.
SCR:013181 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00141" ;
rdfs:label "CancerMutationAnalysis" ;
definition: "Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer." .
SCR:013182 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:syfpeithi",
"nif-0000-21383" ;
rdfs:label "SYFPEITHI: A Database for MHC Ligands and Peptide Motifs" ;
NIFRID:synonym "SYFPEITHI" ;
definition: "SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. It contains a collection of MHC class I and class II ligands and peptide motifs of humans and other species, such as apes, cattle, chicken, and mouse, for example, and is continuously updated. Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database is based on previous publications on T-cell epitopes and MHC ligands. It contains information on: -Peptide sequences -anchor positions -MHC specificity -source proteins, source organisms -publication references Since the number of motifs continuously increases, it was necessary to set up a database which facilitates the search for peptides and allows the prediction of T-cell epitopes. The prediction is based on published motifs (pool sequencing, natural ligands) and takes into consideration the amino acids in the anchor and auxiliary anchor positions, as well as other frequent amino acids. The score is calculated according to the following rules: The amino acids of a certain peptide are given a specific value depending on whether they are anchor, auxiliary anchor or preferred residue. Ideal anchors will be given 10 points, unusual anchors 6-8 points, auxiliary anchors 4-6 and preferred residues 1-4 points. Amino acids that are regarded as having a negative effect on the binding ability are given values between -1 and -3. Sponsors: SYFPEITHI is supported by DFG-Sonderforschungsbereich 685 and theEuropean Union: EU BIOMED CT95-1627, BIOTECH CT95-0263, and EU QLQ-CT-1999-00713." .
SCR:013183 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-32035" ;
rdfs:label "NCJDSU" ;
NIFRID:synonym "National CJD Surveillance Unit",
"National Creutzfeldt-Jakob Disease Surveillance Unit",
"The National Creutzfeldt-Jakob Disease Surveillance Unit" ;
definition: "The incidence of Creutzfeldt-Jakob disease (CJD) is monitored in the UK by the National CJD Surveillance Unit (NCJDSU) based at the Western General Hospital in Edinburgh, Scotland. The Unit brings together a team of clinical neurologists, neuropathologists and scientists specialising in the investigation of this disease. This document is intended to summarise the research in progress at the NCJDSU and also provide some background information about CJD and other human spongiform encephalopathies. We have also provided some links to other resources and contrary points of view available on the Web." .
SCR:013184 a NIFSTD:SIO_000688,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_151628" ;
rdfs:label "RIKEN Tsukuba Institute; Kansai; Japan" ;
NIFRID:synonym "RIKEN Tsukuba Institute" .
SCR:013185 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03646" ;
rdfs:label "Myxopedia" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. An online database containing information aboutMyxococcus xanthus. It provides a genome browser, microarray data, and BLAST functions. MyxoPedia is an online, community driven encyclopedia for information about ''anything Myxo''. Registered community members are welcome to add and edit articles on any aspect of Myxococcus xanthus here. Myxopedia faciliates M.xanthus and other myxobacterial researchers to contribute directly towards the ongoing genome annotation." .
SCR:013186 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-24679" ;
rdfs:label "A Catalogue of Illusions" ;
NIFRID:synonym "Catalogue of Illusions" ;
definition: "Set of different illusions, including color illusions, motion illusions, and optic illusions. Most illusions are from Professor Akiyoshi Kitaoka of the Ritsumeikan University in Kyoto, Japan." .
SCR:013187 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-24776" ;
rdfs:label "Akiyoshis illusion pages" ;
NIFRID:synonym "Illusions Pages" ;
definition: "This portal describes Professor Kitaoka Akiyoshi''s research in the science of visual illusions. Working as an associate professor at the Ritsumeiken University, Department of Psychology, he is one of the few researchers in Japan to be actively researching in this field of study. Professor Kitaoka defines an illusion as a misperception of a real object, adding that defining what is real is a difficult task that depends on recognition and epistemology. An illusion is formed when the perceived characteristics of the object differ from the physical characteristics. Professor Kitaoka first started studying visual illusions when working at the Tokyo Metropolitan Institute for Neuroscience, before coming to RU. He currently researches geometrical, color, lightness, and motion illusions and visual completion, and has become a prominent expert in the field, publishing a wide range of articles on the subject as well as the popular books Trick Eyes, Trick Eyes 2, Trick Eyes Graphics, and the Handbook of the Science of Illusion. To create his illusions, Professor Kitaoka uses graphic design software such as CorelDRAW, Adobe Illustrator, and the drawing software included in Microsoft Word in addition to making use of programming languages like Borland Delphi (Pascal). All of the images set out to test hypotheses that serve to advance his study of illusions and their applications for other visual functions. The goal of his research is to test visual mechanisms through visual illusions." .
SCR:013188 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00981" ;
rdfs:label "muliAlignFree" ;
NIFRID:synonym "muliAlignFree: Multiple Alignment-free Sequence Comparison" ;
definition: "R package intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data." .
SCR:013189 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:polyphen",
"nif-0000-21329",
"nlx_154540",
"OMICS_00136",
"SCR_013200",
"SCR_013238" ;
rdfs:label "PolyPhen: Polymorphism Phenotyping" ;
NIFRID:synonym "Polymorphism Phenotyping",
"Polymorphism Phenotyping v2",
"POLYPHEN",
"PolyPhen",
"PolyPhen-2" ;
definition: """Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations.
PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs.""" .
SCR:013190 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00011" ;
rdfs:label "CongrPE" ;
definition: "A de novo assembly algorithm for Next-Generation Sequencing technology." .
SCR:013191 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-25778",
"r3d100012562" ;
rdfs:label "FishNet2" ;
definition: "FishNet is a collaborative effort by natural history museums and other biodiversity institutions to establish a global network of Ichthyology collections. There is an open invitation for any institution with a fish collection to join. The current portal is an outgrowth of the original FishNet project with improvements in network stability, georeferencing capabilities, and technical support. Users are provided access to searchable, mappable and downloadable data that are cached on a regular basis from participating institutions who have published their data via the DiGIR or TAPIR protocols with a Darwin Core schema. FishNet is also one of four (along with MaNIS, HerpNET, and ORNIS) vertebrate network portals that provide access to specimen collection records from around the world. These web portals, together, comprise VertNet and serve georeferenced, taxon-based data from 72 global institutions. VertNet is a cooperative project working to maintain and expand these distributed database projects. Future plans for VertNet include biodiversity informatics workshops, enhancement of the portal design, better searching capabilities, and a dynamic cache to expand performance and analytic features. :Sponsors: This resource is supported by the National Science Foundation :." .
SCR:013192 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01098" ;
rdfs:label "CallSim" ;
NIFRID:synonym "CallSim - Low-volume read processing base corrector" ;
definition: "A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data." .
SCR:013193 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:plink-seq",
"nlx_154213" ;
rdfs:label "PLINK/SEQ" ;
definition: "An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software)" .
SCR:013194 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01415" ;
rdfs:label "Tuxedo" ;
NIFRID:synonym "Tuxedo: Automated RNA-sequencing Pipeline Script" ;
definition: "Software that manages the RNA-sequencing pipeline based on the TopHat suite of software automatically." .
SCR:013195 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01413" ;
rdfs:label "SAPAS" ;
definition: "A RNA-seq method for polyA research." .
SCR:013196 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-10215",
"OMICS_01169" ;
rdfs:label "AcroMine" ;
NIFRID:synonym "Acromine" ;
definition: "An acronym dictionary which can be used to find distinct expanded forms of acronyms from MEDLINE. This freely available service can be used through your browser or by integrating it with your applications using the ReSTful service. Acromine identifies abbreviation definitions by assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form. Applied to the whole MEDLINE (9,635,599 abstracts), the implemented system extracted 68,007 abbreviation candidates and recognized 467,402 expanded forms. The current Acromine achieves 99% precision and 82-95% recall on our evaluation corpus that roughly emulates the whole MEDLINE." .
SCR:013198 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-10273" ;
rdfs:label "John Hopkins University, In-Vivo Cellular Molecular Imaging Center" ;
NIFRID:synonym "JHU ICMIC" ;
definition: "The vision of the JHU ICMIC is to combine state-of-the-art imaging capabilities with powerful molecular biology techniques to define strategies with intent to cure. It has drawn upon its human resources at JHU to create a center consisting of a multidisciplinary group of premier individuals with diverse skills focused on translating molecular capabilities into imaging possibilities with the single purpose of understanding and curing cancer. Nearly all of the investigators participating in this ICMIC have interactive collaborative projects with one or more of the other investigators. The synergism generated by the collective skills of this unique group of individuals will lead to significant advances in the understanding of cancer and its treatment. The JHU ICMIC structure consists of four interactive and closely related research components focused on hypoxia, HIF-1, and exploiting the hypoxia response element to target cancer cells through choline kinase inhibition. These research components are anchored by the participation of world renowned expertise in HIF-1. The research components utilize MR, PET and Optical Imaging technology to understand cancer vascularization, invasion and metastasis, to achieve effective cancer therapy. The center has selected developmental projects which are highly relevant to the goals of the ICMIC and interactive with the research components. Five resources devoted to adminstration, molecular biology, imaging, probes, and translational application provide the infrastructure to support the research activities of the ICMIC. Research Components in the JHU ICMIC: - Combining Anti-angiogenic therapy with siRNA targeting of choline kinase. - Imaging the Role of HIF-1 in Breast Cancer Progression - Imaging and Targeting Hypoxia in Solid Tumors - Molecular and Functional Imaging of the HER-2/neu Receptor The following are developmental projects currently taking place in ICMIC 1. Receptor imaging using nonparamagnetic MRI contrast agents (2003) 2. New imaging agents for prostate cancer (2003) 3. Non-invasive monitoring of therapeutic effect of siRNA-mediated radiation sensitization in human prostate cancer xenografts (2003) 4. Imaging of the endothelin receptor in cancer (2003) 5. Imaging studies of c-myc regulation of tumor metabolism (2003) 6. Imaging studies of anti-tumorigenic effects of anti-oxidants in vivo (2005) 7. Molecular Imaging with Magnetic Resonance Microsystems (2005) 8. Endogenous angiogenesis inhibitors (2005) 9. MR imaging and spectroscopy in detection and localization of prostate cancer: a prospective trial in patients undergoing cystoprostatectomy and radical prostatectomy. (2005) 10. A versatile visualization system for the analysis of multi-modality and multidimensional cancer imaging (2007) 11. Non-invasive imaging of CXCR4 expression in breast cancer (2007)" .
SCR:013199 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_144045" ;
rdfs:label "SIU Center for Alzheimer's Disease and Related Disorders" ;
NIFRID:synonym "SIU School of Medicine Center for Alzheimer's Disease and Related Disorders" ;
NIFRID:abbrev "SIU CADRD" ;
definition: "Resource center that provides assistance for patients and families affected by Alzheimer's disease and related conditions. The Center provides patient care through the Memory and Aging Clinic as well as through research, education and service to the community. Additionally the Center provides training in dementia care, maintains centralized data collection, and sponsors programs of research that qualify for federal financial participation." .
SCR:013201 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_156805" ;
rdfs:label "NHANES" ;
definition: "Program of studies designed to assess the health and nutritional status of adults and children in the United States. The survey is unique in that it combines interviews and physical examinations." .
SCR:013202 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_155855" ;
rdfs:label "iso2mesh" ;
definition: "A Matlab / Octave-based mesh generation toolbox designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, functioning independently or interfacing with external free meshing utilities. Iso2mesh toolbox can operate directly on 3D binary, segmented or gray-scale images, such as those from MRI or CT scans, making it particularly suitable for multi-modality medical imaging data analysis or multi-physics modeling." .
SCR:013204 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01203" ;
rdfs:label "GoGrid" ;
definition: "Commercial software company offering on-demand cloud, hybrid hosting, hosted private cloud, and dedicated infrastructure for complex needs." .
SCR:013205 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02798" ;
rdfs:label "Endogenous GPCR List" ;
definition: "This database lists the G protein coupled receptors expressed endogenously in various cell lines. In so far as possible, we have tried to follow the receptor nomenclature recommended by IUPHAR. Please refer to the following web sites for additional information on receptor nomenclature: Official database of the IUPHAR committee on receptor nomenclature :http://www.iuphar-db.org/index.jsp British Journal of Pharmacology Volume 150 Issue S1 (February 2007) Guide to Receptors and channels. :http://www.nature.com/bjp/journal/vgrac/ncurrent/index.html The Endogenous GPCR List has been available in various forms since 1994 and seems to have enduring utility. We intend to continue to maintain, and when possible, improve this list. Suggestions for future enhancements are welcome. Information to be added to the database (e.g. additional endogenous receptors) is extremely welcome!" .
SCR:013206 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:telescoper",
"OMICS_00036" ;
rdfs:label "Telescoper" ;
NIFRID:synonym "Telescoper - De novo assembly algorithm" ;
definition: "An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework." .
SCR:013207 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00415" ;
rdfs:label "RegRNA" ;
NIFRID:synonym "RegRNA2.0",
"RegRNA2.0 ? an integrated web server for identifying functional RNA motifs and sites",
"RegRNA 2.0" ;
definition: "An integrated web server for identifying functional RNA motifs in an input RNA sequence." .
SCR:013208 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01678" ;
rdfs:label "dbCAN" ;
definition: "A web server and DataBase for automated Carbohydrate-active enzyme ANnotation, funded by the BioEnergy Science Center of the DOE., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013209 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID: 100008752",
"grid.469719.4",
"ISNI: 0000 0001 0944 4714",
"nif-0000-10649",
"Wikidata: Q4743073" ;
rdfs:label "American Association of Neurological Surgeons" ;
NIFRID:synonym "AANS" ;
definition: "The American Association of Neurological Surgeons is dedicated to advancing the specialty of neurological surgery and serving as the spokes organization for all practitioners of the specialty of neurosurgery, in order to provide the highest quality of care to our patients. :Founded in 1931 as the Harvey Cushing Society, the American Association of Neurological Surgeons (AANS) is a scientific and educational association with over 7,400 members worldwide. The AANS is dedicated to advancing the specialty of neurological surgery in order to provide the highest quality of neurosurgical care to the public. All Active members of the AANS are board certified by the American Board of Neurological Surgery, the Royal College of Physicians and Surgeons of Canada, or the Mexican Council of Neurological Surgery, A.C. Neurosurgery is the medical specialty concerned with the prevention, diagnosis, treatment and rehabilitation of disorders that affect the spinal column, spinal cord, brain, nervous system and peripheral nerves. For more information on what neurosurgeons do, visit our public pages at : :www.NeurosurgeryToday.org : : :. Visitors to our Web site can find Member Counts under membership including demographic details." .
SCR:013210 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02733" ;
rdfs:label "dbRIP" ;
definition: "dbRIP is a database of human Retrotransposon Insertion Polymorphisms (RIPs), in which RIPs are highly integrated into the human genome annotation data provided by UCSC Genome Browser. dbRIP contains all currently known Alu, L1, and SVA polymorphic insertion loci in the human genome. dbRIP can be used for Querying Retrotransposon Insertion Polymorphisms (RIPs), Identifying RIPs associated with particular genes, Genome-wide browsing of RIPs, Verifying newly identified retrotransposon insertions, and viewing a genome-wide view of all RIPs from one selected class or all classes (Genome plots)." .
SCR:013211 a NIFSTD:birnlex_2431,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_inv_1005033" ;
rdfs:label "Center for Scientific Review" ;
NIFRID:abbrev "CSR" ;
definition: "The Center for Scientific Review (CSR) is the portal for NIH grant applications and their review for scientific merit. We receive all research grant applications sent to NIH and handle the review of more than 70% of those by organizing peer review groups (study sections) to evaluate research grant applications. Our mission is to see that NIH grant applications receive fair, independent, expert, and timely reviews — free from inappropriate influences — so NIH can fund the most promising research. The Center specifically: * Serves as the central receipt point for all research and training grant applications submitted to NIH. Also receives some of the applications submitted to other components of the U.S. Department of Health and Human Services (HHS) and refers them to these components; * Assigns all NIH applications to the appropriate NIH institutes or centers for consideration for funding and also to the scientific review groups within CSR or other institutes or centers for review; * Provides the scientific merit review of most research grant and fellowship applications submitted to NIH; * Provides staff support to the Office of the Director, NIH, in the formulation of grant and award policies and procedures; and * Assists other NIH components in providing information on the NIH peer review system and information about the research grant and fellowship application process and procedures to the scientific community, Congress, other NIH staff, and the general public." .
SCR:013212 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:heuraa",
"OMICS_00097" ;
rdfs:label "HeurAA" ;
NIFRID:synonym "heurAA - NGS multiplexed amplicon aligner" ;
definition: "Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing." .
SCR:013213 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00330" ;
rdfs:label "CoNIFER" ;
NIFRID:synonym "Copy Number Inference From Exome Reads" ;
definition: "Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes." .
SCR:013214 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_39873" ;
rdfs:label "HIV-1, Human Protein Interaction Database" ;
NIFRID:synonym "HIV-1 Protein Interaction Database" ;
definition: "The Division of Acquired Immunodeficiency Syndrome (DAIDS) of the National Institute of Allergy and Infectious Diseases (NIAID) has initiated a project, in collaboration with Southern Research Institute and the National Center for Biotechnology Information (NCBI), designed to compile a comprehensive database of the described interactions between HIV-1 and cellular proteins. The goal of this project is to provide scientists in the field of HIV/AIDS research a concise, yet detailed, summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS. This database has been designed to track the following information for each protein-protein interaction identified in the literature: * NCBI Reference Sequence (RefSeq) protein accession numbers. * NCBI Entrez Gene ID numbers. * Amino acids from each protein that are known to be involved in the interaction. * Brief description of the protein-protein interaction. * Keywords to support searching for interactions. * National Library of Medicine (NLM) PubMed identification numbers (PMIDs) for all journal articles describing the interaction." .
SCR:013215 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01330" ;
rdfs:label "DiffSplice" ;
definition: "The Genome-Wide Detection of Differential Splicing Events with RNA-seq." .
SCR:013216 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:MAP",
"OMICS_01424" ;
rdfs:label "MAP" ;
NIFRID:synonym "Metagenomic Assembly Program" ;
definition: "This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013217 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01150" ;
rdfs:label "DynamicProg" ;
definition: "A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms." .
SCR:013218 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01718" ;
rdfs:label "NGS Expert Blog" ;
definition: "Blog including established profound know-how and proprietary protocols to cover a broad range of applications." .
SCR:013219 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.264772.2",
"ISNI:0000 0001 0682 245X",
"nlx_65951",
"Wikidata:Q1495387" ;
rdfs:label "Texas State University; Texas; USA" ;
definition: "Public research university in San Marcos, Texas. Established in 1899 as the Southwest Texas State Normal School, it opened in 1903 to 303 students." .
SCR:013220 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01416" ;
rdfs:label "genCAT" ;
NIFRID:synonym "gencat - Gene''s Comprehensive Annotation Tool" ;
definition: "Software designed as an open platform that allows users to incorporate as many datasets (concepts) as possible to annotate the input gene list, as long as these datasets are prepared in bigwig, BED, BAM/SAM formats." .
SCR:013221 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_13972" ;
rdfs:label "Australian Prostate Cancer Tissue Bank" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 31,2023." .
SCR:013222 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_151321",
"r3d100011087" ;
rdfs:label "doRiNA" ;
definition: "In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions." .
SCR:013223 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00590" ;
rdfs:label "SOCS" ;
definition: "Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences." .
SCR:013224 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_16316" ;
rdfs:label "National Marine Mammal Tissue Bank" ;
definition: "Not yet vetted by NIF curator" .
SCR:013225 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_155725" ;
rdfs:label "CUDA-SPHERE-FWD-MEEG" ;
NIFRID:synonym "CUDA accelerated spherical model forward solution for EEG/MEG",
"CUDA accelerated spherical model M/EEG" ;
definition: "A CUDA C based toolkit which provides a GPU based implementation of the spherical model forward solution for the 306 channel Elekta Neuromag MEG system and the EEG. The 1-Sphere forward solution for the MEG and the 4-Sphere forward solution for the EEG is implemented in CUDA C and an accelerated solution is obtained using the NVIDIA GPU when the solution is calculated for a large number of dipoles (on the order of 15000 and above) and sensor location. Speedup by a factor of 22 and 32 is obtained for the EEG and MEG solution respectively when compared to the fastest CPU implementation available in the public domain. The complete source code and pre-compiled binaries are also made available via an open source license (GPL Version 3). A CUDA enabled NVIDIA graphics card is required to use the software." .
SCR:013226 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03231" ;
rdfs:label "OryGenesDB" ;
definition: "The Oryza sativa database displays sequence information resulting from the research of the Centre de cooperation internationale en recherche agronomique pour le developpement. It also includes related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data, etc.). Genome Browser (Gbrowse), a Web-based application for displaying genomic annotations and other features, is the core of our database. The reference annotation layer consists in the 12 rice pseudomolecules released by the TIGR (Version 5.0, January 2007). All the data are superposed as annotations layers and positioned with respect to these pseudomolecules. We developed a set of tools around GBrowse to retrieve as exhaustively as possible information related to queries with several starting points. These tools allow a molecular geneticist to readily find insertion lines (T-DNA, Tos17, Ds) in genes of interest and to retrieve all the associated annotations related to these sequences." .
SCR:013227 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01773" ;
rdfs:label "Monoclonal Antibody Index" ;
NIFRID:abbrev "MAI" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented September 13, 2016. A searchable biotechnology database e-books with information on more than 9000 monoclonal antibodies. This database has antibodies produced for the diagnosis and therapy of human cancer, Alzheimer's disease, AIDS, and other diseases as well as for biomarker and proteomics research. Information such as antibody name, species, type, characteristics, antigen characteristics, and developer or distributor of antibody as well as mentions in journals, patents, abstracts and reports up until 2012 are included." .
SCR:013228 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00295" ;
rdfs:label "Expectation-Maximization Segmentation" ;
NIFRID:synonym "EMS" ;
definition: "EMS is a freely available suite of Matlab functions and subroutines (with some externally compiled C routines) for fully-automated multi-spectral classification of brain tissues in Magnetic Resonance (MR) images. It uses a model based approach (including an explicit model for MR bias fields) in which all the model parameters are automatically estimated for each individual scan. This enables it to process large amounts of data from normal subjects and subjects suffering from Multiple Sclerosis without need for user intervention or preceeding manual training phase." .
SCR:013229 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:beads",
"OMICS_00466" ;
rdfs:label "BEADS" ;
NIFRID:synonym "BEADS: Bias Elimination Algorithm for Deep Sequencing",
"Bias Elimination Algorithm for Deep Sequencing" ;
definition: "Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data." .
SCR:013231 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:deathdomain",
"nlx_149482" ;
rdfs:label "Death Domain database" ;
NIFRID:synonym "Death Domain database: A manually curated database of protein-protein interactions for Death Domain Superfamily",
"DeathDomain Database",
"DeathDomain.org/" ;
NIFRID:abbrev "DD database" ;
definition: "A manually curated database of protein-protein interactions for Death Domain Superfamily. The Death Domain Database provides a detailed summary of PPI data, which fits into 3 categories: interaction, characterization, and functional role. Users can find in-depth information specified in the literature on relevant analytical methods, structural information. The DD superfamily currently comprises four subfamilies: * Death domain (DD) subfamily * Death effector domain (DED) subfamily * Caspase recruitment domain (CARD) subfamily * Pyrin domain (PYD) subfamily" .
SCR:013232 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00698" ;
rdfs:label "aCGH" ;
definition: "Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects." .
SCR:013233 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:cube-db",
"nlx_149432" ;
rdfs:label "Cube-DB" ;
NIFRID:synonym "Cube-DB: Detection of Functional Divergence in Human Protein Families" ;
definition: "Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orhtologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera)." .
SCR:013234 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00667" ;
rdfs:label "LifeScope" ;
NIFRID:synonym "LifeScope Genomic Analysis Software" ;
definition: "Genomic Analysis Software designed to match the accuracy of the next generation 5500 Genetic Analyzers with Exact Call Chemistry (ECC)." .
SCR:013235 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00112" ;
rdfs:label "RepeatSeq" ;
definition: "Software that determines genotypes for microsatellite repeats in high-throughput sequencing data." .
SCR:013236 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30445" ;
rdfs:label "Description of MORGAM Cohorts" ;
NIFRID:synonym "MORGAM" ;
definition: "The purpose of this document is to give the exact definitions of the MORGAM cohorts and to describe their basic characteristics and data collection procedures, such as the follow-up procedures, the disease end-points recorded and diagnostic procedures. The definition and selection criteria for MORGAM cohort are described in section Definition and selection of cohorts of the MORGAM Manual. For convention, each cohort is assigned appropriate name and code number which is given in Table 1. The baseline characteristics of the MORGAM Cohorts are summarized in Table 2. An overall summary of MORGAM Cohorts along with the objectives of the Project has been published elsewhere [1]. Sponsor. The research was supported by the GenomEUtwin Project grant from the European Commission under the programme `Quality of Life and Management of the Living Resources'' of 5th Framework Programme (no. QLG2-CT-2002-01254) and by the Academy of Finland via its grant number 53646." .
SCR:013237 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_15477" ;
rdfs:label "MIMIC II" ;
NIFRID:synonym "MIMIC",
"Multiparameter Intelligent Monitoring in Intensive Care" ;
definition: "MIMIC II (Multiparameter Intelligent Monitoring in Intensive Care) Database contains comprehensive clinical data from tens of thousands of Intensive Care Unit (ICU) patients. Data were collected between 2001 and 2008 from a variety of ICUs (medical, surgical, coronary care, and neonatal) in a single tertiary teaching hospital. The database contains clinical data from bedside workstations as well as hospital archives. The database also includes thousands of records of continuous high-resolution physiologic waveforms and minute-by-minute numeric time series (trends) of physiologic measurements." .
SCR:013239 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_25072" ;
rdfs:label "ZFIN Protocol Wiki" ;
NIFRID:synonym "ZFIN Protocol",
"ZFIN Protocols Wiki" ;
definition: "ZFIN Protocol Wiki is where zebrafish researchers can share experimental protocols and tips with the rest of the research community. Protocols are organized into sections corresponding to the chapters of The Zebrafish Book, 5th edition (4th edition on-line). Feel free to add new protocols to the appropriate section or add comments to any existing protocol. Sections * General Methods for Zebrafish Care * Breeding * Embryonic and Larval Culture * Imaging * Cellular Methods * Dissociated Cell Culture * Genetic Methods * Antisense Methods * Histological Methods * in situ Hybridization Techniques * Mapping * Transgenesis * Gene Cloning * DNA Analysis * RNA Analysis * Protein Analysis * Microarray * Recipes" .
SCR:013240 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-31387" ;
rdfs:label "QccPack" ;
definition: "QccPack provides an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack has been written to provide very flexible and general implementations of procedures commonly used in coding and compression applications. QccPack is intended for use in the development of prototypes of coding and compression systems, and in academic research. QccPack includes routines for entropy coding, scalar quantization, vector quantization, and wavelet transforms. Additonally, an open-source implementation of SPIHT is available as an optional module. QccPack provides an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack has been written to provide very flexible and general implementations of procedures commonly used in coding and compression applications. The essential component of the QccPack collection is a library (a static library, libQccPack.a, and, if supported on your system, a dynamic library, libQccPack.so) of procedures implementing a large variety of compression and coding algorithms. Application programs may make use of the QccPack library routines by linking the application against the library during compilation. Each library function is very general in its implementation so to be useful in a large variety of applications. Additionally, much of the functionality of the library routines has been provided in the form of stand-alone executable programs. Probably the prime importance of these utility programs is that they provide examples of how to interface with many of the QccPack library routines. The utility programs could also be called from scripts to simulate the operation of complex coding and compression systems before implementing all the system functionality into one stand-alone program. Currently, QccPack consists of over 55,000 lines of C code implementing over 500 library routines and over 50 stand-alone utility programs. The major functionalities currently implemented include: * Entropy coding o Arithmetic coding including multiple-context adaptive and nonadaptive models o Huffman coding o Golomb and adaptive Golomb coding * Scalar Quantization (SQ) o Uniform SQ o Dead-zone SQ o -law and A-law SQ o Lloyd algorithm for optimal SQ design * Vector quantization (VQ) o Generalized Lloyd algorithm (GLA) for VQ-codebook design o Full-search VQ encoding and decoding o Entropy-constrained-VQ (ECVQ) training, encoding, and decoding o Multistage VQ (MSVQ) (also called residual VQ (RVQ)) training, encoding, and decoding * Adaptive vector quantization (AVQ) o The generalized-threshold-replenishment (GTR) algorithm o The Paul algorithm o Gersho-Yano algorithm o Coding of side information * Wavelet transforms, wavelet-based subband coding o Discrete wavelet transform (DWT) using first-generation filter banks and popular orthonormal and biorthogonal wavelets o Lifting implementations of DWT for popular wavelets o Two-dimensional DWT in the form of dyadic subband pyramids o Three-dimensional DWT in the form of dyadic subband pyramids as well as a packet transform o Shape-adaptive DWT (SA-DWT) for 1D and 2D signals o Redundant DWT (RDWT), aka, the algorithme trous o The SR algorithm for wavelet-based image coding o The SFQ algorithm for wavelet-based image coding o The WDR algorithm for wavelet-based image coding o The 3D-WDR algorithm for wavelet-based image-cube coding o The tarp-filter algorithm for wavelet-based image coding o The 3D-tarp algorithm for wavelet-based image-cube coding o The TCE algorithm for wavelet-based image coding o The BISK algorithm for wavelet-based shape-adaptive image coding o The 3D-BISK algorithm for wavelet-based image-cube coding * Error-correcting codes o Field arithmetic, including Gaussian-elimination matrix inversion o Reed-Solomon encoding and decoding o CRC codes o Trellis codes o Hard and soft Viterbi decoding * Image processing o Routines for reading and writing gray and color still images and sequences of images (via PGM and PPM formats) o Routines for reading and writing 3D image-cube volumes o Image and image-sequence deinterlacing o Image differential-pulse-code modulation (DPCM) o Color-space conversions: RGB, YUV, CIE XYZ, CIE UCS, CIE modified UCS o Block-based DCT and inverse DCT * Video coding o The spatial-block algorithm for image-sequence coding o The RDWT-block algorithm for image-sequence coding o The RWMH algorithm for image-sequence coding o Block-based motion estimation and motion compensation o Motion estimation and motion compensation using regular triangle meshes o Encoding and decoding of motion-vector fields * General routines o Vector math (up/down sampling, sorting, dot product, addition/subtraction, etc.) o Matrix math (addition/subtraction, vector-matrix multiplication, etc.) o Linked lists and associated operations o Entropy estimation (first and second order) o General file input and output, including automatic detection and reading/writing of gzip-compressed files o Character bit-packing for binary bitstream input/output o Memory-based fifo for binary bitstreams o Conversion between various file formats used by library routines o Error-message tracking, formatting, and output o Automatic command-line parameter parsing In addition to the standard functionalities listed above, there exist optional modules that can be added to the QccPack library. Usually, these modules are available under licensing terms different from the GPL/LGPL licenses of QccPack and may contain patented algorithms; refer to the documentation included with each module for specific details. These modules are downloaded separately from QccPack and are not enabled by default during the building of QccPack. The currently available optional modules and their functionalities are: * QccPackSPIHT o The Set Partitioning in Hierarchical Trees (SPIHT) algorithm for wavelet-based image coding * QccPackSPECK o The Set-Partitioning Embedded Block (SPECK) algorithm for wavelet-based image coding Abstract: We describe the QccPack software package, an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack is being written to expedite data-compression research and development by providing general and reliable implementations of common compression techniques. Functionality of the current release includes entropy coding, scalar quantization, vector quantization, adaptive vector quantization, wavelet transforms and subband coding, error-correcting codes, image-processing support, and general vector-math, matrix-math, file-I/O, and error-message routines. All QccPack functionality is accessible via library calls; additionally, many utility programs provide command-line access. The QccPack software package, downloadable free of charge from the QccPack Web page, is published under the terms of the GNU General Public License and the GNU Library General Public License which guarantee source-code access and as well as allow redistribution and modification. Additionally, there exist optional modules that implement certain patented algorithms. These modules are downloadable separately and are typically issued under licenses that permit only non-commercial use. This material is based upon work supported in part by the National Science Foundation under Grant No. INT-9600260." .
SCR:013241 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:cem",
"OMICS_01271" ;
rdfs:label "CEM" ;
NIFRID:synonym "CEM: Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads" ;
definition: "An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads." .
SCR:013242 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00619" ;
rdfs:label "Repitools" ;
definition: "Software tools for the analysis of enrichment-based epigenomic data." .
SCR:013243 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00493" ;
rdfs:label "SeqSite" ;
NIFRID:synonym "SeqSite: ChIP-Seq Binding Site Identification" ;
definition: "Software for detecting transcription factor binding sites from ChIP-seq data." .
SCR:013244 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_155711" ;
rdfs:label "BrainCSI" ;
definition: "A tool for analysis of Magnetic Resonance Spectroscopy (MRS) data by registering it to anatomical images. BrainCSI imports LCModel results to calculate absolute metabolite concentrations using tissue water. Corrections to LCModel metabolite concentrations for partial volume of tissues are accomplished by tissue classification of the anatomical images." .
SCR:013245 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01482" ;
rdfs:label "SmashCommunity" ;
definition: "A stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies." .
SCR:013246 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-24171" ;
rdfs:label "Evaluation Instruments Bank" ;
NIFRID:synonym "EIB" ;
definition: "The EIB provides assessment tests for substance disorder related clinical instruments that are freely available. Details regarding copyright and/or possible use restrictions are specified for each instrument. Instruments are generally classed according to the intervention field they are designed to be used in (treatment, prevention, or harm reduction), though some instruments may be usable in more than one field." .
SCR:013247 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:eprobalign",
"OMICS_00975" ;
rdfs:label "eProbalign" ;
NIFRID:synonym "EProbalign",
"eProbalign web server" ;
definition: "Data analysis service that computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities." .
SCR:013248 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_155716" ;
rdfs:label "BrainVisa Morphology extensions" ;
definition: "An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging. The extensions include computation of regional GM thickness, 3D gyrification index, sulcal lenght and depth and sulcal span. These tools are distributed in the form of plugins for a popular analysis package BrainVisa" .
SCR:013249 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30519" ;
rdfs:label "Entrez Utilities" ;
definition: "Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment.
Additional information is available in the NCBI Bookshelf Short Courses Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils) and the NCBI PowerScripting course.
User Requirements: Please read for important information on scripting NCBI servers.
EInfo: Provides field index term counts, last update, and available links for each database.
ESearch: Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user''s environment.
EPost: Posts a file containing a list of primary IDs for future use in the user''s environment to use with subsequent search strategies.
ESummary: Retrieves document summaries from a list of primary IDs or from the user''s environment.
EFetch: Retrieves records in the requested format from a list of one or more primary IDs or from the user''s environment.
ELink: Checks for the existence of an external or Related Articles link from a list of one or more primary IDs. Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs.
EGQuery: Provides Entrez database counts in XML for a single search using Global Query.
ESpell: Retrieves spelling suggestions.
SOAP Interface for Entrez Utilities
PMID to PMC ID Converter
Entrez DTDs
Demonstration Program
Announcement Mailing List
Leasing Data from the National Library of Medicine
Help Desk
User Requirements
Do not overload NCBI''s systems. Users intending to send numerous queries and/or retrieve large numbers of records from Entrez should comply with the following:
Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests.
Send E-utilities requests to http://eutils.ncbi.nlm.nih.gov, not the standard NCBI Web address.
Make no more than 3 requests every 1 second.
Use the URL parameter email, and tool for distributed software, so that we can track your project and contact you if there is a problem.
NCBI''s Disclaimer and Copyright notice must be evident to users of your service. NLM does not claim the copyright on the abstracts in PubMed; however, journal publishers or authors may. NLM provides no legal advice concerning distribution of copyrighted materials, consult your legal counsel.
" .
SCR:013250 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01333" ;
rdfs:label "GPSeq" ;
definition: "A software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013251 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01766" ;
rdfs:label "Antibody Links" ;
NIFRID:synonym "Antibody Link" ;
definition: "An antibody information database where antibodies are organized by the target protein UniProt id." .
SCR:013252 a owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.240023.7",
"ISNI: 0000 0004 0427 667X",
"nlx_143603",
"Wikidata: Q6389637" ;
rdfs:label "Kennedy Krieger Institute" ;
definition: "Located in Baltimore, MD., Kennedy Krieger Institute is an internationally recognized institution dedicated to improving the lives of children and adolescents with pediatric developmental disabilities and disorders of the brain, spinal cord and musculoskeletal system, through patient care, special education, research, and professional training. Patient Care--Specialists from various fields and disciplines work together to evaluate, diagnose, and create individualized treatment plans to guide patients and families through all stages of care. Research and Professional Training--Our innovative research and professional training programs are leading the way in the understanding, prevention, and treatment of a wide range of developmental disabilities. Special Education--We offer a number of school-based, hospital-based, and recreational programs designed to unlock the promise inside our students through innovative and customized educational approaches. Community--We are committed to helping people with developmental disabilities achieve their potential and enjoy success in community life by providing access to resources, services, and model programs." .
SCR:013253 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01251" ;
rdfs:label "SOAPsplice" ;
definition: "A tool for genome-wide ab initio detection of splice junction sites from RNA-Seq, a method using new generation sequencing technologies to sequence the messenger RNA." .
SCR:013254 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03232" ;
rdfs:label "Oryza Tag Line" ;
definition: "Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the Génoplante rice insertion line library. To display the sequence information (Flanking Sequence Tags) resulting from the molecular characterization of the mutagen insertion sites in the collection, Oryza Tag Line is linked to OryGenesDB a GGB-derived interface or FLAGDB++ a Java based interface. Aside from generic data ( production record and seed stock ) Oryza Tag Line includes textual and pictorial information resulting from the following observations: (i.) GUS/GFP expression assays conducted on the primary transformants (T0) and/or T1 progenies (ii.) morpho-physiological alterations detected during the growth of the T1 progenies either in phytotron -up to the 5-6 leaf stage- or under agronomical conditions in the field (collaboration with CIAT, Cali, Colombia)." .
SCR:013255 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01301" ;
rdfs:label "CEDER" ;
definition: "R package intended to implement a program for detecting differentially expressed genes (DEG) using RNA-Seq by combining significance of exons within a gene." .
SCR:013256 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03310" ;
rdfs:label "PlantsP" ;
definition: "A database of plant protein kinases and phosphatases as well as genomic information for these enzymes. Because protein kinases and phosphatases control so many processes in plants, and occur in networks that unite different cellular processes, a genome wide approach is needed to make significant advances in discovering the roles of these enzymes in the regulation of plant function." .
SCR:013257 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00381" ;
rdfs:label "miRSeqNovel" ;
definition: "An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data." .
SCR:013258 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_35625" ;
rdfs:label "Long-term Recordings of Gait Dynamics: Unconstrained and Metronomic Walking" ;
definition: "Stride interval fluctuations were studied in ten young, healthy men. Participants had no history of any neuromuscular, respiratory or cardiovascular disorders, and were taking no medications. Mean age was 21.7 years (range: 18-29 years). Height was 1.77 ���� 0.08 meters (mean ���� S.D.) and weight was 71.8 ���� 10.7 kg. All subjects provided informed written consent. Subjects walked continuously on level ground around an obstacle free, long (either 225 or 400 meters), approximately oval path and the stride interval was measured using ultra-thin, force sensitive switches taped inside one shoe. For more details, please see the accompanying publication. Each subject was given an arbitrary id (si01, si02, ... si10). For each subject, there are six data files: normal (.norm), slow (.slow) and fast (.fast) walking for 1 hour each as well as walking in time to a metronome at normal (.metnrm), slow (.metslw) and fast (.metfst) paces." .
SCR:013259 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_64563",
"nlx_80440" ;
rdfs:label "Japanese Research Center of Genetic Resources NARO Genebank project" ;
NIFRID:synonym "Japanese Research Center of Genetic Resources National Agriculture and Food Research Organization Genebank project",
"NARO Genebank" ;
definition: "Research Center of Genetic Resources is central coordinating institute in Japan for conservation of plants, microorganisms, and animals related to agriculture. NARO Genebank coordinates this activity in collaboration with network of institutes throughout Japan. Conducts exploration, collection, characterization, preservation, and distribution service of microorganism genetic resources, animal genetic resources raised in Japan, and plant genetic resources." .
SCR:013260 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-10275" ;
rdfs:label "Kennedy Krieger Institute: Diagnoses/Disorders" ;
NIFRID:synonym "KKI Diagnoses/Disorders" ;
definition: "Kennedy Krieger Institute is an institution dedicated to improving the lives of children and adolescents with pediatric developmental disabilities through patient care, special education, research, and professional training. Kennedy Kriegers clinical programs offer an interdisciplinary approach in treatment tailored to the individual needs of each child. Services include over 40 outpatient clinics; neurobehavioral, rehabilitation, and pediatric feeding disorders inpatient units; plus several home and community programs providing services to assist families. At Kennedy Krieger, there is no shortage of clinical programs to meet the specialized needs of children and adolescents with developmental disabilities. More than 35 different outpatient clinics, three inpatient units, several home and community programs and clinical laboratories all address the specific conditions of children with a wide range of disorders. Kennedy Krieger is recognized for its range of services in areas including autism, cerebral palsy, spina bifida, neurorehabilitation and feeding disorders. Kennedy Krieger school, is a nationally recognized Blue Ribbon School of Excellence, and is a leader in providing model programs of innovative education for children, adolescents and young adults with a wide range of learning, emotional, physical, neurological, and developmental disabilities. Faculty at Kennedy Krieger are among some of the worlds leading experts in this field and are attuned to the special needs of this population. These faculty have made crucial medical discoveries leading to innovative treatments and have improved the lives of individuals with disabilities. In addition to providing evaluation, rehabilitation, educational services and cutting edge research on behalf of children with brain related disabilities, Kennedy Krieger also provides professional training by renowned experts dedicated to increasing the number of qualified specialists in the United States and abroad. Children treated at Kennedy Krieger are seen by a variety of health care professionals working together in one or more of the Institutes clinical disciplines or departments. These highly trained professionals work directly with the Institutes medical staff to provide coordinated, interdisciplinary care tailored to the special needs of each child. This interdisciplinary approach puts Kennedy Krieger at the forefront in providing patient care for individuals with multiple developmental disabilities. Additionally, Kennedy Krieger Institutes Department of Special Education includes a number of programs that offer service to children with disabilities in a variety of settings. Kennedy Krieger School programs offer special education and related services to students aged 3-21 in three day-school settings and in partnership settings within public schools. For your convenience, a list of diagnoses/disorders treated at Kennedy Krieger Institute has been compiled to provide helpful related information for each diagnosis/disorder and include definitions, symptoms, treatment programs available at Kennedy Krieger, research being conducted at Kennedy Krieger, press releases, Potential articles and links to other helpful additional resources and websites outside the Institute." .
SCR:013261 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154660" ;
rdfs:label "SPREG" ;
NIFRID:synonym "Secondary Phenotype REGression analysis" ;
definition: "Software program for performing regression analysis of secondary phenotype data in case-control association studies. Secondary phenotypes are quantitative or qualitative traits other than the case-control status. Because the case-control sample is not a random sample of the general population, standard statistical analysis of secondary phenotype data can yield very misleading results. SPREG implements valid and efficient statistical methods. (entry from Genetic Analysis Software)" .
SCR:013262 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154041" ;
rdfs:label "MOLKIN" ;
definition: "A population genetics computer program that conducts several genetic analyses on multilocus information in a user-friendly environment. Primary functions carried out by MOLKIN are the computation of the between individuals (and populations) molecular coancestry coefficients, the Kinship distance at individual and population levels. Additionally, users can compute with MOLKIN a set of among populations, genetic distances and F statistics from multilocus information. The program will help researchers or those responsible for population management to assess genetic variability and population structure at reduced costs with respect to dataset preparation (entry from Genetic Analysis Software)" .
SCR:013263 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03074" ;
rdfs:label "KNOTTIN database" ;
NIFRID:abbrev "KNOTTIN Database" ;
definition: "The KNOTTIN database provides standardized data on the knottin structural family (also referred to as the Inhibitor Cystine Knot (ICK) motif/family/fold). Knottins are intriguing miniproteins with strong potential in drug design. This knot is achieved when one disulfide bridge crosses the macrocycle formed by the two other disulfides and the interconnecting backbone." .
SCR:013264 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-21163" ;
rdfs:label "Genetic Association Database" ;
NIFRID:synonym "GAD" ;
definition: "The Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders. The goal of this database is to allow the user to rapidly identify medically relevant polymorphism from the large volume of polymorphism and mutational data, in the context of standardized nomenclature. The data is from published scientific papers. Study data is recorded in the context of official human gene nomenclature with additional molecular reference numbers and links. It is gene centered. That is, each record is a record of a gene or marker. If a study investigated 6 genes for a particular disorder, there will be 6 records. Anyone may view this database and anyone may submit records. You do not have to be an author on the original study to submit a record. All submitted records will be reviewed before inclusion in the archive. Both genetic and environmental factors contribute to human diseases. Most common diseases are influenced by a large number of genetic and environmental factors, most of which individually have only a modest effect on the disease. Though genetic contributions are relatively well characterized for some monogenetic diseases, there has been no effort at curating the extensive list of environmental etiological factors. From a comprehensive search of the MeSH annotation of MEDLINE articles, they identified 3,342 environmental etiological factors associated with 3,159 diseases. They also identified 1,100 genes associated with 1,034 complex diseases from the NIH Genetic Association Database (GAD), a database of genetic association studies. 863 diseases have both genetic and environmental etiological factors available. Integrating genetic and environmental factors results in the etiome, which they define as the comprehensive compendium of disease etiology." .
SCR:013265 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:h-invdb",
"nif-0000-02936" ;
rdfs:label "H-InvDB" ;
NIFRID:synonym "H-InvDB cDNA",
"H-InvDB locus",
"H-InvDB: Annotated Human Gene Database",
"H-Invitational Database" ;
definition: "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups. This database is produced by the Genome Information Integration Project (2005-) based upon the annotation technology established in the H-Invitational Project for annotation of human full-length cDNAs." .
SCR:013267 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00676" ;
rdfs:label "PIA" ;
definition: "A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome." .
SCR:013268 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01324" ;
rdfs:label "SOAPdenovo-Trans" ;
definition: "A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013269 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00260" ;
rdfs:label "Wgsim" ;
definition: "A small tool for simulating sequence reads from a reference genome." .
SCR:013271 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_155838" ;
rdfs:label "VPixx | VIEWPixx" ;
definition: "Research-grade, CRT-replacement LCD display system for vision science and psychophysics. It combines a 22.5″ 1920×1200 industrial LCD (wide 176°/176° viewing angles) with a custom panel/video controller engineered for deterministic stimulus timing and synchronized acquisition. The display supports 12-bit intensity resolution per RGB channel via custom video modes. It uses a scanning RGB LED backlight to improve temporal precision (e.g., crisp frame transitions and reduced motion artifacts) while bypassing consumer “enhancement” processing to keep output predictable for experiments. VIEWPixx also integrates microsecond-synchronized peripherals commonly needed in timing-sensitive paradigms—24-channel TTL I/O (triggers), stereo audio I/O, analog I/O, and a button-box interface—implemented on the same board as the video pipeline for tight hardware-to-video synchronization." .
SCR:013272 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-06697" ;
rdfs:label "Ranking Tables of NIH Funding to US Medical Schools in 2010" ;
NIFRID:synonym "2010 Ranking Tables of NIH Funding" ;
definition: "Excel files available for download of ranking tables of NIH Funding to US Medical Schools in 2010, school and Principal Investigator (PI) rankings by Medical School Department, direct plus indirect costs (excluding both R & D contracts and American Recovery and Reinvestment Act (ARRA) Awards), etc. Categories under the Basic Science Department and Clinical Science Department are available as well as the rank of each School of Medicine from 2001-2010. The data in the 2010 Award files was obtained from the Research Portfolio Online Reporting Tool (RePORT) from the National Institutes of Health at http://report.nih.gov/award/trends/AggregateData.cfm. The Award Data correspond to the US Government fiscal year. Awards for 2010 correspond to those granted from 1 October 2009-30 September 2010. There is considerable variation on how universities credit awards and how the NIH deals with these variations." .
SCR:013273 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-10477" ;
rdfs:label "SPM Anatomy Toolbox" ;
definition: "A MATLAB toolbox which uses three dimensional probabilistic cytoarchitechtonic maps to correlate microscopic, anatomic and functional data of the cerebral cortex. Correlating the activation foci identified in functional imaging studies of the human brain with structural (e.g., cytoarchitectonic) information on the activated areas is a major methodological challenge for neuroscience research. We here present a new approach to make use of three-dimensional probabilistic cytoarchitectonic maps, as obtained from the analysis of human post-mortem brains, for correlating microscopical, anatomical and functional imaging data of the cerebral cortex. We introduce a new, MATLAB based toolbox for the SPM2 software package which enables the integration of probabilistic cytoarchitectonic maps and results of functional imaging studies. The toolbox includes the functionality for the construction of summary maps combining probability of several cortical areas by finding the most probable assignment of each voxel to one of these areas. Its main feature is to provide several measures defining the degree of correspondence between architectonic areas and functional foci. The software, together with the presently available probability maps, is available as open source software to the neuroimaging community. This new toolbox provides an easy-to-use tool for the integrated analysis of functional and anatomical data in a common reference space." .
SCR:013274 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00360" ;
rdfs:label "GLOM MAP is a toolbox written for the MATLAB development enviroment" ;
NIFRID:synonym "GLOM MAP" ;
definition: " :GLOM MAP was written for MATLAB, it works equally as well on the PC as on the MAC. GLOM MAP consists of two components: 1. OBS can be used to map the location of glomeruli in transverse sections of the olfactory bulb. 2. GDB can be used to transform the OBS data and to analyze the collected glomerular activity data. This data can be scored and mapped in the radial and anterio-posterior dimensions as discussed in Salcedo et al, 2005. :" .
SCR:013275 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:genesigdb",
"nlx_149342" ;
rdfs:label "GeneSigDB" ;
NIFRID:synonym "Gene Signature Data Base",
"GeneSigDB - Curated Gene Signatures Database" ;
definition: "Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service." .
SCR:013276 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33024" ;
rdfs:label "i2b2 Research Data Warehouse" ;
NIFRID:synonym "Informatics for Integrating Biology and the Bedside",
"Informatics for Integrating Biology and the Bedside Research Data Warehouse" ;
NIFRID:abbrev "i2b2" ;
definition: "A data warehouse that integrates information on patients from multiple sources and consists of patient information from all the visits to Cincinnati Children' '''s between 2003 and 2007. This information includes demographics (age, gender, race), diagnoses (ICD-9), procedures, medications and lab results. They have included extracts from Epic, DocSite, and the new Cerner laboratory system and will eventually load public data sources, data from the different divisions or research cores (such as images or genetic data), as well as the research databases from individual groups or investigators. This information is aggregated, cleaned and de-identified. Once this process is complete, it is presented to the user, who will then be able to query the data. The warehouse is best suited for tasks like cohort identification, hypothesis generation and retrospective data analysis. Automated software tools will facilitate some of these functions, while others will require more of a manual process. The initial software tools will be focused around cohort identification. They have developed a set of web-based tools that allow the user to query the warehouse after logging in. The only people able to see your data are those to whom you grant authorization. If the information can be provided to the general research community, they will add it to the warehouse. If it cannot, they will mark it so that only you (or others in your group with proper approval) can access it." .
SCR:013277 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_144052" ;
rdfs:label "Loyola University Medical Center / Hines VA Brain Bank" ;
NIFRID:synonym "Loyola University / Hines Brain Bank",
"Loyola University Brain Bank",
"Loyola University Medical Center/Hines VA Brain Bank" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. A medical center with a neuropathology research program focused on the normal and abnormal aging process of the central nervous system and a funding source for research. The center serves as a collection site for brains in order to study normal aging and neurodegenerative diseases like Alzheimer's." .
SCR:013278 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:plantnatsdb",
"nlx_151492" ;
rdfs:label "PlantNATsDB - Plant Natural Antisense Transcripts DataBase" ;
NIFRID:synonym "Plant Natural Antisense Transcripts DataBase" ;
NIFRID:abbrev "PlantNATsDB" ;
definition: "Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources involving approximately 2 million NAT pairs in 69 plant species. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. A ' '''Gene Set Analysis' ''' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs." .
SCR:013279 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_25068" ;
rdfs:label "Trinity Biobank" ;
definition: "The Trinity Biobank was established in 2005 to serve the needs of researchers in the area of genetic epidemiology, population genetics and pharmacogenomics. Its services are available to researchers not only in Trinity College but to other institutions at home and abroad. We provide an automated DNA extraction service purifying large volumes blood (up to 10mL whole blood) and tissue DNA for archival and other purposes. In addition it makes available purified DNA and associated GWAS data from 2000 healthy donors for research use. A key requirement for reliable downstream use of DNA is purity and strand size. The quality of DNA in blood and tissue deteriorates upon storage without purification even at -80 degrees C. We ensure rapid turnaround of biological samples through automated extraction using the Qiagen Autopure system based on optimized ''salting out'' chemistry. The purified DNA sample may then be stored safely at -20 degrees C without deterioration thus freeing up valuable -80 degree C freezer space and the associated capital and maintenance cost as well as security and lab space provision. Automated DNA extraction is particularly suitable for high-throughput sample processing called for in epidemiological studies or simply for clearing sample inventory backlogs. The Trinity Biobank distributes control DNA to researchers as part of its remit to enhance the level of research activity and to synergize molecular medicine research nationally and internationally. The buffy coat collection has been made possible with the cooperation of the Irish Blood Transfusion Service (IBTS). An important requirement to access the collection is that the use of the samples relates only to ethically-approved research and to specifically-nominated research projects. The DNA collection consists of high quality human genomic DNA. Each of the available 2,000 samples is from a single individual and each sample comes with the age and gender data of the donor. The buffy coat sample is derived from the total white cell compliment (50mL buffy coat) of a blood donation (c 400mL). We will endeavor to fulfill samples number requests based on age and gender as best as possible. This collection has also been genotyped using the Affymetrix Genome-Wide Human SNP Array 6.0, featuring 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation (CNV). The DNA comes available as a 100ng/uL in 100uL of TE Buffer, ie in 10ug amounts in a separate screw-cap ampoule. The ampoules are shipped in 100-tube boxes (Sarstedt). Corresponding plasma (ACD) is also available on request. Genotype data is supplied in PLINK binary PED files format (http://pngu.mgh.harvard.edu/~purcell/plink/ )." .
SCR:013280 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02717" ;
rdfs:label "Kyushu University Definitive Haplotype Database" ;
NIFRID:synonym "D-HaploDB" ;
definition: "D-HaploDB genome-wide definitive haplotypes, determined using a collection of 100 Japanese complete hydatidiform moles (CHMs), each carrying a genome derived from a single sperm. The haplotypes incorporate 281 k (D-Haplo Phase I: D1), 581k (D-Haplo Phase II: D2), or 1M (D-Haplo Phase III: D3) SNPs, genotyped with high throughput array-based oligonucleotide hybridization techniques. The Definitive Haplotype Browser can be used to view various information, such as SNP alleles, haplotype blocks, LD-bins and extended shared haplotypes (ESHs) in our study." .
SCR:013281 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:list_ontologies",
"biotools:ontoquest_ws",
"nlx_151737" ;
rdfs:label "OntoQuest" ;
NIFRID:synonym "Ontoquest" ;
definition: "An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework." .
SCR:013282 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00307" ;
rdfs:label "Gtk-based Analyze Image Viewer" ;
NIFRID:synonym "GpetView" ;
definition: "GpetView is light-weight image viewer based on Gtk+ library. The supported image format is ANALYZE(TM) format (Mayo Foundation ). GpetView can run on Unix-systems, such as Linux, Solaris, IRIX, Mac OS-X etc. From Version 2.0, GpetView can also run on Win32 system, if you have installed Glib and Gtk+(2.x). Glib andGtk+ can be found at http://www.gtk.org. For Windows users, you can find Gtk+ libraries at http://gladewin32.sourceforge.net/modules/news/ GpetView has the following features: * very light-weight * view images as transverse, coronal, or sagittal * change color-map (support Analyze lkup file) * zoom images * ROI (Region-Of-Interest) with shapes of circle, ellipse, rectangle, polygon and automatic edge detection * Image histogram and profile Sponsors: This resource is supported by Osaka University. Keywords: Image, Viewer, Software, Transverse, Coronal, Sagittal, Map, Histogram," .
SCR:013283 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:chimeraslayer",
"OMICS_01113" ;
rdfs:label "ChimeraSlayer" ;
definition: "A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp)." .
SCR:013284 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01610" ;
rdfs:label "Mpstruct" ;
NIFRID:synonym "Membrane Proteins of Known 3D Structure" ;
definition: "Table providing information about integral membrane proteins whose crystallographic, or sometimes NMR, structures have been determined to a resolution sufficient to identify TM helices of helix-bundle membrane proteins (typically 4 - 4.5 angstroms). It is based upon Preusch et al. (1998) as revised by White & Wimley (1999). Reference is made to all of the protein types whose structures have been determined. They have attempted to make the database as inclusive as possible." .
SCR:013285 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154549" ;
rdfs:label "PRESTO: Genetic Association Analysis Software" ;
definition: "Software application that performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data." .
SCR:013287 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_56826" ;
rdfs:label "Effect of Deep Brain Stimulation on Parkinsonian Tremor" ;
definition: "Effect of Deep Brain Stimulation on Parkinsonian Tremor: The recordings of this database are of rest tremor velocity in the index finger of 16 subjects with Parkinson''s disease (PD) who receive chronic high frequency electrical deep brain stimulation (DBS) either uni- or bi-laterally within one of three targets: Vim = the ventro-intermediate nucleus of the thalamus (n=3),GPi = the internal Globus pallidus (n=7), or STN = the subthalamic nucleus (n=6)." .
SCR:013289 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154299" ;
rdfs:label "ENDOG" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software application that calculates individual inbreeding (F) and average relatedness (AR) coefficients. Additionally, users can compute useful parameters in population genetics such as: the number of ancestors explaining genetic variability; the genetic importance of the herds; F statistics from genealogical information. (entry from Genetic Analysis Software)" .
SCR:013290 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:RDXplorer",
"OMICS_00349" ;
rdfs:label "RDXplorer" ;
definition: "A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage." .
SCR:013291 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:macs",
"OMICS_00446" ;
rdfs:label "MACS" ;
NIFRID:synonym "MACS2",
"MACS - Model-based Analysis for ChIP-Seq",
"Model-based Analysis for ChIP-Seq" ;
definition: "Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity." .
SCR:013292 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00370" ;
rdfs:label "wapRNA" ;
definition: "A free web-based application for the processing of high-throughput RNA-Seq data from next generation sequencing (NGS) platforms, such as Genome Analyzer of Illumina Inc. (Solexa) and SOLiD of Applied Biosystems (SOLiD)." .
SCR:013293 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30454" ;
rdfs:label "Diogenes" ;
definition: "Diogenes is a pan-European Programme targeting the obesity problem from a dietary perspective: seeking new insights and new routes to prevention. An Integrated Project of the EU Sixth Framework Programme for Research and Technological Development (2005-2009). A new methodology has been developed for consistent assignment of GI values to foods across the five European databases used in the Diogenes intervention study. GI values have been assigned according to five decreasing levels of confidence: (1) Measured values for specific foods; (2) Published values from published sources; (3) Equivalent values where published values for similar foods existed; (4) Estimated values three values selected representing low/medium/high GI ranges; (5) Nominal values assigned as 70, where no other value could be assigned with sufficient confidence. Sponsor. A a r h u s K a r l s h a m n D e n m a r k A / S Products: Vegetable Oils (Maize and Rapeseed) click here for the link to the website of AarhusKarlshamn Denmark B a r i l l a Products: Pasta click here for the link to the website of Barilla B e a u v a i s Products: Canned fish products, jam, soups & convenience foods click here for the link to the website of Beauvais C a m p i n a I n s t i t u t e At the Campina Institute dairy products and science come together. The Campina brands include among others: Optimel/ Optiwel, Vifit, Milner, Valess Click here for the link to the website of Campina Institute C o c a - C o l a S e r v i c e s S . A . Products: beverages click here for the link to the website of Coca-Cola Services S.A. D a l o o n Products: Spring rolls and other convenience foods click here for the link to the website of Daloon D a n g S / A Products: egg products click here for the link to the website of Dang A/S D a n i s c o Products: Sugar (different types) click here for the link to the website of Danisco D a n i s h D a i r y B o a r d Products: Dairy products (milk, yoghurt, cheese) click here for the link to the website of the Danish Dairy Board D a n s k e S l a g t e r i e r Products: Pig Meat Products (various types) click here for the link to the website of Danske Slagterier D r . O e t k e r Products: Ready meals click here for the link to the website of Dr. Oetker E u r o g r a n A / S Products: Instant chocolate, cappuccino, soup and mashed poptatoes click here for the link to the website of Eurogran A/S F r i g o d a n Products: Frozen vegetables click here for the link to the website of Frigodan F r i s k o Products: Ice cream click here for the link to the website of Frisko G a m b a F o o d Products: Frozen fish (different types of European and Asian origin) G i l d e N o r g e B A Products: meat click here for the link to the website of Gilde Norge BA H a t t i n g Products: Bread products (different types) click here for the link to the website of Hatting H e i n z Products: ketchup and a broad range of products under HONIG, Konininklijke de Ruijter, VENZ, Carvan Cevitan, Roosvicee click here for the link to the website of Heinz H j e r t i n g L a k s Products: salmon products click here for the link to the website of Hjerting Laks K e l l o g g '' s D e n m a r k Products: different types of Breakfast Cereals Click here for the link to the website of Kellogg''s Denmark K e l l o g g '' s E u r o p e Products: Ready-To-Eat Cereals and Cereal Bars Click here for the link to the website of Kellogg''s K d b r a n c h e n s F l l e s r d Products: meat: beaf and veal click here for the link to the website of Kdbranchens Fllesrd K r a f t Products: chocolate, Philadelphia cream cheese, pasta, Estrella chips & nuts, mayonaise, salad dressings click here for the link to the website of Kraft L a n t m n n e n M i l l s A / S Products: various grains and flour L U , G e n e r a l B i s c u i t s N e d e r l a n d B . V . Products: biscuits click here for the link to the website of LU L y k k e b e r g A / S Products: Fish (marinated herring) click here for the link to the website of Lykkeberg A/S M a s t e r f o o d s Products: Rice and confectionery click here for the different websites of Masterfoods: Uncle Bens, Mars, Twix, Snickers, M&M''s, Masterfoods N u t r i t i o n e t S a n t / M o d i f a s t Products: Modifast (Low Calorie Diet) click here for the link to the website of Nutrition et Sant click here for the link to the website of Modifast P a r t n e r s h i p f o r D a n i s h P o t a t o e s Products: potatoes (different varieties) click here for the link to the website of the Partnership for Danish Potatoes P a s t a l i f e Products: pasta (with high protein content) click here for the link to the website of Pastalife R a h b e k Products: Frozen, ready-made fish dishes click here for the link to the website of Rahbek R i e b e r & S n D a n m a r k A / S Products: mustard, ketchup, mayonnaise, sanwich filling, spreads and other dressings click on the following links for the different websites of Rieber and Sn Danmark A/S: Rieberson, Bahncke, K-Salat R o y a l G r e e n l a n d A / S Products: cold-water prawns click here for the link to the website of Royal Greenlands A/S S c h u l s t a d Products: Rye bread and wheat bread, including high- and low GI varieties click here for the link to the website of Schulstad S n d e r j y d s k K l Products: Frozen kale, spinach and cabbage. click here for the link to the website of Snderjydsk Kl S u i k e r U n i e Products: different types of sugar click here for the link to the website of Suiker Unie T u l i p F o o d C o m p a n y Products: Meat products (cold cuts, cooked meat, bacon, meat balls, ready-meals, soups etc.) Click here for the link to the website of Tulip Food Company U n i l e v e r Products: a broad range of products under Becel, Bertolli, Calv, Knorr, Iglo, Mora, Conimex, Unox click here for the link to the website of Unilever W a s a b r d A / S Products: Crisp bread click on the following links for the different websites of Wasabrd A/S: Wasa Denmark or Wasa International" .
SCR:013294 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01013" ;
rdfs:label "SeqTRACS" ;
NIFRID:synonym "SeqTRACS: LIMS for sequencing core facilities" ;
definition: "Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility." .
SCR:013295 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30439" ;
rdfs:label "Swiss-PdbViewerDeepViewv4.0" ;
NIFRID:synonym "DeepView" ;
definition: "First of all, and most importantly, PC and Mac versions have been resynchronized. Support for direct login modelling submissions and result retrieval to/from the SwissModel Workspace Enhanced Import Menu Enhanced user interface with taxonomy support, and new sequence alignment features. New 3D Motif Searching feature Easy access to external user defined scripts directly from the interface Revised Help files accessible from the interface Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modeling tools are integrated and command files for popular energy minimization packages can be generated. Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images." .
SCR:013296 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:macie",
"nif-0000-03093" ;
rdfs:label "MACiE" ;
NIFRID:synonym "Annotation and Classification in Enzymes",
"Mechanism",
"The MACiE Database" ;
definition: "MACiE, which stands for Mechanism, Annotation and Classification in Enzymes, is a collaborative project on enzyme reaction mechanisms. MACiE currently contains 223 fully annotated enzyme reaction mechanisms, which comprise 218 EC numbers (161 EC sub-subclasses) and 310 distinct CATH codes. It is a joint effortbetween the Mitchell Group at the Unilever Centre for Molecular Informatics part of the University of Cambridge and the Thornton Group at the European Bioinformatics Institute." .
SCR:013297 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_71249" ;
rdfs:label "Apnea-ECG Database" ;
definition: "Apnea-ECG Database has been assembled for the PhysioNet/Computers in Cardiology Challenge 2000. It consists of 70 ECG recordings, each typically 8 hours long, with accompanying sleep apnea annotations obtained from study of simultaneously recorded respiration signals, which are included for 8 of the recordings." .
SCR:013298 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:chimerascan",
"OMICS_01343" ;
rdfs:label "chimerascan" ;
definition: "Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data." .
SCR:013299 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_155833" ;
rdfs:label "VPixx | PROPixx" ;
NIFRID:synonym "PROPixx DLP LED projector" ;
NIFRID:abbrev "PROPixx" ;
definition: "Unique DLP LED projector which has been designed to be the most flexible display solution for vision research and neuroscience research. The PROPixx features a native resolution of 1920 x 1080, and can be driven with refresh rate up to 500Hz with deterministic timing. The PROPixx uses high brightness LEDs as a light source, giving a wide colour gamut and much longer lifetime than halogen light sources. It features high-bit depth, up to 12-bit per color for high-frequency full colour stimulation. For stereo vision applications, our high-speed ferro-electric circular polarizer can project stereoscopic stimuli with the use of passive glasses at up to 400Hz. In addition the PROPixx includes an array of peripherals which often need to be synchronized to video during an experiment, and with perfect microsecond precision." .
SCR:013300 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00233" ;
rdfs:label "NIDA Drug Supply Program" ;
definition: "Supplies chemicals and research probes that are either unavailable, difficult to obtain, or very expensive to buy to researchers. In addition, this program also provides analytical services for the analysis of researchers experimental samples. The NIDA Drug Supply Program is administered by the Chemistry & Physiological Systems Research Branch." .
SCR:013301 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154239" ;
rdfs:label "BEAGLECALL" ;
definition: "Software package for simultaneous genotype calling and haplotype phasing for unrelated individuals. BEAGLECALL produces output posterior genotype probabilities and output phased haplotypes. BEAGLECALL generates extremely accurate genotype calls because it uses both allele signal intensity data and inter-marker correlation to call genotypes. BEAGLECALL is designed for use with high-density SNP arrays, and it uses the BEAGLE haplotype frequency model to model inter-marker correlation. (entry from Genetic Analysis Software)" .
SCR:013302 a NIFSTD:NEMO_0569000,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.471400.6",
"ISNI:0000 0001 2301 2088",
"nlx_144491",
"Wikidata:Q4120165" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA" ;
NIFRID:synonym "Perelman School of Medicine",
"Raymond & Ruth Perelman School of Medicine",
"University of Pennsylvania Perelman School of Medicine",
"University of Pennsylvania School of Medicine" ;
NIFRID:abbrev "Penn Medicine" ;
definition: "Medical school of the University of Pennsylvania. It is located in the University City section of Philadelphia." .
SCR:013303 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154370" ;
rdfs:label "GWASELECT" ;
definition: "Software application that implements a novel variable selection method for GWAS data and is able to handle more than half million SNPs. Extensive simulation studies and real data analysis show that this method enjoys high power and low false discovery rate compared to existing variable selection methods. The variables selected by GWASelect can be readily placed into a logistic regression model for disease prediction. The current release is designed for binary outcome under the additive mode of inheritance. (entry from Genetic Analysis Software)" .
SCR:013304 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154396" ;
rdfs:label "HEGESMA" ;
NIFRID:synonym "HEterogeneity and GEnome Search Meta Analysis" ;
definition: "Software application for performing genome scan meta-analysis, a quantitative method to identify genetic regions (bins) with consistently increased linkage score across multiple genome scans, and for testing the heterogeneity of the results of each bin across scans. The program provides as an output the average of ranks and three heterogeneity statistics, as well as corresponding significance levels. (entry from Genetic Analysis Software)" .
SCR:013305 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02935",
"OMICS_01887" ;
rdfs:label "Human Transcriptome Database for Alternative Splicing" ;
NIFRID:synonym "H-DBAS - Human-transcriptome DataBase for Alternative Splicing" ;
NIFRID:abbrev "H-DBAS" ;
definition: "A specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. H-DBAS offers unique data and viewer for human Alternative Splicing (AS) analysis. It contains: * Genome-wide representative alternative splicing variants (RASVs) identified from following datasets * H-Inv full-length cDNAs (resource summary): H-Invitational cDNA dataset * H-Inv all transcripts (resource summary): Published human mRNA dataset * Mouse full-length cDNAs (resource summary): Mouse cDNA dataset * RASVs affecting protein functions such as protein motif, GO, subcellular localization signal and transmembrane domain * Conserved RASVs compared with mouse genome and the full-length cDNAs (H-Inv full-length cDNAs only)" .
SCR:013306 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:crossbow",
"OMICS_00284" ;
rdfs:label "Crossbow" ;
definition: "A scalable software pipeline for whole genome resequencing analysis." .
SCR:013308 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152415" ;
rdfs:label "MP Biomedicals" ;
definition: "An Antibody supplier" .
SCR:013309 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154019" ;
rdfs:label "SNIPPEEP" ;
definition: "Software application that is an interactive graphic interface to visualise results from whole genome genotyping. It allows one to visualise single subjects and groups of subjects, and provides a direct connection with the UCSC Genome Browser. (entry from Genetic Analysis Software)" .
SCR:013310 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152294" ;
rdfs:label "Bender MedSystems" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017.\\\\\\\\\\\\
\\\\\\\\\\\\
An Antibody supplier." .
SCR:013311 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152292" ;
rdfs:label "BD Biosciences" ;
NIFRID:synonym "BD Biosciences - Discovery Labware" ;
definition: "An Antibody supplier" .
SCR:013312 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_156921",
"r3d100010859" ;
rdfs:label "WoRMS" ;
NIFRID:synonym "World Register of Marine Species" ;
definition: "An authoritative and comprehensive list of names of marine organisms, including information on synonymy. While highest priority goes to valid names, other names in use are included so that this register can serve as a guide to interpret taxonomic literature. The content of WoRMS is controlled by taxonomic experts, not by database managers. WoRMS has an editorial management system where each taxonomic group is represented by an expert who has the authority over the content, and is responsible for controlling the quality of the information. Each of these main taxonomic editors can invite several specialists of smaller groups within their area of responsibility to join them. This register of marine species grew out of the European Register of Marine Species (ERMS), and its combination with several other species registers maintained at the Flanders Marine Institute (VLIZ). Rather than building separate registers for all projects, and to make sure taxonomy used in these different projects is consistent, VLIZ developed a consolidated database called ''Aphia''. A list of marine species registers included in Aphia is available below. MarineSpecies.org is the web interface for this database. The WoRMS is an idea that is being developed, and will combine information from Aphia with other authoritative marine species lists which are maintained by others (e.g. AlgaeBase, FishBase, Hexacorallia, NeMys). Resources to build MarineSpecies.org and Aphia were provided mainly by the EU Network of Excellence ''Marine Biodiversity and Ecosystem Functioning'' (MarBEF), and also by the EU funded Species 2000 Europe and ERMS projects. Intellectual property rights of the European part of the register is managed through the Society for the Management of Electronic Biodiversity Data (SMEBD). Similar solutions are now being investigated for the other parts of the register." .
SCR:013313 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30585" ;
rdfs:label "Francisella tularensis Genome Research" ;
NIFRID:synonym "Francisella tularensis" ;
definition: "Francisella tularensis is a Gram-negative bacteria that causes the disease tularemia. The genus also includes the strains Francisella novicida and Francisella holarctica, both of which are important research organisms. The biology, genomes and virulence capabilities of these organism are under active investigation in research institutions throughout the world. Our goal for the francisella.org website is to foster communication and collaboration among the Francisella tularensis research community. rancisella tularensis is a Gram-negative bacteria that causes the disease tularemia. The genus also includes the strains Francisella novicida and Francisella holarctica, both of which are important research organisms. The biology, genomes and virulence capabilities of these organism are under active investigation in research institutions throughout the world. Our goal for the francisella.org website is to foster communication and collaboration among the Francisella tularensis research community. Please visit the following sections of the website for more details about the tools currently available and those to be available in the near future. News 04/17/2008 F. novicida transposon mutant orders are now being handled by BEI Resources. 03/25/2008 New features have been added to the PSAT synteny analysis tool including a printer friendly version of the genomic neighborhood graphic, a text output of homologs in a region in spreadsheet format, and an option for displaying multiple alignments for a gene against a single comparison genome. 02/07/2008 Proteomics experimental data for F. novicida are now integrated into our genome browser. 02/05/2008 Updated genome annotations can now be submitted using the Panda tool. Your participation is encouraged. Please see the Panda page for more information. 02/04/2008 F. holarctica FTA is now available from Genbank (NC_009749) and has been added to our genome browser Tools Name Description Get surrounding sequence Given a gene, other genome feature, or genome coordinate, displays in FASTA format the surrounding sequence a specified number of nucleotides upstream and downstream Synteny Tool Analyze potential regions of local synteny between the Francisella genomes and any other published bacterial genome" .
SCR:013314 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02861" ;
rdfs:label "FusionDB" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. FusionDB is a database of bacterial and archaeal gene fusion events - also known as Rosetta stones. Gene-fusion events are not the only resource to determine functional links between two proteins. Similar phylogenetic profiles and conserved chromosomal co-localization can also be used as an indicator for such interactions." .
SCR:013315 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01241" ;
rdfs:label "HMMSplicer" ;
definition: "An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets." .
SCR:013316 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00371" ;
rdfs:label "MicroRazerS" ;
definition: "A software tool optimized for mapping short RNAs onto a reference genome." .
SCR:013317 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-10200" ;
rdfs:label "Computational Neurobiology and Imaging Center" ;
NIFRID:abbrev "CNIC" ;
definition: "Center to advance research and training in mathematical, computational and modern imaging approaches to understanding the brain and its functions. Software tools and associated reconstruction data produced in the center are available. Researchers study the relationships between neural function and structure at levels ranging from the molecular and cellular, through network organization of the brain. This involves the development of new computational and analytic tools for imaging and visualization of 3-D neural morphology, from the gross topologic characteristics of the dendritic arbor to the fine structure of spines and their synapses. Numerical simulations of neural mechanisms based on these structural data are compared with in-vivo and in-vitro electrophysiological recordings. The group also develops new theoretical and analytic approaches to exploring the function of neural models of working memory. The goal of this analytic work is to combine biophysically realistic models and simulations with reduced mathematical models that capture essential dynamical behaviors while reproducing the functionally important features of experimental data. Research areas include: Imaging Studies, Volume Integration, Visualization Techniques, Medial Axis Extraction, Spine Detection and Classification, Applications of Rayburst, Analysis of Spatially Complex Structures, Computational Modeling, Mathematical and Analytic Studies" .
SCR:013318 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152414" ;
rdfs:label "Molecular Probes" ;
NIFRID:synonym "Invitrogen",
"Molecular Probes (Invitrogen)" ;
definition: "An Antibody supplier and subset of ThermoFisher Scientific which provides fluorescence reagents for various experiments and methods." .
SCR:013319 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152291" ;
rdfs:label "BBInternational" ;
NIFRID:synonym "BBI Solutions" ;
definition: "An Antibody supplier" .
SCR:013320 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152057" ;
rdfs:label "New Beneficiary Data System" ;
NIFRID:synonym "New Beneficiary Data System (NBDS)" ;
NIFRID:abbrev "NBDS" ;
definition: "Data set of extensive information on the changing circumstances of aged and disabled beneficiaries - Living, noninstitutionalized population of the continental United States from the Social Security Administration' '''s Master Benefit Record who were new recipients of Social Security benefits (first payment in mid-1980 through mid-1981) or who had established entitlement to Medicare and were eligible for, but had not received, Social Security benefits as of July 1982. Based initially on a national cross-sectional survey of new beneficiaries in 1982, the original data base was expanded with information from administrative records and a second round of interviews in 1991. Variables measured in the original New Beneficiary Survey (NBS) include demographic characteristics; employment, marital, and childbearing histories; household composition; health; income and assets; program knowledge; and information about the spouses of married respondents. The 1991 New Beneficiary Follow-up (NBF) updated marital status, household composition, and the economic profile and contains additional sections on family contacts, postretirement employment, effects of widowhood and divorce, major reasons for changes in economic status, a more extensive section on health, and information on household moves and reasons for moving. Disabled-worker beneficiaries were also asked about their efforts to return to work, experiences with rehabilitation services, and knowledge of SSA work incentive provisions. The NBDS also links to administrative files of yearly covered earnings from 1951 to 1992, Medicare expenditures from 1984 to 1999, whether an SSI application has ever been made and payment status at five points in time, and dates of death as of spring 2001. For studies of health, the Medicare expenditure variables include inpatient hospital costs, outpatient hospital costs, home health care costs, and physicians' ''' charges. The survey data cover functional capacity including ADLs and IADLs. For studies of work in retirement, the survey includes yearly information on extent of work, characteristics of the current or last job, and reasons for working or not working. No other data set has such detailed baseline survey data of a population immediately after retirement or disability, enhanced with subsequent measures over an extended period of time. The data are publicly available through NACDA and the Social Security Administration Website. * Dates of Study: 1982-1991 * Study Features: Longitudinal * Sample Size: ** 18,136 (NBS 1981) ** 12,677 (NBF 1991) Links: * 1982 (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/08510 * 1991 (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06118" .
SCR:013321 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:psrnatarget",
"OMICS_00414" ;
rdfs:label "psRNATarget" ;
NIFRID:synonym "psRNATarget: A Plant Small RNA Target Analysis Server" ;
definition: "A plant small RNA target analysis server which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to ?open? secondary structure around miRNA?s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript. PsRNATarget is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded miRNAs and transcript sequences; and outputs a comprehensive list of miRNA / target pairs along with the online tools for batch downloading, key word searching and results sorting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013322 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:trans-abyss",
"OMICS_01326" ;
rdfs:label "Trans-ABySS" ;
definition: "A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data." .
SCR:013323 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03450" ;
rdfs:label "SeedGenes" ;
definition: "A database of genes that give a seed phenotype when disrupted by mutation. The long-term goal of this project is to establish a comprehensive dataset of essential genes. The updated project database (December, 2007) presents information on 358 genes and 605 mutants. More than 60% of these mutants have been analyzed in the Meinke laboratory (Stillwater, OK)." .
SCR:013324 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01281" ;
rdfs:label "NEUMA" ;
NIFRID:synonym "Normalization by Expected Uniquely Mappable Area" ;
definition: "Software for estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency (''consistency coefficient'') for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data." .
SCR:013325 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01715" ;
rdfs:label "Homologus" ;
definition: "A blog on transcriptomics, bioinformatics and computational biology." .
SCR:013326 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_38706" ;
rdfs:label "ZFIN Antibody Wiki" ;
NIFRID:synonym "ZFIN Community Antibody Wiki" ;
definition: "A catalog of antibodies important for zebrafish research, maintained by ZFIN. ZFIN Antibody Wiki is where zebrafish researchers can help each other by sharing antibody information - new antibodies, protocols, tips - anything that might be helpful." .
SCR:013327 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID: 501100000038",
"grid.452912.9",
"ISNI: 0000 0004 0408 2381",
"nlx_39429",
"Wikidata: Q2993807" ;
rdfs:label "Natural Sciences and Engineering Research Council of Canada" ;
NIFRID:synonym "Conseil de recherches en sciences naturelles et en genie du Canada" ;
NIFRID:abbrev "CRSNG",
"NSERC" ;
definition: "NSERC aims to make Canada a country of discoverers and innovators for the benefit of all Canadians. The agency supports university students in their advanced studies, promotes and supports discovery research, and fosters innovation by encouraging Canadian companies to participate and invest in postsecondary research projects. NSERC researchers are on the vanguard of science, building on Canada''s long tradition of scientific excellence." .
SCR:013328 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03221" ;
rdfs:label "OperonDB" ;
definition: "Operon DB is a method to detect and analyze conserved gene pairs - pairs of genes that are located close on the same DNA strand in two or more bacterial genomes. For each conserved gene pair, we calculate an estimate of probability that the genes belong to the same operon. The algorithm takes into account several alternative possibilities. One is that functionally unrelated genes may have the same order due simply because they were adjacent in a common ancestor. Other possibilities are that genes may be adjacent in two genomes by chance alone, or due to horizontal transfer of the gene pair." .
SCR:013329 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01351" ;
rdfs:label "FusionSeq" ;
definition: "A modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data." .
SCR:013330 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03289" ;
rdfs:label "Pig Genomic Informatics System" ;
NIFRID:abbrev "PigGIS" ;
definition: "It presents accurate pig gene annotations in all sequenced genomic regions. It integrates various available pig sequence data, including 3.84 million whole-genome-shortgun (WGS) reads and 0.7 million Expressed Sequence Tags (ESTs) generated by Sino-Danish Pig Genome Project, and 1 million miscellaneous GenBank records. The Pig Analysis Database has covered nearly 50% of the whole pig genome and over 70% of the coding sequences (CDS), and aims to provide the most complete pig gene set to date. In addition to gene annotations, the PigGIS also presents expressional information from 98 EST libraries, SNPs detected from both WGS reads and ESTs, oligos that can be used in microarray design and relevant evolutionary data. SIFT analysis of deleterious mutations will come in future." .
SCR:013331 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03314",
"r3d100011569",
"SCR_017665" ;
rdfs:label "PlasmoDB" ;
NIFRID:synonym "PlasmoDB 5.5",
"Plasmodium genome-resource",
"Plasmodium Genomics Resource" ;
definition: "Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene." .
SCR:013332 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00985" ;
rdfs:label "Probalign" ;
NIFRID:synonym "Probalign: multiple sequence alignment using partition function posterior probabilities" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software that uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. Computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.Produces accurate alignments on long and heterogeneous length datasets containing protein repeats." .
SCR:013333 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00461" ;
rdfs:label "Center for New Technology Enterprise" ;
NIFRID:synonym "The Center for New Technology Enterprise" ;
NIFRID:abbrev "CNTE" ;
definition: "It is an independent nonprofit organization established to provide meaningful trans-disciplinary experiential education to students by making the most cutting-edge instructional methods and technologies available to them to bring new inventions to the marketplace and to encourage knowledge sharing and collaboration among its numerous constituencies. The Center provides a comprehensive program in which its students learn and acquire real-world experience by assisting universities, private and public research institutions, companies, and entrepreneurs to evaluate new technologies and facilitate the creation and development of new ventures. By offering a virtual venue for students and other constituencies worldwide, our stakeholders and collaborators can connect and share knowledge, expertise, resources, best practices, and other important information. Employers, investors and others searching for talent place a premium on relevant experience. However, students, individuals seeking a change in their careers, and prospective entrepreneurs often find it difficult to obtain positions that can provide needed experience, even if they are willing to work without compensation. This conundrum often leads to people taking or staying in positions for which they have no passion and which do not make the best use of their abilities. The Centers program is designed to provide extensive, intensive and relevant experience to its participants, with particular emphasis on teaching them to adapt to and thrive in our lightning fast, rapidly changing and increasingly flat world. As an independent organization, the Centers program and activities are not restricted to any particular institution or jurisdiction. Thus the Center can attract students, clients, professionals and other stakeholders, establish collaborations, and pursue other opportunities appropriate to its mission almost anywhere. eductional resource." .
SCR:013334 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02670" ;
rdfs:label "CnidBase" ;
definition: "CnidBase, the Cnidarian Evolutionary Genomics Database, is a tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians. In turn, CnidBase will help to illuminate the role of specific genes in shaping cnidarian biodiversity in the present day and in the distant past. CnidBase highlights evolutionary changes between species within the phylum Cnidaria and structures genomic and expression data to facilitate comparisons to non-cnidarian metazoans. CnidBase aims to further the progress that has already been made in the realm of cnidarian evolutionary genomics by creating a central community resource which will help drive future research and facilitate more accurate classification and comparison of new experimental data with existing data." .
SCR:013335 a owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_43313" ;
rdfs:label "Blue Ridge Institute for Medical Research; North Carolina; USA" ;
NIFRID:synonym "Blue Ridge Institute for Medical Research" ;
NIFRID:abbrev "BRIMR" ;
definition: "The goal of the Institute is to explore the interfaces of fundamental biological science, clinical science, and clinical care with a special emphasis on targeted cancer therapy. The current focus centers on signaling by protein kinases. These enzymes (protein kinases) play a key regulatory role in nearly every aspect of cell biology. Owing to the myriad actions of protein kinases, it is imperative that they be stringently regulated because aberrant activity of these enzymes can lead to a variety of diseases including, inter alia, cancer, diabetes and autoimmune, cardiovascular, degenerative, inflammatory, and nervous disorders. Because mutations and dysregulation of protein kinases play causal roles in human disease, these enzymes represent attractive drug targets. Our research focuses on the epidermal growth factor receptor protein-tyrosine kinase, Raf/Mek/Erk protein kinases, and on the regulation of tyrosine hydroxylase activity by protein phosphorylation. The Blue Ridge Institute for Medical Research is a Federal tax exempt 501(c)(3) non-profit organization incorporated in the State of North Carolina on 24 March 2006 (EIN 20-4665742; DLN 17053144012016)." .
SCR:013336 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-23920" ;
rdfs:label "Alcohol and Drug Abuse Institute (ADAI) Library: Alcohol, Drugs and Tobacco Web Links" ;
NIFRID:synonym "Alcohol Drugs and Tobacco" ;
definition: "This database contains links to 600+ Alcohol, Tobacco, and Other Drugs (ATOD) organizations and resources on the web. It can be viewed by name in the A-to-Z list, by category or you can type any keyword or phrase into the search box to find links that match your search term. The categorical list includes ATOD Research Centers, Information Resources, Treatment, Training, U.S. Gov''t Agencies, Internat''l Gov''t Agencies, Recovery, Washington State, Organizations/Advocacy, Professional Societies, Journals/Newsletters, Other Sites" .
SCR:013337 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30382" ;
rdfs:label "Functional Glycomics Research" ;
NIFRID:synonym "Functional Glycomics" ;
definition: "This Gateway is a collaboration between the Consortium for Functional Glycomics (CFG) and Nature Publishing Group (NPG), providing a comprehensive resource for functional glycomics research. Use this site to stay up-to-date on glycomics news, request CFG resources, and search databases of glycan-binding proteins, glycan structures, and glycosyltransferases. The Functional Glycomics Update provides a one-stop overview of the latest research in glycobiology for specialists and non-specialists alike. It is updated monthly to bring you the latest news and selected highlights from Nature journals. In addition, it will provide two featured articles a month on the most relevant advances in the field published in NPG and other top journals. By collating new articles into a key worded research library, we hope to provide a continuously updated and broad overview of the field. Sponsor. The CFG is a large international research initiative funded by NIGMS to elucidate the roles of carbohydrate-protein interactions in cell communication at the cell surface." .
SCR:013338 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154670" ;
rdfs:label "TAGIMPUTE" ;
NIFRID:synonym "TAGging-snp based IMPUTATE" ;
definition: "A command-line program for the imputation of untyped SNPs. tagIMPUTE is based on a few flanking SNPs that can optimally predict the SNP under imputation. (entry from Genetic Analysis Software)" .
SCR:013339 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154647" ;
rdfs:label "SNPMSTAT" ;
NIFRID:synonym "SNP Missing data STATistics" ;
definition: "A command-line program for the statistical analysis of SNP-disease association in case-control/cohort/cross-sectional studies with potentially missing genotype data. SNPMStat allows the user to estimate or test SNP effects and SNP-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty, study design and gene-environment dependence. For SNPs without missing data, the program performs the standard association analysis. For typed SNPs with missing data or untyped SNPs, the program performs the maximum-likelihood analysis. (entry from Genetic Analysis Software)" .
SCR:013340 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:snp_hitlink",
"nlx_154644" ;
rdfs:label "SNP HITLINK" ;
NIFRID:synonym "SNP HIgh-Throughput LINKage analysis system" ;
definition: "Software program providing a useful pipeline to directly connect SNP data and linkage analysis program. SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro. (entry from Genetic Analysis Software)" .
SCR:013341 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154070" ;
rdfs:label "MECPM" ;
NIFRID:synonym "Maximum Entropy Conditional Probability Moldeling" ;
definition: "Software application (entry from Genetic Analysis Software)" .
SCR:013342 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152282" ;
rdfs:label "Assay Biotech" ;
definition: "An Antibody supplier" .
SCR:013343 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152281" ;
rdfs:label "AS Diagnostik" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017.\\\\\\\\\\\\
\\\\\\\\\\\\
An Antibody supplier" .
SCR:013344 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03408" ;
rdfs:label "Rice Pipeline" ;
definition: "A unification tool which dynamically collects and compiles data from scientific databases in National Institute of Agrobiological Sciences (NIAS), and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Oryza sativa into easy to navigate. The mission of Rice PIPELINE is to provide a unique scientific resource of rice that pools publicly available data commonly sought after for any clone sequence, clone name, GenBank accession number, or keyword." .
SCR:013345 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00366" ;
rdfs:label "Coordination and sustainability of international mouse informatics resources" ;
NIFRID:synonym "CASIMIR" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2022. Much of the current effort in functional genomics, and our understanding of the biology of human disease, is underpinned by informatics infrastructures served by the scattered collection of relevant databases which exists in Europe. This infrastructure is essential for the support of a European Research Area in mouse functional genomics. CASIMIR, a coordination action of the 6th Framework Programme of the European Commission, will focus on co-ordination and integration of databases set up in support of FP5 and FP6 projects containing experimental data, including sequences, and material resources such as biological collections, relevant to the use of the mouse as a model organism for human disease. Interoperability of disseminated databases potentially provides enormous synergy in the provision, integration and analysis of a wide range of data with concomitant added value for research projects. Having set standards and benchmarks the proposed action will then reach out to co-ordinate other European and International databases and consult with the Community. EU FlagThe CASIMIR 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-2006-037811" .
SCR:013346 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:plan2l",
"OMICS_01192" ;
rdfs:label "PLAN2L" ;
NIFRID:synonym "PLAN2L: Plant Annotation to Literature",
"Plant annotation to literature" ;
definition: "A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned." .
SCR:013347 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154111",
"nlx_154582",
"SCR_000830" ;
rdfs:label "R/FEST" ;
NIFRID:synonym "FEST" ;
definition: "An R package for simulations and likelihood calculations of pair-wise family relationships using DNA marker data. (entry from Genetic Analysis Software)" .
SCR:013348 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03341" ;
rdfs:label "PROCOGNATE" ;
definition: "A database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam. The database contains an assignment of PDB ligands to the domains of structures as classified by the CATH, SCOP and Pfam databases. Cognate ligands have been identified using data from the ENZYME and KEGG databases and compared to the PDB ligand using graph matching to assess chemical similarity. Cognate ligands from the known reactions in ENZYME and KEGG for a particular enzyme are then assigned to enzymes structures which have EC numbers." .
SCR:013349 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152022" ;
rdfs:label "aGEM" ;
NIFRID:synonym "anatomic Gene Expression Mapping" ;
definition: "Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013350 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03177" ;
rdfs:label "National Antisense Transcript Database" ;
NIFRID:abbrev "NATsDB" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A resource that allows users to identify cis-NATs in eleven eukaryotic species, screening eight of these species for the first time and bringing the number of candidate SA pairs in human to 7,246. We construct this free and publicly accessible database that allows researchers to query the dataset." .
SCR:013351 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154452" ;
rdfs:label "MAOS" ;
NIFRID:synonym "Meta-Analysis with Overlapping Subjects" ;
definition: "Software application that implements valid and efficient statistical methods for meta-analysis of genomewide association studies with overlapping subjects. The current release performs logistic regression analysis of individual level data under the additive mode of inheritance. Data from genome-wide association studies are often analyzed jointly for the purposes of combining information from multiple studies of the same disease or comparing results across different disorders. In many instances, the same subjects appear in multiple studies. Failure to account for overlapping subjects can greatly inflate type I error when combining results from multiple studies of the same disease and can drastically reduce power when comparing results across different disorders. (entry from Genetic Analysis Software)" .
SCR:013352 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:dsap",
"OMICS_00357" ;
rdfs:label "DSAP" ;
definition: "A web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013353 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_49103" ;
rdfs:label "Alu Pairs Database" ;
definition: "On line database of alu pairs. This map file is a subfile of repbase (Genetic Information Research Institute(GIRI)), derived by comparing genomic sequences in the GenBank database (release 112.0, National center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD) with the Alu consensus sequence, was made in April 1999 and is maintained at the GIRI), Sunnyvale, CA). The Alu map includes the following information in columnar form: locus, beginning sequence position, ending sequence position, fragment start relative to repeat consensus, type of Alu sequence, the fragment start relative to repeat consensus, the fragment end relative to repeat consensus, the orientation of the sequence (D, denoting direct, versus C, denoting complementary), the percent similarity to the Alu consensus sequence, the ratio of mismatches to matches, and the alignment score. The database is available for download. An Alu element is a short stretch of DNA originally characterized by the action of the Alu (Arthrobacter luteus) restriction endonuclease. Alu elements of different kinds occur in large numbers in primate genomes. In fact, Alu elements are the most abundant Transposable elements in the human genome. They are derived from the small cytoplasmic 7SL RNA, a component of the signal recognition particle. The event, when a copy of the 7SL RNA became a precursor of the Alu elements, took place in the genome of an ancestor of Supraprimates. (from Wikipedia)." .
SCR:013354 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02849" ;
rdfs:label "FlyTrap- GFP Protein Trap Database" ;
NIFRID:synonym "FlyTrap" ;
definition: "The FlyTrap database presents the current results of large scale protein trapping screens that provide both information on which cells express each tagged gene, and subcellular localization of GFP-tagged proteins. Expression is under the control of endogenous promoter and enhancer elements, allowing for visualization of normal expression patterns. Drosophila proteins tagged with Green Fluorescent Protein (GFP) were created by insertion into genes of an artificial exon encoding GFP flanked by splice acceptor (SA) and splice donor (SD) sequences so that expression of GFP relies on splicing into mature mRNAs and in-frame fusion." .
SCR:013355 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_151843" ;
rdfs:label "Longitudinal Studies of Aging" ;
NIFRID:synonym "Longitudinal Studies of Aging (LSOAs)",
"LSOA - Longitudinal Studies of Aging" ;
NIFRID:abbrev "LSOA",
"LSOAs" ;
definition: "A data set of a multicohort study of persons 70 years of age and over designed primarily to measure changes in the health, functional status, living arrangements, and health services utilization of two cohorts of Americans as they move into and through the oldest ages. The project is comprised of four surveys: * The 1984 Supplement on Aging (SOA) * The 1984-1990 Longitudinal Study of Aging (LSOA) * The 1994 Second Supplement on Aging (SOA II) * The 1994-2000 Second Longitudinal Study of Aging (LSOA II) The surveys, administered by the U.S. Census Bureau, provide a mechanism for monitoring the impact of proposed changes in Medicare and Medicaid and the accelerating shift toward managed care on the health status of the elderly and their patterns of health care utilization. SOA and SOA II were conducted as part of the in-person National Health Interview Survey (NHIS) of noninstitutionalized elderly people aged 55 years and over living in the United States in 1984, and at least 70 years of age in 1994, respectively. The 1984 SOA served as the baseline for the LSOA, which followed all persons who were 70 years of age and over in 1984 through three follow-up waves, conducted by telephone in 1986, 1988, and 1990. The SOA covered housing characteristics, family structure and living arrangements, relationships and social contracts, use of community services, occupation and retirement (income sources), health conditions and impairments, functional status, assistance with basic activities, utilization of health services, nursing home stays, and health opinions. Most of the questions from the SOA were repeated in the SOA II. Topics new to the SOA II included use of assistive devices and medical implants; health conditions and impairments; health behaviors; transportation; functional status, assistance with basic activities, unmet needs; utilization of health services; and nursing home stays. The major focus of the LSOA follow-up interviews was on functional status and changes that had occurred between interviews. Information was also collected on housing and living arrangements, contact with children, utilization of health services and nursing home stays, health insurance coverage, and income. LSOA II also included items on cognitive functioning, income and assets, family and childhood health, and more extensive health insurance information. The interview data are augmented by linkage to Medicare enrollment and utilization records, the National Death Index, and multiple cause-of-death records. Data Availability: Copies of the LSOA CD-ROMs are available through the NCHS or through ICPSR as Study number 8719. * Dates of Study: 1984-2000 * Study Features: Longitudinal * Sample Size: ** 1984: 16,148 (55+, SOA) ** 1984: 7,541(70+, LSOA) ** 1986: 5,151 (LSOA followup 1) ** 1988: 6,921 (LSOA followup 2) ** 1990: 5,978 (LSOA followup 3) ** 1994-6: 9,447 (LSOA II baseline) ** 1997-8: 7,998 (LSOA II wave 2) ** 1999-0: 6,465 (LSOA II wave 3) Link: * LSOA 1984-1990 ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/08719" .
SCR:013356 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00941" ;
rdfs:label "MEDEA" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVCE, documented June, 2019.Comparative Genomic Visualization with Adobe Flash." .
SCR:013357 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:cnv-seq",
"OMICS_00339" ;
rdfs:label "CNV-seq" ;
definition: "A method for detecting DNA copy number variation (CNV) using high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013358 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_61725" ;
rdfs:label "Mouse Brain Image Visualizer (MBIV)" ;
NIFRID:synonym "Mouse Brain Image Visualizer" ;
NIFRID:abbrev "MBIV" ;
definition: "The Mouse Brain Image/Atlas Visualizer (MBIV) is a Java-based 2D visualization tool, available both as a web-based applet or downloadable application, for browsing high resolution 3D MRI mouse brain images and their associated atlases. A user can dynamically access images and atlases in our mouse brain database through the interface provided by MBIV and then select from the database the datasets they wish to upload and browse on their local machine." .
SCR:013359 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-31494" ;
rdfs:label "Operational Criteria" ;
NIFRID:synonym "OPCRIT" ;
definition: "The operational criteria OPCRIT checklist for psychotic and affective illness has been designed to facilitate a polydiagnostic approach to mental illness. The package is specifically for the needs of the researcher and is intended to be used by clinicians or investigators trained in clinical research. It is not recommended for use by raters without previous experience in psychopathology and psychiatric diagnosis. Click the Download link below to download Opcrit. This download is compressed zip file which will yield the actual installer files. Open WinopInstallerFiles.zip and when prompted extract the contents to a temporary location. One of the files extracted is Setup.exe. Run this setup file and follow the instructions to install the Opcrit. Depending on your system type and version of Windows, you may need to reboot your system once installation is complete. After installation, you will also need to download and run the installer for the october 2009 update (see below)." .
SCR:013360 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154665" ;
rdfs:label "SUPERLINK" ;
definition: "Software program that performs exact linkage analysis with the same input-output relationships as in standard genetic linkage programs such as LINKAGE, FASTLINK, VITESSE, but can run larger files than previous programs. (entry from Genetic Analysis Software)" .
SCR:013361 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_149218" ;
rdfs:label "EASE: the Expression Analysis Systematic Explorer" ;
NIFRID:synonym "Expression Analysis Systematic Explorer" ;
NIFRID:abbrev "EASE" ;
definition: "Windows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatible" .
SCR:013362 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:genscan",
"OMICS_01494" ;
rdfs:label "GENSCAN" ;
NIFRID:synonym "GENSCAN Web Server at MIT" ;
NIFRID:abbrev "genscan" ;
definition: "Web server for identification of complete gene structures in genomic DNA.Tool for predicting locations and exon-intron structures of genes in genomic sequences from variety of organisms. Used for prediction of complete gene structures in human genomic DNA." .
SCR:013363 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02921" ;
rdfs:label "GPCR Natural Variants database" ;
NIFRID:synonym "GPCR NaVa database" ;
definition: "The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans. The GPCR NaVa database includes: 1) rare mutations (frequency < 1%); 2) polymorphisms (frequency > 1%), including Single Nucleotide Polymorphisms (SNPs); 3) variants without estimates of allele frequency. The GPCR NaVa database aids GPCR research by categorising and integrating information on variants from databases and scientific papers. Moreover, the GPCR NaVa database is linked with the reputable GPCRDB. In case of missing NaVas, please help our users by sending a completed Excel-file to Jeroen Kazius. human G Protein-Coupled Receptors, human G Protein, human G-protein" .
SCR:013364 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02807" ;
rdfs:label "EPGD" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. EPGD isfocused on the paralogs and the duplication events in the evolution. It is gene-centered and organized by paralog family. The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website in plain text files. The database will be very useful for both experimentalists and bioinformaticians for the study of duplication events or paralog families." .
SCR:013365 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-31385" ;
rdfs:label "Linkage Disequilibrium Analyses for Quantitative and Discrete Traits" ;
NIFRID:synonym "QTDT" ;
definition: "How is association mapping going to help me find genes? During the past decade, the genes for a large number of rare mendelian traits have been identified. However, traditional linkage analyses lack power and precision when applied to complex disease. Association mapping, which compares the effects of different chromosomal variants, may be more successful at identifying genes of small effect. How does QTDT help association mapping? Association mapping can produce misleading results when the study population is not homogeneous, but includes individuals with different genetic backgrounds. Family based association tests, commonly referred to as TDTs (Transmission Disequilibrium Tests), do not produce misleading results in these circumstances. QTDT can use all the information in a pedigree to construct powerful tests of association that are robust in the presence of stratification. What does the Q stant for ? Q stands for Quantitative. Quantitative traits provide effective descriptions of many complex diseases, including asthma. For many of these conditions, all or nothing definitions of disease are arbitrary and unsatisfactory. QTDT incorporates variance components methodology in the analysis of family data and includes exact estimation of p-values for analysis of small samples and non-normal data. The QTDT abbreviation (for Quantitative Transmission Disequilibrium Tests) was first used by David Allison in his 1997 paper. This research was supported in part by the intramural program of the National Eye Institute and by National Institutes of Health Grants EY016862, EY007758, EY09859, EY012118, P30-EY014801, EY-014458, EY014467, HL084729, and HG002651, by the Foundation Fighting Blindness, the Macula Vision Research Foundation, the American Health Assistance Foundation, Research to Prevent Blindness, the Pew Charitable Trusts, the Mayo Clinic Foundation, the Casey Macular Degeneration Center Fund, the Marion W. and Edward F. Knight AMD Fund, the Harold and Pauline Price Foundation, National Genotyping Centre of Spain, and the Elmer and Sylvia Sramek Foundation. The Center for Inherited Disease Research, fully funded through a federal contract (HHSN268200782096C) from National Institutes of Health to" .
SCR:013366 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03060" ;
rdfs:label "JAIL- Just Another Interface Library" ;
NIFRID:synonym "JAIL" ;
definition: "JAIL is a database that classifies the interfaces between domain architectures and those between protein chains and between proteins and nucleic acids. Interacting proteins are difficult to crystallize and rarely present within the Protein Data Base. Nevertheless, it is essential to analyze the interacting parts of the proteins to understand the process of protein-protein docking. To overcome this problem we have built up the JAIL database. Since interacting domains exhibit similar structural features than proteins, all known interfaces between interacting domains of the SCOP database were extracted and classified in JAIL. Only a part of all protein structures are included in SCOP. Particularly, new PDB entries are not yet annotated. To overcome this problem additionally all interfaces between protein chains were calculated and included in the database. This type of interface also comprises the interacting parts of the assumed biological units. The last important type of interfaces provided here is composed of the interacting parts between proteins and nucleic acids. Overall the data set consists of about 180,000 interfaces. JAIL is a comfortable tool to browse through the interface library and to analyze single interfaces. However, more general questions require large-scale analysis. For this purpose, a detailed form enables the compiling of comprehensive non redundant data sets for download." .
SCR:013367 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30518" ;
rdfs:label "Ensembl Genome Browser" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17,2022. Genome databases for vertebrates and other eukaryotic species. Analysis and annotation maintained on current data.Distribution of analysis to other bioinformatics laboratories. Ensembl concentrates on vertebrate genomes, but other groups have adapted system for use with plant and fungal genomes (see Powered by Ensembl list on website)." .
SCR:013368 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-31885" ;
rdfs:label "The Delarue Group" ;
NIFRID:synonym "Delarue Group" ;
definition: "This site provides online servers for algorithms such as normal mode calculation, structural refinement, solvation, and mutation. The primary application is for biological macromolecules like proteins or DNA, but they can certainly be used for general structures." .
SCR:013369 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152410" ;
rdfs:label "Meridian Life Science" ;
NIFRID:synonym "Meridian Life Science inc." ;
definition: "An Antibody supplier" .
SCR:013370 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152408" ;
rdfs:label "MediMabs" ;
definition: "An Antibody supplier" .
SCR:013371 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-20819" ;
rdfs:label "Biological Interaction database for Protein-nucleic Acid" ;
NIFRID:abbrev "BIPA" ;
definition: "A database for protein-nucleic acid interaction that provides various features of protein-nucleic acid interfaces.
There are 2333 protein-nucleic acid PDB complexes, 9547 SCOP domains, and 9633 domain-nucleic acid interfaces in BIPA. BIPA also provides a multiple structural alignment of representative structures at the SCOP family level using the program SALIGN, and the structural alignments were further annotated using the program JOY to detect local environments of amino acids.
" .
SCR:013372 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00245" ;
rdfs:label "International Gene Trap Consortium Pathways" ;
NIFRID:synonym "IGTC Pathways" ;
definition: "IGTC uses GenMapp to provide maps of public gene trap data from members of the International Gene Trap Consortium (IGTC) to map sets of biological pathways and gene groupings. Users can browse the pathway diagrams and view which genes within the pathway have been trapped. Genes with gene trap insertions are colored on the pahtway diagram depending upon the number of traps of the gene. Clicking on a gene of interest will bring up a backpage of annotation data and detailed information about the gene trap cell lines." .
SCR:013373 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:alta-cyclic",
"OMICS_01149" ;
rdfs:label "Alta-Cyclic" ;
definition: "An Illumina Genome-Analyzer (Solexa) base caller." .
SCR:013374 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03068" ;
rdfs:label "Kidney Development Database" ;
NIFRID:synonym "KDD" ;
definition: "The Kidney Development Database was created to collect in one place the data from a large number of developmental studies that have a bearing on the study of kidney development. With its oldest parts dating back to 1993/4, it is, as far as we know, the earliest computer database in the field of vertebrate organogenesis. Data are displayed in tables, arranged according to a standard scheme of kidney development explained in the key. Many of the entries are derived from low-power in situs or published text-only descriptions, and should therefore be interpreted with mild caution." .
SCR:013375 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-11635" ;
rdfs:label "American Parkinson's Disease Association Information and Referral Center" ;
NIFRID:synonym "APDA I and R Center" ;
definition: "A patient resource to provide Parkinson's disease patients and their families with information and resources to help understand and manage Parkinson's disease and improve the quality of life for both patient and caregiver, while increasing public awareness about the disease. The website also connects users with resources, such as therapy groups, physical exercise classes, and patient care resources. It gives users access to mailing lists, support group information, and other Parkinson's-related event information for Parkinson's patients and their families. Based at Stanford University Medical Center, it is a partnership between the American Parkinson Disease Association, Inc. and Stanford University." .
SCR:013376 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154517" ;
rdfs:label "PEDFIDDLER" ;
NIFRID:synonym "PEDPACK in PANGAEA" ;
definition: "Software suite of six programs that can be used as a stand-alone extension of the pedigree drawing facilities found in the publicly available version of PEDPACK. (entry from Genetic Analysis Software)" .
SCR:013377 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02908",
"r3d100012458" ;
rdfs:label "GiardiaDB" ;
definition: "GiardiaDB is a resource for information on Giardia lamblia. It contains gene information, including genomic attributes, protein expression patterns, evolution, and EST sequence information. The website provides tools for BLASTing, sequence retrieval, graphic visualization, and PubMed information." .
SCR:013378 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154688" ;
rdfs:label "VG" ;
NIFRID:synonym "Visual Genotype" ;
definition: "Software program that presents complete raw datasets of individuals'' genotype data using a display format with samples as rows and polymorphisms as columns. The color code is: (1) blue: homozygous genotype for the common allele; (2) red: heterozygous genotype; (3) yellow: homozygous genotype for the rare allele; and (4) grey: missing data (entry from Genetic Analysis Software)" .
SCR:013379 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152407" ;
rdfs:label "Mediagnost" ;
NIFRID:synonym "Mediagnost Gesellschaft für Forschung und Herstellung von Diagnostika GmbH" ;
definition: "An Antibody supplier" .
SCR:013380 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03097" ;
rdfs:label "MALISAM: Manual ALIgnments of Structurally Analogous Motifs" ;
NIFRID:synonym "MALISAM" ;
definition: "MALISAM is a database of pairwise, structure-based alignments for structurally analogous motifs in proteins. Homology and analogy are two alternative scenarios to explain structural similarities among proteins. Homologs inherit similar features from their common ancestor, while analogs converge to similar structures due to a limited number of energetically favorable ways to pack secondary structural elements. Analogous pairs in this database are in three categories: a hybrid motif and a core motif, an interface motif and a core motif, an artificial protein and a natural protein. During evolution, a protein family usually preserves a common core while accumulating insertions and deletions in the periphery. A core motif is composed entirely of secondary structure elements belonging to the evolutionary core. A hybrid motif consists of both core elements and peripheral insertions that are not present in the majority of the family members. An interface motif uses secondary structural elements from two or more domains or subunits contacting along that interface." .
SCR:013381 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03237",
"r3d100012084" ;
rdfs:label "Phenylalanine Hydroxylase Locus Knowledgebase" ;
NIFRID:synonym "Phenylalanine Hydroxylase Database" ;
NIFRID:abbrev "PAHdb" ;
definition: "A database of centralized mutation data on the PAH gene. Searchable fields of the database available to users are: mutation name, polymorphic haplotype, population, geographic location, gene region, codon number, mutation type, substitution, phenotype, author's name and many more. The complete information provided for each mutation is regularly updated from both published data and personal communications." .
SCR:013382 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154395" ;
rdfs:label "HAPSTAT" ;
definition: "Software interface for the statistical analysis of haplotype-disease association. HAPSTAT allows the user to estimate or test haplotype effects and haplotype-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty and study design. The current version considers cross-sectional, case-control and cohort studies. (entry from Genetic Analysis Software)" .
SCR:013383 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152406" ;
rdfs:label "MD Biosciences" ;
NIFRID:synonym "MD Bioproducts" ;
definition: "An Antibody supplier" .
SCR:013384 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.433005.1",
"ISNI: 0000 0004 0546 7056",
"nif-0000-10195" ;
rdfs:label "Children and Adults with Attention Deficit/Hyperactivity Disorder" ;
NIFRID:abbrev "CHADD" ;
definition: "Non-profit organization serving individuals with attention deficit-hyperactivity disorder (AD/HD) and their families. CHADD has over 16,000 members in 200 local chapters throughout the U.S. Chapters offer support for individuals, parents, teachers, professionals, and others. CHADD''s primary objectives are: to provide a support network for parents and caregivers; to provide a forum for continuing education; to be a community resource and disseminate accurate, evidence-based information about AD/HD to parents, educators, adults, professionals, and the media; to promote ongoing research; and to be an advocate on behalf of the AD/HD community. In general, CHADD works to improve the lives of people affected by AD/HD through: Collaborative Leadership, Advocacy, Research Education and, Support CHADD has three current priority objectives: (1) to serve as a clearinghouse for evidence-based information on AD/HD, (2) to serve as a local face-to-face family support group for families and individuals affected by AD/HD, and (3) to serve as an advocate for appropriate public policies and public recognition in response to needs faced by families and individuals with AD/HD. CHADD is a membership organization, produces the bi-monthly Attention! magazine (for members), and sponsors an annual conference. The National Resource Center on AD/HD (NRC) is the CDC-funded national clearinghouse for evidence-based information about AD/HD." .
SCR:013385 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152849" ;
rdfs:label " Renin Angiotensin System Study " ;
NIFRID:synonym "Renin Angiotensin System Blockage-DN (RASS)",
"Renin Angiotensin System Study (RASS/B-RASS)" ;
NIFRID:abbrev "RASS",
"RASS/B-RASS" ;
definition: "Randomized, multicenter, double-blind study to determine if renin angiotensin medications, either losartan (angiotensin II blocker) or enalapril (converting enzyme inhibitor), can prevent or delay the onset of diabetic kidney disease in patients with type 1 diabetic patients who do not have hypertension, diabetic nephropathy, or predictive levels of microalbuminuria. Two hundred eight five patients ages 16-61 with 2-20 yrs of Type 1 Diabetes Mellitus and no renal functional abnormalities were randomized into a parallel, double-blind, placebo-controlled study involving 3 groups (95 patients/group). Each group received an angiotensin-converting enzyme inhibitor (ACEI) (enalapril), or an angiotensin II receptor blocker (Losartan), or placebo. All patients had their usual Diabetes Mellitus (DM) management. Baseline studies included measures of glomerular filtration rate (GFR), urinary albumin excretion rate (UAE), blood pressure (BP), and a percutaneous renal biopsy. Patients were followed by quarterly measures of BP, HbA1C, UAE, and drug compliance. There were annual measures of GFR and a repeat renal biopsy after 5 yrs in the study. The main endpoint is kidney structural changes over time, especially mesangial fractional volume (v(Mes/glom)). Secondary endpoints will be other DN structural measures and measures of kidney function (UAE, GFR). These studies will determine whether rennin angiotensin system blockage in the early stages of DN can prevent the early kidney structural changes in this important disorder. Ancillary studies will evaluate the effects of treatment group on the development and progression of diabetic retinopathy and will develop predictors of study participants' ''' compliance. Baseline, 2.5 and 5 year retinal fundus photographs in the RASS patients were obtained." .
SCR:013386 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30186" ;
rdfs:label "BioMoby" ;
definition: "The MOBY-S system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next. The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. Sponsors: Funding was provided by Genome Prairie and Genome Alberta A Bioinformatics Platform for Genome Canada''; Canadian Institutes for Health Research; The Natural Sciences and Engineering Research Council of Canada; The Heart and Stroke Foundation for BC and Yukon; The EPSRC through the myGrid (GR/R67743/01, EP/C536444/1, EP/D044324/1, GR/T17457/01) e-Science projects; The Spanish National Institute for Bioinformatics (INB) through Fundacin Genoma Espaa; The Generation Challenge Programme (GCP; http://www.generationcp.org) of the Consultative Group for International Agricultural Research. :Keywords: Ontology, Messaging, Standard, Client, Automatically, Discovery, Biological, Data, ANalytical, Service, Model, Organism, Database, Java, Platform, Semantic, Bioinformatics," .
SCR:013387 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-11885" ;
rdfs:label "Cortical Box Method: Quantitative analysis for gene expressions in rodent cortex" ;
NIFRID:synonym "Cortical Box Method" ;
definition: "The Cortical box method is an analytical method that standardizes the serial coronal sections of rodent cortex for quantitative analysis (details are written in the manual document). There are several tools necessary for this analysis. Currently, a program CxStand which is a core program of Cortical Box method is available for download. It standardizes a set of serial sections of rat cortex into standard rectangulars. Cortical box method was developed by Dr. Junya Hirokawa in the Yamamori Lab to map c-fos immunoreactivity in the rat cortex. This method was now applied to analyze the in situ data. From the original image, the cortical region is taken out and transformed, then normalized. You do this to a set of coronal sections of a rat cortex. Then, the cortex becomes a box. You can now slice the cortical box at desired lamina positions for layer maps. For more information, please refer to, http://www.nibb.ac.jp/brish/Gallery/corticalboxE.html. Requirements Cortical Box Method software is written in Labview and requires Labview version 7.0 (or later) and Vision development version 7.0 (or later). Labview and Vision are products of National Instruments (http://www.ni.com/ ). I confirmed (*) the Cortical box software works in the latest versions of Labview (ver.8.6) and Vision development (ver. 8.6), which can be downloaded without charge in the National Instruments web site (http://www.ni.com/ ) and can be used as evaluation softwares for 30 days. I tested the programs on PCs running the Windows family of operating systems. *A VI called image to image does not exist in Labview 8.6, please replace it into image to image 2. Programs CxStand ver 1.01 - (English, 680KB, Latest Version (2008/09/25 Update)) Standardization of a part of cortex into a rectangular. CBanalysis - construct 3D cortical box and create specific layer maps. DensityMap - Creating denisty map of staining signals. Copyright (c) 2008 Junya Hirokawa. All rights reserved. This program is free software; you can redistribute it and/or modify it." .
SCR:013388 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_151869" ;
rdfs:label "National Survey of Families and Households" ;
NIFRID:synonym "National Survey of Families and Households (NSFH)" ;
NIFRID:abbrev "NSFH" ;
definition: "A national sample survey dataset covering a wide variety of issues on American family life beginning in 1987-88 and at two subsequent timepoints1992-93 and 2001-03. Topics covered included detailed household composition, family background, adult family transitions, couple interactions, parent-child interactions, education and work, health, economic and psychological well-being, and family attitudes. The first wave interviewed 13,017 respondents, including a main cross-section sample of 9,643 persons aged 19 and over plus an oversample of minorities and households containing single-parent families, step-families, recently married couples, and cohabiting couples. In each household, a randomly selected adult was interviewed. In addition, a shorter, self-administered questionnaire was filled out by the spouse or cohabiting partner of the primary respondent. Interviews averaged about 100 minutes, although interview length varied considerably with the complexity of the respondent''s family history. In 1992-94, an in-person interview was conducted of all surviving members of the original sample, the current spouse or cohabiting partner, and with the baseline spouse or partner in cases where the relationship had ended. Telephone interviews were conducted with focal children who were aged 5-12 and 13-18 at baseline. Short proxy interviews were conducted with a surviving spouse or other relative in cases where the original respondent died or was too ill to interview. A telephone interview was conducted with one randomly selected parent of the main respondent. In 2001-03, telephone interviews were conducted with: Surviving members of the original respondents who had a focal child age 5 or over at baseline; the baseline spouse/partner of these original respondents, whether or not the couple was still together; the focal children who were in the household and aged 5-18 at baselinemost of whom were interviewed at wave 2; and all other original respondents age 45 or older in 2000, and their baseline spouse/partner. Oversamples: Blacks, 9.2%; Mexican-Americans, 2.4%; Puerto Ricans, 0.7% * Dates of Study: 1987-2003 * Study Features: Longitudinal, Minority Oversampling * Sample Size (original respondents): ** Wave I (1987-88): 13,017 ** Wave II (1992-93): 10,007 ** Wave III (2001-03): 8,990 Links: * Wave I (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06041 * Wave II (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06906 * Wave III (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00171" .
SCR:013389 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152405" ;
rdfs:label "MBL International" ;
NIFRID:synonym "MBL International Corporation" ;
definition: "An Antibody supplier" .
SCR:013390 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152404" ;
rdfs:label "Matreya LLC" ;
definition: "An Antibody supplier" .
SCR:013391 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154101" ;
rdfs:label "QTDT" ;
NIFRID:synonym "Quantitative (Trait) Transmission/Disequilibrium Test" ;
definition: "Software application that performs linkage disequilibrium (TDT) and association analysis for quantitative traits. Includes support for the methods of Abecasis et al. (2000), Fulker et al. (1999), Monks et al. (1998), Allison (TDTQ5, 1997) and Rabinowitz (1997). Supports families of any size, with or without parental information. Includes simple variance components modelling. Interfaces with SimWalk2 for IBD estimation. (entry from Genetic Analysis Software)" .
SCR:013392 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03152" ;
rdfs:label "Mobile group II introns database" ;
definition: "It aims to provide correct information on introns, particularly in bacteria. Information in the web site includes: (1) introductory information on group II introns; (2) detailed information on subfamilies of intron RNA structures and intron-encoded proteins; (3) a listing of identified introns with correct boundaries, RNA secondary structures and other detailed information; and (4) phylogenetic and evolutionary information. The comparative data should facilitate study of the function, spread and evolution of group II introns." .
SCR:013393 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01604" ;
rdfs:label "RosettaDock" ;
definition: "Predicts the structure of a protein-protein complex from the individual structures of the monomer components." .
SCR:013394 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_153888" ;
rdfs:label "PiGenome" ;
NIFRID:synonym "Pig Genome Database",
"Pigenome database",
"Sus scrofa Genome database" ;
definition: "Database for ESTs (Expressed Sequence Tags), consensus sequences, bacterial artificial chromosome (BAC) clones, BES (BAC End Sequences). They have generated 69,545 ESTs from 6 full-length cDNA libraries (Porcine Abdominal Fat, Porcine Fat Cell, Porcine Loin Muscle, Liver and Pituitary gland). They have also identified a total of 182 BAC contigs from chromosome 6. It is very valuable resources to study porcine quantitative trait loci (QTL) mapping and genome study. Users can explore genomic alignment of various data types, including expressed sequence tags (ESTs), consensus sequences, singletons, QTL, Marker, UniGene and BAC clones by several options. To estimate the genomic location of sequence dataset, their data aligned BES (BAC End Sequences) instead of genomic sequence because Pig Genome has low-coverage sequencing data. Sus scrofa Genome Database mainly provide comparative map of four species (pig, cattle, dog and mouse) in chromosome 6." .
SCR:013395 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00180" ;
rdfs:label "Collaborative Study on the Genetics of Alcoholism" ;
NIFRID:abbrev "COGA" ;
definition: "A multi-site, multi-disciplinary undertaking with the overall goals of characterizing the familial transmission of alcoholism and related phenotypes and identifying susceptibility genes using genetic linkage. The study is being coordinated by the SUNY Health Science Center at Brooklyn (HSCB) under the leadership of Henri Begleiter. The study was initially funded by the National Institute of Alcohol Abuse and Alcoholism (NIAAA) in 1989. Additional useful information at http://www.niaaa.nih.gov/ResearchInformation/ExtramuralResearch/SharedResources/projcoga.htm" .
SCR:013396 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-32868" ;
rdfs:label "TCMGeneDIT" ;
definition: "TCMGeneDIT is a database system providing association information about traditional Chinese medicines (TCMs), genes, diseases, TCM effects and TCM ingredients automatically mined from vast amount of biomedical literature. Integrated protein-protein interaction and biological pathways information collected from public databases are also available. In addition, the transitive relationships among genes, TCMs and diseases could be inferred through the shared intermediates. Furthermore, TCMGeneDIT is useful in deducing possible synergistic or antagonistic contributions of the prescription components to the overall therapeutic effects. TCMGeneDIT is a unique database of various association information about TCMs. The database integrating TCMs with life sciences and biomedical studies would facilitate the modern clinical research and the understanding of therapeutic mechanisms of TCMs and gene regulations." .
SCR:013397 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154215" ;
rdfs:label "GRIDQTL" ;
definition: "Publicly available Web-based application that can perform QTL mapping on a variety of population types. GridQTL will extend the functionality of QTLExpress by adding new and advanced approaches for modelling QTL analysis in simple and complex populations. These new methods will be available on a Grid system that will offer flexible workflow management, resource allocation, data persistence, detached execution of simulations and the scalability required for the increase in data volume, data sources and complexity required by the new models. (entry from Genetic Analysis Software)" .
SCR:013398 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.452552.1",
"nlx_152403" ;
rdfs:label "MABTECH" ;
NIFRID:synonym "Mabtech AB" ;
definition: "An Antibody supplier" .
SCR:013399 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03120",
"OMICS_01842" ;
rdfs:label "MethyCancer" ;
NIFRID:synonym "database of human DNA Methylation and Cancer" ;
definition: "Database to study interplay of DNA methylation, gene expression and cancer that hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer information from public resources, and the CpG Island (CGI) clones derived from our large-scale sequencing. Interconnections between different data types were analyzed and presented. Search tool and graphical MethyView are developed to help users access all the data and data connections and view DNA methylation in context of genomics and genetics data. The search tool and graphical MethyView are developed to help users access all the data and data connections and view DNA methylation in context of genomics and genetics data. As part of the Cancer Epigenomics Project in China, MethyCancer serves as a platform for sharing data and analytical results from the Cancer Genome/Epigenome Project in China with colleagues all over the world." .
SCR:013400 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:enigma",
"nlx_144365" ;
rdfs:label "ENIGMA" ;
definition: "A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007" .
SCR:013401 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03588" ;
rdfs:label "Tree families database" ;
NIFRID:synonym "TreeFam" ;
definition: "A database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S. cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members.TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations.The basic elements of TreeFam are gene families that can be divided into two parts: TreeFam-A and TreeFam-B families. TreeFam-B families are automatically created. They might contain errors given complex phylogenies. TreeFam-A families are manually curated from TreeFam-B ones. Family names and node names are assigned at the same time. The ultimate goal of TreeFam is to present a curated resource for all the families. phylogenetic tree, animal, vertebrate, invertebrate, gene, ortholog, paralog, evolutionary history, gene families, single-metazoan animals, outgroup genes like yeast (S. cerevisiae and S. pombe), plant (A. thaliana), historical duplications, speciations, losses, Human, Genome, comparative genomics" .
SCR:013402 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154689" ;
rdfs:label "VH" ;
NIFRID:synonym "visual haplotype" ;
definition: "Software application for displaying estimated haplotype data (entry from Genetic Analysis Software)" .
SCR:013403 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01489" ;
rdfs:label "MED" ;
definition: "A non-supervised gene prediction algorithm for prokaryotic genomes with multivariate entropy distance method." .
SCR:013404 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03058" ;
rdfs:label "IVDB - Influenza Virus Database" ;
definition: "IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. For the convenience of efficient data utilization, our Q-Filter system classifies and ranks all nucleotide sequences into 7 categories according to sequence content and integrity. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively. A searching system is developed for users to retrieve a combination of different data types by setting various search options. To facilitate analysis of the global viral transmission and evolution, the IV Sequence Distribution Tool (IVDT) is developed to display worldwide geographic distribution of the viral genotypes and to couple genomic data with epidemiological data. The BLAST, multiple sequence alignment tools and phylogenetic analysis tools were integrated for online data analysis. Furthermore, IVDB offers instant access to the pre-computed alignments and polymorphism analysis of influenza virus genes and proteins and presents the results by SNP distribution plots and minor allele distributions. IVDB aims to be a powerful information resource and an analysis workbench for scientists working on IV genetics, evolution, diagnostics, vaccine development, and drug design." .
SCR:013405 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152402" ;
rdfs:label "MabTag GmbH" ;
NIFRID:synonym "MabTag" ;
definition: "An Antibody supplier" .
SCR:013406 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.488037.0",
"nlx_152401" ;
rdfs:label "List Biological Laboratories" ;
NIFRID:synonym "List Biological Laboratories Inc",
"List Biological Labs Inc",
"List Biological Labs Inc.",
"List Labs" ;
definition: "Organization which manufactures bacteria for research and clinical investigations. List Biological Laboratories cultivates native and recombinant microorganisms and purifies, formulates, and lyopholizes enzyme products, virulence factors, and microbial cell wall components. Products include antibodies, microbial toxins, peptides, and virulence factors. Services include live biotherapeutics for clinical trials, contracting research capabilities, GMP regulatory support, lyopholization services and support, and toxin compliance." .
SCR:013407 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02929" ;
rdfs:label "Greglist" ;
definition: "A database listing potential G-quadruplex regulated genes. G-rich DNA sequences can form G-quadruplexes, a four-stranded structure that is stabilized by planar arrays of four guanines associated with hydrogen bonds. Promoter G-quadruplexes have emerged as a new way to regulate gene transcription, such as in c-MYC expression. Further, G-quadruplex motifs are highly enriched in gene promoter regions in humans and other mammals. Greglist contains genes whose promoter regions have G-quadruplex motifs, and these genes are highly likely to be regulated by G-quadruplexes." .
SCR:013408 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30034" ;
rdfs:label "CBiS" ;
NIFRID:synonym "Centre for Bioinformation Science",
"The Centre for Bioinformation Science" ;
definition: "It is part of the Institute for Advanced Studies at The Australian National University (ANU). CBiS forms a bridge between two areas of major strength at ANU, mathematics and biological sciences. CBiS brings together researchers with backgrounds in mathematics, statistics and quantitative biology with the goal of developing a conceptual architecture for an information-based, integrative approach to complex biological systems. Software available for download or use is: * Pozitiv * GE Bi-Plot * Chip Stability * PyEvolve * Vestige Most software is freely available under the GPL or similar licenses. For details, see each individual package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013409 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pcs",
"nlx_33020" ;
rdfs:label "Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers" ;
NIFRID:synonym "Pairwise Conservation Scores" ;
NIFRID:abbrev "PCS" ;
definition: "A stand-alone package to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3''-UTRs." .
SCR:013410 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03600" ;
rdfs:label "U12DB: The U12 Intron Database" ;
NIFRID:synonym "U12DB" ;
definition: "This is a searchable database of U12-type introns. U12-type introns are spliced by the U12-dependent spliceosome and are present in the genomes of many higher eukaryotic lineages including plants, chordates and some invertebrates. Investigations into the evolution and mechanism of U12-depending splicing would be facilitated by access to a catalog of such introns. However, due to their relatively recent discovery and a systematic bias against recognition of non-canonical splice sites in general, the introns defined by U12-type splice sites are under-represented in genome annotations. Such under-representation compounds the already difficult problem of determining gene structures. It also impedes attempts to study these introns genome-wide or phylum-wide. The resource described here, the U12 Intron Database (U12DB), aims to catalog the U12 introns of completely sequenced eukaryotic genomes and associate orthologous introns with each other.Two pathways for the removal of eukaryotic spliceosomal introns exist: a major pathway that is dependent on the main U2 snRNA-containing spliceosome and a minor pathway that is dependent on the low abundance U12 snRNA-containing spliceosome. The two spliceosomes share only one snRNA, U5, but have many of the same protein components in common. They are distinguished mainly by the splice signal sequences in the pre-mRNA to which they bind. U12 consensus sequences for the donor site, RTATCCTTT, and branch point, TTCCTTRAY, are highly conserved and distinct from the U2 consensi. The two spliceosomes also differ in the order of spliceosomal assembly. U11 and U12 form a dimer which then recognizes the donor site and branch point simultaneously, whereas U1 and U2 recognize these sites independently before associating.Computational scans for U12 introns have previously been performed for human (Levine and Durbin, 2001) and Arabidopsis (Zhu and Brendel, 2003). Both scans used similar methodology, essentially predicting introns and confirming them using alignment to expressed sequence. We extended this approach to 20 genomes using spliced alignment of sequence flanking known introns or transcript-confirmed intron predictions to the genomic sequence of orthologous genes. Details can be found in forthcoming article in the Nucleic Acids Research database issue." .
SCR:013411 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152389" ;
rdfs:label "IMMUNOSTEP, S.L." ;
NIFRID:synonym "IMMUNOSTEP" ;
definition: "An Antibody supplier" .
SCR:013412 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02836" ;
rdfs:label "Fusarium graminearum Genome Database" ;
NIFRID:synonym "FGDB" ;
definition: "The MIPS Fusarium graminearum Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Fusarium graminearum (Anamorph of Gibberella zeae). The goal is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The underlying sequence is the initial release of the high quality draft sequence of the Whitehead Center for Genome Research." .
SCR:013413 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-10222" ;
rdfs:label "eQTL Visualization Tool" ;
NIFRID:synonym "eQTLexplorer" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics." .
SCR:013414 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152400" ;
rdfs:label "LifeSpan" ;
NIFRID:synonym "LifeSpan Biosciences",
"LifeSpan Biosciences Inc." ;
definition: "An Antibody supplier" .
SCR:013415 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152398" ;
rdfs:label "Life Sciences Advanced Technologies inc" ;
NIFRID:synonym "Life Sciences Advanced Technologies inc.",
"Life Sciences Inc",
"Life Sciences Inc." ;
definition: "An Antibody supplier" .
SCR:013416 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_143962" ;
rdfs:label "SAPALDIA" ;
NIFRID:synonym "SAPALDIA Cohort",
"SAPALDIA Cohort Study",
"Swiss study on Air Pollution and Lung Disease in adults" ;
definition: "SAPALDIA (Swiss study on Air Pollution and Lung Disease in adults) is a multi-center study in eight geographic areas representing the range of environmental, meteorological and socio-demographic conditions of Switzerland, which studies the effects of air pollution on the respiratory and cardiovascular health in adults. Local centers are: Aarau, Basel, Davos, Geneva, Lugano, Montana, Payerne, and Wald. It was initiated in 1991 (SAPALDIA 1) with a follow-up assessment in 2002 (SAPALDIA 2). This study has allowed to assess 1) prevalence and development of major respiratory and allergic symptoms and diseases and the age-related decline in lung function, 2) the distribution of heart rate variability in the general population over age 50, 3) the association of these health indicators with individual long term exposure to air pollution, other toxic inhalants, life style and molecular factors. Another follow-up examination (SAPALDIA 3) started in January 2010. This study is well positioned to address crucial questions of air pollution epidemiology and important environmental health policy-related questions in the coming years. When SAPALDIA was initiated in 1991, 9' '''651 subjects, aged 18 to 60 years, were recruited for a detailed computer-based interview and more than 90% of them underwent lung function and atopy testing. More than 7' '''000 of the subjects had bronchial reactivity tested by a methacholine challenge. SAPALDIA shares parts of its study protocol with the European Community Respiratory Health Survey (ECRHS) with which it is linked through the study center of Basel. Since 1991 SAPALDIA has been carefully following address histories of its participants. In the 2002 follow-up, 8' '''047 (83%) provided health information, 6' '''528 persons underwent physical re-examination, and 6' '''345 provided blood samples to establish an extensive blood, plasma, serum and DNA bank. In addition, 1' '''813 subjects aged 50 or older participated in 24h-ECG Holter monitoring to provide detailed data on parameters of heart rate variability. With the inclusion of cardiovascular endpoints, SAPALDIA is one of the first studies examining effects from long-term exposure to air pollution on cardiovascular health parameters as well as mutual influence between the respiratory and the cardiovascular system. The SAPALDIA bio-bank has allowed scientific publications on the association between some genetic profiles (gene polymorphism) and the propensity to develop asthma, allergic diseases, or accelerated lung function decline with age. Ongoing studies are focusing on gene-environment interactions a crucial question to understand why some persons suffer more from the effect of air pollution than others." .
SCR:013417 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02760" ;
rdfs:label "DomIns: A Web Resource for Domain Insertions in Known Protein Structures" ;
NIFRID:synonym "DomIns" ;
definition: "DomIns is a web resource aimed at providing comprehensive information on domain insertions in proteins of known structure. We have followed the definition of protein domains as in the SCOP (Structural Classification of Proteins) database in order to identify insertions. We have considered only the major five classes (All-alpha, All-beta, alpha/beta, alpha+beta and Small Proteins), the fold and the superfamily level of SCOP hierarchy for identifying insertions. Apart from browsing insertions in whole PDB, we also provide an option to browse insertions in a pre-computed list of non-redundant PDB chains provided by PDB_Select with a sequence identity threshold of 90%." .
SCR:013418 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02725" ;
rdfs:label "DBAli. A Database of Structure Alignments." ;
NIFRID:synonym "DBAli" ;
definition: "DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. It is not currently being updated; however, updates should resume in the near future. All pairwise structural comparisons in DBAli have been obtained using the MAMMOTH program developed in the group of Prof. Angel R. Ortiz. All multiple structure alignments in DBAli have been obtained using the SALIGN command in MODELLER developed in the group of Prof. Andrej Sali." .
SCR:013419 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02722" ;
rdfs:label "Database of Germline p53 Mutations" ;
definition: "The database of germline p53 mutations is a comprehensive database covering all published cases of germline p53 mutations. The current version lists 580 tumors in 448 individuals belonging to 122 independent pedigrees. The database describes each p53 mutation (type of the mutation, exon and codon affected by the mutation, nucleotide and amino acid change), each family (family history of cancer, diagnosis of Li-Fraumeni syndrome), each affected individual (sex, generation, p53 status, from which parent the mutation was inherited) and each tumour (type, age of onset, p53 status-loss of heterozygosity, immunostaining). Each entry contains the original reference(s)." .
SCR:013420 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02706" ;
rdfs:label "CutDB" ;
definition: "The CutDB focuses on the annotation of individual proteolytic events, both actual and predicted. Its offers searchable lists of proteases, Merops code, substrate, and diseases from which users can specify their desired queries in order to obtain more specific information. CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate and cleavage site. Currently, CutDB integrates 3070 proteolytic events for 470 different proteases captured from public archives (such as MEROPS and HPRD) and publications. CutDB supports various types of data searches and displays, including clickable network diagrams. Most importantly, CutDB is a community annotation resource based on a Wikipedia approach, providing a convenient user interface to input new data online. A recent contribution of 568 proteolytic events by several experts in the field of matrix metallopeptidases suggests that this approach will significantly accelerate the development of CutDB content." .
SCR:013421 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02660" ;
rdfs:label "Chloroplast Genome Database" ;
definition: "The Chloroplast Genome Database contains annotated chloroplast/plastid genomes from the NCBI Organelle Genomes section at NCBI. Users can search for genes by their annotated names, conduct flexible BLAST searches, download protein and nucleotide sequences extracted from a selected chloroplast genome, and browse the putative protein families (tribes) created using TribeMCL." .
SCR:013422 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00278" ;
rdfs:label "CARDinal Plane VIEWing System" ;
NIFRID:synonym "Cardviews" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Cardviews is a CARDinal plane VIEWing System developed at the Center for Morphometric Analysis at the Massachusetts General Hospital. It is a tool for brain morphometry (including volumetric analysis using xvol) and this program emerged as a product of our methodological development. While some of its functionality is specifically tailored for our general segmentation and neocortical parcellation routines, the imaging interface, segmentation tools, and localization capacity have utility extending beyond the specific aims motivating its initial conception. :" .
SCR:013423 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02644",
"r3d100010131" ;
rdfs:label "CCDB - The CyberCell Database" ;
NIFRID:synonym "CCDB" ;
definition: "The CyberCell database (CCDB) is a comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli (strain K12, MG1655). It is intended to provide sufficient information and querying capacity for biologists and computer scientists to use computers or detailed mathematical models to simulate all or part of a bacterial cell at a nanoscopic (10-9 m), mesoscopic (10-8 m) and microscopic (10-6 m) level. The CCDB database is actually several databases: CCDB contains quantitative proteomic, genomic and metabolic information about E. coli. CC3D contains 3D structural data for E. coli structural proteomics work CCRD contains detailed information on E. coli RNA molecules CCMD database contains quantitative information on E. coli metabolites. Each database is presented as a re-formattable synoptic table which allows users to casually browse the databases. Detailed information about each gene, protein, RNA, structure or metabolite may be obtained by clicking on the *Card button on the left column. Each card contains more than 60 fields concerning all aspects of the sequence, function or structure of a given molecule. CCDB users may also perform text searches (using the Search button), BLAST sequence searches (using the BLAST button) or conduct more detailed data extraction or relational data searches (using the Extract button)." .
SCR:013424 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154598" ;
rdfs:label "R/QTLDESIGN" ;
definition: "Software application to help plan quantitative trait locus (QTL) experiments. (entry from Genetic Analysis Software)" .
SCR:013425 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154559" ;
rdfs:label "PYPOP" ;
NIFRID:synonym "PYthon for POPulation genetics" ;
definition: "Software application (entry from Genetic Analysis Software)" .
SCR:013426 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154226" ;
rdfs:label "ANTMAP" ;
definition: "Software application based on the Ant Colony Optimization to solve the special case of the traveling salesman problem of ordering markers when the number of loci is large. ANYMAP performs segregation test, linkage grouping and locus ordering, and constructs a linkage map rapidly. (entry from Genetic Analysis Software)" .
SCR:013427 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154096" ;
rdfs:label "MDR" ;
NIFRID:synonym "Multifactor Dimensionality Reduction" ;
definition: "Software application that is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions. (entry from Genetic Analysis Software)" .
SCR:013428 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03296",
"OMICS_00557" ;
rdfs:label "PLACE- A Database of Plant Cis-acting Regulatory DNA Elements" ;
NIFRID:abbrev "PLACE" ;
definition: "A database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also contains a brief description of each motif and relevant literature with PubMed ID numbers. DDBJ/EMBL/GenBank nucleotide sequence databases accession numbers will be also included. Note: As of January 2007, PLACE is no longer updated or maintained." .
SCR:013429 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03394" ;
rdfs:label "REDIdb- RNA Editing Database" ;
NIFRID:synonym "RNA Editing Database" ;
NIFRID:abbrev "REDIdb" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A relational database in which all editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored and maintained in ad hoc designed textual flat files. Individual genes of interest can be searched by appropriate query strings containing the gene name or the intracellular location or the molecular type (as tRNA, rRNA, intron) or the organism or a combination of the previous terms. Moreover, each record of the REDIdb database can be also retrieved according to its specific accession number (more help on how to perform a REDIdb search is available at the ?help? page). To make easier the browsing of each REDIdb entry and quicker the identification of editing sites, two alternative but complementary facilities have been provided either to graphically display genomic and cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are shown by mousing over." .
SCR:013430 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.420010.7",
"ISNI: 0000 0004 0566 5896",
"nlx_152397",
"Wikidata: Q6458581" ;
rdfs:label "LI-COR Biosciences" ;
definition: "An Antibody supplier" .
SCR:013431 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30411" ;
rdfs:label "DC Analysis programs" ;
NIFRID:synonym "DOS" ;
definition: "These programs have been written over the last 20 years for analysis of our own results. They all do some things that are still not available in any commercial program. The programs are written in protected-mode 32-bit Fortran 90, with some assembler subroutines for fast graphics, and the Gino graphics library. Thus they are essentially DOS programs, though they are usually run from Windows, either via a desktop icon (the .ico files) or in the DOS box. The manuals (now in pdf format), have now all been collected into a single document, DCMANUALS.PDF, which should be downloaded, and the bits that you need can then be printed. Note that some sections are common to many or all programs, e.g. the notes on the graph and histogram drawing subroutines, and it is important to read this before using any of the programs (though there is a lot of online help (hit F1) for the graphics, and also in SCAN. Sponsor. Our work was supported by the Wellcome Trust (project grant 074491) and the Medical Research Council (programme grant G0400869)." .
SCR:013432 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03420" ;
rdfs:label "RNAJunction" ;
definition: "It is a database of RNA Junction and Kissing Loop Structures. RNA is versatile in both its structure and function. Within this database you will to able to find more than 12,000 extracted three-dimensional junction and kissing loop structures as well as detailed annotations for each. If you are interested in RNA as a building block for nano-scale design or if you are analyzing the properties of specific RNA motifs you should find utility in this site. The junctions in this database were extracted using a junction scanning algorithm from a number of structures from the Protein Data Bank. Coming from parent structures, both NMR and crystal, these junctions may be under contextual constraints. It is possible that these constraints play a critical role in the junction's conformation and stability." .
SCR:013433 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:dali",
"nlx_77142" ;
rdfs:label "Dali Server" ;
NIFRID:synonym "Dali" ;
definition: "Network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB). You receive an email notification when the search has finished. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. Requests can also be submitted by e-mail to dali-server at helsinki dot fi. The body of the e-mail message must contain atomic coordinates in PDB format. If you want to know the structural neighbours of a protein already in the Protein Data Bank (PDB), you can find them in the Dali Database. If you want to superimpose two particular structures, you can do it in the pairwise DaliLite server. Academic users may download the DaliLite program for local use." .
SCR:013434 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_76473" ;
rdfs:label "Plant DNA C-values Database" ;
definition: "The DNA amount in the unreplicated gametic nucleus of an organism is referred to as its C-value, irrespective of the ploidy level of the taxon. The Plant DNA C-values Database currently contains data for 7058 plant species. It combines data from the Angiosperm DNA C-values Database, Gymnosperm DNA C-values Database, the Pteridophyte DNA C-values Database, the Bryophyte DNA C-values Database, together with the addition of the Algae DNA C-values database." .
SCR:013435 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_66534" ;
rdfs:label "Ohio U Diabetes Endocrine Biorepository" ;
NIFRID:synonym "Diabetes / Endocrine Diseases Biorepository",
"Ohio University Diabetes / Endocrine Diseases Biorepository" ;
NIFRID:abbrev "Ohio University Diabetes/Endocrine Diseases Biorepository" ;
definition: "Plasma and cell fractions obtained from patients with Diabetes and endocrine diseases and their first degree relatives who agreed to participate in the development of the biorepository. Plasma is aliquoted into multiple specimen containers and stored at -80C. Cell fractions are subjected to DNA and RNA fractionation, aliquoted into multiple specimen containers, and frozen at -70 to -80 degrees centigrade. Anyone who would like to obtain samples from the Biorepository must provide evidence that they have adequate training in the use of bloodborne pathogens, as outlined by OSHA. The investigator must agree to indemnify and hold harmless the Ohio University Diabetes/Endocrine Diseases Biorepository, the Appalachian Rural health Institute, and the Ohio University College of Osteopathic Medicine from any claims, liability, costs, and damages." .
SCR:013436 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152395" ;
rdfs:label "Lab Vision" ;
definition: "An Antibody supplier" .
SCR:013437 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30294" ;
rdfs:label "Sequencing of Candida Albicans" ;
NIFRID:synonym "Candida Albicans" ;
definition: "The Stanford Genome Technology Center began a whole genome shotgun sequencing of strain SC5314 of Candida albicans. After reaching its original goal of 1.5X mean coverage of the haploid genome (16Mb) in summer, 1998, Stanford was awarded a supplemental grant to continue sequencing up to a coverage of 10X, performing as much assembly of the sequence as possible, using recognizable genes as nucleation points. Candida albicans is one of the most commonly encountered human pathogens, causing a wide variety of infections ranging from mucosal infections in generally healthy persons to life-threatening systemic infections in individuals with impaired immunity. Oral and esophogeal Candida infections are frequently seen in AIDS patients. Few classes of drugs are effective against these fungal infections, and all of them have limitations with regard to efficacy and side-effects." .
SCR:013438 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02770" ;
rdfs:label "DroSpeGe: Drosophila Species Genomes" ;
NIFRID:synonym "DroSpeGe" ;
definition: "DroSpeGe provides a preview of newly sequenced Drosophila genomes, with genome maps and BLAST sequence search. Genome maps include D. melanogaster genome homology, homologies to nine eukaryote proteomes, marker gene locations, and Drosophila microsatellites. Current genome assemblies can be BLASTed, with links to genome maps of your BLAST matches. Annotation data are available in Gene Finding Format (GFF) for these whole genome comparisons." .
SCR:013439 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-10515" ;
rdfs:label "Montage RTS2000" ;
definition: "Software program for creating montages from multiphoton microscopy." .
SCR:013440 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-10463" ;
rdfs:label "L2L Microarray Analysis Tool" ;
NIFRID:synonym "L2L MDB",
"L2L Microarray Analysis Tool: A simple tool for discovering the hidden biological significance in microarray expression data",
"L2L Microarray Database" ;
NIFRID:abbrev "L2L" ;
definition: "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.
Database of published microarray gene expression data, and a software tool for comparing that published data to a user' '''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don' '''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible" .
SCR:013441 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-21118",
"OMICS_01894" ;
rdfs:label "Drosophila melanogaster Exon Database" ;
NIFRID:synonym "DEDB - Drosophila melanogaster Exon Database",
"DEDB : Drosophila melanogaster Exon Database" ;
NIFRID:abbrev "DEDB" ;
definition: "Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers." .
SCR:013442 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:weighted_fdr",
"nlx_154604",
"nlx_154690",
"SCR_000848" ;
rdfs:label "WEIGHTED FDR" ;
NIFRID:synonym "R/WEIGHTED_FDR" ;
definition: "Software application (entry from Genetic Analysis Software)" .
SCR:013443 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152394" ;
rdfs:label "Kokusan Chemical" ;
NIFRID:synonym "Kokusan Chemical Co. Ltd." ;
definition: "An Antibody supplier" .
SCR:013444 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152393" ;
rdfs:label "Kamiya Biomedical Company" ;
definition: "An Antibody supplier" .
SCR:013445 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.435318.8",
"ISNI: 0000 0004 6010 2746",
"nlx_152392",
"Wikidata: Q30289951" ;
rdfs:label "Innovative Research" ;
definition: "An Antibody supplier" .
SCR:013446 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02601" ;
rdfs:label "BGI-RISe - Beijing Genomics Institute Rice Information System" ;
NIFRID:synonym "BGI-RIS" ;
definition: "Integrated information resource for rice genomes as well as a workbench for comparative genomic analysis among cereal crops. Sequence contigs of Beijing indica and Syngenta japonica have been further assembled and anchored onto the rice chromosomes. The rice genomes have been annotated for gene content, repetitive elements, and SNPs. Sequence polymorphisms between different rice subspecies have also been identified. Designed as a basic platform for rice study, the sequenced genomes and related information is presented in systematic and graphical ways for the convenience of in-depth comparative studies. In addition to the comprehensive data of Oryza sativa L. ssp. indica sequenced, BGI-RIS will host carefully curated genome information of Oryza sativa L. ssp. japonica." .
SCR:013447 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_155766" ;
rdfs:label "GenGen" ;
NIFRID:synonym "GenGen: Genetic Genomics Analysis of Complex Data" ;
definition: "A suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated." .
SCR:013448 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03449" ;
rdfs:label "Secreted Protein Database" ;
NIFRID:abbrev "SPD" ;
definition: "A collection of secreted proteins from Human, Mouse and Rat proteomes, which includes sequences from SwissProt, Trembl, Ensembl and Refseq. The 18,152 entries are classified into fourteen functional categories, including "apolipoprotein", "cytokine", "protease", "toxin", etc. To make the dataset more comprehensive, nine related datasets were also collected, such as SPDI, Riken mouse secretome, SwissProt vertebrate secreted proteins, SubLoc etc." .
SCR:013449 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:tHESIAS",
"nlx_154102",
"OMICS_19747" ;
rdfs:label "THESIAS" ;
NIFRID:synonym "Testing Haplotype EffectS In Association Studies" ;
definition: "Software program that performs haplotype-based association analysis in unrelated individuals. This program is based on a maximum likelihood model described in Tregouet et al. 2002 and is linked to the stochastic EM (SEM) algorithm. THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, both quantitative and qualitative phenotypes can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. (entry from Genetic Analysis Software)" .
SCR:013450 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03319" ;
rdfs:label "PMDB - Protein Model Database" ;
NIFRID:synonym "Protein Model DataBase" ;
NIFRID:abbrev "PMDB" ;
definition: "It collects three dimensional protein models obtained by structure prediction methods. Users can both contribute new models and search for existing ones. The database currently stores all models submitted to the last four editions of the CASP experiment." .
SCR:013451 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02624" ;
rdfs:label "BSORF - Bacillus Subtilis Genome Database" ;
NIFRID:synonym "BSORF" ;
definition: "This website provides a resource for the Bacillus subtilis genome. It provides a list of mutants, DNA array data, and search features against both the whole genome and coding sequences. It also contains Kegarrays and access to the KEGG Expression Database." .
SCR:013453 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:toxodb",
"nif-0000-03572",
"r3d100012266" ;
rdfs:label "ApiDB ToxoDB" ;
NIFRID:synonym "ToxoDB",
"Toxoplasma Genomics Resource" ;
definition: "A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info" .
SCR:013454 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154218" ;
rdfs:label "DMLE" ;
NIFRID:synonym "Disease Mapping using Linkage disEquilibrium" ;
definition: "Software application for high-resolution mapping of the position of a disease mutation relative to a set of genetic markers using population linkage disequilibrium (LD). (entry from Genetic Analysis Software)" .
SCR:013455 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:cryptodb",
"nif-0000-02698",
"r3d100012265" ;
rdfs:label "ApiDB CryptoDB" ;
NIFRID:synonym "CryptoDB",
"Cryptosporidium Genomics Resource" ;
definition: "An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data" .
SCR:013456 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152056" ;
rdfs:label "National Survey of Self-Care and Aging" ;
NIFRID:abbrev "NSSCA" ;
definition: "Data set on the prevalence of self-care behaviors by non-institutionalized older adults. Personal interviews were conducted with 3,485 individuals 65 years of age and older, with oversampling of the oldest old. Questions were asked about the type and extent of self-care behaviors for activities of daily living, management of chronic conditions (through self-care activities, equipment use, and environmental modifications), medical self-care for acute conditions, health promotion/disease preventions, social support, health service utilization, and socio-demographic/economic status. A follow-up study by telephone was conducted in 1994 to continue examination of subjects. Many of the same questions from the baseline were asked, along with questions regarding change in health status since baseline and nursing home visits. For subjects who had been institutionalized since baseline (Part 2), information was gathered (by proxy) regarding demographic status, living arrangements prior to institutionalization, and reasons for institutionalization. For subjects who had died since baseline (Part 3), information was again gathered through interviews with proxies. Questions covered nursing home admissions and date and place of death. In both waves, a proxy was substituted if the subject was hospitalized (or institutionalized since baseline), too ill, cognitively not able to respond, or deceased. Survey data were linked to Medicare/Medicaid health utilization records. The baseline data are archived at NACDA as ICPSR Study No. 6718, and the followup data are archived as ICPSR Study No. 2592 and linkable to the baseline data. * Dates of Study: 1990-1994 * Study Features: Longitudinal * Sample Size: ** 1990-1: 3,485 (Baseline) ** 1994: 2,601 (Followup) Links: * 1990-1991 Baseline ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06718 * 1994 Follow-up ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/02592" .
SCR:013457 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00562" ;
rdfs:label "RARTF" ;
NIFRID:synonym "RARTF: RIKEN Arabidopsis Transcription Factor database",
"RIKEN Arabidopsis Transcription Factor database" ;
definition: "Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available." .
SCR:013458 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_18589" ;
rdfs:label "pTARGET" ;
NIFRID:synonym "pTARGET: Prediction server for protein subcellular localization" ;
definition: "pTARGET is a computational method to predict the subcellular localization of only eukaryotic proteins from animal species that include fungi and metazoans. Predictions are carried out based on the occurrence patterns of protein functional domains and the amino acid compositional differences in proteins from different subcellular locations. This method can predict proteins targeted to nine distinct subcellular locations that include cytoplasm, endoplasmic reticulum, extracellular/secreted, Golgi, lysosomes, mitochondria, nucleus, peroxysomes and plasma membrane. Current predictions are based on Pfam database version 19.0. Datasets used for developing pTarget method are available., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013459 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03196" ;
rdfs:label "NoPdb: Nucleolar Proteome Database" ;
NIFRID:synonym "Nucleolar Proteome Database" ;
NIFRID:abbrev "NoPDB" ;
definition: "It archives data on more than 700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene its domain structures and relevant protein homologues across species as well as documenting its MS identification history including all the peptides sequenced by tandem MS/MS. Moreover, data showing the quantitative changes in the relative levels of 500 nucleolar proteins are compared at different timepoints upon transcriptional inhibition. Correlating changes in protein abundance at multiple timepoints highlighted by visualization means in the NOPdb provides clues regarding the potential interactions and relationships between nucleolar proteins and thereby suggests putative functions for factors within the 30% of the proteome which comprises novel/ uncharacterized proteins. The NOPdb is searchable by either gene names protein sequences Gene Ontology terms or motifs or by limiting the range for isoelectric points and/or molecular weights and links to other databases (e.g. LocusLink OMIM and PubMed)." .
SCR:013460 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154054" ;
rdfs:label "SGS" ;
definition: "Software application (entry from Genetic Analysis Software)" .
SCR:013461 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152390" ;
rdfs:label "ImmuQuest" ;
NIFRID:synonym "ImmuQuest Ltd." ;
definition: "An Antibody supplier" .
SCR:013462 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_19923" ;
rdfs:label "miRNA viewer" ;
NIFRID:synonym "Human miRNA Targets" ;
definition: "Although hundreds of miRNAs have been discovered in mammalian genomes, the function of less than a handful of miRNAs is known. This viewer allows access to the predicted protein coding gene targets that are conserved between human and mouse/rat. Searching by miRNA will display a ranked list of gene targets and allow you to analyze each conserved target gene/sites in detail. Similarly, searching by gene name/identifier will display the sequence of the three prime UTR and the positions of the miRNA sites along the sequence, allowing you to analyze the target sites in detail. * View miRNA target sites for any target gene * View target genes and sites for any miRNA" .
SCR:013463 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03484" ;
rdfs:label "The Soybean GBrowse Database" ;
definition: "It provides the mapping of relationships between soybean genomic features in a way that is presentable in GBrowse. It combines Perl MySQL database programming with Gbrowse to provide an integrated way of presenting soybean genomic features. The database is also searchable for listings of these relationships." .
SCR:013464 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-21055" ;
rdfs:label "BioIE: Extracting Informative Sentences From the Biomedical Literature" ;
NIFRID:synonym "BioIE" ;
definition: "BioIE is a rule-based system that extracts informative sentences relating to protein families, their structures, functions and diseases from the biomedical literature. Based on manual definition of templates and rules, it aims at precise sentence extraction rather than wide recall. After uploading source text or retrieving abstracts from MEDLINE, users can extract sentences based on predefined or user-defined template categories. BioIE also provides a brief insight into the syntactic and semantic context of the source-text by looking at word, N-gram and MeSH-term distributions. Important Applications of BioIE are in, for example, annotation of microarray data and of protein databases." .
SCR:013465 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03501" ;
rdfs:label "STRBase" ;
definition: "A database of information on short tandem repeat systems. It contains facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes." .
SCR:013466 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_151824" ;
rdfs:label "Epidemiology of Chronic Disease in the Oldest Old" ;
NIFRID:synonym "Kaiser Permanente Study of the Oldest Old" ;
definition: "A collection of data of an epidemiological study of chronic disease in the oldest old based on information collected from Kaiser Permanente facilities in Northern California (KPNC). The initial sample was drawn from the Kaiser''s active membership lists for the years 1971 and 1980. The sample was restricted to members that had a Multiphasic Health Checkup examination (MHC) within 7 years of the baseline date. The sample was stratified to attain equal numbers of observations (1,000 in each) in three sex-age cells for each cohort: 65-69, 70-79, and 80+. Each cohort was followed for 9 years through existing medical records and computerized hospitalization tapes. Mortality data was collected by matching the sampled data with state Vital Statistics data for an additional 3 years for a total follow-up time of 12 years. Part 1 of the data collections consists of Master Records, which includes information from the morbidity review, in which over 35 chronic conditions or diagnoses were abstracted from the member charts, as well as detailed diagnostic criteria for the major conditions. A prevalence review was done, which included the 4 years prior to the baseline date for these same conditions. Recurrent disease is included for the following conditions: cancers, myocardial infarction, and various forms of strokes. A detailed account of outpatient health services use, and data from the multiphasic health checkup, which was administered to each participant during the nine yearly follow-ups, are also included in the Master Records file. The labs and procedures included: chemistry, hematology, urinalysis, bacteriology, chest x-ray, GI x-ray, ultrasound, CT/MRI, mammogram, resting ECG, treadmill ECG, echocardiograms, nuclear scans, outpatient breast biopsy, cystoscopy, and cataract surgery. Inpatient utilization includes all hospitalizations, procedures done during a hospital stay, length of stay, admitting/discharge diagnosis. Part 2, Hospitalization, contains records of causes and dates of hospitalizations and discharges and nursing home admissions. There is also a section on incomplete reviews and the reasons for them. Demographic information and some lifestyle information from the multiphasic health checkup (e.g., smoking, alcohol, and Body Mass Index) are also in this file. Data Availability: These datasets have been documented extensively and are available from the ICPSR (Study No. 4219). * Dates of Study: 1971-1992 * Study Features: Longitudinal, Anthropometric Measures * Sample Size: ** 1971 cohort: 2,877 (baseline) ** 1980 cohort: 3,113 (baseline) ** 1971 & 1980: 5,990 ** Hospitalization: 14,730 Links: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04219 * HSRR: http://wwwcf.nlm.nih.gov/hsrr_search/view_hsrr_record_table.cfm?TITLE_ID=381&PROGRAM_CAME=toc_with_source2.cfm" .
SCR:013467 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00566" ;
rdfs:label "National Cell Culture Center" ;
NIFRID:abbrev "NCCC" ;
definition: "Provides access to large scale cell culture at reasonable cost. The Cell Culture Center has experience with the production of over 1700 cell lines. Numerous common cell lines, such as HeLa, CHO, 293, BHK, and hybridomas are routinely produced at the Center. We will adapt your cell line or custom protocol to large scale production then deliver the cells in the quantity and frequency you need. Large Scale Production Services: Mammalian cells: Suspension culture (1 to 400 liters per day), Anchorage dependent culture (1 to 200 roller bottles per batch), Purified monoclonal antibodies (10 mg to 100 grams), Non-hybridoma cell secreted proteins, Conditioned media Secreted proteins from suspension cultures can be produced in automated hollow fiber bioreactor systems. These systems may be considered after initial static culture production yields are determined. Upon determining the quantities requested by the investigator, the appropriate automated system will be used. For more information on the automated instrumentation available for the use of secreted protein production, please refer to the Biovest International web page (www.biovest.com). Working with our experienced personnel and quality controlled, state-of-the-art facilities also permits access to large quantities of cells or protein so you aren''t limited by the cell culture capacities of your own laboratory. The Center fulfills the needs of small research laboratories as well as those of larger institutions. Customers from all sectors of the research and industrial community are welcome to inquire about our services. If you''d like to inquire about using our services, use the contact infromation below. Key words: Cell, cells, culture, monoclonal, antibodies, antibody." .
SCR:013468 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03459" ;
rdfs:label "ShiBASE" ;
definition: "A database of the genomes of representative strains of the four Shigella species and comparative genomic hybridization (CGH) of 43 different serotypes of Shigella strains by microarray. The intra-species comparison of Shigella genomes are presented at several different levels in the database, including not only basic genome features, structure of genomes and orthologs ordering, but also metabolic pathways and virulence factors. Moreover, the CGH results on 43 different serotypes of Shigella strains were also integrated into ShiBASE. The newly developed online sequence comparison visualization service, Shi-align, offers an easy way for biologists to perform comparative analysis on their own data." .
SCR:013469 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02573" ;
rdfs:label "Active Sequence Collection" ;
NIFRID:synonym "ASC" ;
definition: "A collection of Active protein Sequences, or protein fragments or subsequences, collected in the form of function-oriented databases. Since its first release, ASC has extended its topics to other specific functions as well as by including databases with structural peculiarities. The current release (Spring 2005) includes seven databases: - AIRS: a database of Auto Immune Related Sequences. The collected information comes from the literature and each entry reports the peptide sequence, information about its biological activity, the reference (with hyperlink to Medline or other similar service). - BAC: a database of Bio ACtive peptides. The collected information comes from the literature and each entry reports the peptide sequence, its biological activity, the reference (with hyperlink to Medline or other similar service). - CHAMSE: a database of CHAMeleon SEquences. This name indicates the structural feature of some segments which have been observed to assume both alpha helix and beta strand structure in 3D models of proteins. - DORRS: a Database Of RGD Related Sequences which collects active linear and cyclized short peptide sequences taken from literature. - DVP: a database of Delivery Vector Peptides. The collected information comes from the literature and each entry reports the peptide sequence and the reference (with hyperlink to Medline or other similar service). - SSP: a Database of Structures of Solved Peptides. - TRANSIT: a database of TRANsglutamination SITes which collects information from literature about protein amino acids substrates of the transglutaminase enzyme (E.C. 2.3.2.13 - click the number for the ENZYME database link at the ExPASy Molecular Biology Server)." .
SCR:013470 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-31779" ;
rdfs:label "Manipulate and Display a DNA Sequence" ;
NIFRID:synonym "Manipulate Display a DNA Sequence" ;
definition: "A software tool that allows users to input a DNA (or RNA) sequence and obtain its inverse, complement or inverse complement. The program can also be used to display a DNA sequence and its complement in double-stranded format. Functions after users paste a DNA sequence into the upper text box, then click the appropriate button to place a manipulated form of the sequence in the lower text box." .
SCR:013471 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-21402" ;
rdfs:label "Therapeutically Relevant Multiple Pathways Database" ;
NIFRID:synonym "TRMP" ;
definition: "The Therapeutically Relevant Multiple Pathways Database is designed to provide information about such multiple pathways and related therapeutic targets described in the literatures, the targeted disease conditions, and the corresponding drugs/ligands directed at each of these targets. This database currently contains 11 entries of multiple pathways, 97 entries of individual pathways, 120 targets covering 72 disease conditions along with 120 sets of drugs directed at each of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name. Additional information provided include protein name, synonyms, Swissprot AC number, species, gene name and location, protein sequence (AASEQ) and gene sequence (NTSEQ) as well as potential therapeutic implications while applicable. Cross-links to other databases are provided which include Genecard, GDB, Locuslink, NCBI, KEGG, OMIM, SwissProt to facilitate the access of more detailed information about various aspects of the particular target or non-target protein. Queries can be submitted by entering or selecting the required information in any one or combination of the fields in the form. User can specify full name or any part of the name in a text field, or choose one item from an selection field. Sponsors: TRMP is supported by the National University of Singapore." .
SCR:013472 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02564" ;
rdfs:label "ArchDB - Biological Database of Protein Loops" ;
NIFRID:synonym "ArchDB" ;
definition: "
ArchDB is a compilation of structural classifications of loops extracted from known protein structures.
ArchDB includes 4 classifications:
* ArchDB40 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 40% sequence identity.
* ArchDB95 contains the classification of loops extracted from proteins domains of ASTRAL SCOP with less that 95% sequence identity.
* ArchDB-EC is a classification of loops extracted from proteins with known enzymatic function
* ArchDB-KI is a curated classification database of kinase loops EC number 2.7.X.X with functional information of residues.
Futhermore, the functional annotation of residues in this database are further classified in four categories:
1. ATP interaction: for residues involved on ATP binding/interaction.
2. Substrate binding: for residues involved in substrate interaction/binding with the exception of ATP
3. Ion interaction: for residues involved in ion interaction/binding of ions needed for the catalytic mechanism
4. Catalytic: involved in reaction, the stabilization of a transition state or the activation of substrates.
Additionally, three different approaches were applied to identify functional residues of the loops of the sub-classes:
1. Residues found within a cut-off distance of 6���� from an heteroatom, ligand, inhibitor, cofactor or complex partner molecule (protein or DNA), with the exception of D2O or crystallization buffer molecules.
2. Residues identified by functional information from ACTSITE and SITE records in the RCSB protein data bank.
3. Residues identified by the functional annotation collected from the literature and assigned to specific motifs of kinases.
Lastly, the multiple ways to browse and query in ArchDB are:
* Search by sequence: Users can search for classified loop(s) with sequence similarity to a query sequence.
* Search by structure: Users can upload protein coordinates in PDB format and its loops will be extracted and compared with those from the classification. First: structural class is assigned comparing loop geometry and, second: the loop conformation is compared among the subclasses within the assigned class.
* Search subclasses and/or Search Loops: A range of options are offered for subclass or loop searches. Users can query ArchDB asking for subclasses or loops with specific flanking secondary structures, length of loops or phi/psi loop conformation. Also, users can retrieve all subclasses or loops with PDB SITE annotations and contacts with co-crystallized ligands. Finally, users can search for subclasses that have SCOP, GO or EC annotations conserved at different percentage levels.
* Search structures: Users can search for classified PDB structures in ArchDB with specific Sprot. Annotation/Keyword, GO annotation, SCOP and EC codes.
* Specific queries for ArchDB-KI: Users can list functional subclasses or loops classified in ArchKI.
:Sponsors: ArchDB is funded by grants from Fundacin Areces (Spain), Ministerio de Ciencia y Tecnologa Spain (MCYT; BIO2002-03609, BIO2001-246 and BIO2001-264), Centre de Referncia en Biotecnologia Generalitat de Catalunya (CERBA), and the Generalitat de Catalunya
:
:Enzyme-specific classification,
:Kinase proteins, ligand, Protein residue, Protein motif, Protein loop,
" .
SCR:013473 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152388" ;
rdfs:label "ImmunoStar" ;
NIFRID:synonym "Diasorin",
"Immuno Nuclear",
"Immunonuclear",
"ImmunoStar inc.",
"Incstar" ;
definition: "An Antibody supplier" .
SCR:013474 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03143" ;
rdfs:label "MitoDrome" ;
definition: "It has been developed with the aim to annotate the complete set of Drosophila melanogaster nuclear genes encoding for mitochondrial proteins in order to contribute to their functional characterization. The data collected in MitoDrome derive from the comparison of Human mitochondrial proteins available in SWISSPROT vs. the Drosophila genome, ESTs and cDNA sequences available in the FlyBase database. According to the results, each Drosophila gene sharing significant homology with a human mitochondrial protein was classified as a putative Drosophila mitochondrial gene and annotated in MitoDrome." .
SCR:013475 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152387" ;
rdfs:label "Immunosolution" ;
definition: "An Antibody supplier" .
SCR:013476 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03115" ;
rdfs:label "Metagrowth" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database aiming to guide experimental studies and in silico simulation studies on the culture conditions of obligate parasitic bacteria. Now we are gathering biological data relevant to the improvement of culture conditions of different obligate parasitic bacteria, and organizing a database named Metagrowth. The data were collected from literature, genomic sequence information, metabolic databases and transporter databases. Each database entry is composed of evidences and derived hypotheses. The hypotheses are physical conditions or supplementation of molecules in culture media, that may lead to the improvement of the bacterial growth. Currently about 200 entries are available for six different bacteria." .
SCR:013477 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02816" ;
rdfs:label "Essential genes in E. coli" ;
definition: "The Essential Genes in E. Coli website provides links to data on essential genes in E. coli, and shows a short list of E. coli essential genes identified from the Neidhardt E. coli books. Essential genes are defined as those genes which are required in WT strain MG1655 for the formation of colonies on solid rich medium within 24 hours of incubation at 37 degrees C." .
SCR:013478 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03285" ;
rdfs:label "PHYTOPROT" ;
definition: "A database of protein domains shared by different sequence clusters. These were assembled by performing an "all-by-all" comparison of (putative) protein sequences with the BIOFACET software, building clusters of sequences based on their similarity and finally displaying à la Prodom the domains shared by the sequences in each cluster." .
SCR:013479 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bayesfst",
"nlx_154236" ;
rdfs:label "BAYESFST" ;
definition: "Software application for Bayesian estimation of the coancestry coefficient FST (entry from Genetic Analysis Software)" .
SCR:013480 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154404" ;
rdfs:label "HWMET" ;
definition: "Software application for Bayesian estimation of the population inbreeding coefficient f (entry from Genetic Analysis Software)" .
SCR:013481 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03635" ;
rdfs:label "VirOligo: Virus Oligonucleotide Database" ;
NIFRID:synonym "VirOligo" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of virus-specific oligonucloetides and their primers. It allows users to search based on virus name, PMID, VirOligoID, or taxonomy ID. The VirOligo database is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place. To this end, researchers are also exploring Virus Signature Hybridization (ViSH) and Virus Signature Amplification (ViSA), microarray-based methods for hybridization and PCR amplification. The site employs Universal PCR techniques, a PCR that amplifies DNA fragments from more than one viral species, such as family- or genus-specific PCR." .
SCR:013482 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:huge",
"nif-0000-02990" ;
rdfs:label "HUGE - Human Unidentified Gene-Encoded large proteins" ;
NIFRID:synonym "HUGE" ;
definition: "The HUGE protein database has been created to publicize the Human cDNA project at the Kazusa DNA Research Institute. This project will sequence and analyze long (>4 kb) human cDNAs and establish methods by using the sequence data how to predict the primary structure of proteins of various biological activities. Currently, it focuses on the analysis of cDNA clones encoding particularly large proteins (>50 kDa). The HUGE protein database contains various types of information derived from the predicted primary structure data of newly identified human proteins. The HUGE protein database are expected to cover various sets of large human proteins of hitherto unidentified functions. They are likely to be involved in cellular structure/motility (such as cytoskeleton, membrane skeleton, and motor proteins), gene expression and nucleic acid metabolism, cell signaling/communication (such as cellular adhesion, signal transduction, channels, and receptors), and so on." .
SCR:013483 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00163" ;
rdfs:label "DsTool" ;
definition: "Software package providing an interactive graphical interface for computations in dynamical systems and visualization of resulting geometric structures, designed for researchers and educators studying dynamical systems (both differential equations and discrete time systems). DsTool readily produces nice pictures for both discrete and continuous systems." .
SCR:013484 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152386" ;
rdfs:label "ImmunoDiagnostics" ;
NIFRID:synonym "ImmunoDiagnostics inc." ;
definition: "An Antibody supplier" .
SCR:013485 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152385" ;
rdfs:label "Immuno-Biological Laboratories" ;
NIFRID:synonym "IBL",
"Immuno-Biological Laboratories Co",
"Ltd." ;
definition: "An Antibody supplier" .
SCR:013486 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-20850" ;
rdfs:label "Glycosylation Pathways Database" ;
NIFRID:synonym "GTDB" ;
definition: "A pathway-based graphical interface for navigating the glycoenzyme database. The goal of the project is to define the paradigms by which carbohydrate binding proteins function in cellular communication. These pages are divided into six categories: -Glycosphingolipid: Sub-categories are Isogloboseries, Globoseries, Neo-lactoseries, Lactoseries and Ganglioseries - N-linked: Sub-categories are High-mannose, Hybrid and Complex -Mucin -Terminal Core 1 -Other O-linked -Terminal All: Includes all potential terminal structures for each glycan category" .
SCR:013487 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-21124" ;
rdfs:label "DOLOP: A Database of Bacterial Lipoproteins" ;
NIFRID:synonym "DOLOP" ;
definition: "DOLOP is an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. This website along will have additional information on the biosynthetic pathway, supplementary material and other related figures. DOLOP also contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. Additionally, the website features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins." .
SCR:013488 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:inclusive",
"OMICS_00766" ;
rdfs:label "INCLUSive" ;
definition: "A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements." .
SCR:013489 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03639" ;
rdfs:label "VKCDB - Voltage-gated K Channel Database" ;
NIFRID:synonym "VKCDB" ;
definition: "Voltage-gated potassium channel database (VKCDB) is designed to serve as a resource for research on voltage-gated potassium channels. Protein sequences, references, functional data and many other relevant data are included in this database. Mysql is used as the underlying database management system to meet the requirements of future development plans. VKCDB will allow you to browse and search using different annotation criteria, and search against the sequences in VKCDB with VKCBLAST. Displayed entries can be selected to download as multiple sequences in FASTA format for further analyses, such as ClustalW alignment. Several computational tools are being developed to help guide structure function analysis of voltage-gated potassium channels and other protein families in general. VKCDB currently stores 346 voltage-gated potassium channel entries, including some "unknown proteins" annotated by automatic genome annotation projects which share a high degree of sequence similarity with voltage-gated potassium channels. VKCDB was populated using automatic parsing of BLASTP search output. Entries were checked manually for redundancy, sequence conflicts, and isoforms, and they are hyperlinked to their variant entries as well as to entries with sequence conflicts. All entries contain GenBank annotations and Swissprot annotations if available. Current annotations were updated with Swissprot release 43.1 (Apr 2004) and GenBank as of Apr 2004. The snapshot version 3 of VKCDB in XML format as of Apr 2004 can be downloaded here. We collected available electrophysiological data and pharmacological data from over 200 journal articals and stored them in VKCDB. VKCDB is updated regularly from BLAST searches of new entries in GenBank and Swissprot. VKCBLAST are updated to include new sequences within a few days after new entries are added into VKCDB. Sequences of all VKCDB entries were sent to TMHMM and PHD for membrane domain prediction. Both results were parsed and linked to each VKCDB entry page. Multiple alignment of T1 and six transmembrane domains of Kv1-4 and KCNQ (Kv7) family are also presented here. VKCDB is a part of an ongoing high throughput voltage-gated potassium channel sequencing project in the laboratories of Dr. Warren J. Gallin and Dr. Andy N. Spencer at the University of Alberta, Canada." .
SCR:013490 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154467" ;
rdfs:label "MAPPOP" ;
definition: "Software application that selects high resolution mapping subsamples and performs bin mapping (entry from Genetic Analysis Software)" .
SCR:013491 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03395" ;
rdfs:label "SBM DB" ;
NIFRID:synonym "Systems Biology and Medicine Database" ;
definition: "It is a comprehensive database of Gene Expression Profiles, which enable to compare the transcriptome of various tissues, organs and experiments. mRNA expression levels of thousands of genes are measured with oligo-nucleotide DNA microarray "GeneChip". All gene expression data in this database is produced by LSBM (Laboratory for Systems Biology and Medicine) and the collaborators. SBM DB provides two different databases: A reference database for fur expression analysis (RefEXA) and LSMB GeNet, a database of various organisms, tissues, and experiences. RefEXA provides a comprehensive gene expression database of Human normal tissues, normal cultured cells and cancer cell lines with GeneChip HG-U133A, can help investigation of Human disease. LSMB provides" .
SCR:013492 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152417" ;
rdfs:label "myNeuroLab.com" ;
definition: "An Antibody supplier" .
SCR:013493 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152416" ;
rdfs:label "MyBioSource" ;
NIFRID:synonym "MyBioSource Inc",
"MyBioSource Inc.",
"MyBioSource.com" ;
definition: "An Antibody supplier" .
SCR:013494 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00826" ;
rdfs:label "ArrayOligoSelector" ;
definition: "Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene." .
SCR:013495 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID: 501100000266",
"grid.421091.f",
"ISNI: 0000 0004 0394 8681",
"nlx_10253",
"Wikidata: Q5377871" ;
rdfs:label "Engineering and Physical Sciences Research Council" ;
NIFRID:synonym "UK EPSRC" ;
NIFRID:abbrev "EPSRC" ;
definition: "EPSRC is the main UK government agency for funding research and training in engineering and the physical sciences, investing more than £850 million a year in a broad range of subjects from mathematics to materials science, and from information technology to structural engineering. We support research into engineering, mathematics, physics, chemistry, materials science, information and communications technologies. EPSRC is a non-departmental public body funded by the UK government through the Department for Universities, Innovation and Skills. We employ around 300 staff in Swindon. We manage our portfolio through programmes. Research base programmes focus on investigator-led research and training. Business innovation programmes deliver our priority research themes and maximise the economic and social impact of the research and training we fund." .
SCR:013496 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154365" ;
rdfs:label "GRR" ;
NIFRID:synonym "Graphical Representation of Relationships" ;
definition: "A graphical tool designed for detection of errors in relationship specification in general pedigrees by use of genome scan marker data. (entry from Genetic Analysis Software)" .
SCR:013497 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30418" ;
rdfs:label "DINO" ;
definition: "DINO is a realtime 3D visualization program for structural biology data. It runs under X-Windows and uses OpenGL. Supported architectures are Linux-i586 and Mac OSX. Versions for IRIX, OSF1 and SunOS are made available sporadically, usually upon request. DINO is distributed in binary form only, the current DINO version is 0.9.1. Structural Biology is a multidisciplinary research area, including x-ray crystallography, structural NMR, electron microscopy, atomic-force microscopy and bioinformatics (molecular dynamics, structure predictions, surface calculations etc). The data produced by these different research areas is very diverse: atomic coordinates (models and predictions), electron density maps, surface topographs, trajectories, molecular surfaces, electrostatic potentials, sequence alignements etc... DINO aims to visualize all this structural data in a single program and to allow the user to explore relationships between the data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar fields (electron densities and electrostatic potentials), topographs (surface topography scans) and geom (geometric primitives such as lines). The number and size of the data the program can handle is only limited by the amount of RAM present in the system. No artifical limits are set. Supported input file formats are PDB (coordinates), X-PLOR/CNS (coordinates, electron densities and trajectories), CHARMM (coordinates, trajectories and scalar fields), CCP4 (electron densities), UHBD (el, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013498 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02546" ;
rdfs:label "Aminoacyl-tRNA synthetase database" ;
NIFRID:synonym "AARS DB" ;
definition: "The AARSs database is the collection of amino acid sequences of all published AARSs. Currently it contains 1047 primary structures of cytoplasmic and organellar AARSs from various organisms. The entries are grouped according to AARS amino acid specificity. They are based on EMBL/SWISS-PROT format. Each includes the AARS amino acid sequence, its SWISS-PROT name and the accession number, a short description of the sequence, its source (organism name with taxonomic classification) and bibliographic information. For the enzymes whose sequences were determined at the nucleotide level, the appropriate EMBL/GenBank or TIGR entries are included, and for those with already known 3D structure, the cross-references to the Brookhaven Protein Data Base are indicated. The partial sequences of AARSs are also included in the database. According to the original SWISS-PROT description, some of the entries have been marked as putative or probable." .
SCR:013499 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33081" ;
rdfs:label "Extensible MATLAB Medical image Analysis" ;
NIFRID:synonym "EMMA",
"MINC-EMMA" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. EMMA (Extensible MATLAB Medical image Analysis) is a toolkit designed to ease the use of MATLAB in the analysis of medical imaging data. It provides functions for reading and writing MINC files, viewing images, performing ROI operations, and performing several popular analyses. Also, there are toolkits for performing kinetic analysis of dynamic PET rCBF (regional cerebral blood flow) and FDG data. The goal for this site is to provide a centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools that are of use to the general community." .
SCR:013500 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_151355" ;
rdfs:label "Aging Status and Sense of Control (ASOC)" ;
NIFRID:synonym "Aging Status and Sense of Control",
"Aging Status Sense of Control (ASOC)" ;
NIFRID:abbrev "ASOC" ;
definition: "A dataset generated longitudinal study that aims to explain the relationship between age and changes in the sense of control over one' '''s life, over two follow-up periods. The main hypotheses are (a) over a period of time, the sense of control declines by an amount that increases with age; (b) the change in sense of control reflects an underlying change in biosocial function, which accelerates with age; (c) higher social status slows the decline in the sense of control, possibly by preserving biosocial function; and (d) changes in biosocial function and in the sense of control have deviation-amplifying reciprocal effects that accelerate age-dependent changes in the sense of control. This was a three-wave panel survey with fixed 3-year intervals and repeated assessments of the same variables. Questionnaire topics focused on: physical health (subjective health; activities of daily living; height and weight; health conditions; expected personal longevity); health behavior (exercise, smoking, diet, alcohol use); use of medical services (medical insurance coverage, prescription drug use); work status (current employment status; title of current job or occupation and job description; types of work, tasks, or activities; description of work or daily activity and interactions; supervisory status; management position and level; work history); sense of controlextent of agreement or disagreement with planning and responsibility versus luck and bad breaks; sense of victimhood versus control; social support and participation; personal and household demographics; marital and family relations; socioeconomic status; history of adversity. * Dates of Study: 1994-2001 * Sample Size: 2,593 (Waves 1-2); 1.144 (Wave 3) * Study Features: Longitudinal Data Archives: http://www.sscnet.ucla.edu/issr/da/da_catalog/da_catalog_titleRecord.php?studynumber=I3334V1" .
SCR:013501 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-21131" ;
rdfs:label "Drug ADME Associated Protein Database" ;
NIFRID:synonym "ADMEAP" ;
definition: "A database for facilitating the search for drug Absorption, Distribution, Metabolism, Excretion (ADME) associated proteins. It contains information about known drug ADME associated proteins, functions, similarities, substrates / ligands, tissue distributions, and other properties of the targets. Associated references are also included. Drug absorption, distribution, metabolism and excretion (ADME) often involve interaction of a drug with specific proteins. Knowledge about these ADME-associated proteins is important in facilitating the study of the molecular mechanism of disposition and individual response as well as therapeutic action of drugs. It is also useful in the development and testing of pharmacokinetics prediction tools. Several databases describing specific classes of ADME-associated proteins have appeared. A new database, ADME-associated proteins (ADME-AP), is introduced to provide comprehensive information about all classes of ADME-associated proteins described in the literature including physiological function of each protein, pharmacokinetic effect, ADME classification, direction and driving force of disposition, location and tissue distribution, substrates, synonyms, gene name and protein availability in other species. Cross-links to other databases are also provided to facilitate the access of information about the sequence, 3D structure, function, polymorphisms, genetic disorders, nomenclature, ligand binding properties and related literatures of each protein. ADME-AP currently contains entries for 321 proteins and 964 substrates. ADME Class Based on their respective role of pharmacokinetics, ADME-associated proteins can be classified into four categories: A: This Category includes proteins involved in the absorption or re-absorption of drugs into systemic system. D: This category includes proteins responsible for facilitating the distribution of drugs from the systemic system to the target sites or away from the target sites back to the systemic system. Certain plasma proteins and intracellular binding proteins may alter free drug concentration by acting as drug storage depot. These proteins thus play a regulatory role in drug distribution and they are thus included in Category D. Based on their role in drug distribution, proteins in this category can be further divided into three groups D1, D2, and D3. The first group D1 includes transporters capable of transporting chemicals across membranes of various tissue barriers from the systemic system into the target sites. Blood-brain barrier and placenta barrier are examples of tissue barrier. Proteins in the second group D2 are responsible for transporting drugs back into the systemic system. Proteins in the third group D3 mainly function as drug storage depot. These include ligand binding proteins in plasma and intracellular proteins. M: Proteins in category M are drug-metabolizing enzymes. These enzymes can be further divided into two separate groups M1 and M2, according to whether the corresponding enzymatic reaction is phase I or phase II. E: This category E includes proteins that enable the excretion or presystemic elimination of drugs. Some proteins belong to more than one category: e.g. P-glycoprotein both limits intestinal absorption and excludes drugs from the brain back to the blood. It thus belongs to both Category E and D. For those proteins capable of transporting natural substrates without literature report of interaction with a drug, a postfix potential is attached to their respective classification to indicate that their specific role in ADME is yet to be confirmed. Use of ADME-AP for commercial purposes is not allowed." .
SCR:013502 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_15565" ;
rdfs:label "StemCord Cord Blood Bank" ;
definition: "Not yet vetted by NIF curator" .
SCR:013503 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01574" ;
rdfs:label "TreeView" ;
definition: "Software to graphically browse results of clustering and other analyses from Cluster." .
SCR:013504 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00719",
"OMICS_00752",
"SCR_013506" ;
rdfs:label "dChip Software" ;
NIFRID:synonym "dChip Software: Analysis and visualization of gene expression and SNP microarrays" ;
NIFRID:abbrev "dChip" ;
definition: "Software for analysis and visualization of gene expression and SNP microarrays." .
SCR:013505 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_01571" ;
rdfs:label "Cluster" ;
NIFRID:synonym "Cluster 3.0" ;
definition: "Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets." .
SCR:013507 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_00846" ;
rdfs:label "ScanAlyze" ;
definition: "Software to process fluorescent images of microarrays." .
SCR:013508 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30508" ;
rdfs:label "EISEN LAB" ;
definition: "Welcome to Michael Eisens lab in the Howard Hughes Medical Institute (HHMI) at University of California at Berkeley (UCB) and the Lawrence Berkeley National Lab (LBNL). We are part of the Department of Molecular and Cell Biology of UCB and the Genomics Division of LBNL, and the. We are located in Stanley Hall on the Berkeley campus.Our lab applies computational and experimental genomic approaches to study how genome sequences specify organismal form and function. We are particularly interested in the regulation of gene expression, and focus on how the information that specifies when and where genes are expressed is encoded in genome sequences, the role that regulated gene expression plays in animal development and the response of microbes to their environments, and how variation in and evolution of gene expression contributes to phenotypic variation and the remarkable diversity of life on Earth. This site contains a more detailed description of our research projects, an introduction to members of the lab, reprints of all of our publications, free downloadable and web-based software. Sponsor. Experimental work described here was supported by a Howard Hughes Medical Institute Investigator award to MBE and by National Institutes of Health (NIH) grant GM704403 to MBE and MDB. Computational analyses were supported in by NIH grant HG002779 to MBE. Work at Lawrence Berkeley National Laboratory was conducted under Department of Energy contract DE-AC02-05CH11231. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." .
SCR:013509 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-02731" ;
rdfs:label "dbQSNP" ;
definition: "THe dQSNP database accumulates and presents experimental data of sequences and allele frequencies of SNPs in promoter regions. The regions studied here were mainly 1.0 kb upstream and 0.2 kb downstream of transcriptional start regions (TSS), which have been defined as the 5'' end of full length cDNA, obtained from the database of transcription start sites. Users can search dbQSNP records by Blast-search against STS sequences in this database, by key word or by chromosomal location." .
SCR:013510 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154235" ;
rdfs:label "AUTOSCAN" ;
definition: "A helper program to automate the tedious process of the creation of input files from genotype data of genome-wide scans (entry from Genetic Analysis Software)" .
SCR:013511 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-20958" ;
rdfs:label "Kazusa Arabidopsis data opening site" ;
NIFRID:synonym "KAOS" ;
definition: "This site has been developed by Kazusa DNA Research Institute for the purpose of offering the science community the analyzed sequence data produced by a multi-national Arabidopsis genome sequencing project coordinated by the Arabidopsis Genome Initiatives (AGI). The aim of this service is to enable users to browse the annotated sequence data produced by all the sequencing teams of AGI through an user-friendly graphic display system and search engines. Gene structures proposed on the annotated sequences as well as those predicted by computer programs are presented and each graphic item has a hyperlink to detailed information of the corresponding area. The nucleotide sequence data deposited in GenBank by AGI was downloaded, re-computer-analyzed at Kazusa and parsed results are displayed graphically." .
SCR:013512 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_154683" ;
rdfs:label "TRIMHAP" ;
NIFRID:synonym "TRIMmed-HAPlotype (previously named HAL: Haplotype ALgorithm)" ;
definition: "Software application for linkage disequilibrium mapping based on ancestral founder haplotypes. Method uses haplotype data from general pedigrees. (entry from Genetic Analysis Software)" .
SCR:013513 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30381" ;
rdfs:label "Conquest DICOM software 1.4.15" ;
NIFRID:synonym "Conquest DICOM" ;
definition: "Fast error free and transparent compression (>2x) of image data on disk with NKI private or JPEG compression. A database browser and slice viewer integrated in the PACS system with options for: viewing DICOM header, creating BMP files (ideal for slides), sending selected images, printing, database fix tools such as changing patient IDs, deleting and anonymizing studies and series, and splitting and merging series. Uses drag and drop to load DICOM and HL7 files. A simple query/move user interface for diagnostic purposes, to improve your knowledge of DICOM, and to grab missing data from another server. Elementary DICOM print server and client - prints to the default printer. Correct display of JPEG and RLE compressed images in browser. Flexible configuration of JPEG and NKI private compression with optional (de)compression of incoming, dropped, transmitted and archived files. The JPEG compression is done using executables from the OFFIS DICOM toolkit (DCMTK version 3.5.4), developed by Kuratorium OFFIS e.V. A simple DICOM Modality Worklist implementation with HL7 import with configurable translation. A CGI WEB interface with several possible viewers (especially important for the Linux version without a GUI). The server can act as an advanced scriptable DICOM image forwarder and/or DICOM image cache. The server integrates an advanced DICOM viewer based on K-PAC DICOM training and testing Demonstration and research image archives Image format conversion from a scanner with DICOM network access DICOM image viewing and slide making DICOM image selection, (limited) editing, and splitting and merging of series Advanced scriptable image modification, filtering, forwarding and conversion DICOM caching and archive merging DICOM web access for viewing and data management (scriptable)" .
SCR:013514 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03345" ;
rdfs:label "PromEC" ;
definition: "A compilation of E. coli mRNA promoter sequences. It includes documentation on the location of experimentally identified mRNA transcriptional start sites on the E. coli chromosome, as well as the actual sequences in the promoter region. The database is currently updated as of July 2000 and includes 471 entries." .
SCR:013515 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-20851" ;
rdfs:label "Heart and Calcium Functional Network Database" ;
NIFRID:synonym "Heart and Calcium Functional Network" ;
NIFRID:abbrev "HCNet" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A specialized database for mouse heart and calcium signaling toolkit genes. It contains the functional gene modules pre-calculated from the microarray data compendium using various algorithms for genetic network analyses. The Heart and Calcium functional Network (HCNet) database is a collection of functional gene clusters calculated from microarray data compendium obtained from the Korea Systems Biology Initiative and from the publicly available GEO database. It was designed to assist experimentalists especially in the field of cardiac and calcium signaling research to detect potential network motifs and gene clusters that are functionally related or co-regulated by common transcription factors. Genes of defined numbers are classified into two categories, 1) heart-specific genes and 2) heart-specific genes plus calcium signaling toolkit-genes." .
SCR:013516 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152357" ;
rdfs:label "Epitomics" ;
definition: "Original provider of rabbit monoclonal antibodies. Important Note for Epitomics Customers in the U.S.: As of Jan. 28, 2013, orders for Epitomics products will now be handled directly by Abcam." .
SCR:013517 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID: 100004774",
"grid.273406.4",
"ISNI: 0000 0004 0376 1796",
"nlx_152420",
"Wikidata: Q17134414" ;
rdfs:label "New England Biolabs" ;
definition: "An Antibody supplier." .
SCR:013518 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152419" ;
rdfs:label "Neuromics" ;
definition: "An Antibody supplier" .
SCR:013519 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152418" ;
rdfs:label "Nacalai Tesque" ;
NIFRID:synonym "Nacalai Tesque Inc",
"Nacalai Tesque Inc." ;
definition: "An Antibody supplier" .
SCR:013520 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00444" ;
rdfs:label "Congressionally Directed Medical Research Program Grants Database" ;
NIFRID:synonym "Congressionally Directed Medical Research Program" ;
definition: "This is a database of awards granted by the Department of Defense congressionally directed research program. Vision: Find and fund the best research to eradicate diseases and support the warfighter for the benefit of the American public. :Mission: We provide hope by promoting innovative research, recognizing untapped opportunities, creating partnerships, and guarding the public trust. :Grants; funding :" .
SCR:013521 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33207" ;
rdfs:label "Merge Healthcare Incorporated" ;
NIFRID:synonym "Merge Healthcare" ;
NIFRID:abbrev "Merge" ;
definition: "Merge Healthcare Incorporated develops solutions that automate healthcare data and diagnostic workflow to enable a better electronic record of the patient experience, and to enhance product development for health IT, device and pharmaceutical companies. Merge products, ranging from standards-based development toolkits to sophisticated clinical applications, have been used by healthcare providers, vendors and researchers worldwide for over 20 years. Merge Healthcare utilizes decades of technology, expertise, intellectual property, innovative software development and expert services to build IT solutions for healthcare and biopharmaceutical customers worldwide. Merge Healthcares OEM applications and toolkits improve the process of transferring diagnostic data and images, and support integration of data from imaging procedures into broader health IT applications. These solutions provide an advanced start to software development, and are quietly inside many of today''s health IT systems. Merge Healthcares Medical Imaging Solutions bring mission-critical improvements for imaging workflow, from scheduling to billing through disaster recovery. Our Perioperative Solutions provide enhanced workflow for the entire surgery experience. Our customers, from the largest outpatient center chains to rural hospitals, have relied on Merge to bring them the solutions and services needed to run clinically and financially successful businesses. Merge Healthcares eClinical business unit, recently added through the acquisition of etrials Worldwide Inc., provides adaptive web-based tools that coordinate to transform data into intelligence and speed the path to an actionable study endpoint for clinical trials. Pharmaceutical, biotechnology, medical device and contract research organizations use integrated trial, site and patient solutions for real-time access to the high quality data they need to make informed decisions." .
SCR:013522 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152348" ;
rdfs:label "Dualsystems Biotech AG" ;
definition: "An Antibody supplier" .
SCR:013523 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152347" ;
rdfs:label "Diatheva" ;
NIFRID:synonym "DIATHEVA s.r.l." ;
definition: "An Antibody supplier" .
SCR:013524 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152346" ;
rdfs:label "Diagnostic Systems Laboratories" ;
NIFRID:synonym "Diagnostic Systems Laboratories inc." ;
definition: "An Antibody supplier. Is part of Beckman Coulter." .
SCR:013525 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152345" ;
rdfs:label "Diagnostic Consulting Network" ;
NIFRID:synonym "Diagnostic Consulting Network (DCN)" ;
definition: "An Antibody supplier" .
SCR:013526 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152344" ;
rdfs:label "Diaclone" ;
NIFRID:synonym "Diaclone SAS" ;
definition: "An Antibody supplier" .
SCR:013527 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.482683.3",
"nlx_152343" ;
rdfs:label "DSHB" ;
NIFRID:synonym "Developmental Studies Hybridoma Bank",
"Developmental Studies Hybridoma Bank at the University of Iowa" ;
definition: "An antibody supplier which banks and distributes hybridomas and monoclonal antibodies for use in research. The bank includes antibodies against targets such as GFP, transcription factors, stem cells, and human." .
SCR:013528 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152341" ;
rdfs:label "Detroit R&D" ;
NIFRID:synonym "Detroit R&D Inc" ;
definition: "An Antibody supplier" .
SCR:013529 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152340" ;
rdfs:label "Deciphergen Biotechnology" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017.\\\\\\\\\\\\
\\\\\\\\\\\\
An Antibody supplier" .
SCR:013530 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152339" ;
rdfs:label "Dako" ;
NIFRID:synonym "Dako inc" ;
definition: "An Antibody supplier; Dako was purchased by Agilent in 2012 and several years later the websites began to reflect the Dako products as part of the Agilent catalog." .
SCR:013531 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33266" ;
rdfs:label "Clinical Trial Management Application" ;
NIFRID:synonym "Clinical Trial Management Application (CTMA)" ;
NIFRID:abbrev "CTMA" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 11, 2012. The Clinical Trials Management Tools are Java-based suite (accessed via a secure intranet) for managing various aspects of a clinical trial, research protocols, outcomes initiatives, statistical research analysis, as well as CTEP/CDUS reporting. Developed in collaboration with the Clinical Research Services (CRS) Office at the UPCI, this research-based application provides an integrated tool for managing administrative (e.g. IRB submissions and approvals) and clinical (e.g. tumor measurements, registrations/ screenings) functions for the collection and analysis of data generated from a clinical trial. More information can be found here, http://www.upci.upmc.edu/spore/skin/coreD.cfm" .
SCR:013532 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152338" ;
rdfs:label "Cytoskeleton" ;
NIFRID:synonym "Cytoskeleton inc." ;
definition: "An Antibody supplier" .
SCR:013533 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152280" ;
rdfs:label "ARP American Research Products" ;
NIFRID:synonym "ARP American Research Products Inc",
"ARP American Research Products Inc." ;
NIFRID:abbrev "ARP" ;
definition: "An Antibody supplier" .
SCR:013534 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152279" ;
rdfs:label "Arbor Assays" ;
definition: "An Antibody supplier" .
SCR:013535 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00467" ;
rdfs:label "Foundation for Biomedical Research" ;
NIFRID:synonym "FBR" ;
definition: "Established in 1981, the Foundation for Biomedical Research (FBR) is the nation''s oldest and largest organization dedicated to improving human and veterinary health by promoting public understanding and support for humane and responsible animal research. FBR is the leading voice of scientific reason and medical progress in the ongoing, sometimes violent debate that surrounds animal research. Their mission is to educate the public about the essential role of humane animal research in the quest for medical advancements, treatments and cures for both humans and animals. And through its innovative educational programs, FBR works to inform the news media, teachers, students and parents, pet owners and other groups about the essential need for lab animals in medical and scientific research and discovery. It serves as an accessible, reliable resource for the news media and works to bring American journalists and scientists together to promote exceptional and ongoing news coverage that contributes to public appreciation and respect for responsible animal research." .
SCR:013536 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00466" ;
rdfs:label "Faculty for Undergraduate Neuroscience" ;
NIFRID:synonym "FUN" ;
definition: "FUN is an international organization that is focused on neuroscience education and research at the undergraduate level. FUNs members and supporters include businesses and organizations; private liberal arts colleges, state and research university departments and programs; and individual faculty and students, all sharing a common interest in undergraduate neuroscience." .
SCR:013537 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152314" ;
rdfs:label "Biotrend" ;
definition: "An Antibody supplier" .
SCR:013538 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152313" ;
rdfs:label "Biotium inc" ;
definition: "An Antibody supplier" .
SCR:013539 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152312" ;
rdfs:label "Bioss Inc" ;
NIFRID:synonym "Bioss Inc." ;
definition: "An Antibody supplier" .
SCR:013540 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152311" ;
rdfs:label "Biosense Laboratories" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017.\\\\\\\\\\\\
\\\\\\\\\\\\
An Antibody supplier." .
SCR:013541 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152310" ;
rdfs:label "BioSell Solutions" ;
definition: "An Antibody supplier" .
SCR:013542 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152309" ;
rdfs:label "Biorbyt" ;
definition: "An Antibody supplier" .
SCR:013543 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152308" ;
rdfs:label "BIOPUR" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017.\\\\\\\\\\\\
\\\\\\\\\\\\
An Antibody supplier" .
SCR:013544 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152307" ;
rdfs:label "BioPorto Diagnostics" ;
definition: "An Antibody supplier" .
SCR:013545 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152306" ;
rdfs:label "BIOMOL" ;
definition: "An Antibody supplier" .
SCR:013546 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152305" ;
rdfs:label "Biomedical technologies" ;
definition: "An Antibody supplier" .
SCR:013547 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152304" ;
rdfs:label "Biomedica Medizinprodukte GmbH" ;
NIFRID:synonym "Biomedica",
"Biomedica Medizinprodukte GmbH & Co KG" ;
definition: "An Antibody supplier" .
SCR:013548 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.470243.6",
"nlx_152300" ;
rdfs:label "BioChain" ;
NIFRID:synonym "BioChain Institute Inc",
"BioChain Institute Inc." ;
definition: "An Antibody supplier" .
SCR:013549 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152299" ;
rdfs:label "BIOCARE MEDICAL" ;
definition: "An Antibody supplier" .
SCR:013550 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID: 100001305",
"grid.428260.a",
"ISNI: 0000 0001 0302 6132",
"nif-0000-00463",
"Wikidata: Q3075422" ;
rdfs:label "Christopher and Dana Reeve Foundation" ;
NIFRID:synonym "Christopher & Dana Reeve Foundation" ;
definition: "This foundation is dedicated to curing spinal cord injury by funding innovative research, and improving the quality of life for people living with paralysis through grants, information and advocacy." .
SCR:013552 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152298" ;
rdfs:label "BioAssay Works" ;
NIFRID:synonym "BioAssay Works L.L.C.",
"BioAssay Works LLC" ;
definition: "An Antibody supplier" .
SCR:013554 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152295" ;
rdfs:label "Bethyl" ;
NIFRID:synonym "Bethyl Laboratories" ;
definition: "An Antibody supplier" .
SCR:013555 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00399" ;
rdfs:label "Ontology-based Knowledgebase for Human Cell Adhesion Molecules" ;
NIFRID:synonym "OKCAM" ;
definition: "OKCAM (Ontology-based Knowledgebase for Cell Adhesion Molecules) is an online resource for human genes known or predicted to be related to the processes of cell adhesion. These genes include members of the cadherin, immunoglobulin/FibronectinIII (IgFn), integrin, neurexin, neuroligin, and catenin families. :We have mapped these genes onto a novel cell adhesion molecule ontology (CAMO) that provides a hierarchical description of cell adhesion molecules and their functions. It is intended to provide a means to facilitate better and better understanding of the global and specific properties of CAMs through their genomic features, regulatory modes, expression patterns and disease associations become clearer. :Cadherins, IgCAMs, Integrins, Neurexins, Neuroligins, Catenins :" .
SCR:013556 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152271" ;
rdfs:label "AngioBio" ;
definition: "An Antibody supplier" .
SCR:013557 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00401" ;
rdfs:label "PainConsortium News" ;
definition: "NIH Pain Research Pain Information Index:The National Institutes of Health consists of many different institutes and centers. This site is an index to various NIH publications about pain symptoms, conditions and treatments of pain. :General Pain, Acupuncture, AIDS/HIV, Arachnoiditis, Arthritis, Avascular Necrosis, Back Pain, Behavioral and Relaxation Approaches, Behet''s Disease, Cancer Pain, Carpal Tunnel Syndrome, Central Pain Syndrome, Chiropractic Use, Chronic Pain, Complex Regional Pain Syndrome, Diabetic Neuropathy, Epidermolysis Bullosa, Fibromyalgia, Glossopharyngeal Neuralgia, Gout, Headache, Heritable Disorders of Connective Tissue, HIV/AIDS, Herpes Zoster Oticus, Hip Replacement, Juvenile Rheumatoid Arthritis, Knee Problems, Lichen Sclerosus, Lupus, Magnets, Manipulative and Body-Based Practices, Marfan Syndrome, Medicines by Design, Meralgia Paresthetica, Migrane, Omega-3 Fatty Acids, Osteoarthritis, Paresthesia, Peripheral Neuropathy, Pelvic Pain, Pinched Nerve, Piriformis Syndrome, Polymyalgia Rheumatica and Giant Cell Arteritis, Prescription Drugs and Pain Medications, Progressive Locomotor Ataxia, Prostate Problems, Psoriasis, Raynaud''s Phenomenon, Reflex Sympathetic Dystrophy, Repetitive Motions Disorders, Rheumatoid Arthritis, Scleroderma, Scoliosis, Shingles, Shoulder Pain, Sjogren''s Syndrome, Spinal Stenosis, Sports Injuries, Sprains and Strains, Tarlov Cysts, Temporomandibular Joint Disorders, Tethered Spinal Cord Syndrome, Third Molar (Wisdom Tooth) Removal, Thunder God Vine, Trigeminal Neuralgia Information Page, Whiplash, Wisdom Tooth Removal :" .
SCR:013558 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.483224.b",
"nlx_152290",
"Wikidata: Q4838851" ;
rdfs:label "BACHEM" ;
definition: "An Antibody supplier" .
SCR:013559 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152289" ;
rdfs:label "B-Bridge International" ;
NIFRID:synonym "B-Bridge International Inc",
"B-Bridge International Inc." ;
definition: "An Antibody supplier" .
SCR:013560 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152288" ;
rdfs:label "Aviva Systems Biology" ;
definition: "An Antibody supplier" .
SCR:013561 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33362" ;
rdfs:label "TranscriptionDetector" ;
NIFRID:synonym "Transcription Detector" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2015. TranscriptionDetector is a tool for finding probes measuring significantly expressed loci in a genomic array experiment. TranscriptionDetector was originally created to analyze the transcriptome of Drosophila melanogaster. The study, a collaboration with Kevin White's Lab at Yale, is described in our 2004 Science paper. Later on, it has been elaborated and more recently presented in Gabor Halasz et al. in Genome Biol. 2006 July 19; 7(7):R59 The TranscriptionDetector algorithm requires that a set of negative control probes (NCPs) be included on each microarray used in the study. The significance of a data probe is evaluated relative to these NCPs, which represent non-specific binding." .
SCR:013562 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33391" ;
rdfs:label "Jambalaya" ;
definition: "Jambalaya is a plug-in created for Protg which uses Shrimp to visualize the knowledge bases the user has created. Protg is an ontology editor and a knowledge-base editor which allows domain experts to build knowledge-based systems by creating and modifying reusable ontologies and problem-solving methods." .
SCR:013563 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152284" ;
rdfs:label "ATGen" ;
definition: "An Antibody supplier" .
SCR:013564 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152283" ;
rdfs:label "Astra Biotech GmbH" ;
NIFRID:synonym "Astra Biotech" ;
definition: "An Antibody supplier" .
SCR:013565 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00397" ;
rdfs:label "Barrow Neurological Institute (BNI)" ;
NIFRID:synonym "BNI" ;
definition: "Barrow Neurological Institute of St. Joseph''s Hospital and Medical Center in Phoenix, Arizona, is internationally recognized as a leader in neurological research and patient care. :Established in 1962 under the auspices of Dr. John Green, Barrow has been brought into the twenty-first century under the guiding influence of Dr. Robert Spetzler. :Barrow treats patients with a wide range of neurological conditions, including brain and spinal tumors, cerebrovascular conditions, and neuromuscular disorders. Barrow''s clinicians and researchers are devoted to providing excellent patient care and finding better ways to treat neurological disorders. :Barrow Neurological Institute of St. Joseph''s Hospital and Medical Center, Phoenix, Arizona :department portal :" .
SCR:013566 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152267" ;
rdfs:label "Amersham Biosciences" ;
definition: "An Antibody supplier" .
SCR:013568 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152264" ;
rdfs:label "Alpha Diagnostic International" ;
NIFRID:synonym "Alpha Diagnostic International Inc",
"Alpha Diagnostic International Inc.",
"Alpha Diagnostic Intl. Inc." ;
NIFRID:abbrev "ADI" ;
definition: "An Antibody supplier" .
SCR:013569 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152263" ;
rdfs:label "Alpco Diagnostics" ;
definition: "An Antibody supplier" .
SCR:013570 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152262" ;
rdfs:label "Alomone Labs" ;
NIFRID:synonym "Alomone Labs Ltd." ;
definition: "An Antibody supplier" .
SCR:013571 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152261" ;
rdfs:label "AllStar Scientific" ;
definition: "An Antibody supplier" .
SCR:013572 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00396" ;
rdfs:label "Neurotrophic Lab" ;
NIFRID:synonym "NeurotrophicLab" ;
definition: "We are interested on the mechanisms by which environmental factors affect neuronal health. We have found that trophic factors endogenous to the brain and spinal cord can be induced by the practice of select behaviors. We have recently reported that physical activity, learning, and nutritional factors control neurotrophins in the brain. These findings opened the exciting possibility that regulation of trophic factors by behavior can be a pivotal mechanism by which specific experiences can impact the structure and function of the CNS. It may account for the improvement of CNS function after trauma provided by rehabilitative therapies. On the contrary, it may explain the decay in function in aging or degenerative diseases following a lack of stimulation. These two avenues provide direction for my research program: 1) How trophic factors induced by activity can help functional recovery following brain and spinal cord trauma. We are using several exercise models to boost the production of trophic factors in the brain and spinal cord. Our goal is to provide critical information to guide the design of behavioral therapies for the reduction of the severity of insult or disease, and to increase CNS function. 2) We are evaluating the effects of lifestyle on trophic factor production, with resulting effects on circuit remodeling, synaptic function, and cognition. We believe that changes in trophic factor as a result of select experiences can affect neuronal health with profound consequences for cognitive function. :lab :" .
SCR:013573 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152260" ;
rdfs:label "Alexis" ;
definition: "An Antibody supplier" .
SCR:013574 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152259" ;
rdfs:label "AgriSera" ;
definition: "An Antibody supplier" .
SCR:013575 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152258" ;
rdfs:label "Agilent Technologies" ;
definition: "Company provides laboratories worldwide with analytical instruments and supplies, clinical and diagnostic testing services, consumables, applications and expertise in life sciences and applied chemical markets." .
SCR:013576 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00293" ;
rdfs:label "Edgewarp3D" ;
NIFRID:synonym "Edgewarp 3D",
"Edgewarp 3D Browser",
"The Edgewarp3D Browser",
"The Edgewarp 3D Browser" ;
definition: "Edgewarp3D is a sophisticated workstation package for manipulation of 2D and 3D biomedical images and related data structures by a combination of landmark location, thin-plate spline, and image unwarping and averaging. Utilizes NLM Visible Human data set" .
SCR:013577 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152257" ;
rdfs:label "Advansta" ;
NIFRID:synonym "Advansta Inc",
"Advansta Inc." ;
definition: "An Antibody supplier" .
SCR:013578 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00286" ;
rdfs:label "Dend" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. An interactive program for resectioning and deriving measurements from contoured structures. It creates structural measurements obtaining lengths, surfaces, and volumes from volume data. Investigation of 3D structures and communication to others are greatly facilitated by this computer-based visualization." .
SCR:013579 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152254" ;
rdfs:label "Advanced Biotechnologies" ;
NIFRID:synonym "Advanced Biotechnologies Inc" ;
definition: "An Antibody supplier" .
SCR:013580 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152253" ;
rdfs:label "Advanced BioSciences Laboratories" ;
NIFRID:synonym "Advanced BioSciences Laboratories Inc" ;
definition: "An Antibody supplier" .
SCR:013581 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.418415.d",
"ISNI: 0000 0004 0507 1772",
"nif-0000-33410",
"Wikidata: Q1055390" ;
rdfs:label "Cerner Millenium" ;
NIFRID:abbrev "Cerner" ;
definition: "A global health company contributing to the systemic improvement of health care delivery and the health of communities. We are transforming health care by eliminating error, variance and waste for health care providers and consumers around the world. Our solutions optimize processes for health care organizations ranging from single-doctor practices to entire countries, for the pharmaceutical and medical device industries, and for the field of health care as a whole. Our solutions are licensed by more than 9,000 facilities worldwide. We invite you to join us in our quest to make health care become all it should be. Since our company began, we have been committed to transformational change in the vital task of keeping people well. Now more than ever, our focus is on developing the innovations that will help improve the entire health care system. Ultimately, as our CEO Neal Patterson has said, health care is personal. Because in the end, nothing matters more than our health and our families. We''re changing the way people: * Use and share information ** We empower providers to base decisions on best clinical evidence. ** We coordinate care across traditionally fragmented health care systems. ** We provide clinical organizations with the reliability, flexibility and continuous innovation available through cloud-based intelligence. ** We provide contextually relevant information to the right people at the right time. * Pay for health and care ** We believe IT investment must be matched with innovative payment models that are much easier to navigate. ** We are replacing the current, claims-based system with streamlined electronic payments. ** We develop ways to reward people and their providers for proactively achieving positive health goals. * Think about health ** We empower people to actively engage in their health by providing them with a standards-based, lifetime Personal Health Record. ** We are replacing the reactive sick care model with a proactive, personalized plan for health." .
SCR:013582 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00394" ;
rdfs:label "International Behavioral Neuroscience Society" ;
NIFRID:synonym "IBNS" ;
definition: "The International Behavioral Neuroscience Society (IBNS) was formed to encourage research and education in the field of behavioral neuroscience. Founded in 1992, the IBNS has approximately 719 members which derive from 36 different countries and consist of scientists, clinicians, teachers, and others with a background and interest in the relationship between brain and behavior. :" .
SCR:013583 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00289" ;
rdfs:label "diffusion TENSOR Visualizer" ;
NIFRID:synonym "dTV" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The diffusion TENSOR Visualizer (dTV) is an analysis tool for diffusion MRI including diffusion tensor images. Several basic functions are available in dTV: fiber tracking and 3D display; diffusion profile visualization as ellipsoid, etc.; compute grey/color-coded FA map, ADC map, etc.; analysis DT-related values within ROI; ans customizing MPG data Current version is dTV.II SR (Second Release). The dTV works as an extension software, i.e. plugin, for a volume data viewer software VOLUME-ONE, which is also in this database." .
SCR:013584 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152255" ;
rdfs:label "Advanced Immunochemical" ;
NIFRID:synonym "Advanced Immunochemical Inc" ;
definition: "An Antibody supplier" .
SCR:013585 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33412" ;
rdfs:label "Open Clinical Report Repository" ;
NIFRID:synonym "Open clinical report and annotation repository" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Repository of de-identified clinical reports available for NLP researchers has been designed. Work with the AMIA NLP working group in designing annotation schemas and obtaining annotations, design a repository for shareable annotations, help design and execute a shared task in IE from clinical reports. The University of Pittsburgh NLP Repository contains clinical reports that are available to the community for NLP research purposes and comprises: # Report Repository - one month of de-identified clinical reports from multiple hospitals and # Annotation Repository - annotations performed on reports from the Report Repository. Anyone performing annotations on reports from the NLP Repository is required to deposit their annotations. The Repository contains reports of the following types generated from multiple hospitals during a single month: * History and Physicals * Progress Notes * Consultation Reports * Radiology Reports * Surgical Pathology Reports * Emergency Department Reports * Discharge Summaries * Operative Reports * Cardiology Reports" .
SCR:013586 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33434" ;
rdfs:label "Concept Hub" ;
NIFRID:synonym "ConceptHub" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. A database built up with software and services that maintains multiple versions of terminologies, map sets, and values sets concurrently. HDD Access has superseded Concept Hub." .
SCR:013587 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00385" ;
rdfs:label "Spike Train Computational Neuroscience Portal" ;
NIFRID:synonym "SpikeTrain" ;
definition: "This database contains hundreds of links to functional neuroscience databases, software, books, articles, research labs and institutions :link aggregation site; portal; :" .
SCR:013588 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00428" ;
rdfs:label "DementiaNet" ;
definition: "DementiaNet is a Community on the Internet where people affected by dementia and their relatives have the opportunity to meet and exchange experiences as well as finding information and help. :Danish, English, Dementia, Dementia Diseases, Diagnosis, Treatment, Dementia-like Conditions, psychosocial aspects, pharmacological treatment, non-pharmacological treatment, Acetylcholinesterase inhibitors, NMDA receptor antagonists, Pharmaceutical Benefits Scheme (PBS), Alzheimer''s disease, beta-amyloid deposits, Secretory inhibitors, protein deposit inhibitors, beta-amyloid, Ginkgo Biloba, Alzheimer''s Medication, Medication Subsidies, Dementia-like Conditions, Social Perceptions :" .
SCR:013589 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.421926.a",
"ISNI: 0000 0004 0618 5755",
"nlx_152252" ;
rdfs:label "Active Motif" ;
definition: "An Antibody supplier" .
SCR:013590 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00375" ;
rdfs:label "XooNIps - Neuroinformatics Base Platform System" ;
NIFRID:synonym "XooNIps" ;
definition: "Neuroinformatics (NI) is a new discipline that challenges the understanding of the structure and mechanism of the brain by combining neuroscience and information technology. The global collaborations in this field have been actively started with the support of the International Neuroinformatics Coordinating Facility (INCF) launched in November 2005. The Laboratory for Neuroinformatics at RIKEN Brain Science Institute (BSI) is involved in developing various cutting-edge technologies related to NI such as XooNIps. XooNIps succeeded the concept and basic feature of the vision science platform; Visiome, constructed by the NRV (i.e., Neuroinformatics Research in Vision) Project and has been developed based on a content management system (CMS); XOOPS, as infrastructure for NI databases to share different types of data on the Internet. :XooNIps has three features: :The first is the flexibility of developing databases. CMS-based XooNIps makes it easy to change the design or to extend the functions of databases by combining the different modules available on XOOPS. Therefore, even those who are not expert in computer system can develop their database on XooNIps. :The second is the diversity and extensibility of the data which can be handled by XooNIps. In order to handle different types of actual data, it provides not only the various data forms per se, but also the extension method to handle a new data form, which enables to deal easily with even a non-standardized data form. :The third is the facility to distribute metadata. XooNIps implements OAI-PMH (i.e., Open Archive Initiative-Protocol for Metadata Harvesting) which is one of the standard protocols to distribute metadata. This enables to collect information on other databases which are developed on XooNIps or to coordinate databases by exchanging metadata with other databases which implement OAI-PMH than those on XooNIps. :Since April 2007, Neuroinformatics Japan Center (NIJC) at RIKEN BSI takes charge of extending and maintaining XooNIps, and is committed to manage the documentation hereafter. :NIJC, as a national node of INCF, is developing and operating various NI platforms in neuroscience based on XooNIps to establish and facilitate NI research in Japan. XooNIps is also being applied to databases or organizational repositories in several institutions and universities, and laboratory groupware in various fields. We hope XooNIps will be of universal use in and out of Japan. :database; binary executable; software development tool; metadata; data set; :" .
SCR:013591 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00276" ;
rdfs:label "btrack" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. It analyzes and graphs time-lapse imaging data as acquired by a Bio-Rad confocal microscope, for experiments using nonratiometric fluorescent indicator dyes. Btrack can accommodate changes in the positions of imaged cells/tissue regions and can be used for analyzing an unlimited number of areas (cells/tissue regions) in an imaged field." .
SCR:013592 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152248" ;
rdfs:label "Abnova Corporation" ;
definition: "An Antibody supplier" .
SCR:013593 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_12927" ;
rdfs:label "LifeCell Corporation" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016." .
SCR:013594 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00374" ;
rdfs:label "Samurai Graph: A highly functional and user-friendly graph plotter" ;
NIFRID:abbrev "Samurai Graph" ;
definition: "Samurai Graph is a highly functional and user-friendly graph plotter. It can plot the graphs from the scalar to vector type 2-dimensional data. Samurai Graph is an open source development project, released under the GNU Lesser General Public License (LGPL). Samurai Graph is Java-based and platform-independent application. It runs on most major operating systems including MS-Windows, Linux, MacOS X, FreeBSD., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013595 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00441" ;
rdfs:label "Neurogenerator" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A database project for the neuroimaging community NeuroGenerator is a database project funded by the European Commission. The overall purpose is to make databases with data in comparable and compatible formats suited for meta research and for making models of the cerebral cortex of the human brain. Researchers can submit their own raw PET-data and fMRI data to NeuroGenerator. The data are analyzed with the statistical software package FSL. In this way databases are produced of PET and fMRI data in standard anatomical format Data as statistical parametric images in standard anatomical format immediately comparable due to the uniform processing Cytoarchitectural data (from post mortem brains) in standard anatomical format." .
SCR:013596 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152243" ;
rdfs:label "Abbiotec" ;
NIFRID:synonym "Abbiotec LLC" ;
definition: "An Antibody supplier" .
SCR:013597 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00197" ;
rdfs:label "Neuromantic" ;
definition: "Neuromantic is a freeware reconstruction tool for Windows-based machines. It is designed to allow the efficient creation of 3D neuronal reconstructions from serial stacks of images. :Neuron, Morphological Reconstruction, Morphology, Freeware, Software, Dendritic Morphology : :May be used as a freeware alternative to Neurolucida or Neuron_Morpho for the 3D reconstruction of neurons from serial image stacks." .
SCR:013598 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00420" ;
rdfs:label "Theoretical and Computational Biophysics Group (TCBG)" ;
NIFRID:synonym "TCBG" ;
definition: "The Theoretical and Computational Biophysics Group (TCBG), an NIH Resource for Macromolecular Modeling and Bioinformatics, was founded by Professor Klaus Schulten in 1989 and is located at the Beckman Institute of the University of Illinois at Urbana-Champaign (UIUC). The group is led by Professor Klaus Schulten (Physics, Biophysics, Chemistry) with Professors Laxmikant Kale (Computer Science), Zaida Luthey-Schulten (Chemistry) and Alek Aksimentiev (Physics), and with the Resource''s assistant director Dr. Emad Tajkhorshid (Biophysics). Research and development activities of the TCBG center on the structure and function of supramolecular systems in the living cell, and on the development of new algorithms and efficient computing tools for structural biology. :The TCBG brings the most advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance. We extend, refine and deliver these technologies in response to experimental progress and emerging needs of the wide biomedical research community. We magnify the impact of our work through direct collaboration with experimental researchers, the distribution of cutting-edge and user-friendly software, and via extensive training, service, and dissemination efforts. :cell, algorithm, simulation software, membrane potential, genome, molecule, ion channel, chromatin, Image Processing software, data Data visualization software, simulation software; Membrane Biophysics, Mechanobiology, Nanoengineering, Bioenergetics, Neurobiology, Molecular Dynamics, cellular membrane, osmotic pressure, proteins (use protein), Gatekeeper Protein, membrane, mechanosensitive channel of small conductance (MscS), Visual Molecular Dynamics (VMD), Quantum Biology, quantum chemistry, Molecular Dynamics Simulator, Nanoscale Imaging, cellular membrane tension, bacterial cell, electron paramagnetic measurements, computer modeling, atomic detail, computational microscope, Lipoproteins [high density lipoproteins (HDL)], Petascale Computing, Macromolecular Modeling, Bioinformatics, supramolecular systems, living cell, algorithms (use algorithm), computing tools, structural biology, molecular modeling, computational technologies, membrane proteins, structural information, molecular visualization, Molecular modeling tools, structural information, bioinformatics databases, molecular dynamics simulations, interactive modeling, collaborations, theoretical, experimental researchers, light energy, electrical membrane potentials (use membrane potential, add term as syn), synthesis of ATP, photosynthetic systems, storage and control of genetic information, classical and quantum dynamical motion of biopolymers, numerical experiments, non-equilibrium statistical mechanics, elasticity theory, theory of disordered systems, collaborative environment, Software Development, cells (use cell), molecular graphics viewer, static and dynamic structures, DNA sequencing, genomes (use genome), direct manipulation and observation, single molecules (use molecule), bioenergetic proteins, nanotechnology, steered/interactive molecular dynamics, dissemination, coarse-graining methods, residue-based and shape-based coarse graining, CG, polymeric systems, Computational Environment, Training, Workshops, Tutorials, Case Studies, Classes, research, Highly Cited, compute power, visualization equipment, desktop workstations, lipid bilayers, allow passage of ions across the membrane (use ion channel), mechanotransduction, membrane tension, 3-D graphics, built-in scripting, animating, analyzing, ideal DNA interbasepair helical parameters, plugin, nucleosomes, antialiasing, depthcueing, Molecular Representations, analysis and Data visualization software (use Image Processing software, and data Data visualization software, add terms as syn.), computer simulations (use simulation software), photosynthetic systems, computational clusters :" .
SCR:013599 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00306" ;
rdfs:label "genomics Workbench" ;
NIFRID:synonym "geWorkbench" ;
definition: "geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data. Example use cases include: * loading data from local or remote data sources. * visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways. * providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory networks reconstruction, BLAST searches, pattern/motif discovery, etc. * validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks (one of the 7 National Centers for Biomedial Computing funded through the NIH Roadmap). Additionally, geWorkbench is supported by caBIG, NCI''s cancer Biomedical Informatics Grid initiative." .
SCR:013600 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00433" ;
rdfs:label "Psychotropics" ;
definition: "The Lundbeck Institute is pleased to present Psychotropics Online, a comprehensive guide to CNS compounds and products. A database of psychotropic and neurological drugs. Generic name, Trade name, Description, Code numbers, Monographies, Tranquilizers - Anxiolytics, Anxiolytics / Antipsychotics, Neuroleptics and Antipsychotics, Monoamine Oxidase Inhibitors, Antidepressants, Antidementia drugs, Sympathomimetics, Antiparkinsonians, Anticonvulsants, Hallucinogenic Agents, Additional Group, Biochemical profiles, Side-effects, Antipsychotics, Tranquilizers - anxiolytics, Tricyclic Antidepressants (TCAs), Selective Serotonin Reuptake Inhibitors (SSRIs), Selective Serotonin and Noradrenaline Reuptake Inhibitors (SNRIs), Selective Noradrenaline Reuptake Inhibitors (NARIs), MAO inhibitors (MAOIs), Sympathomimetics, Anticonvulsants, Lithium, Barbiturates, Street names, Terminal plasma half-lives, Orphan drugs" .
SCR:013601 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00129" ;
rdfs:label "Alzforum Antibody Directory for Neuroscience Research" ;
NIFRID:synonym "Alzforum Antibody Directory" ;
definition: "The Alzheimer Research Forum is the web''s most dynamic scientific community dedicated to understanding Alzheimer''s disease and related disorders. It also contains a database of providers of antibodies directed against several hundred molecules and proteins of relevant to research on Alzheimer and other neurodegenerative diseases. The web site reports on the latest scientific findings, from basic research to clinical trials; creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across the numerous disciplines that can contribute to the global effort to cure Alzheimer''s disease. The ARF team of professional science writers and editors, information technology experts, web developers and producers all work closely with our distinguished and diverse Advisory Board to ensure a high-quality of information and services. We very much welcome our readers'' participation in all aspects of the web site. Sponsors: The Alzheimer Research Forum is an independent nonprofit organization. It is supported by grants and individual donations." .
SCR:013602 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00355" ;
rdfs:label "VTK CISG Registration Toolkit" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This software package provides two voxel-based image registration algorithms that are based on maximising Normalised Mutual Information (NMI). They are incorporated in a user-friendly command-line and graphical interface that includes a visualisation tool for 3D image pairs to permit analysis of registration results. These algorithms have been demonstrated on range of medical applications including brain, breast, liver, and cardiac data and results have been published." .
SCR:013603 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00352" ;
rdfs:label "VOLUME-ONE" ;
definition: "Last update 2004. :VOLUME-ONE is a general-purpose software for viewing volumetric image data. :" .
SCR:013604 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00311" ;
rdfs:label "Head Circumference" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 09, 2013. This tool is a program that allows you to calculate the head circumference based on MRI data. Using Fourier harmonics to parameterize the contour of the head this tool gives the length of the contour. This embedded tutorial software can automatically store the results in a Excel spreadsheet." .
SCR:013605 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-10162" ;
rdfs:label "Baylor College of Medicine Human Genome Sequencing Center" ;
NIFRID:synonym "BCM HGSC",
"Human Genome Sequencing Center" ;
NIFRID:abbrev "BCM-HGSC" ;
definition: "Center for high-throughput DNA sequence generation and the accompanying analysis. The sequence data generated by the center's machines are analyzed in a complex bioinformatics pipeline, and the data are deposited regularly in the public databases at the National Center for Biotechnology Information (NCBI)." .
SCR:013606 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00422" ;
rdfs:label "Scholarpedia" ;
definition: "A peer-reviewed encyclopedia written by the leading experts in their respective fields. It does not publish research or position papers, but rather living reviews that will be maintained by the future generation of experts via the process of curatorship. :Computational neuroscience, Neuroscience, Electrophysiology, Neuron, Network Dynamics , Brain Models, Synapse, Memory, Conditioning, Consciousness, Vision, Olfaction, Neuroimaging, Dynamical Systems, Oscillators, Synchronization, Pattern Formation, Chaos, Bifurcations, Simulation Environment, Artificial Neural Networks, Models of Neurons, Spiking Networks, Brain Theory, Recurrent Networks, Feedforwar, Networks, Graph Theory, Reinforcement Learning, Evolutionary Computation, Information Theory, Statistics, Signal Analysis, Pattern Recognition, Navigation and Control, Robotics :" .
SCR:013607 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00351" ;
rdfs:label "Videoscribbler" ;
definition: "VideoScribbler is a program that makes it possible to trace directly onto live video. It was developed to provide a way to outline and count cells in a video image. The program displays the live video image in a 640x480 window. Userrs can click and drag the mouse to outline cells, while releasing the mouse button will complete the outline and increment the \"Object Count\" display at the bottom of the window." .
SCR:013608 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00348" ;
rdfs:label "Unys" ;
NIFRID:synonym "Unyu" ;
definition: "Unys is a Java Web Start application for viewing Synu polygonal and MicroBrightField Neurolucida datasets. Other formats, such as OBJ and COLLADA will be added shortly. Unys is still in a state of being actively developed. This software has replaced the previously existing Synuview application. Requirements: Java 1.5 or more recent. No software installation is required but Java Web Start must be pre-installed. Most modern computers will have this installed. Sponsors: this software is supported by the National Center for Microscopy and Imaging Research. Keywords: Dataset, Neurolucida, Software, Java, Application, Synu polygonal, Viewing," .
SCR:013609 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00330" ;
rdfs:label "mri3dX" ;
NIFRID:synonym "MRI3dX",
"MRI structural/functional Visualization and Analysis" ;
definition: "A tool for visualization of structural and functional MRI volumes. Features include structural and functional overlay display of volume sections, volume annotation, ROI analysis, interfacing with FSL''s brain extraction, and 3D rendering. mri3dX should run on most unix workstations, but requires Motif and OpenGL/Mesa graphics libraries." .
SCR:013610 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00331" ;
rdfs:label "MRIVIEW" ;
NIFRID:synonym "MRIVIEW - An Interactive Tool for Brain Imaging" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016.
MRIVIEW is a software tool for viewing and manipulating volumetric MRI head data, and for using this data as an anatomical reference in studies of brain function. MRIVIEW supplies methods for reading in raw MRI data, segmenting structures in the data, reconciling coordinate systems between multiple imaging modalities, viewing combinations of anatomical and functional information, and building models of structures within the head. Recent extensions to MRIVIEW include an MEG/EEG forward simulator, and a parallelized multi-start multi-dipole MEG/EEG inverse procedure." .
SCR:013611 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00345" ;
rdfs:label "Stroketool-CT" ;
definition: "Stroketool-CT is a user friendly MS-Windows based software system for calculation and visualization of enhanced CT perfusion imaging data sets of the brain. It contains features such as quantitative perfusion using SVD algorithms; DICOM compatibility; rapid calculations of rCBF, MTT, rCBV, TTP,Tmax; and interactive and automatic AIF-detection." .
SCR:013612 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152477" ;
rdfs:label "Synaptic Systems" ;
NIFRID:synonym "SY SY",
"Synaptic Systems GmbH" ;
definition: "An Antibody supplier" .
SCR:013613 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152476" ;
rdfs:label "Symansis" ;
definition: "An Antibody supplier" .
SCR:013614 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152475" ;
rdfs:label "Syd Labs" ;
NIFRID:synonym "Syd Labs Inc",
"Syd Labs Inc." ;
definition: "An Antibody supplier" .
SCR:013615 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00312" ;
rdfs:label "iiV (internet image Viewer)" ;
definition: " :iiV is an interactive brain imaging data display tool written in Java. It displays 3-D data set as slices perpendicular to the 3 major axis. Individual slice voxels are mapped thru a linear scaling, threshold and color table to displayable pixel values. Any number of slices from any number of data files may be arranged, annotated, overlaid, cropped, zoomed and rotated. iiV maintains the original data internally for mouse selection and display of original voxel values. If input locations map to a real world valued coordinates that mapping may be applied to display selected voxel locations in real coordinates. Slices may also include tracking crosshairs and automatically update to display the same region of the brain as selected in another slice. iiV includes a fairly complete set of editing commands including selection, drag, group, delete, and undo/redo commands. It also includes a script language for saving and reloading of the interactive display and creating animated demos. iiV supports reading ANALYZE, ECAT, ECAT7, DICOM, GIF, JPEG, PPM, Stimulate SDT, and raw data formats and saving what is displayed as scripts, GIF and PPM files. :" .
SCR:013616 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00341" ;
rdfs:label "PV-Wave" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2015. PV-Wave is a interactive programming language designed for data analysis. We have several programs written for creating, viewing, and measuring MRI images of brains. PV-Wave is a very powerful programming language with a very simple syntax. We reuse code from one program to write a new program that does something slightly different. This only takes us a few hours. If we used another language, like C++, our program turn around time would be days instead of hours." .
SCR:013617 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00334" ;
rdfs:label "NeuroServ" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A Java-based tool for managing and sharing MRI/DTI datasets, and related subject and protocol metadata. Data entry, data access, general query, reporting, analysis, and administrative operations occur through browser-based forms. NeuroServ works with a webserver (Tomcat) and a backend database (e.g., Postgres); a schema and over 40 forms are provided in the distribution. Support for DTI includes entry of multi-orientation raw DWI files, semi-automated normalization to the B0 image and quality filtering. Planned extensions include full DTI processing through image production and data sharing using the SSC incremental visiblity model." .
SCR:013618 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:osirix",
"nif-0000-00340" ;
rdfs:label "OsiriX Medical Imaging Software" ;
NIFRID:synonym "OsiriX" ;
definition: " :OsiriX is an image processing software dedicated to DICOM images (.dcm / .DCM extension) produced by medical equipment (MRI, CT, PET, PET-CT, ...) and confocal microscopy (LSM and BioRAD-PIC format). It can also read many other file formats: TIFF (8,16, 32 bits), JPEG, PDF, AVI, MPEG and Quicktime. It is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or medical imaging modality (STORE SCP - Service Class Provider, STORE SCU - Service Class User, and Query/Retrieve) . OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images: 2D Viewer, 3D Viewer, 4D Viewer (3D series with temporal dimension, for example: Cardiac-CT) and 5D Viewer (3D series with temporal and functional dimensions, for example: Cardiac-PET-CT). The 3D Viewer offers all modern rendering modes: Multiplanar reconstruction (MPR), Surface Rendering, Volume Rendering and Maximum Intensity Projection (MIP). All these modes support 4D data and are able to produce image fusion between two different series (for example: PET-CT). Osirix is at the same time a DICOM PACS workstation for medical imaging and an image processing software for medical research (radiology and nuclear imaging), functional imaging, 3D imaging, confocal microscopy and molecular imaging. :" .
SCR:013619 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00338" ;
rdfs:label "Nonparametric Prediction Activation Influence Reproducibility re-Sampling" ;
NIFRID:synonym "NPAIRS" ;
definition: "The NPAIRS (Nonparametric, Prediction, Activation, Influence, Reproducibility, re-Sampling) package provides a statistical resampling framework with GLM, PCA and CVA data analysis options forming the basic building blocks for benchmarking and comparing data processing choices and preprocessing pipelines using prediction and reproducibility performance metrics. The distribution package also includes flexible visualization and plotting tools for displaying the results of NPAIRS analyses. :" .
SCR:013620 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00413" ;
rdfs:label "Sigpath" ;
definition: "SigPath is a prototype of an information system for cell signaling pathways and networks. A primary emphasis of SigPath is that biochemical information can be stored both at the qualitative and quantitative levels. When information is stored quantitatively, SigPath can assist users in generating quantitative models that can be used to simulate how the concentrations of the molecules involved in a model change over time. For background, design goals, tutorials, and contact information, visit the SigPath Project Pages :Gs pathway, LSD_binds_serotonin 2AR, MAPK cascade, EGFR signaling and MAP kinase cascade, EGF receptors, mGluR activation :" .
SCR:013621 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00328" ;
rdfs:label "The MNI AutoReg Software Package" ;
NIFRID:synonym "MNI_AutoReg" ;
definition: "Web site last updated August 26, 1998 Automatic method for comparing different MRI datasets by visual inspection of equivalent anatomical planes. Implementation is based on multi-scale, three dimensional (3D) cross-correlation, to register a given volumetric data set to an average MRI brain (n > 300) aligned with the Talairach stereotaxic coordinate system. :" .
SCR:013622 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152474" ;
rdfs:label "Swant" ;
NIFRID:synonym "Swant Inc." ;
definition: "An Antibody supplier" .
SCR:013623 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.295067.f",
"ISNI: 0000 0004 0506 0213",
"nlx_152473",
"Wikidata: Q30253595" ;
rdfs:label "SurModics" ;
NIFRID:synonym "SurModics inc." ;
definition: "An Antibody supplier" .
SCR:013624 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-32929" ;
rdfs:label "NEMO Analysis Toolkit" ;
NIFRID:synonym "NEMO ERP Analysis Toolkit" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. NIH tombstone webpage lists Project Period : 2009 - 2013. The NEMO ERP Analysis Toolkit includes tools for EEG/ERP and MEG data decomposition, and ontology-based mark-up, annotation, and labeling of patterns in EEG and MEG data. These tools have been implemented in MATLAB by Robert Frank, a mathematician and data analyst for NEMO. The current NEMO analysis pipeline has been designed with the aim to support cross-lab, cross-experiment meta-analysis of EEG and MEG data. The current proposed processing pipeline consists of the following steps: * Step 1: Decomposing ERP data (continuous data are transformed into discrete patterns for analysis) o PCA/ ICA/Microstate * Step 2: Marking up the analysis results o Each pattern is annotated with labels that relate pattern attributes to NEMO ontology concepts * Step 3: Clustering the observed patterns within and across experimental groups * Step 4: Labeling the cross-experiment clusters Each item in the above list is a step/phase in the processing pipeline and is associated with a set of matlab scripts in our NEMO ERP Analysis Toolkit, which is implemented by a collection of MATLAB scripts." .
SCR:013625 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33010" ;
rdfs:label "XV" ;
definition: "XV is an interactive image manipulation program for the X Window System. It can operate on images in the GIF, JPEG, TIFF, PBM, PGM, PPM, XPM, X11 bitmap, Sun Rasterfile, Targa, RLE, RGB, BMP, PCX, FITS, and PM formats on all known types of X displays. It can generate PostScript files, and if you have ghostscript (version 2.6 or above) installed on your machine, it can also display them. XV allows users to: display an image on the root window, in a variety of styles; grab any rectangular portion of the screen and turn it into an image; arbitrarily stretch, compress, rotate or flip the image; view files as ASCII text or hexadecimal data; determine pixel values and x,y coordinates in the image; apply different gamma functions to the Red, Green, and Blue color components, to correct for non-linear color response; and run a number of image-processing algorithms on any rectangular portion of the image, among other functions." .
SCR:013626 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00406" ;
rdfs:label "Syracuse Biomaterials Institute" ;
definition: "Welcome to the Syracuse Biomaterials Institute! We are a new, interdisciplinary institute focused on research in biomaterials, smart medical devices, and biological/tissue-engineered constructs. Biomaterials are natural and synthetic substances designed to treat, augment, or replace tissues and organs of the human body as treatments to disease or injury. An outgrowth of the long-standing Biomaterials Group in the Biomedical and Chemical Engineering Department, the Syracuse Biomaterials Institute (SBI) was launched in Fall, 2007, through strategic investments by Syracuse University, New York State Foundation for Science, Technology and Innovation (NYSTAR), and private donations. SBI is a cohesive collection of highly collaborative faculty spanning eight (8) academic units, including faculty from SUNY Upstate Medical University and SUNY College of Environmental Science and Forestry. Our researchers are engaged in a wide spectrum of problems, ranging from fundamental studies of the biochemical and physical processes controlling cell functions to the development of new technologies for biomedical applications. In addition to our collaborative research and teaching activities, we are excited to be designing our future SBI home, planned for Fall 2009, that will collocate our research groups and central laboratory facilities. :jobs board, postdoctoral training program, graduate training program, portal :" .
SCR:013627 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00335" ;
rdfs:label "NIS (NeuroImaging Statistics)" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Collection of Unix-based programs for pre-processing and analyzing neuroimaging datasets. This includes tools for mean-normalization of images, image registration, ANOVA, post-hoc contrast analysis, region-of-interest identification and examination (including time series). Includes a test data set." .
SCR:013628 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33052" ;
rdfs:label "SBIA" ;
NIFRID:synonym "Section for Biomedical Image Analysis",
"The Section for Biomedical Image Analysis" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. A section of the Penn department of radiology, it is devoted to the development of computer-based image analysis methods and their application to clinical research studies. Image analysis methodologies include image registration, segmentation, population-based statistical analysis, biophysical modeling of anatomical deformations, and high-dimensional pattern classification. Clinical research studies spans a variety of clinical areas and organs, and they include brain diseases such as Alzheimer's disease and schizophrenia, evaluation of treatment effects in large clinical trials, diagnosis of cardiac diseases, and diagnosis prostate, breast and brain cancer. SBIA also performs small animal imaging research aiming to understand brain development in mouse models. It has multiple resources which can be accessed by researcher." .
SCR:013629 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33133" ;
rdfs:label "Informatics for Integrating Biology and the Bedside" ;
NIFRID:abbrev "i2b2" ;
definition: "i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origin. For some resources (e.g. software) the use of the resource requires accepting a specific (e.g. OpenSource) license." .
SCR:013630 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33136" ;
rdfs:label "Quovadx, Inc." ;
NIFRID:abbrev "Quovadx" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 10, 2012. With Cloverleaf Integration Services from Quovadx, Inc., the FDOH now provides managers and policy makers with access to critical data residing in various counties across the state. The Cloverleaf engine is used to map legacy electronic billing formats for Medicaid to HIPAA compliant formats for three of the largest patient care systems in the state without the need to make programming changes to the existing systems that bill Medicaid. The Cloverleaf solution also guarantees the delivery of messages, enables rapid development and deployment of application interfaces between systems and provides a means of maintaining compliance with any new HIPAA format changes. While making the data available to a larger audience, the privacy and security of sensitive health data is also maintained by the solution''s ability to manage security and business rules for each system." .
SCR:013631 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00408" ;
rdfs:label "Hasenwinkel Research Group" ;
definition: "Hasenwinkel Research Group is interested in creating absorbable biopolymeric gels for the prevention of post-surgical tissue adhesions, novel two-solution bone cements fro fixation of total join replacements, nerve and soft tissue regeneration, surface modification of materials to enhanve and promote biological function and biocompatibility, studying effects of chemical, mechanical, and electrical environments on the development of three-dimensional tissue scaffolds in culture. :datum, lab web page :" .
SCR:013632 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00534" ;
rdfs:label "Stroke Trials Registry" ;
definition: "Stroke Trials Registry is a continuously updated registry of randomized clinical trials in stroke and cerebrovascular disease. This project is a free public service from the Internet Stroke Center at Washington University School of Medicine; with support from the American Stroke Association and the National Institute of Neurological Disorders and Stroke. This registry will meet technical standards for inclusion in the International Clinical Trials Registry Platform of the World Health Organization. The information on this site is intended for health professionals. SPOTRIAS is an NIH-funded network of stroke research centers that perform early phase clinical projects, share data, and promote new approaches to therapy for acute stroke. clinical data, human, homo sapien, stroke, translational medicine" .
SCR:013633 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00535" ;
rdfs:label "Neurology Image Library from The Internet Stroke Center" ;
NIFRID:synonym "Neurology Image Library" ;
definition: "The Internet Stroke Center at Washington University is pleased to offer this module for viewing CT, MR, and angiogram images of cerebrovascular and neurological diseases. While this project is still being perfected -- and many more cases have yet to be added -- we hope that you will find this collection useful in your education and practice. The images presented here are for educational use only. This information may not be used for diagnosis or treatment. All images are protected property of the Internet Stroke Center at Washington University and may not be reproduced without permission. Permission may be granted to students and professionals to borrow images from this site for educational purposes and/or presentations; we just ask that an email be sent detailing both the desired material and the intended use. Please direct all comments, questions, and requests to the Site Editor of the Internet Stroke Center." .
SCR:013634 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00337" ;
rdfs:label "Northern Eclipse 6.0" ;
definition: "Northern Eclipse 6.0 software is a Windows based full Image Analysis and Archiving System with a full suite of Image Processing techniques, Morphological and Densitometry measuring routines, digital and analogue camera control, SDK for custom camera driver solutions, 3D-Reconstruction, De-Convolution and programmable via 3 levels of automation plus access to hundreds of OLE applications and thousands of scripts." .
SCR:013635 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152471" ;
rdfs:label "StressMarq Biosciences" ;
NIFRID:synonym "StressMarq Biosciences Inc" ;
definition: "An Antibody supplier" .
SCR:013637 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152469" ;
rdfs:label "Stemgent" ;
NIFRID:synonym "Stemgent Inc." ;
definition: "An Antibody supplier" .
SCR:013638 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00520" ;
rdfs:label "G-Protein Coupled Receptor Oligomerization Knowledge Base (GPCR-OKB) ontology project" ;
NIFRID:synonym "GPCR-OKB" ;
definition: "G-Protein Coupled Receptor Oligomerization Knowledge Base (GPCR-OKB) ontology project offers an ontology that can be downloaded. :G Protein-Coupled Receptors (GPCRs) are a large and diverse family of membrane proteins whose members participate in the regulation of most cellular and physiological processes and therefore represent key pharmacological targets. Although several bioinformatics resources support research on GPCRs, most of them have been designed based on the traditional assumption that monomeric GPCRs constitute the functional receptor unit (Figure 1 below). The increase in the frequency and number of reports about GPCR dimerization/oligomerization and the implication of oligomerization in receptor function makes necessary the ability to store and access information about GPCR dimers/oligomers electronically. :We present here the design blueprint for an information system that can manage the elements of information required to describe comprehensively the phenomena of both homo- and hetero-oligomerization of GPCRs. Specifically, we present the ontology (Figures 2-4 below) that we plan to use for the development of an intuitive and user-friendly GPCR-Oligomerization Knowledge Base (GPCR-OKB). This information system is being designed in close collaboration with experimental colleagues working on GPCR oligomerization, and adopts the list of recommendations recently stipulated by the NC-IUPHAR subcommittee for the recognition and nomenclature of GPCR multimers. :Our long term goal is to disseminate to the scientific community organized, curated, and detailed information about GPCR dimerization/oligomerization, and its related structural context. :Skrabanek L, Murcia M, Bouvier M, Devi L, George SR, Lohse MJ, Milligan G, Neubig R, Palczewski K, Parmentier M, Pin JP, Vriend G, Javitch JA, Campagne F, Filizola M. Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base. BMC Bioinformatics. 2007 May 30;8:177. PMID 17537266 :The ontology files (developed in Protege) can be downloaded. :" .
SCR:013639 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.437840.c",
"nif-0000-00499" ;
rdfs:label "SimulConsult Neurological Syndromes" ;
NIFRID:synonym "Simulconsult" ;
definition: "Clinicians can get a simultaneous consult about their patient''s diagnosis using SimulConsult''s diagnostic decision support software. After some patient findings are entered into the software, it provides an initial differential diagnosis and suggests other useful findings, including tests. The database used by the software has > 2,300 diagnoses, focused on genetic neurological and metabolic diseases, but is expanding with increasing content on non-neurological genetics and non-genetic neurology. The information about diseases is entered by clinicians, referenced to the literature and peer-reviewed by experts. The information includes many types of information ignored in other diagnostic approaches, allowing the software to take into account pertinent negatives, temporal information, and cost of tests. The approach is also flexible enough allow rapid addition of newly recognized diseases. SimulConsult enables both generalists and specialists to transform medical diagnosis, by lowering costs, reducing errors and eliminating the medical diagnostic odysseys experienced by far too many patients and their families. SimulConsult also enables researchers to find diseases with clinical presentations that are similar to other diseases or individual patients, assisting in identifying mechanisms of diseases. The software may be used only by medical professionals (doctors, nurse practitioners, genetic counselors, medical librarians and supervised trainees in these professions), who may register on the site or use the software through institutional access of their medical center. Keywords: diagnosis, diagnostic, software, neurology, genetic, neurological, metabolic, metabolism, human" .
SCR:013640 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33158" ;
rdfs:label "Simbiome" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2015. Simbiome is a curated, online electronic resource that organizes and presents relevant resources for physics-based simulation of biomedical structures and related entities in biology and life sciences." .
SCR:013641 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00545" ;
rdfs:label "Chronic Fatigue Syndrome" ;
NIFRID:abbrev "CFS" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This website endeavors to provide information on the Chronic Fatigue Syndrome Working Group (CFSWG) and its programs that is helpful to researchers, health care providers, people with CFS and their families, and the general public. :The mission of the Trans-NIH Working Group for Research on Chronic Fatigue Syndrome is to: :* Stimulate and support research on CFS within the context of the missions of all Institutes, Centers and Offices. :* Collaborate and coordinate the research agendas of all Institutes, Centers and Offices to issue on a regular basis joint Program Announcements or theme related Request for Applications to further interdisciplinary research in CFS. :* Present new knowledge to and facilitate novel theoretical approaches to CFS among NIH scientists. :* Plan and sponsor scientific symposia to foster awareness, provoke new scientific interest, and generate interdisciplinary collaboration on CFS among both the NIH and Academic medical community." .
SCR:013642 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152468" ;
rdfs:label "STEMCELL Technologies" ;
NIFRID:synonym "STEMCELL Technologies Inc.",
"StemCell Technologies Inc." ;
definition: "An Antibody supplier" .
SCR:013643 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152467" ;
rdfs:label "Stage 1 Diagnostics" ;
definition: "An Antibody supplier" .
SCR:013644 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152466" ;
rdfs:label "Spring Bioscience" ;
definition: "An Antibody supplier" .
SCR:013645 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00557" ;
rdfs:label "Mouse Genome Project" ;
definition: "The goal of the mouse genome project is to determine the function of genes on mouse Chromosome 11 by saturating the chromosome with recessive mutations. The distal 40 cM of mouse Chr 11 exhibits linkage conservation with human Chromosome 17. We are using the chemical N-ethyl-N-nitrosourea (ENU) to saturate wild type chromosomes with point mutations. By determining the function of genes on a mouse chromosome, we can extrapolate to predict function on a human chromosome. We expect many of the new mutants to represent models of human diseases such as birth defects, patterning defects, growth and endocrine defects, neurological anomalies, and blood defects. Because many of the mutations we expect to isolate may be lethal or detrimental to the mice, we are using a unique approach to isolate mutations. This approach uses a balancer chromosome that is homozygous lethal and carries a dominant coat color marker to suppress recombination over a reasonable interval. On this site one can obtain a list of mutations on chromosome 11." .
SCR:013646 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152722" ;
rdfs:label "PhenoGO" ;
NIFRID:synonym "Phenotype Context Database for Gene Ontology Annotations" ;
definition: "PhenoGO is a computed database designed for high throughput mining that provides phenotypic and experimental context - such as the cell type, disease, tissue, and organ - to existing annotations between gene products and Gene Ontology (GO) terms, as specified in the Gene Ontology Annotations (GOA) for multiple model organisms. Phenotypic and Experimental (P&E) contexts to identifiers are computationally mapped to general biological ontologies, including: the Cell Ontology (CO), phenotypes from the Unified Medical Language System (UMLS), species from Taxonomy of the National Center for Biotechnology Information (NCBI) taxonomy, and specialized ontologies such as Mammalian Phenotype Ontology (MP) and Mouse Anatomy (MA)." .
SCR:013648 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00410" ;
rdfs:label "Graduate School Guide" ;
NIFRID:synonym "Graduate School",
"The Graduate School Guide" ;
definition: "This web resource allows the user to search and rank 23,517 programs at 2,356 universities based on the users priorities. Data come from the National Science Foundation, the National Research Council, and the National Center for Education Statistics. The graduate school guide has been made possible by generous support from: :* The Alfred P. Sloan Foundation :* The Burroughs Wellcome Fund :The Center for Science and the Media served as the fiscal sponsor for the project. :Jobs board, Career development, Graduate training program list :" .
SCR:013649 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00403" ;
rdfs:label "CSIT" ;
NIFRID:synonym "Centre for Scientific Investigations and Training",
"The Centre for Scientific Investigations and Training" ;
definition: "It fosters Interdisciplinary research, teaching, and service activities linked to health and development in Nigeria and resource limited settings of the developing world. :OBJECTIVES OF THE CENTRE: The Institute helps strengthen and sustain the interests and activities of the science community by: :Facilitation of international contacts for program development and training. :* Advocacy for better equity in global health investments. :* Assistance in securing resources for international activities. :* Standardization and facilitation of overseas administrative approaches. :* Improved communication through grand rounds, seminars, and discussion forums. :* Taking up public enlightenment campaigns and public health education :* Active partnerships with institutions in Nigeria and abroad that share the Institute''s goals and wish to partner with CSIT faculty, staff, and students. :* Publishes the JEN Biomedicine, an international journal that gives unfettered access to research from Nigeria and other parts of Africa and the world. :* It''s CSIT Service Centre that helps with works and writing of scientists to make them acceptable for publication. The centre is equipped with research aids and staff that can help out with planning, executing, writing, graphic works including black and white and colour photos, editing research papers to make them acceptable by journals of interest. You can also undertake statistical analyses. In particular preparing journal figures, peer-review before publication, and statistical analyses. :* It''s Teaching Aids Centre that provides teaching aids to institutions and for workshops and conferences. Has in store models for studying behaviour including Elevated plus, Y, T, Radial-arm, Light/Dark Box, Open Box mazes. Available also are projectors, image analysers, computers, scanners, microscopes, microscope slides, animal skeletons, fixed animal tissues for biology and anatomy, patch clamping, stereotaxic equipment and methods, etc. The Centre can also teach you how to use any of the above. :" .
SCR:013650 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152490" ;
rdfs:label "Zyagen" ;
NIFRID:synonym "Zyagen Laboratories" ;
definition: "An Antibody supplier" .
SCR:013651 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152487" ;
rdfs:label "Wako" ;
NIFRID:synonym "Wako Chemicals USA inc." ;
definition: "An Antibody supplier" .
SCR:013652 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152486" ;
rdfs:label "Ventana Medical Systems inc." ;
definition: "An Antibody supplier" .
SCR:013653 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152484" ;
rdfs:label "US Biological" ;
NIFRID:synonym "United States Biological" ;
definition: "An Antibody supplier" .
SCR:013654 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nlx_152483" ;
rdfs:label "Tulip Biolabs" ;
definition: "An Antibody supplier" .
SCR:013655 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-32932" ;
rdfs:label "Human Brain Project" ;
NIFRID:abbrev "HBP" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 16, 2013. The resource redirects to its parent, OSSP. Project seeking to increase the transparency and accessibility of the scientific research process by connecting researchers with an additional source of funding - microinvestments received from the broader online community. In exchange for these public investments, researchers will maintain research logs detailing the play-by-play progress made in their project, as well as publishing all of their data in a public database under a science commons license. These research projects, in turn, will serve to continually update a research-based neuroscience-based human brain & body curriculum." .
SCR:013656 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00528" ;
rdfs:label "Center for Cell Analysis and Modeling" ;
NIFRID:synonym "CCAM - Computational Facility" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 26,2023. CCAM is one of five National Technology Centers for Networks and Pathways, NTCNP, funded throught the NIH Technology Center for Networks and Pathways, TCNP. CCAM integrates new microscope technologies for making quantitative in vivo live cell measurements with new physical formulations and computational tools that will produce spatially realistic quantitative models of intracellular dynamics. :The overarching rationale for CCAMs research as a TCNP is that polarity in networks and pathways is determined by the spatial organization, subcellular distribution, dynamic behavior, interactions and functions of specific molecules within the cell. To investigate these relationships, we use a tripartite approach described as: :1) Measure - develop new tools for measuring spatially resolved dynamic behavior of molecules in cells, :2) Model - develop new methods for spatial modeling of biological systems. :3) Manipulate - develop new techniques for manipulating the spatial distribution of molecules in living cells. :Microscopy contrast enhancement protocol, biophotonics, subcellular :" .
SCR:013657 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00395" ;
rdfs:label "Cure PSP: Society for Progressive Supernuclear Palsy" ;
NIFRID:synonym "CurePSP" ;
definition: "Progressive Supranuculear Palsy (PSP) is a little known but fatal degenerative brain disease that is often misdiagnosed as Alzheimers or Parkinsons disease. Only by becoming more aware of PSP and the devastating effects on its victims and their families can we begin to work toward more effective treatments and eventually a cure. :CurePSP has always believed that truly effective clinical interventions will follow good, solid basic scientific research. For this reason, CurePSP promotes research that helps generate an integrated picture of PSP and CBD at the molecular and cellular levels. CurePSP believes that in the long term, research of this nature will prove indispensable in developing a prevention or cure for PSP and CBD. :CurePSP has carefully structured its research program and has identified the programs that have been the most successful and those that need strengthening. With an increased research budget made possible through improved donor support, CurePSP will be able to markedly intensify the efforts to cure the disease in a way that promises relief for those afflicted today as well as hope for those who may be afflicted tomorrow. :grant :" .
SCR:013658 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00419" ;
rdfs:label "Animal Diversity Web" ;
definition: "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology at the University of Michigan :Animal Diversity Web Has: Thousands of species accounts about individual animal species. These may include text, pictures of living animals, photographs and movies of specimens, and/or recordings of sounds. Students write the text of these accounts and we cannot guarantee their accuracy. Descriptions of levels of organization above the species level, especially phyla, classes, and in some cases, orders and families. Hundreds of hyperlinked pages and images illustrate the traits and general biology of these groups. Professional biologists prepare this part. :Animal Diversity Web Is An Online Encyclopedia: ADW is a large searchable encyclopedia of the natural history of animals. Every day, thousands of classroom students and informal visitors use it to answer animal questions. Other sites specialize in local, endangered, or particular kinds of animals. We aim to be as comprehensive as possible. :A Science Learning Tool: ADW facilitates inquiry-driven learning, that is, teaching about science by leading students to use the methods of science. Our large database is structured, providing consistent information for all species to foster comparisons. An advanced search tool allows a user to call up species accounts fitting any combination of descriptors. Students can explore for patterns and relationships, learn how to frame and answer scientific questions and, with the help of a good teacher, experience the excitement and satisfaction of doing science. Our long-term goal is to create a database rich enough that students can discover for themselves basic concepts in ecology and conservation biology. :A Virtual Museum: ADW provides a way to make the contents of research museums available globally for teaching and research. So far, our efforts have been directed mainly at mammals. Photographs of scientific specimens are available for representative species from most mammal families. We''ve also included several hundred Quick Time Virtual Reality Movies of skulls. These allow the user to rotate the specimen, providing an excellent impression of its 3-dimensional structure. We''ve written in depth about and illustrated many of the characteristics of interest to students of mammals. An important goal for the future is to expand to cover other groups of animals and include other media such as animal behavior video. :Wiki features, database, teaching tool :" .
SCR:013659 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID: 100000958",
"grid.27324.30",
"ISNI: 0000 0000 9804 9902",
"nif-0000-00440",
"Wikidata: Q40358" ;
rdfs:label "AAAS" ;
NIFRID:synonym "American Association for the Advancement of Science",
"The American Association for the Advancement of Science" ;
definition: "It is an international non-profit organization dedicated to advancing science around the world by serving as an educator, leader, spokesperson and professional association. In addition to organizing membership activities, AAAS publishes the journal Science, as well as many scientific newsletters, books and reports, and spearheads programs that raise the bar of understanding for science worldwide. :AAAS History: Founded in 1848, AAAS serves some 262 affiliated societies and academies of science, serving 10 million individuals. Science has the largest paid circulation of any peer-reviewed general science journal in the world, with an estimated total readership of one million. The non-profit AAAS is open to all and fulfills its mission to advance science and serve society through initiatives in science policy; international programs; science education; and more. For the latest research news, log onto EurekAlert!, the premier science-news Web site, a service of AAAS. :Membership and Programs: Open to all, AAAS membership includes a subscription to Science. Four primary program areas fulfill the AAAS mission: * Science and Policy * International Activities * Education and Human Resources * Project 2061 :AAAS Mission: AAAS seeks to advance science, engineering, and innovation throughout the world for the benefit of all people. To fulfill this mission, the AAAS Board has set these broad goals: * Enhance communication among scientists, engineers, and the public; * Promote and defend the integrity of science and its use; * Strengthen support for the science and technology enterprise; * Provide a voice for science on societal issues; * Promote the responsible use of science in public policy; * Strengthen and diversify the science and technology workforce; * Foster education in science and technology for everyone; * Increase public engagement with science and technology; and * Advance international cooperation in science. :" .
SCR:013660 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00465" ;
rdfs:label "EURAXESS Links" ;
definition: "A networking tool for European researchers abroad. It provides information about research in Europe, European research policy, opportunities for research funding, for international collaboration and for trans-national mobility. Membership is free. :The objective of EURAXESS Links is a flourishing network of European researchers, scientists and scholars abroad. The network is already running in the USA since 2005 and has been launched in Japan in June 2008. The members of the network are informed about European Union research policies and made aware of career opportunities in Europe as well as opportunities for collaboration with Europe. The multidisciplinary network involves researchers at all stages of their careers and allows them to become well connected amongst themselves and in Europe, ensuring that they are recognised as an important resource for the European Research Area, whether they remain abroad or choose to return. :Through the success of the network, EURAXESS Links is intended to contribute to the improvement of Europe''s position in the global competition for talent, and the reinforcement of research collaboration. :EURAXESS Links focuses on three types of activity: networking of researchers, information dissemination and helping expatriate researchers to collaborate with colleagues in Europe or to return to rewarding careers in Europe. Membership of EURAXESS Links is free. :social networking; people resource :" .
SCR:013661 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00427" ;
rdfs:label "NeuGen" ;
definition: "NeuGen is a tool for the efficient generation and description of dendritic and axonal morphology of realistic neurons and neural networks in 3D. :NeuGen builds real neural network geometries and is based on experimental data. The ''in silico'' neurons are based on cells of cortical columns in the neocortex. :L4 spiny stellate neurons, L2/3 pyramidal cells, L5A and L5B pyramidal cells, L4 star pyramidal cells, measuring of morphological paprameters (This is misspelled so not sure we can use), .hoc files, .dx resp. .net files, Via .net files, Data visualization software, OpenDX DataExplorer, simulation software, NEURON, Anatomical Fingerprints, stochastic model, Electromagnetic Simulation Software :" .
SCR:013662 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00425" ;
rdfs:label "Small-world Network Analysis and Partitioning" ;
NIFRID:synonym "SNAP" ;
definition: "SNAP (Small-world Network Analysis and Partitioning) is an extensible parallel framework for exploratory analysis and partitioning of large-scale networks. SNAP is implemented in C, uses OpenMP primitives for parallelization, and targets sequential, multicore, and symmetric multiprocessor platforms. Our intent with SNAP is to provide a simple and intuitive interface for network analysis and application design, hiding the parallel programming complexity from the user. In addition to path-based, centrality, and community identification queries on large-scale graphs, we support commonly-used preprocessing kernels and quantitative measures that help understand the global network topology. The latest version of SNAP (0.4) was released in August 2010. Sponsors: This work was supported in part by NSF Grants CAREER CCF-0611589, NSF DBI-0420513, ITR EF/BIO 03-31654, IBM Faculty Fellowship and Microsoft Research grants, NASA grant NP-2005-07-375-HQ, and DARPA Contract NBCH30390004. Keywords: network, analysis, software, graph, traversal, betweenness centrality, community, identification, multicore," .
SCR:013663 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-00356" ;
rdfs:label "Volume Visualization and Navigation Tool" ;
NIFRID:synonym "VVNT" ;
definition: "Volume Visualization and Naviagtion Tool (VVNT) is a platform to visualize, navigate, process and analyze the multi-modality multi-dimensional medical images. Image processing functions from the Insight Registration and Segmentation tool kit (ITK), Volume visualization functionality from the Visualization tool kit (VTK) are seamlessly integrated into this application. It is built as a Multi-Document Interface (MDI) application, so that several windows can be opened, several operations compared.Some of the current features include * Opens all formats of the DICOM files. * Performs basic image processing functions, contrast brightness adjustments, zooming, panning and other operations. * Surface rendering and Maximum Intensity Projections. * Rotate the rendered volume by specified direction and angle * Automatic segmentation / object extraction * Voxel counts and statisticsSeveral volume measurements and processing functions are currently being added." .
SCR:013664 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "The Northwestern University Neuroimaging Data Archive" ;
NIFRID:abbrev "NUNDA" ;
definition: "A resource for managing study data collected by the Northwestern University neuroimaging community. It includes a secure database, automated pipelines for processing managed data, and tools for exploring and accessing the data. Access to data in the NUNDA is restricted to users authorized by the specific study's investigators. The NUNDA is hosted by the Neuroimaging & Applied Computational Anatomy Lab, and it is modeled after the Washington University's Central Neuroimaging Data Archive (CNDA). The NUNDA is powered by XNAT, an open source software package for managing neuroimaging and related data." .
SCR:013665 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012858" ;
rdfs:label "Mass spectrometry Interactive Virtual Environment (MassIVE)" ;
NIFRID:synonym "Mass spectrometry Interactive Virtual Environment",
"MassIVE" ;
definition: "Mass spectrometry Interactive Virtual Environment (MassIVE) is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. Data repository for proteomics data." .
SCR:013666 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciTran" ;
definition: "Scientific Transparency (SciTran) is a software project that has grown out of the Project on Scientific Transparency at Stanford University. At the heart of SciTran is a scientific data management system – SDM – designed to enable and foster reproducible research. SciTran SDM delivers efficient and robust archiving, organization, and sharing of scientific data. We have developed the system around neuroimaging data, but our goal is to build a system that is flexible enough to accomodate all types of scientific data – from paper-and-pencil tests to genomics data. SDM will also allow for the sharing of data and computations between remote sites. SciTran is open-source software, released under the MIT license. Our code is hosted on GitHub. Feel free to try it out or to contribute. Commercial support for SciTran SDM is available through our partners at Flywheel. Check out their demo, if you''d like to give SDM a quick try." .
SCR:013667 a owl:NamedIndividual ;
rdfs:label "Neuroimaging Data Model" ;
NIFRID:abbrev "NIDM" ;
definition: "Collection of specification documents that define extensions the the W3C PROV standard for the domain of human brain mapping. NIDM uses provenance information as a means to link components from different stages of the scientific research process from dataset descriptors and computational workflow, to derived data and publication." .
SCR:013668 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SciRes_000197" ;
rdfs:label "FP-CIT SPECT brain template in MNI space" ;
definition: "The FP-CIT SPECT brain template has been created using a fully automatic procedure involving posterization of the source image to three levels: background, brain and striatum. We performed a spatial affine registration of these 40 posterized source images to a posterized reference image in the MNI space. The intensity values of the transformed images is normalized linearly, assuming that the histogram of the intensity values follows an alpha-stable distribution. Lastly, we built the [123I]FP-CIT SPECT template by the mean of the transformed and normalized images. More info: 1) Salas-Gonzalez et al. Building a FP-CIT SPECT brain template using a posterization approach. Accepted in Neuroinformatics. 2) Salas-Gonzalez et al. Linear intensity normalization of FP-CIT SPECT brain images using the alpha-stable distribution. NeuroImage, Volume 65, 2013, pp. 449-455. http://dx.doi.org/10.1016/j.neuroimage.2..." .
SCR:013669 a owl:NamedIndividual ;
rdfs:label "Open Humans Project" ;
NIFRID:abbrev "open humans" ;
definition: "A project''s launch partners are three research studies that have an established record crowd-sourcing health data for research studies. One initiatives is the Personal Genome Project, established at geneticist George Church''s Harvard lab, which creates a freely available scientific resource that brings together genomic, environmental and human trait data. These data are donated by volunteers enrolled in a PGP study from our global network. A second partner is the GoViral project, started by researchers at Harvard University and New York University, which enables volunteers to provide easy-to-collect specimens when sick with a respiratory infection, and get confirmation of what type of viral illness they have. By testing samples when symptoms occur, participants can validate symptomatic reports as well as enable a better understanding of the representativeness of self-reported data and symptom profiles for different acute respiratory illnesses. Third on the list is the American Gut project, based at the University of California-San Diego and the University of Chicago, which is studying the vast microbial flora that inhabit the human digestive system from crowd-sourced (and properly sealed) samples of feces or skin swabs." .
SCR:013670 a owl:NamedIndividual ;
rdfs:label "Cancer Genomics of the Kidney (CAGEKID)" ;
NIFRID:abbrev "CAGEKID" ;
definition: "The Cancer Genomics of the Kidney (CAGEKID) consortium brings together expertise in clinical care and epidemiology with genomic expertise. This consortium is an effort of the larger International Cancer Genome Consortium (ICGC), which has the goal of obtaining a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumour types and/or subtypes with the aim of elucidating the genomic changes present in the many forms of cancers that contribute to the burden of disease throughout the world." .
SCR:013671 a owl:NamedIndividual ;
rdfs:label "Care Connectivity Consortium" ;
NIFRID:abbrev "CCC" ;
definition: "The Care Connectivity Consortium (CCC) is working to address and overcome the most critical and key challenges to effective health information exchange (HIE), to make HIE technologies more versatile and valuable for patients, caregivers, and health care organizations. By developing improved technologies for comprehensive, secure, reliable and innovative HIE, the CCC aims to enable health care provider organizations nationwide to deliver better, timelier, and more informed patient care." .
SCR:013672 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_014248",
"SCR_015958" ;
rdfs:label "ZEISS ZEN Microscopy Software" ;
NIFRID:synonym "ZEISS Efficient Navigation",
"ZEISS Efficient Navigation (ZEN)",
"ZEN Blue",
"ZEN Digital Imaging for Light Microscopy",
"ZEN Microscopy Software" ;
NIFRID:abbrev "ZEN" ;
definition: "User interface software for Carl Zeiss light microscopy imaging systems. ZEN is the universal user interface you will see on every imaging system from ZEISS. After selecting fluorophore, ZEN applies the necessary settings to collect and organize data." .
SCR:013673 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica Application Suite X" ;
NIFRID:synonym "LAS X",
"LASX",
"Leica Application Suite X (LAS X)",
"Leica LAS",
"Leica LAS AF Image Acquisition Software",
"Leica LAS X Life Science Microscope Software",
"Leica LAS X Life Science software",
"Leica LAS X LS" ;
definition: "Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes." .
SCR:013674 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Corel Graphics Suite" ;
definition: "Software package for editing and preparation of bitmap and vector graphics" .
SCR:013675 a owl:NamedIndividual ;
rdfs:label "Somatostatin Receptor SSTR2A Peptide Fragment" ;
definition: "This is the synthetic antigen sequence from which Biotrend anti-SST2A antibodies are raised." .
SCR:013678 a owl:NamedIndividual ;
rdfs:label "BioMedical Materials Consortium" ;
NIFRID:abbrev "BMM" ;
definition: "The BioMedical Materials (BMM) consortium focuses on advancing the use of new materials to biomedical research. As a public-private partnership, the consortium includes the participation of over 50 leading institutions, corporations, and health foundations, with support from the government of the Netherlands. The activities of this consortium have ended. The website and materials will be available until 12-31-2015." .
SCR:013679 a owl:NamedIndividual ;
rdfs:label "Cell4Cure (C4C) Consortium" ;
NIFRID:abbrev "C4C" ;
definition: "The Cell4Cure consortium aims to advance the cGMP production of therapeutic cell therapies. The consortium is led by Cellectis, a biotech focused in the development of adoptive immunotherapies and CELLforCURE, the largest commercial industrial facility for the production of therapeutic cell therapies in Europe. The consortium also includes seven public-sector organizations and university medical centers, who collaborate with the private sector companies." .
SCR:013680 a owl:NamedIndividual ;
rdfs:label "Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB)" ;
NIFRID:abbrev "CAACB" ;
definition: "The Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB) aims to advance the safe and reliable production of biopharmaceuticals by mitigating the risk of cell culture contamination through agents such as viruses or mycoplasma, by creating a central database of accumulated industry knowledge. Currently, industrial knowledge about contaminating adventitious agents and successful approaches to combat these specific agents is largely limited to each company''s individual experience. The collection, analysis and dissemination of the full body of industry experience would enhance the reliable manufacture and supply of such safe and effective medications. This consortium operates under the umbrella of MIT Center for Biomedical Innovation (CBI)." .
SCR:013681 a owl:NamedIndividual ;
rdfs:label "Collaboratory of AIDS Researchers for Eradciation (CARE)" ;
NIFRID:abbrev "CARE" ;
definition: "The Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV." .
SCR:013682 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.494009.0" ;
rdfs:label "Consortia Advancing Standards in Research Administration Information" ;
definition: "The Consortia Advancing Standards in Research Administration Information (CASRAI) is dedicated to reducing the administrative burden on researchers and improving business intelligence capacity of research institutions and funders.The Consortia Advancing Standards in Research Administration Information (CASRAI) aim is to improve the flow of information within and between research stakeholders by developing and maintaining a common and extensible dictionary of terms and exchangeable business objects to advance collaboration. The members include research-performing and research-funding organizations, as well as the service providers that support them. CASRAI goal is to create a central and standardized method for research teams to quickly produce any documents needed by funders and institutions. CASRAI aims to have the following outcomes: save time for researchers in applying & reporting to their funding agencies; Improve access to quality data for institutions and funders; Simplify the measurement of research impacts on society; Provide peer networking opportunities for teams tackling administrative data issues" .
SCR:013683 a owl:NamedIndividual ;
rdfs:label "Centre for Commercialization of Regenerative Medicine (CCRM)" ;
NIFRID:abbrev "CCRM" ;
definition: "The Centre for Commercialization of Regenerative Medicine''s (CCRM) is an industry consortium that aims to accelerate the application of regenerative medicine to clinical practice. Stakeholder in the consortium include the pharmaceutical, devices, reagents, tools, biomaterials and cell therapeutic companies." .
SCR:013685 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.440037.4",
"Wikidata: Q5062415" ;
rdfs:label "Centre for Drug Research and Developement (CDRD)" ;
definition: "The Centre for Drug Research and Development (CDRD) is a Canadian consortium that serves as an integrated national drug development and commercialization center. CDRD''s mandate is to de-risk discoveries stemming from publicly-funded health research and transform them into viable investment opportunities for the private sector." .
SCR:013686 a owl:NamedIndividual ;
rdfs:label "Clinical Decision Support Consortium" ;
NIFRID:abbrev "CDS" ;
definition: "The Clinical Decision Support (CDS) Consortium aims to enable the use of electronic health records (EHRs) to improve the safety and quality of medical care by pairing these data resources with clinical decision support systems to effectively influence physician behavior. CDS aims to advance a variety of techniques designed to facilitate and guide doctors'' decision making toward evidence‐based practice." .
SCR:013687 a owl:NamedIndividual ;
rdfs:label "Centre for Drug Safety Science" ;
NIFRID:abbrev "CDSS" ;
definition: "The Centre for Drug Safety Science (CDSS) aims to coordinate the fundamental clinical and basic research into the causes, characteristics and consequences of adverse drug reactions (ADRs). It was established as a joint venture between the Universities of Liverpool and Manchester to bring together a critical mass of knowledge and technologies in order to advance our understanding of Adverse Drug Reactions." .
SCR:013688 a owl:NamedIndividual ;
rdfs:label "Global CEO Initiative on Alzheimer's Disease" ;
NIFRID:abbrev "CEOAD" ;
definition: "The Global CEO Initiative on Alzheimer's Disease is a public- private partnership that aims to stop Alzheimer's disease and dementia. The consortium brings together international public authorities with the private sector to serve as the leading business voice on Alzheimer's disease." .
SCR:013689 a owl:NamedIndividual ;
rdfs:label "Consortium for Functional Glycomics (CFG)" ;
NIFRID:abbrev "CFG" ;
definition: "The Consortium for Functional Glycomics (CFG) serves to combine the expertise and glycomics resources to reveal functions of glycans and glycan-binding proteins (GBPs) that impact human health and disease. The CFG offers resources to the community free of charge, including glycan array screening services, a reagent bank, and access to a large glycomics database and data analysis tools." .
SCR:013690 a owl:NamedIndividual ;
rdfs:label "Colon Therapy Research Consortium (COLTHERES)" ;
NIFRID:abbrev "COLTHERES" ;
definition: "The Colon Therapy Research (COLTHERES) consortium brings together clinical centers and translational researchers funded in the European Union to define and perform biomarker driven clinical trials to improve cancer therapy outcomes. This 4-year consortium will use comprehensively molecularly-annotated colon cancers as a \"test-bed\" to define specific biomarkers of response or resistance to signaling pathway agents." .
SCR:013692 a owl:NamedIndividual ;
rdfs:label "European Clinical Research Infrastructures Network (ERCRIN)" ;
NIFRID:abbrev "ECRIN" ;
definition: "The European Clinical Research Infrastructures Network (ECRIN) is focused on synergizing and connecting the clinical research capabilities within the European continent." .
SCR:013693 a owl:NamedIndividual ;
rdfs:label "European Management Platform for Emerging and Re-Emerging Infectious Disease Entities (EMPERIE)" ;
NIFRID:abbrev "EMPERIE" ;
definition: "The European Management Platform for Emerging and Re-emerging Infectious Disease Entities (EMPERIE) consortium brings together international experts of different disciplines in an efficient and decisive collaborative network, to coordinate the response and control of an emerging new disease." .
SCR:013694 a owl:NamedIndividual ;
rdfs:label "European Network for Genetic and Genomic Epidemiology (ENGAGE)" ;
NIFRID:abbrev "ENGAGE" ;
definition: "The European Network for Genetic and Genomic Epidemiology (ENGAGE) consortium aims to translate data emerging from large-scale research efforts in molecular epidemiology into information of direct relevance to future advances in clinical medicine. The ENGAGE consortium will integrate and analyze one of the largest ever human genetics dataset (more than 80,000 genome-wide association scans and DNAs and serum/plasma samples from over 600,000 individuals). One goal is to demonstrate that the findings from ENGAGE can be used as diagnostic indicators for common diseases that will help us to understand better risk factors, disease progression and why people differ in responses to treatment." .
SCR:013695 a owl:NamedIndividual ;
rdfs:label "MicroRNAs in the Pathogenesis Treatment and Prevention of Epilepsy (EpimiRNA) Consortium" ;
NIFRID:abbrev "EpimiRNA" ;
definition: "The MicroRNAs in the Pathogenesis, Treatment and Prevention of Epilepsy (EpimiRNA) consortium aims to understand molecular mechanisms, diagnostics and develop novel therapeutics for epilepsy. The consortium aims to apply recent scientific breakthroughs that identified a new family of molecules that affect brain cell structure and function called microRNAs, to better understand medical products targeted to epilepsy." .
SCR:013696 a owl:NamedIndividual ;
rdfs:label "Markers for Sub-Clinical Cardiovascular Risk Assessment (EU-MASCARA)" ;
NIFRID:abbrev "EU-MASCARA" ;
definition: "The Markers for Sub-Clinical Cardiovascular Risk Assessment (EU-MASCARA) consortium aims to improve diagnosis of cardiovascular diseases and prediction of cardiovascular risk by analyzing a panel of biomarkers. EU-MASCARA aims to validate biomarkers that have been proposed to be associated with cardiovascular disease and risk across different disease entities and also in independent general population samples. The most robust biomarkers will be implemented in novel biochip based assays for clinical use." .
SCR:013697 a owl:NamedIndividual ;
rdfs:label "European large-scale functional genomics in the rat for translational research (EURATRANS)" ;
NIFRID:abbrev "EURATRANS" ;
definition: "The European large-scale functional genomics in the rat for translational research (EURATRANS) consortium brings together investigators who will use next-generation sequencing technologies to generate genomic, transcriptomic and epigenomic datasets. The goal is to create quantitative metabonomic and proteomic datasets to give significant depth of coverage, at multiple levels, across pathophysiological phenotypes. The aim is to enable insights into disease mechanisms, through an integrative, cross-disciplinary approach to understanding large-scale functional genomic datasets in rats and humans." .
SCR:013698 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BEI Resource Repository" ;
NIFRID:synonym "BEI Resource" ;
definition: "Central data repository that supplies organisms and reagents to the broad community of microbiology and infectious diseases researchers." .
SCR:013699 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Immune Tolerance Network TrialShare" ;
NIFRID:synonym "Immune Tolerance Network",
"ITN",
"Trial Share",
"TrialShare" ;
NIFRID:abbrev "ITN TrialShare" ;
definition: "Immune tolerance data management and visualization portal for studies sponsored by Immune Tolerance Network (ITN) and collaborating investigators. Data from published studies are accessible to any user; data from current in-progress studies are accessible to study investigators and collaborators. Includes links to published Figures, tools for visualization and analysis of data, and ability to query study data by subject, group, or any other study parameter." .
SCR:013700 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011129" ;
rdfs:label "Nanomaterial Registry" ;
NIFRID:abbrev "MIAN" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 9,2023. Registry that archives curated nanomaterial research data and their biological and environmental implications. The Registry provides data management plans for researchers, and accepts users' public-ready data, archive them, integrate them into the registry, allowing for the data to be shared publicly. Users can request more information on specific nanomaterial records, compare multiple nanomaterials, and export data to their desktop." .
SCR:013701 a owl:NamedIndividual ;
rdfs:label "European Network for Translational Research in Atrial Fibrillation (EUTRAF)" ;
NIFRID:abbrev "EUTRAF" ;
definition: "The European Network for Translational Research in Atrial Fibrillation (EUTRAF) consortium brings together investigators aiming to accelerate knowledge in the pathophysiology and treatment of Atrial Fibrillation. By integrating the mutually complementary strengths and expertise from molecular and cellular electrophysiology to the study of large cohort of patients, EUTRAF aims to develop approaches for increasing knowledge of the arrhythmogenic substrate, with the ultimate goal of developing novel treatments and diagnostic tools." .
SCR:013702 a owl:NamedIndividual ;
rdfs:label "Fatty Liver Inhibition of Progression (FLIP)" ;
NIFRID:abbrev "FLIP" ;
definition: "The Fatty Liver: Inhibition of Progression consortium (FLIP) aims to study the mechanisms of progression of liver disease in NAFLD to provide strategies for prevention and therapy. The project is based on the largest European cohort of patients with histologically diagnosed NAFLD, assembled with clinical and epidemiological data, and with biobanks of DNA, frozen liver tissue and serum. The consortium''s efforts span all the steps of the disease for studying cellular mechanisms of progression, with a goal of answering key issues dealing with the interplay of metabolic, inflammatory and fibrotic factors in the initiation and perpetuation of liver injury." .
SCR:013703 a owl:NamedIndividual ;
rdfs:label "Genetic Association Information Network (GAIN)" ;
NIFRID:abbrev "GAIN" ;
definition: "The Genetic Association Information Network (GAIN) supports a series of Genome-Wide Association Studies (GWAS) designed to identify specific points of DNA variation associated with the occurrence of a particular common disease. Initially focusing on six major common diseases, GAIN focused on combining the results with clinical data to create a significant new resource for genetic researchers." .
SCR:013705 a owl:NamedIndividual ;
rdfs:label "NeuroML Database" ;
definition: "The NeuroML database is a curated relational database that provides for the storage and retrieval of computational neuroscience models expressed in NeuroML, which is an extensible XML-based language for describing complex mathematical models of neurons and neuronal networks. NeuroML models are unique in their modular and multi-scale structure, where subcomponents of models can correspond to neuroscience models. In particular, the NeuroML database allows for efficient searches over the components of models and metadata that are associated with a hierarchical NeuroML model description." .
SCR:013707 a owl:NamedIndividual ;
rdfs:label "Global Research in Paediatrics (GRIP)" ;
NIFRID:abbrev "GRIP" ;
definition: "The Global Research in Paediatrics (GRiP) consortium focuses on the lack of appropriate testing of pediatric drugs. In particular, most pediatric medications having inadequate information about dosing regimen, dose adjustment and administration. GRiP partners are working to build and maintain an infrastructure matrix, which has the core aim of reducing the current fragmentation of the efforts to study and develop the use of medicine in children. By linking the existing pediatric research networks, GRIP will involve more than 1000 institutions worldwide." .
SCR:013708 a owl:NamedIndividual ;
rdfs:label "Glycomics by High-throughput Integrated Technologies (GLYCOHIT)" ;
NIFRID:synonym "GLYCOHIT" ;
definition: "The Glycomics by High-throughput Integrated Technologies (GlycoHIT) consortium aims to advance the development of reliable and fast diagnostic tests for the early detection of cancer. By creating high-throughput technologies to analyze altered sugars, or glycobiomarkers, the consortium aims to allow scientists to diagnose different forms of cancer from a simple blood test without the need for biopsy. GlycoHIT will also further develop sugar testing technologies to allow this rapid form of diagnosis to be used in a clinical setting." .
SCR:013709 a owl:NamedIndividual ;
rdfs:label "Imaging of Neuroinflammation in Neurodegenerative Diseases (INMiND)" ;
NIFRID:abbrev "INMiND" ;
definition: "The goal of the Imaging of Neuroinflammation in Neurodegenerative Diseases (INMiND) consortium is to identify novel biological targets of neuroinflammation for both diagnostic and therapeutic purposes, and to translate this knowledge into clinical application and patient benefit. The consortium supports collaborative research on molecular mechanisms that link neuroinflammation with neurodegeneration." .
SCR:013710 a owl:NamedIndividual ;
rdfs:label "Inflammatory Bowel Disease Biomarkers Consortium (IBD BIOM)" ;
definition: "The Inflammatory Bowel Disease Biomarkers Consortium (IBD-BIOM) addresses the need to improve our understanding of inflammatory bowel disease (IBD) through new biomarkers into molecular dysfunctions that give rise to IBD. The biomarkers targeted by the consortium will be translated into early-detection clinical diagnostic tests for IBD patients." .
SCR:013711 a owl:NamedIndividual ;
rdfs:label "Mendelian Forms of Parkinson's Disease (MEFOPA)" ;
NIFRID:abbrev "MEFOPA" ;
definition: "The Collaborative Project on Mendelian Forms of Parkinson's Disease (MEFOPA) is a consortium that advances the basic and clinical research on rare Mendelian forms of Parkinson's disease (PD) by identifying and validating relevant disease-related molecular pathways, drug-targets and biomarkers for disease susceptibility and progression." .
SCR:013712 a owl:NamedIndividual ;
rdfs:label "Multiple Sclerosis Outcome Assessments Consortium (MSOAC)" ;
NIFRID:abbrev "MSOAC" ;
definition: "The Multiple Sclerosis Outcome Assessments Consortium (MSOAC) is a public-private partnership which aims to accelerate the development of new therapies for MS by generating new tools for measuring outcomes in clinical trials. It is collecting, standardizing, and analyzing data about MS with the goal of qualifying new measures of disability for the disease. MSOAC is the newest of the eight consortia of Critical Path Institute (C-Path), a nonprofit organization that is dedicated to accelerating drug development by delivering on the mission outlined by FDA' '''s critical path initiative." .
SCR:013713 a owl:NamedIndividual ;
rdfs:label "OPTObacteria" ;
NIFRID:abbrev "OPTO" ;
definition: "The OPTObacteria consortium aims to develop a multianalyte and automatic laboratory detector (ALD) for antibiotic resistant infections. The goal is to detect these analytes within 4-6 hours from the sample collection, providing a report with the actual patient status, and predicting emerging drug resistance through the companion epidemiology software. The platform technology for this consortium is an opto electronic device, in which the appropriate ligand-probe, linked onto an opto electronic surface, will be able of specifically recognize biomolecules of the resistant infections." .
SCR:013714 a owl:NamedIndividual ;
rdfs:label "Osteoarthritis Biomarkers Project (OABP)" ;
NIFRID:abbrev "OABP" ;
definition: "The Osteoarthritis Biomarkers Project (OABP) is a consortium designed to identify and classify biological markers of progression of knee osteoarthritis. Their goal is to advance the ability to predict the individual risk of developing severe OA and to monitor progression of OA." .
SCR:013715 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_014211" ;
rdfs:label "Image Studio Lite" ;
NIFRID:synonym "Image Studio Lite Software",
"Image Studio Lite version 3.1",
"LI-COR Image Studio Lite Software",
"LICOR Image Studio Lite Software" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 28,2023. Software application which can analyze basic Western blot data and export them for use in spreadsheet programs. Users can create standardized or custom lab reports and can share them with colleagues. Image Studio Lite has been discontinued and replaced with Empiria Studio Software." .
SCR:013716 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ARRS GoldMiner" ;
definition: "An image repository that provides access to published, peer-reviewed medical images from biomedical journals." .
SCR:013717 a owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100010574" ;
rdfs:label "Cancer Nanotechnology Laboratory (caNanoLab)" ;
NIFRID:synonym "caNanoLab",
"Cancer Nanotechnology Laboratory" ;
definition: "Data sharing portal designed to facilitate information sharing across international biomedical nanotechnology research community to expedite and validate use of nanotechnology in biomedicine." .
SCR:013718 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FDA Adverse Event Reporting System Data" ;
NIFRID:synonym "Adverse Event Reporting System",
"Adverse Event Reporting System Data" ;
NIFRID:abbrev "FAERS" ;
definition: "Database that contains information on adverse event and medication error reports submitted to FDA. The database is designed to support the FDA's post-marketing safety surveillance program for drug and therapeutic biologic products." .
SCR:013719 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "InterNano Process Database" ;
NIFRID:synonym "InterNano Resources for Nano Manufacturing" ;
NIFRID:abbrev "InterNano" ;
definition: "Database and knowledge base of techniques for processing nanoscale materials, devices, and structures that includes step-by-step descriptions, images, notes on methodology and environmental variables, and associated references and patent information. The purpose of the Process Database is to facilitate the sharing of appropriate process knowledge across laboratories.The processes included here have been previously published or patented" .
SCR:013720 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dietary Restriction Gene Database" ;
NIFRID:synonym "The GenDR Database of Dietary Restriction-Related Genes" ;
NIFRID:abbrev "GenDR" ;
definition: "Database of genes associated with dietary restriction. It includes genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of dietary restriction and genes robustly altered due to dietary restriction, derived from a meta-analysis of microarray studies in mammals." .
SCR:013721 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Drug Code Directory" ;
NIFRID:abbrev "ndc" ;
definition: "Drug database published by the Food and Drug Administration of unique universal product identifiers for all drugs manufactured, prepared, propagated, compounded, or processed by it for commercial distribution." .
SCR:013722 a owl:NamedIndividual ;
rdfs:label "Open Colleges Group" ;
definition: "Online higher education which offers vocational and professional courses to adults." .
SCR:013724 a owl:NamedIndividual ;
rdfs:label "ProteinSimple: FluorChem™ E System" ;
definition: "Imaging system for detection of chemiluminescent, colorimetric and UV fluorescent gels and blots." .
SCR:013725 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UN-SCAN-IT Graph Digitizer Software" ;
NIFRID:synonym "UN-SCAN-IT" ;
NIFRID:abbrev "USI" ;
definition: "Digitizer software which can convert graph images to useful (x,y) data by turning a scanner into an automatic graph digitizer. UN‑SCAN‑IT works with most image formats (TIFF, JPG, BMP, GIF, etc.) from any scanner, digital camera, or other image source to digitize plots, instrumental output, published graphs, etc. Its features include: automatically digitizing strip chart and xy recorder output, digitizing graphs that are on different scales to compare results, comparing data with published graphs of other investigators, digitizing old plots and charts for comparison with new data, and re‑scaling and appending existing printed graphs." .
SCR:013726 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "G*Power" ;
NIFRID:synonym "G Power",
"G Star Power",
"G*Power - Statistical Power Analyses for Windows and Mac" ;
definition: "Data analytics software to compute statistical power analyses for many commonly used statistical tests in social and behavioral research. It can also be used to compute effect sizes and to graphically display the results of power analyses." .
SCR:013727 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Approved Drug Products with Therapeutic Equivalence Evaluations" ;
NIFRID:abbrev "Orange Book" ;
definition: "Database that contains drug products approved on the basis of safety and effectiveness by the Food and Drug Administration." .
SCR:013728 a owl:NamedIndividual ;
rdfs:label "ExtrAvidin FITC, Sigma-Aldrich" ;
definition: "Avidin is a tetrameric or dimeric biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs.5 It consists of four high affinity binding sites for biotin. ExtrAvidin is prepared from egg white avidin. It is a modified form of affinity purified avidin and combines high specific activity of avidin with the low background staining of streptavidin. It is a biotin binding protein produced by the bacteria Streptomyces avidinii.6 ExtrAvidin has been conjugated to fluorescein isothiocyanate (FITC) and is used for various techniques." .
SCR:013729 a owl:NamedIndividual ;
rdfs:label "dkNET Community Pilot Funding Opportunities" ;
definition: "A list of community-based funding opportunities provided by projects or organizations other than government funding opportunities. They are available via various NIDDK-supported centers, e.g., pilot projects, training opportunities, etc." .
SCR:013731 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Xenopus Resource" ;
NIFRID:abbrev "NXR" ;
definition: "National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics)." .
SCR:013732 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EchinoBase" ;
NIFRID:synonym "Echino Base",
"Echinoderm genomic database",
"Gene Library Resource for the Sea Urchin Strongylocentrotus purpuratus",
"Sea Urchin Genome Database",
"SpBase" ;
definition: "Database that provide a genomic information and comparative genomics platform on sea urchins and related echinoderms. It provide collection of information to directly support experimental work on these useful research models in cell and developmental biology." .
SCR:013733 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_014203" ;
rdfs:label "WormGUIDES" ;
NIFRID:synonym "Global Understanding in Dynamic Embryonic Systems" ;
definition: "A worm atlas that provides an interactive 4D atlas of nuclear positions, from zygote until hatching which can be used to guide cell identification. The tools enable examination of the connectome during development from integrate knowledge of C. elegans embryogenesis to widely used resources, such as WormAtlas and WormBase." .
SCR:013735 a owl:NamedIndividual ;
rdfs:label "Volcano Web Service crawled by BCube" ;
definition: "This web service provides volcano and earthquake information. It also has tsunami events and tsunami tide gauges, and plate boundaries. BPR and DART stations. Also volcanic eruptions." .
SCR:013736 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain RNA-Seq" ;
NIFRID:synonym "Barres Brain RNA-Seq" ;
definition: "Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain." .
SCR:013737 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:kaviar" ;
rdfs:label "KAVIAR" ;
NIFRID:synonym "Known VARiants",
"queryable database of known variants" ;
definition: "A database containing a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants." .
SCR:013738 a "resource",
owl:NamedIndividual ;
rdfs:label "USAspending.gov" ;
definition: "Database of resources receiving federal financial assistance of more than $25,000. The Federal Funding Accountability and Transparency Act of 2006 was mandated to provide the public access to information regarding organizations and other entities receiving federal funding." .
SCR:013739 a "resource",
owl:NamedIndividual ;
rdfs:label "National Institute of Health Data Book" ;
NIFRID:synonym "NIH Data Book" ;
definition: "Database of summary statistics of resources receiving funding from the National Institutes of Health. The resources listed includes extramural grants and contract awards, grant applications, NIH supported organizations, trainees, and fellows, and the national biomedical workforce." .
SCR:013740 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenAIRE" ;
NIFRID:synonym "Open Access Infrastructure for Research in Europe" ;
definition: "A research portal to share and obtain research data and journal articles openly accessible to all disciplines. Established to support the Open Access Policy, as set out by the ERC Scientific Council Guidelines for Open Access and the Open Access pilot launched by the European Commission." .
SCR:013741 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Patent Full-Text Database" ;
NIFRID:abbrev "PatFT" ;
definition: "Full text database of all patents granted in the United States since 1976, and the patent number, issue date, and current US classification for all patents granted from 1790 through 1975." .
SCR:013742 a owl:NamedIndividual ;
rdfs:label "Human Brain Transcriptome" ;
NIFRID:abbrev "HBT" ;
definition: "A data repository containing transcriptome and associated metadata for the developing and adult human brain. It provides genome-wide, exon-level transcriptome data from both sexes and multiple ethnicities." .
SCR:013743 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spatio-temporal transcriptome of the human brain" ;
definition: "A research paper with supplementary materials reporting the generation and analysis of exon-level transcriptome and associated genotyping data. The experiment represented both males and females of multiple ethnicities and examines gene regulation and expression in different areas of the brain. A data set on the human brain transcriptome as well as insights into the transcriptional foundations of human neurodevelopment is provided." .
SCR:013744 a owl:NamedIndividual ;
rdfs:label "Beijing Natural History Museum" ;
NIFRID:synonym "Beijing Museum of Natural History",
"BNHM" ;
definition: "A museum whose three main focuses are its specimen collection, academic research, and the popularization paleontology, zoology, botany, and anthropology." .
SCR:013745 a owl:NamedIndividual ;
rdfs:label "WinMDI Software" ;
NIFRID:synonym "Windows Multiple Document Interface for Flow Cytometry",
"Windows Multiple Document Interface software" ;
definition: "Software to analyze flow cytometry listmode data files." .
SCR:013746 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NURSA Transcriptomine" ;
NIFRID:synonym "Transcriptomine" ;
definition: "A database of tissue specific nuclear receptor transcriptomes based on annotated published genome wide transcriptional profiling experiments in the field of nuclear receptor signaling. Queries can include single and multiple genes, Gene Ontology terms, disease terms, and uploaded custom gene lists." .
SCR:013747 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.452221.2",
"ISNI: 0000 0004 0502 0676",
"Wikidata: Q2909651" ;
rdfs:label "Bombay Natural History Museum" ;
NIFRID:synonym "Bombay Natural History Society" ;
NIFRID:abbrev "BNHS" ;
definition: "A non-governmental wildlife research institution involved in the conservation of nature, primarily biological diversity and threatened species through action based on research, education and public awareness. Contains publications, collections, and educational materials as well as information on current research." .
SCR:013748 a owl:NamedIndividual ;
rdfs:label "Biotechnology Culture Collection Institution Pusat Penelitian dan Pengembangan Bioteknologi-LIPI" ;
NIFRID:synonym "Biotechnology Culture Collection Institution",
"Pusat Penelitian dan Pengembangan Bioteknologi-LIPI" ;
definition: "An institutional resource focusing on research in biotechnology. Their goals include becoming a reliable reference in the biotechnological field and improving the performance and professionalism of research institutes." .
SCR:013749 a NIFSTD:birnlex_2085,
owl:NamedIndividual ;
rdfs:label "University of South Florida Center for Biological Defense" ;
NIFRID:synonym "USF Center for Biological Defense" ;
NIFRID:abbrev "USF CBD" ;
definition: "An institutional resource focusing on biological defense and infectious disease research. The institution teaches preparation and response to catastrophes, especially bioterrorism preparedness, to local communities and conducts research in detecting and fighting biological agents and infectious diseases." .
SCR:013750 a owl:NamedIndividual ;
rdfs:label "National Bank for Industrial Microorganisms and Cell Cultures" ;
NIFRID:synonym "Bulgarian national collection for microorganisms and cell culture",
"Bulgarian Type Culture Collection",
"NBIMCC" ;
definition: "An institutional and material resource housing over 7400 strains of bacteria, yeasts, fungi, plant and animal viruses, and animal cell cultures. Certified for preservation, supply, import, and export of strains. An international depository which applies their collected strains in research, education, health services, industry, and agriculture." .
SCR:013751 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Digital Resource Tools" ;
NIFRID:abbrev "DiRT" ;
definition: "A software registry containing digital research tools ranging from content management systems to statistical analysis packages and mind mapping software. The site contains detailed descriptions, license information, and links to software developer websites and downloads." .
SCR:013752 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Connected Researchers" ;
definition: "A software registry providing links to software programs designed to aid researchers. Connected Researchers actively adds new resources to its registry along with descriptions and links to the software developer's site." .
SCR:013753 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DH Writer" ;
definition: "Software tool for reformatting abstracts from original submission formats into a text encoding format for publishing on-line and book abstracts." .
SCR:013754 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multi-Disciplinary Approach to the Study of Chronic Pelvic Pain" ;
NIFRID:synonym "MAPP Research Network",
"Multidisciplinary Approach to the Study of Chronic Pelvic Pain Research Network" ;
NIFRID:abbrev "MAPP" ;
definition: "Collaborative research network specializing in urological chronic pelvic pain disorders. Project involves conducting research primarily on interstitial cystitis/painful bladder syndrome and chronic prostatitis/chronic pelvic pain syndrome and involves researchers from multiple disciplines. MAPP Network includes researchers with clinical, epidemiological, and basic research expertise." .
SCR:013755 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cancer3D" ;
definition: "Database that allows for the exploration of cancer on somatic missense mutations from the Cancer Genome Atlas and Cancer Cell Line Encyclopedia. The site maps proteins and mutations using 3D models and is an interface to the algorithms e-Driver and e-Drug allowing for the prediction of novel cancer drivers or drug biomarkers." .
SCR:013756 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BibSonomy" ;
definition: "A software application which assists in managing and sharing scientific literature. Users can collect and share publications, collaborate with other researchers, and find new resources and publications for research." .
SCR:013757 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CaptoMe" ;
definition: "A software application which contains a collection of biomedical resources and assist in the management resources. Resources consist of clinical trials, publications, abstracts, patents, news and events. Users can search, save, and make notes on publications." .
SCR:013758 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CiteULike" ;
definition: "A web application which stores and organizes scholarly papers and references. Papers of interest identified from the web can be added to the users' personal library and the associated references will be automatically extracted." .
SCR:013759 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colwiz" ;
NIFRID:synonym "collective wizdom" ;
definition: "A reference manager software tool which manages references and journal articles. Individual users can search for and save references or share a library of resources with identified group members who can annotate and comment on the references" .
SCR:013760 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ContentMine" ;
definition: "A web application which provides public access to scientific literature through text and data mining." .
SCR:013761 a owl:NamedIndividual ;
rdfs:label "Tip Calculator" ;
definition: "calculates tips" .
SCR:013762 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Data Elixir" ;
definition: "A web-based information resource providing current news and resources relevant to data science. Users can subscribe to the weekly newsletter by providing an email address or visit the site. The site displays the current week's news and houses an archive of their past newsletters." .
SCR:013763 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepDyve" ;
definition: "A web application which enables users to access fee based scientific journals and articles. Users can rent peer-reviewed journals and articles from the website, regardless of their academic institution or library affiliations." .
SCR:013764 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:evidence_finder" ;
rdfs:label "EvidenceFinder" ;
definition: "A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched." .
SCR:013765 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MyScienceWork" ;
definition: "A web-based collaboration tool specializing in sharing and promoting research. Users can share their research and collaborate with others or search the site for publications. Relevant scientific news is also available for users to view." .
SCR:013766 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nowomics" ;
definition: "A web application that allows users to track new biomedical papers from the PubMed database. Users can search for articles concerning genes, species, disease, techniques, and other related topics and create a personalized Newsfeed related to bookmarked papers. New articles are also displayed in Newsfeed format." .
SCR:013767 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Paperity" ;
definition: "A web application containing Open Access journals and papers from multiple disciplines. Relevant resources are collected from all fields of research, from the natural and physical sciences to the social sciences and humanities. Users can search for journals and papers or expose their papers to a wider audience." .
SCR:013768 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Paperscape" ;
definition: "A web application tool which visualizes papers collected in arXiv. Users can search for papers and create an interactive graph to organize their resources. The graph shows the relationships between papers, the dates they were published, and other relevant information. Papers can be tagged and graphs can be shared with colleagues." .
SCR:013769 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PubChase" ;
definition: "A web application that recommends biomedical scientific articles based on articles saved to the users' ''' library. Users can search the National Library of Medicine databases and store articles of interest in a cloud library, which can be accessed on a computer or mobile device and can be shared with colleagues." .
SCR:013770 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PubGet" ;
definition: "A web application which allows users to access life science research articles in PDF format. Users can search across all affiliated institution's subscriptions. Tools are provided to manage papers, which include downloading citations and creating email alerts for new, relevant articles." .
SCR:013771 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PubPeer" ;
definition: "A software application that enables users to peer review published research articles. Users must have a previous publication and an email address at an academic or research institution. Comments can be made in any article published with a digital object identifier, PubMed identifier or a preprint in arXiv. Authors are notified of any comments their paper has received and may respond to comments." .
SCR:013772 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Culture Collection of Algae at the University of Cologne" ;
NIFRID:abbrev "CCAC" ;
definition: "An institution and biomaterial supply resource which houses more than 3500 strains of algae. The majority of the strains are derived from freshwater/terrestrial habitats while 15% are representative of marine and brackish water strains. 15% of the strains are axenic. 50% of the strains are currently available to the public and can be ordered from the CCAC's main site." .
SCR:013773 a NIFSTD:birnlex_2085,
owl:NamedIndividual ;
rdfs:label "Universidade Federal do Ceara, Centro Ciencias Agrarias" ;
NIFRID:synonym "Federal University of Ceará Center for Agricultural Sciences" ;
NIFRID:abbrev "CCA" ;
definition: "An institution focused on furthering research and higher education in the field of agriculture." .
SCR:013774 a NIFSTD:NEMO_0569000,
owl:NamedIndividual ;
rdfs:label "Central College of Bangalore" ;
NIFRID:synonym "Bangalore University" ;
NIFRID:abbrev "BU" ;
definition: "An institution located in Bangalore focused on higher education. The university has established Gandhi Bhavan, Dr. B.R. Ambedkar Study and Research Centre, and Centre for Study of Social Exclusion and Inclusive policy as well as schools of biological sciences, social sciences, and business studies." .
SCR:013775 a NIFSTD:birnlex_2085,
owl:NamedIndividual ;
rdfs:label "Culture Collection of Fungi" ;
NIFRID:abbrev "CCF" ;
definition: "An institution which serves as a deposit of saprotrophic ascomycete and zygomycete strains. 3400 isolates are contained, 2400 of which are available to the public. The collection also provides atlases of each. While some strains are provided for free, other services, such as providing strains for teaching or research or identifying cultures, are provided for a charge." .
SCR:013776 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.487518.7" ;
rdfs:label "Carter County Museum" ;
NIFRID:abbrev "CCM" ;
definition: "An institution which records the natural history of Ekalaka county, Montana. The museum contains artifacts from 80 million years ago to the present, including fossils, arrowheads, and early pioneer artifacts. Another focus of the museum are vertebrates and invertebrates found in the area. Items are available to research by appointment." .
SCR:013777 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReadCube" ;
definition: "A software resource application which organizes research literature. Users can import PDF articles into the application and create a searchable library. ReadCube enables users to perform keyword searches and provides references as well as note-taking tools. ReadCube also recommends articles to users based on library contents. For publishers, ReadCube enables interactive PDF versions of articles with tools for readers to make notes or perform author and keyword searches." .
SCR:013778 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciCurve" ;
definition: "A software application that provides visual representations and organization for systematic literature searches. Users can observe trends in scientific literature through graphic visualizations while using keyword searches to find related articles or compare trends within a given graphic. SciCurve also allows users to locate journals which publish literature in users' fields of interest." .
SCR:013779 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011280" ;
rdfs:label "FLOWRepository" ;
NIFRID:synonym "FLOW Repository",
"FlowRepository" ;
definition: "A database of flow cytometry experiments where users can query and download data collected and annotated according to the MIFlowCyt data standard." .
SCR:013780 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sciencescape" ;
definition: "A web application which organizes current scientific literature by fields, people, institutes, labs, places, and historical sets they are a part of. Sciencscape allows users to subscribe to topics to receive new material, as well as provides visual representations to organize recent and most cited papers." .
SCR:013781 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scizzle" ;
definition: "A web application which finds new and relevant scientific literature based on keyword searches and filters. Users can also share, organize, and collaborate on papers using tools within Scizzle." .
SCR:013782 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sparrho" ;
definition: "A web application which organizes and recommends new scientific literature to users' news feeds based on keyword searches and user preferences. The site contains materials such as articles, posters, patents, grants, videos, and events." .
SCR:013783 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Wiki Journal Club" ;
NIFRID:abbrev "WJC" ;
definition: "A database which holds summaries of landmark clinical trials. The topics of contributed articles range across various biomedical fields and disciplines such as immunology, nephrology, and urology." .
SCR:013784 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zotero" ;
definition: "A software application that allows users to add and store research content directly from the web. Users can use the tool to add research content and bibliographic references directly to their Zotero library from their browser. The application stores PDFs, images, audio and video files, and snapshots of web pages on a single searchable interface." .
SCR:013785 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ACS ChemWorx" ;
definition: "A web application which provides tools to share references and generate bibliographies with colleagues, organize and access references, and track metrics for ACS articles. Articles are automatically synced to user libraries and are accessible from multiple devices." .
SCR:013786 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pathway_tools" ;
rdfs:label "Pathway Tools" ;
NIFRID:synonym "Pathway Tools Bioinformatics Software",
"Pathway Tools Software" ;
definition: "A software application which supplies software tools to develop and maintain pathway/genome databases (PGDBs). These include the development of organism-specific databases, metabolic reconstruction and metabolic-flux modeling, scientific visualization and web publishing of organism-specific databases, analysis of gene-expression and metabolomics datasets, comparative genome and pathway analyses, and analysis of biological networks." .
SCR:013787 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RefSeqGene" ;
NIFRID:synonym "NCBI RefSeqGene",
"RefSeqGene Project" ;
definition: "A data set of defined genomic sequences used as reference standards for well-characterized genes. These standard nucleotide sequences serve as foundations for locating mutations, establishing conventions for numbering exons and introns, and defining the coordinates of other variations. Sequences are aligned to reference chromosomes. RefSeqGene is a subset of NCBI RefSeq." .
SCR:013788 a owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100010905" ;
rdfs:label "Trace Archive" ;
NIFRID:synonym "NCBI Trace Archive" ;
definition: "An online repository which houses sequencing data from gel and capillary platforms (such as Applied Biosystems ABI 3730®). Most sequences are derived from Whole Genome Shotgun sequencing. Large data sets as well as only a few sequences can be obtained." .
SCR:013789 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCBI Viral Genomes" ;
NIFRID:synonym "Viral Genomes" ;
definition: "A database which provides viral and viroid genome sequence data and resource tools. Al viral genomes are downloadable and a complete RefSeq release of viral and viroid genome sequences are available." .
SCR:013790 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Virus Variation" ;
NIFRID:synonym "NCBI Virus Variation" ;
definition: "A repository which supports the search, retrieval, and display of large virus sequence data sets concerning the viruses of Dengue, West Nile, and Influenza. Users can search sequences based on a number of biological and clinical criteria and selected sequences can be downloaded or analyzed using a variety of web-based tools and displays. Virus Variation is an extension of NCBI's Influenza Virus Resource." .
SCR:013791 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clone DB" ;
NIFRID:synonym "NCBI Clone DB" ;
definition: "A database which integrates information about genomic clones and libraries, including sequence data, map positions and distributor information. A clone's standardized name in Clone DB is comprised of its microtiter plate address with plate number row and column, prefixed by the standard library abbreviation, to provide a unique clone name. Libraries with records may be accessed via the genomic or cell-based library browsers." .
SCR:013792 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biospecimen Repository and Processing Core" ;
NIFRID:abbrev "BRPC" ;
definition: "A biomaterial supply and access service resource which provides a shared resource for coordinated tissue processing and biorepository services. Services include patient identification and informed consent, specimen collection, processing and banking, and annotation of banked specimens and specimen distribution. They provide biospecimen inventory management, services, and equipment. It is a shared resource of Duke University." .
SCR:013794 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Metabolomics_Workbench",
"r3d100012314" ;
rdfs:label "Metabolomics Workbench" ;
NIFRID:synonym "Metabolomics Workbench (MetWB)",
"MetWB",
"UCSD Metabolomics Workbench" ;
definition: "Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops." .
SCR:013795 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Database for Clinical Trials related to Mental Illness" ;
NIFRID:abbrev "NDCT" ;
definition: "A database which houses human subjects clinical trial data. NDCT currently contains data on 13,409 subjects and has access to data on 100,500 subjects from the NIMH Data Archive. Users can also sign up for news updates and watch video tutorials. " .
SCR:013796 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RDoCdb" ;
NIFRID:synonym "Research Domain Criteria Database" ;
definition: "A database that houses human subjects data related to mental health research. Data from 691 subjects are shared in RDoCdb and data from 100,500 subjects are shared in the NIMH Data Archive. Users can plan for data submission, share data, query data, or share their results related to a publication or finding." .
SCR:013797 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Sartorius | Ambr 15 Cell Culture Generation 2" ;
definition: """Automated, high throughput microscale bioreactor system that replicates laboratory
scale bioreactor performance., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.""" .
SCR:013798 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuronStudio" ;
NIFRID:synonym "NeuronStudio (Beta)" ;
definition: "A software application which allows reconstruction of neuronal structures from confocal and multi-photon images. NeuronStudio provides tools for manual, semi-manual, and automatic tracing of the dendritic arbor, as well as manual and automatic detection and classification of dendritic spines. Advanced 2D and 3D visualization techniques facilitate the verification of the reconstruction, as well as allowing accurate manual editing. The most current version is Version 0.9.92 which was last updated on November 19, 2009." .
SCR:013799 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rayburst Open-Source Code " ;
definition: "A software application which provides the source code for the Rayburst Algorithm. The fully automated algorithm casts rays in a 2D/3D dataset without the use of pre-generated ray tables. It is implemented in ANSI C as a single module. The most current version is Version 1.1, last updated on Aug. 15, 2006." .
SCR:013800 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Volume Integration and Alignment System" ;
NIFRID:abbrev "VIAS" ;
definition: "A software application designed to allow multiple stacks of tiled optical sections obtained from Laser Scanning Microscopy to be integrated into a single volumetric dataset. VIAS allows the user to select the individual image stacks from disk and to adjust their relative position on the screen interactively. By using a global 3D coordinate system, users can manipulate stacks and execute the integration of the data after all the stacks of images have been correctly positioned. VIAS was designed with large datasets in mind. The current version of VIAS is Version 2.4, last updated on January 26, 2009." .
SCR:013801 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Volume Integration and Alignment System Source Code " ;
NIFRID:synonym "Volume Integration and Alignment System (VIAS) Source Code" ;
definition: "The source code for VIAS software Version 2.4. The code is written in the C programming language and uses Win32 for the graphical user interface. " .
SCR:013802 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Polygonized Viewer" ;
NIFRID:synonym "P-View",
"PView" ;
definition: "A software application which enables the visualization of datasets obtained from Confocal Laser Scanning Microscopy (CLSM). P-View allows users to interact with a pre-computed model using a flight simulator type interface. The program makes use of several optimizations to allow visualization of large objects using standard PC workstation hardware, including the speed up techniques Level of Detail and Frustum Culling. The current version of this software is Version 1.2.1, last updated on October 1, 2002." .
SCR:013803 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroGL" ;
definition: "A software application which is used to create navigable visuals of neural structures. The current version of the program accepts NeuroZoom ASCII files as input. Users can visit CNIC's online repository for a full list of free, available models. The current version of the software available is Version 1.2, last updated on July 13, 2004." .
SCR:013804 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TIFF Stack Sub-Sampler" ;
NIFRID:abbrev "TSS" ;
definition: "A software application which reduces the number of voxels used to represent a volumetric dataset by means of subsampling, i.e., computes a smaller version of a given dataset. Stacks can be selected from the disk by point and click and users are free to specify the new dimensions as actual pixels or as a percent of the original dimensions. The current version is Version 1.0, last updated on February 10, 2003." .
SCR:013805 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vienna Drosophila Resource Center " ;
NIFRID:abbrev "VDRC" ;
definition: "Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID." .
SCR:013807 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-03236",
"SCR_007842" ;
rdfs:label "Proteome Analyst" ;
NIFRID:abbrev "PA" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Web-based tool that predicts subcellular localization and GO molecular function of proteins. Proteome Analyst has the ability to explain its predictions and gives users the ability to run a large set of tools on their proteins." .
SCR:013808 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "InterMOD" ;
NIFRID:synonym "InterMine",
"InterMod Consortium" ;
definition: "An international consortium whose goals are to enable faster comparative studies and develop tools that make analysis accessible to the wider scientific community. InterMOD is an open source data warehouse where users can query and input their own data, access analysis tools, and create their own InterMine. Five core mines make make up InterMOD: RGD, SGD ZFIN, MGI, and WormBase." .
SCR:013809 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eLife Lens" ;
definition: "A web application which modifies the online use of scientific articles published in eLife. eLife Lens is a tool created by eLife that enables users to explore figures, figure descriptions, and references while keeping their place in the article text. Users can search for papers by subject, organism, article type, and/or top authors. " .
SCR:013811 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Elsevier" ;
NIFRID:synonym "Elsevier B.V.",
"Elsevier BV" ;
definition: "A publishing company which aims to produce intellectual content as well as research platforms and intelligence solutions. Elsevier publishes works related to science, health, and technology in physical copies and online. The company also provides integrated technology and analytics which allows users to to interact with, manipulate, share, and extract informant from various resources." .
SCR:013812 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Article of the Future" ;
NIFRID:synonym "Elsevier - Article of the Future" ;
definition: "A web application which provides interactive and in depth reading of online scientific articles published in Elsevier. While reading an article, users can access interactive data sources such as Protein Viewer and Google Maps as well as links to references and databases. Prototypes for seven different scientific areas are currently available for more specific research, but all scientific disciplines are represented within Article of the Future. " .
SCR:013813 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Interactive Science Publishing" ;
NIFRID:synonym "OSA ISP" ;
NIFRID:abbrev "ISP" ;
definition: "A software application which allows for interactive viewing and publishing of a wide range of 2D and 3D image data formats. Users can use the tool to build custom views of image data that can be saved, integrated with peer-reviewed articles, and shared with readers through the Optical Society's journals. ISP supports DICOM, TIFF, and JPEG image formats." .
SCR:013814 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PubReader" ;
definition: "A web application which serves as an alternate way to read scientific literature in PubMed Central and Bookshelf. PubReader features an easy-to-read multi-column display, a figure strip for access to figures, and a search function. It is designed especially to support reading on tablets and other smaller devices but is available for reading on laptops and desktops." .
SCR:013815 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SHERPA RoMEO" ;
NIFRID:synonym "RoMEO" ;
definition: "A database which houses publisher policies regarding the self- archiving of journal articles on the web and in Open Access repositories. RoMEO contains publishers' general policies on self-archiving of journal articles and certain conference series. Each entry provides a summary of the publisher's policy, including what version of an article can be deposited, where it can be deposited, and any conditions that are attached to that deposit." .
SCR:013816 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Wiley Anywhere Article " ;
NIFRID:synonym "Anywhere Article" ;
definition: "A web application which enhances online reading of articles from the Wiley Online Library. Wiley Anywhere Article is an alternate HTML version of articles found on the Wiley Online Library that is supported on all desktop, tablet, and mobile devices. Readers have access to sidebar and tray functions which display references, figures, and other important information while keeping their place in the article. " .
SCR:013817 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Wiley Smart Article" ;
NIFRID:synonym "Smart Article" ;
definition: "A web application which provides article tools specifically for the chemistry journals Applied Organometallic Chemistry, Chemistry – An Asian Journal, Chirality, Journal of Heterocyclic Chemistry, and Journal of Physical Organic Chemistry. The addition of Smart Article to these journals allows researchers to search across all five journals and to index and browse facilities for detailed information on compounds." .
SCR:013818 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SlideShare" ;
definition: "A collaboration tool which allows users to upload and share presentations, infographics, documents, videos, PDFs, and webinars. Individual slideshows are available for download and are easily uploaded to other websites and blogs. " .
SCR:013819 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Trellis" ;
NIFRID:synonym "Trelliscience" ;
definition: "A collaboration tool designed specifically for scientists as a place to collaborate and engage in activities with others. Users can create and manage a professional profile, meet new people and build their professional network, find the latest news and updates in science, participate in online conversations, upload and manage documents, and host a journal club, a live chat-based Q&A, or a presentation series." .
SCR:013820 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Academic Joy" ;
definition: "A collaboration tool that aims to spread the stories and advice of researchers in the sciences, engineering, and the humanities. Researchers can share and collaborate on ideas, find resources and tools, and read the stories of other researchers. " .
SCR:013821 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Assay Depot" ;
NIFRID:synonym "AssayDepot" ;
definition: "A web application containing access to research services and products. Users can create custom services, find research services and compare them, request price quotes, exchange files and upload reports, place orders, and track studies. Assay Depot regularly updates its page with new services." .
SCR:013825 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MSDF Drug Development Pipeline" ;
NIFRID:synonym "Drug-Development Pipeline",
"MSDF Drug-Development Pipeline" ;
definition: "A database providing information about compounds under investigation for therapeutic use. There are currently 44 compounds on record with 100 compounds in the process of being uploaded to the database. " .
SCR:013826 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MSGene" ;
NIFRID:synonym "MSGene database" ;
definition: "A database which provides a comprehensive and regularly updated collection of genetic association studies performed on multiple sclerosis phenotypes. Eligible publications are identified following systematic searches of scientific literature databases as well as the table of contents of journals in genetics, neurology, and immunology. " .
SCR:013827 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Statistics Calculator" ;
definition: """A set of many statistics calculators, including a confidence interval calculator.
""" .
SCR:013829 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sLORETA" ;
NIFRID:synonym "Standard Low Resolution Brain Electromagnetic Tomography",
"Standardized low-resolution brain electromagnetic tomography" ;
definition: "A software application which computes images of electric neuronal activity from EEG and MEG. Standard Low Resolution Brain Electromagnetic Tomography, or sLORETA, localizes “test point sources” exactly (under ideal conditions) when estimating electric neuronal generators. This property can be generalized to any source distribution, based on the principles of linearity and superposition. However, it would be noted that sLORETA has very low spatial resolution." .
SCR:013830 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "exact Low Resolution Electromagnetic Tomography" ;
NIFRID:synonym "Exact Low Resolution Brain Electromagnetic Tomography" ;
NIFRID:abbrev "eLORETA" ;
definition: "Software application which computes cortical three-dimensional distribution of current density of the brain based on the scalp-recorded electric potential distribution. The exact low resolution brain electromagnetic tomography method has the property of exact localization to test point sources, yielding images of current density with exact localization, albeit with low spatial resolution. eLORETA has no localization bias even in the presence of structured noise. Deep structures, such as the anterior cingulate cortex and mesial temporal lobes, can be correctly localized with these methods." .
SCR:013831 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReMoto" ;
definition: "A neuronal simulation software application used to study spinal cord neuronal network systems for muscle control. Users can investigate phenomena at several levels of organization, such as the neuronal membrane level or the whole muscle behavior level. ReMoto can be used to interpret results, validate experimental protocols, and teach neurophysiology. " .
SCR:013833 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurofly" ;
NIFRID:synonym "Virtual Insect Brain Lab" ;
definition: "An on-going atlas project of the Virtual Insect Brain Project with the goal of reconstructing and standardizing Gal4 expression patterns in Drosophila brains. Neurofly will be a web-based tool that will enable the online comparison of mutations and Gal4 expression patterns in the Drosophila brain. To this end, a database of reconstructed and standardized Gal4 expression patterns - on the basis of the existing Drosophila StandardBrain - was developed along with tools for 3D image data set processing. Users will be able to evaluate the expression patterns intersections of various Gal4 driver lines and/or mutations." .
SCR:013834 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Free Statistical Software " ;
definition: "A software registry which offers links to various free statistical software programs for stand-alone computing. The software programs are split into different categories: General Packages, Subset Packages, Curve Fitting and Modeling, Biostatistics and Epidemiology, Surveys, Testing and Measurement, Excel Spreadsheets and Add-ins, Programming Languages and Subroutine Libraries, Scripts and Macros, Miscellaneous, and Other Collections. " .
SCR:013836 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011819" ;
rdfs:label "Cancer Cell Line Encyclopedia" ;
NIFRID:abbrev "CCLE" ;
definition: "A collaborative project between the Broad Institute and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation, with the goal of conducting a detailed genetic and pharmacologic characterization of a large panel of human cancer models. The CCLE also works to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines. " .
SCR:013837 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Brain Tissue Bank" ;
NIFRID:synonym "Budapest Human Brain Tissue Bank",
"Human Brain Tissue Bank Budapest" ;
NIFRID:abbrev "HBTB" ;
definition: "A biomaterial resource which stores and distributes dissected human brain samples and topographically oriented tissue blocks. Most brains were removed from the skull and frozen within 2-6 hours after death. The microdissection of 260 different brain nuclei is performed on frozen brains and the samples are kept in -70ºC. Materials must be studied in the course of an approved research project, which has scientific aims and is devoid of any commercial profit for the researches involved and for their respective institutions." .
SCR:013838 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Maritime Brain Tissue Bank" ;
NIFRID:abbrev "MBTB" ;
definition: "A biomaterial supply resource which supplies brain tissue for researchers studying dementia and other neurodegenerative diseases. The Maritime Brain Tissue Bank archives tissues related to Alzheimer's Disease, mixed dementias, Lewy Body Disease, and Huntington's Disease, among others." .
SCR:013839 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRC London Neurodegenerative Diseases Brain Bank" ;
NIFRID:synonym "The Brain Bank" ;
definition: "A biomaterial supply resource which provides high quality, clinically and neuropathologically well-characterised human brain and spinal cord tissue. The Brain Bank focuses on neurodegenerative diseases such as Alzheimer’s Disease (AD), Frontotemperal dementias (FTD) and Motor Neurone Disease (MND). However, it also contains tissues for the study of HIV, Autism and Schizophrenia, and movement disorders." .
SCR:013841 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Netherlands Brain Bank" ;
NIFRID:abbrev "NBB" ;
definition: "A biomaterial supply resource which collects, stores, and disseminates diseased and healthy brain tissue. The Netherlands Brain Bank currently contains more than 3600 samples, and each sample includes a neuropathological report and donor medical history. The samples can additionally be matched with ante-mortem parameters and post-mortem parameters upon request. Sample types include cortex, spinal cord, cerebrospinal fluid, plasma, and DNA, among others. Database mining is available with a financial contribution. " .
SCR:013842 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroBioTec" ;
NIFRID:synonym "NeuroBioTec Banque" ;
definition: "A biomaterial supply resource which collects, stores, and disseminates biomaterial and clinical data relating to neurological disorders, psychiatric disorders, cardiology pathologies, and pneumology pathologies. NeuroBioTec has 18 collections with a total of 100,000 samples of serum, plasma, cerebrospinal fluid, PBMC, urine, tissue, DNA and RNA. Some samples can be made available to external researchers under certain conditions. " .
SCR:013843 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Newcastle Brain Tissue Resource" ;
definition: "A biomaterial supply resource which archives and disseminates brain tissue for the study of normal brain aging and brain disorders. Researchers must create an account in order to browse the database of available tissue. Samples are distributed to researchers in such a way that the identity and personal information of donors is protected. " .
SCR:013844 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "ProteoGenex" ;
NIFRID:synonym "ProteoGenex Corporation" ;
definition: "Commercial biomaterial supply resource which provides an extensive biorepository as well as an exclusive human tissue-based research service. The biobank contains defined and categorized clinical samples of tissues, blood, serum, bone marrow, and tissue microarrays. ProteoGenex collects biomaterials for a variety fields, including oncology, neurology, and immunology. Normal tissues are collected, as well. All samples are supported by pathology information and patient clinical history documentation. ProteoGenex also offers custom collection design." .
SCR:013845 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sera Laboratories International" ;
NIFRID:synonym "Seralab" ;
definition: "A biomaterial supply resource which provides human and animal biological matrices and services. Human biomaterials and tools include hepatocytes, clinical samples, normal samples, subcellular fractions, immunology products, renal cells, cell cultures, and diagnostic tools. Animal biomaterials include hepatocytes, blood, fluid, and tissue samples, subcellular fractions, and cell cultures. Custom cells and clinical samples are available for purchase, as are hepatocyte and renal media. " .
SCR:013846 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EPBscore" ;
definition: "A software application which tracks EPBs. EPBscore tool uses maximal intensity for the following reasons: 1) the integrated intensity is affected by the sampling density and it is not clear how large an area one should integrate over. This is often determined by ad- hoc criteria with no theoretical justification. 2) The integrated intensity is susceptible to movement artifacts. 3) As shown in (Grillo et al. 2013), the maximal intensity scales over the whole range of EPB intensities is considered. Importantly, the tool successfully minimizes human input by automating the EPB scoring and measurement steps., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013850 a owl:NamedIndividual ;
rdfs:label "Residual Variation Intolerance Score (RVIS)" ;
NIFRID:synonym "Residual Variation Intolerance Score" ;
NIFRID:abbrev "RVIS" ;
definition: "A gene-based score intended to help in the interpretation of human sequence data. The score is designed to rank genes in terms of whether they have more or less common functional genetic variation relative to the genome wide expectation given the amount of apparently neutral variation the gene has. A gene with a positive score has more common functional variation, and a gene with a negative score has less and is referred to as intolerant." .
SCR:013851 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "InnoCentive" ;
definition: "A global network group resource which provides crowdsourcing services for “innovation solutions.” InnoCentive utilizes an innovation framework, called Challenge Drive Innovation, which is based on leveraging open innovation and crowdsourcing. Software tools are available for idea management, innovation management, and external crowdsourcing programs and competitions." .
SCR:013852 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kaggle" ;
definition: "A group resource which connects organizations to data scientists who produce accurate predictive models. Kaggle uses competition to incentivize data scientists to create the most accurate and precise predictive models for an organization’s sets of data. The data scientist or team of data scientists who creates the best model is awarded a prize and the organization receives the predictive model. " .
SCR:013853 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Benefunder" ;
NIFRID:synonym "benefunder" ;
definition: "A funding resource which allows researchers to receive funding from citizen and organizational donors. Benefunder encourages relationships between the donor(s) and researcher(s) as well as wealth management which facilitates long-term funding and low overhead." .
SCR:013854 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Experiment" ;
definition: "A for-profit funding resource which funds research through the contributions of donors and backers. Scientists can create project profiles which include stated funding goals that must be reached before the end of the campaign. Projects which do not achieve their funding goals will be dropped and no funding from Experiment backers will be received. Three basic criteria must be met before an experiment can receive consideration for funding: The experiment seeks to answer a specific research question, the process and results can be shared openly and transparently, and the researchers have the expertise needed to meet the goals. Additional criteria must be met for academic scientists, individual scientists, and corporate scientists, respectively. Experiments are reviewed by Experiment staff before they are accepted." .
SCR:013855 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Consano" ;
definition: "A non-profit funding resource that allows academic medical researchers to receive funding from donors. Researchers set a fixed amount for donor funding which must be reached within two months to ensure the continuation of the campaign. Consano allows quarterly communication between donors and researchers throughout the term of the project. Some non-academic research is approved to be funded through Consano. " .
SCR:013856 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Asana" ;
definition: "A computational hosting resource designed to replace email as the primary means of team communication by allowing teams to manage, plan, and organize on the same interface. Asana provides an interface with different panels that organize team members’ tasks, meetings, projects, comments, and inboxes. It is compatible with a variety of software and web tools such as DropBox, GitHub, Evernote, WordPress, and JIRA. " .
SCR:013857 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ELabInventory" ;
NIFRID:synonym "eLabInventory" ;
definition: " A computational hosting resource which organizes lab inventories, including communal stocks, samples, and chemicals. Users can organize by predefined or custom sample types and store information for each type using specific fields. Samples can be stored in defined custom storage units and can be added to or searched within those storage units. ELabInventory supports 2D barcoding to identify samples. " .
SCR:013858 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LabCritics" ;
NIFRID:synonym "Labcritics" ;
definition: "A registry for reviewed material resources such as lab equipment, consumables, and services. LabCritics provides comparison charts, location of distributors, and distributor ratings along with extensive material reviews." .
SCR:013859 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LabGuru" ;
definition: "A computational hosting resource which provides lab management and collaboration in one location. When users create a new experiment, they can take note of the experimental design in LabGuru by searching for and adding protocols and reagents to the project main page. Information for reagents such as batch number and concentration are retained in the records. Users can also track the progress of experiments and receive results using a variety of tools provided by LabGuru. " .
SCR:013860 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StrainControl" ;
definition: "A computational hosting resource used for keeping track of reagents and materials in wet-labs. Users can store and manage strains, cell-lines, proteins, plasmids, oligos, chemicals, inventories, and more, as well as search StrainControl for other such reagents and materials. Users can also customize text, columns, and modules to match their lab needs. Data is stored on a secure database on a user’s computer or computer network. " .
SCR:013861 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Docollab" ;
definition: "An web-based computational hosting resource which allows users to document scientific research and collaborate with others. Users can store experiments and protocols, organize and manage projects, share and collaborate with colleagues, and publish findings within their Docollab account. " .
SCR:013869 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-30108",
"r3d100010875" ;
rdfs:label "Cellosaurus" ;
definition: "Database of all cell lines used in biomedical research which include immortalized cell lines, naturally immortal cell lines (stem cells), widely used and distributed finite life cell lines, vertebrate cell lines (majority being human, mouse, and rat), and invertebrate (insects and ticks) cell lines, as well as cell line synonyms. Each cell line is provided with the following information: the recommended name (the name which appears in the original publication), a list of synonyms, a unique accession number, comments on a number of topics including misspellings and gene transfection, information on the tissue/organ origin with the UBERON code, the NCI Thesaurus or Orphanet ORDO code for the disease(s) the individual suffered from (for cancer and human genetic disease lines only), the species of origin, the parent cell line, cross-references of sister cell lines, the sex of the individual, the category in which the cell line belongs (Adult stem cell; Cancer cell line; Embryonic stem cell; Factor-dependent cell line; Finite cell line; Hybrid cell line; Hybridoma; Induced pluripotent stem cell; Spontaneously immortalized cell line; Stromal cell line; Telomerase immortalized cell line; Transformed cell line; Undefined cell line type), web links, publication references, and/or cross-references to cell line catalogs/collections, ontologies, cell lines databases/resources, and to databases that list cell lines as samples." .
SCR:013955 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Benchling" ;
definition: "An online resource which helps researchers manage and organize labs and experimental results by supplying molecular biology software tools for experimental design and data analysis. Benchling provides tools for functions such as primer design and colony counting as well as CRISPR guide design and automated Gibson and Golden Gate cloning. Users can take notes in line with data, link data across entries, keep files and data in one place, and manage and keep track of team progress. An enterprise version of Benchling is available for scientists working within an organization with additional administrative, compliance, and security protocols." .
SCR:013956 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BiomedUSA" ;
definition: "An access service resource which serves as a global open access hub for the sharing and licensing of Biological Research Materials and related technologies with researchers. Biomedical researchers from research institutions and industry can connect with Technology Transfer Offices owning proprietary Biological Research Materials or rights to relevant technologies. Users can also search BioMedUSA's aggregated resources, such as biorepositotires and biologicals to share/license, for materials and technologies." .
SCR:013957 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biowebspin" ;
definition: "A collaboration tool and job resource which connects academic and industrial researchers and scientific professionals across various fields and discipines. Users can create their own profile and be matched with other users, follow news and events, search for jobs, Ph.D, and career opportunities, and use PubAdvanced, an app which searches PubMed with added features." .
SCR:013958 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DIRECT2experts" ;
NIFRID:synonym "DIRECT2experts network",
"Distributed Interoperable Research Experts Collaboration Tool" ;
definition: "An on-going project and collaboration tool where biomedical researchers can access to expertise and related resources across institutions, regardless of local platforms and tools. Users can work with participating institutions in order to connect to their existing research networking tools. Biomedical institutions that wish to participate must have a mature, deployed research networking tool and can commit resources to assessments." .
SCR:013959 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Florida ExpertNet" ;
NIFRID:synonym "ExpertNet" ;
definition: "A portal that connects users to reserch expertise and resources within Florida's universities. Users can search for experts (principal investigators), funded research projects, centers and institutes, technology licensing opportunities, speakers, and instructional programs." .
SCR:013960 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GlobalEventList" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on March, 4, 2021. A meeting resource which lists current and up-coming scientific and medical events by discipline, location, and date." .
SCR:013961 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LabRoots" ;
NIFRID:synonym "labroots" ;
definition: "A video resource which provides access to webinars and educational materials in various scientific fields. Users can also create communities in which to share materials and news." .
SCR:013962 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MalariaWorld" ;
definition: "A portal for malaria researchers and professionals. The site provides links to articles, news, discussion forums, the MalariaWorld journal, weblogs, events, and job listings." .
SCR:013963 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nanoHUB" ;
definition: "A portal which provides simulation programs for nanoscale phenomena, online presentations, courses, learning modules, podcasts, animations, and teaching materials. Researchers can also collaborate with others and publish content." .
SCR:013964 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Piirus" ;
definition: "A database and collaboration tool which allows researchers to make contacts or find collaborators within their field or from a different discipline. Users can create a profile detailing their collaboration interests, research areas, and methodologies as well as add links to external sites such as LinkedIn and Academia.edu. Piirus takes the information from users' profiles to suggest researchers with whom they may be interested in collaborating with. Users can also search for users with particular interests, expertise, or techniques." .
SCR:013965 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ResearchConnection" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented June 21, 2018.
A service resource and collaboration tool which connects academically affiliated researchers to undergraduate and graduate students. Researchers can advertise their lab and open positions as well as organize and manage applicants. Students can browse labs based on university and field(s) of interest and apply directly for lab positions or jobs. Universities must officially partner with ResearchConnection to advertise labs." .
SCR:013967 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DrawScience" ;
definition: "A production service resource which transforms scientific articles into infographics. In order to make an infograph, users must submit a package to DrawScience containing a scholarly article(s) to base the infographic on, a summary of the rationale and conclusions of the research, and definitions for 5 or less terms necessary to understand the research. Users may also make an infographic which will be attributed to them." .
SCR:013968 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Useful Science" ;
definition: "A collection of concise summaries of scientific articles that link back to the physical article. Users can contribute resources to the site and may choose to provide a summary; if they do not, Useful Science will do so. Summaries are then tagged with the appropriate topic. Topics that relate to everday life such as health, fitness, nutrition, and sleep are the main focus of the site." .
SCR:013969 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zooniverse" ;
definition: "A production service resource which allows researchers to enlist the help of volunteers in projects. Researchers can build web-based projects where volunteers can assist in identification, classification, and/or characterization of specific \"items\" in images. An example of a project is having volunteers mark the instances when nematode worms lay eggs as part of a larger project concerning genes and behavior." .
SCR:013970 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Life Technologies Instrument Management" ;
NIFRID:synonym "Life Technologies Instrument Management Tool",
"Life Technologies Lab Management Tool" ;
definition: "A web application which allows users to record, organize, and manage lab equipment online. Instrument Management provides tools to view service history and field service reports, request service or service quotes online, monitor warranty or contract statuses, and view instrument details." .
SCR:013971 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "elabFTW" ;
NIFRID:synonym "elabftw" ;
definition: "An open access electronic lab notebook which helps users design and organize lab experiments. Users can upload files and embed images of any type into the ELN, as well as export in PDF or zip archive into the electronic notebook. The database stores reagents, protocols, and other lab and experiment necessities for different kinds of labs. It is a PHP + MySQL application that users install on a server. After it is installed, the ELN is located in the browser." .
SCR:013972 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Findings App" ;
NIFRID:synonym "FindingsApp" ;
definition: "An ELN (electronic lab notebook) software application that allows researchers to organize and manage experiment tasks, protocols, and results. Users can divide experiments into tasks spread across weeks and keep track of multiple experiments and protocols using a variety of apps, such as timestamps and completion markers. Files can be stored in the Findings library and opened in a given application." .
SCR:013973 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LabArchives" ;
definition: "An ELN (electronic lab notebook) software application where researchers can record and organize their data in lieu of a paper notebook. Users can store and edit texts, PDFs, spreadsheets, images, sample collections, and other types of data. LabArchives automatically backs up data and data can be accessed anywhere. Users can choose to use the professional edition of LabArhives, the classroom edition, or to purchase an enterprise license." .
SCR:013974 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "labfolder" ;
NIFRID:synonym "LabFolder",
"Labfolder" ;
definition: "An ELN (electronic lab notebook) software application where researchers can record and organize their data by recording, dragging, and dropping elements. Users can utilize tools and features such as image annotation, search and filter, protocol templates, and team communication. The format of the ELN is customizable and can be rearranged at any point." .
SCR:013975 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LabLog" ;
NIFRID:synonym "Laboratory Logbook" ;
definition: "An ELN (electronic lab notebook) software application which can be used to document neuroscience projects and store metadata. LabLog is meant to constitute a laboratory's long term memory for project related information. To do this, project information is stored in a central laboratory database and can be easily retrieved by searching and filtering." .
SCR:013976 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Emerald Cloud Lab" ;
definition: "A production service resource which allows researchers to conduct experimental procedures through the cloud. Researchers can ship samples for an experiment to Emerald, then design the experiment(s) over the web using ECL software. Emerald then conducts the experiment(s) in an automated lab as specified, organizing the data into a database in the cloud. Samples are then shipped back to the lab (within a metter of days) and results can be analyze ECL's data analysis suite. Standard experiment types include but are not limited to: analytical balance readings, light microscopy, solid phase extraction, flourescence thermodynamics, RNA extraction/cDNA prep, and Western blot. Additional experiment types may be contributed." .
SCR:013977 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TetraScience" ;
definition: "A software provider which supplies researchers with software that enables remote monitoring and management of experiments. TetraScience provides software for managing lab cameras, sensors, electrical switches, adapters, and timers. Users are notified by text or email of lab proceedings and alerts." .
SCR:013978 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Transcriptic" ;
definition: "A web-based production service resource which provides access to remote life science research labs powered by custom robotic automation. The typical Transcriptic deployment happens in three stages. Transcriptic first executes a proof-of-concept (POC) to gather important reliability and sensitivity data that will inform the handling of the project and generate validation data for the customer. Once a POC has been successfully completed, w a four-to-six week pilot study is run where the customer provides real samples at small scale. Once the process is stable, scale up occurs and a larger number of samples can be processed. Users can access results, environmental monitoring data, and all workcell actions, as well as remotely monitor all environmental parameters taking place inside the enclosed, sterile automated lab (temperature, humidity and atmospheric composition)." .
SCR:013979 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biorepositories and Biospecimens Research Branch" ;
NIFRID:synonym "Biorepositories and Biospecimen Research Branch of the Cancer Diagnosis Program",
"Biorepositories and Biospecimen Research Branch of the CDP" ;
definition: "A portal to numerous programs and databases associated with the BBRB, a department of the NCI which aims to improve the collection and dissemination of high-quality biosecimens used in cancer research. The BBRB hopes to do this by improving the quality and consistency of human biospecimens and developing biorepository standards and facilitating Biospecimen Science studies that form the basis of evidence-based practices. The site provides acces to the Biospecimen Research Database, which contains peer-reviewed primary and review articles as well as standard operating procedures in human biospecimen science. The BBRB also directs programs such as the Biospecimen Pre-Analytical Variables Program and the Cancer Human Biobank (caHUB)." .
SCR:013980 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Duke Human Heart Repository" ;
definition: "A biomaterial supply resource which collects and disseminates human heart tissue. Samples include both failing and non-failing hearts, RNA/DNA analysis, tissue staining and immunofluorescence samples.The tissue that has been flash frozen and stored at -80˚C is acquired from distinct regions of the heart such as the LV free wall, septum, and valve leaflets. Individual sample sizes are typically 100-300mg for flash frozen tissues. The DHHR also serves as a resource for assay development, target identification, and sponsored research, capable of isolating cardiomyocytes from hearts and using them for in-vitro assays such as calcium handling, enzyme activity, signalling pathways and other biochemical research activities" .
SCR:013981 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CDE Tool" ;
NIFRID:synonym "CDEpack" ;
definition: "A software application which automatically packages up the code, data, and environment required to deploy and run Linux programs on other machines without any installation or configuration. Users can prepend any set of Linux commands with the \"cde\" binary, and CDE will run them and automatically package up all files accessed during execution. A package is a directory that can be compressed and delivered to any x86-Linux machine and contains all the files and environment variables required to run the original commands. After receiving the package, the user can run those same commands from within the package on any modern x86-Linux distro., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:013982 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dexy" ;
NIFRID:synonym "dexy" ;
definition: "A multi-purpose project automation tool written in Python which helps create technical documents. Dexy is a free-form literate documentation tool for writing any kind of technical document incorporating code. It provides a consistent interface to tools and scripts and keeps track of what to run, in which order, and with what parameters." .
SCR:013983 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GitLab" ;
definition: "A software application which provides Git repository management with fine grained access controls, code reviews, issue tracking, activity feeds, wikis, and continuous integration. Four different versions are available, each with different packaging pricing: Community edition, Enterprise edition, Continuous integration, and GitLab.com." .
SCR:013984 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IPython Notebook" ;
definition: "A web application and interactive computational environment where users can combine code execution, rich text, mathematics, plots, and rich media. IPython Notebook consists of two parts, the web application and plain texts. The Ipython Notebook web application is used for interactive authoring of literate computations, in which explanatory text, mathematics, computations, and rich media output may be combined. Input and output are stored in persistent cells that may be edited in-place. The plain text documents, called notebooks, record and distribute the results of the rich computations. Saved files in the notebook can be put under version control and shared with colleagues." .
SCR:013985 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mercurial" ;
definition: "A software application which provides distributed source control management for projects. Using Mercurial, each developer has a local copy of the project development history. Mercurialhas a user friendly interface, is written mostly in Python, and works independently of network access or a central server. Functionality can be increased using extensions, either by downloading them or writing new ones." .
SCR:013986 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rOpenSci" ;
definition: "A software repository which provides and builds open source tools for open science. rOpenSci provides packages that allow access to data repositories through the R statistical programming environment. R packages are grouped by what the tools do: acquire data, full-text of journal articles, altmetrics, data-publication, reproducibility, and data visualization." .
SCR:013987 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sweave" ;
definition: "NO LONGER AVAILABLE. Documented on May 19, 2020. Software R tool for creating dynamic reports and reproducible research using LaTeX. Enables embedding of R code within LaTeX documents to generate PDF file that includes narrative and analysis, graphics, code, and results of computations. Software tool for complete data analyses in LaTex documents." .
SCR:013988 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenomeCompiler" ;
definition: "A software platform which enables users to conduct genetic engineering with genomic manipulation tools (provided in the platform). Genome Compiler includes multiple DNA synthesis providers, lab facility services, and advanced bioinformatics tools and genetic repositories. Data can be imported from VectorNTI, SnapGene, ApE, Clone Manager, and others. The Gibson Assembly and Restriction Ligation methods are supported by Genome Compiler." .
SCR:013989 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kitware" ;
definition: "A software repository which provides open source software and technology for visualization, computer vision, medical imaging, data publishing, and quality software process solutions. Kitware also provides services such as creating customized applications for clients, porting their open-source tools to specialized computing platforms, and supporting their open-source software tools with documentation, professional consulting services, and software training." .
SCR:013990 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "machine learning open source software" ;
NIFRID:synonym "mloss.org" ;
NIFRID:abbrev "mloss" ;
definition: "A software repository which provides open source software for machine learning. Software entries include information such as author, license, data format, and programming language. The ultimate goal of mloss.org is to create a comprehensive open source machine learning environment where open source machine learning software can compete with comercial closed source solutions." .
SCR:013991 a owl:NamedIndividual ;
rdfs:label "Plotly" ;
definition: "Web application to collaboratively create interactive graphs and share them with others. JavaScript toolbox plotly.js enables users with little to no web development skills to make scientific charts." .
SCR:013992 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StatCrunch" ;
definition: "A web application which allows users to collect data, perform complex analyses, and generate results. Users can upload data sets from their computer or from the internet for data analysis and graph creation which can be saved, printed, and downloaded. More than 15,000 statistical data sets are available." .
SCR:013993 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "surf-incontext" ;
NIFRID:synonym "InContext" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented July 21, 2015. Web based software which allows users to navigate through RDF relations. Its features include: a light weight client side JavaScript solution using HTML5 and CSS3; the ability to hide and show detailed information of the center object; being tested in IE6+, Firefox 2+, Safari 2+, Chrome 3+; a \"More Info\" button which can be configured to be handled by the server, to allow specific page rendering options; the ability to run as a sandbox in memory: no conflicts with JQuery; and the option for the history manager to be switched off to enable the existing history manager of a website to take over." .
SCR:013994 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tableau Desktop" ;
definition: "A software application which utilizes drag-and-drop to create data visualizations of various formats. Users can collaborate on and discuss data and graphs that can be created from spreadsheets, databases, and big data sources. Three versions of Tableau Desktop are available: Tableau Server, Tableau Online, and Tableau Reader." .
SCR:013995 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Wakari" ;
definition: "A web application which performs Python data analysis. Users can create IPython notebooks to hold uploaded data and use various tools to describe, analyze, and visualize the data. Notebooks, data, and Anaconda environments can be shared as \"bundles\" with other users, who can edit and download them." .
SCR:013996 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WebPlotDigitizer" ;
NIFRID:synonym "WebPlotDigitizer Version 4.1",
"WebPlotDigitizer Version 4.2" ;
definition: "Web based tool to extract data from plots, images, and maps. HTML5 based online tool to extract numerical data from plot images. Used to reverse engineer images of data visualizations to extract underlying numerical data." .
SCR:013997 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WINGS" ;
NIFRID:synonym "Workflow Instance Generation and Specialization" ;
definition: "A software application which assists scientists with designing computational experiments. WINGS is a semantic workflow system which incorporates semantic constraints about datasets and workflow components into its workflow representations. The workflow system has an open modular design and can be easily integrated with other existing workflow systems and execution frameworks to extend them with semantic reasoning capabilities. WINGS also allows users to express high-level descriptions of their analysis goals, and assists them by automatically and systematically generating possible workflows that are consistent with that request. In cases where privacy or off-line use are important, WINGS can submit workflows in a scripted format for execution in the local host. It uses Pegasus or OODT as the execution engine for large-scale distributed workflow execution." .
SCR:013998 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Grant Forward" ;
definition: "A database of searchable grants and other funding opportunities for researchers and institutions. Grant Forward's Database contains more than 19,000 opportunities including 8,000+ federal and foundation opportunities each." .
SCR:013999 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pivot" ;
NIFRID:synonym "COS Pivot",
"ProQuest Pivot" ;
definition: "A database of funding opportunities for research administrators, research development professionals, and institutions. Researcher profiles are matched to current funding opportunities in the COS database using a proprietary algorithm. Users may also find funding opportunities by searching the database., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014000 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CitationStyles" ;
definition: "A database that contains different CSL citation styles. Styles can be searched by name, journal title, or by example and then viewed or installed. Users can also edit current styles and save them." .
SCR:014001 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EndNote" ;
definition: """A software application which helps users build a bibliography as they write formatted papers, manuscripts and other research-rich documents. Users can search multiple databases and collect PDFs as references for papers, then organize them within EndNote. Bibliographies and citations can be compiled within Microsoft Word using built-in tools. Papers are stored within an EndNote library and can be shared with colleagues.
""" .
SCR:014002 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Paperpile" ;
definition: "A web application which allows users to find reference papers and cite them during the authoring process. Paperpile utilizes Google and Chrome apps in order to directly download PDFs from various databases to Google Drive. If writing in Google Docs, users can search for certain reference papers and insert them into their draft as citations using the Google Drive Paperpile tool. Users can also collaborate on papers and add different citations." .
SCR:014003 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Asciidoctor" ;
NIFRID:synonym "Asciidoctor Project" ;
definition: "A software application which translates plain text written in AsciiDoc syntax to HTML5, DocBook 5, and other backends. Asciidoctor reads and parses text written in the AsciiDoc syntax, then feeds the parse tree into a set of built-in templates to produce HTML5. Users can write their own converter or provide Tilt-supported templates to customize the generated output or produce alternative formats. Asciidoctor also recognizes additional markup and formatting options, such as font-based icons and UI elements." .
SCR:014004 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Penflip" ;
definition: "A web application which allows users to collaboratively write documents and books with version control and revision history. Users can write in plain text or with Markdown and invite others to collaborate on their work. Math equations can be written with LaTeX or MathML with MathJax. eBooks can be downloaded and compiled into forms such as PDF, ePub, Word, and HTML . Works can be made public or kept private." .
SCR:014005 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Poetica" ;
definition: "A web-based authoring platform for Wordpress which allows users to write, edit, and track changes and revisions. Users can see all revisions and edits to an artcle and decide which ones may be kept or reverted. After creating an article, users can upload it directly to WordPress." .
SCR:014006 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Writefull" ;
definition: "A software application which provides feedback on writing, wording, and frequency of text by checking against databases of correct language. Users can highlight a chunk of text and use Writefull to see how often the specific text appears in different language databases. Writefull can also offer synonyms and suggestions for wording. Writefull is supported by numerous writing tools which include MS Word and Gmail." .
SCR:014007 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Peerage of Science" ;
definition: "A peer review service resource which allows researchers to dictate the time constraints in which their manuscripts are peer reviewed. Authors submit their manuscript to Peerage of Science before submitting to any journal and decide the deadlines for the four stages of the process (which are \"Submission and Reviews,\" \"Peer-review-of-peer-review,\" \"Manuscript revision upload or withdrawal for re-submission,\" and \"Final evaluation of the revised manuscript\"). Once submitted, any qualified, non-affiliated Peer can choose to review the manuscript. The peer reviews are peer reviewed and are also available to all subscribing journals with automated event tracking. Authors may accept a direct publishing offer from a subscribing journal, or choose to export the peer reviews to any journal of their choice." .
SCR:014008 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Collage Authoring Environment" ;
NIFRID:synonym "Collage Authoring Environment for Executable Publications" ;
definition: "A web application which provides the framework for collaborative preparation and publication of computational experiments that can back executable papers. The Collage environment enables researchers to embed chunks of executable code and data into scientific publications and facilitate repeated execution of such codes on underlying computing and data storage resources. Executable papers made with Collage can be embedded into a web site." .
SCR:014009 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Exec&Share" ;
NIFRID:synonym "Exec and Share",
"exec and share",
"exec&share" ;
definition: "A database and storage service resource that allows researchers to create a companion website, a website which allows people to run the computer codes associated with a scientific publication. Users upload or paste data, choose the value of the parameters, and click on the Exec&Share button. All calculations are done on a dedicated cloud computer and are automatically displayed to the user. It is also possible to only make the code downloadable, but not executable. In that case, users can download the code and run it on their own computer. Companion websites can currently be made from a code written in R, MATLAB©, C++, Fortran, and Rats." .
SCR:014010 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Google Charts" ;
definition: "A web application which allows users to create data visualizations using JavaScript that can be embedded in a web page. Users can load some Google Chart libraries, list the data to be charted, select options to customize their chart, and create a chart object with a personally chosen id. Then, in the web page, users create a with that id to display the Google Chart. Charts are customizable and interactive, and since they are rendered using HTML5/SVG technology, charts are cross-browser compatibility and cross platform portability to iPhones, iPads and Android." .
SCR:014011 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100010418" ;
rdfs:label "RunMyCode" ;
definition: "A database and storage service resource which allows users to create, view, share, and download information from companion websites. RunMyCode allows users to create companion websites for their scientific publications. Users can share and download computer code and data from companion websites made with RunMyCode. Any software and data format is compatible with RunMyCode." .
SCR:014012 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cofactor Science" ;
definition: "A training service which offers publishing advice and editorial support for scientific researchers. Cofactor Science offers workshops and editorial services on multiple levels of completeness and depth. Their Journal Selector tool selects journals from the Cofactor Science database that best fits a user's publishing criteria. Journals include Nature, PLOS One, PeerJ, and Genome Medicine." .
SCR:014013 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Edanz's journal advisor" ;
definition: "A training service which offers English editorial support for primarily non-native English speaking scientific researchers. Users answer a questionairre concerning their progress with their manuscript and Edanz suggests which of its services users should utilize. Services include Journal Advisor, English Editing, Expert Scientific Review, Cover Letter Development, Review Editing, Abstract Development, Response Letter Edit and Manuscript Check, Author-guided Rewriting, and Reviewer Recommendation. Edanz also offers training workshops and seminars for non-native English speakers." .
SCR:014014 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JournalReviewer" ;
definition: "A database which allows researchers to view and comment on the logistics of scientific journals' review processes. JournalReviewer collects and aggregates feedback from users who have submitted manuscripts to journals in order to provide information for others considering journal submissions. Statistics such as turnaround rate, review length and quality, journal recommendations, and desk reject plausabilities are compiled from commentors' ratings." .
SCR:014015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Journalysis" ;
definition: "A database where researchers can read and post reviews of publishing experiences with scientific journals. When writing comments, reviewers are adivsed to provide facts where possible, be specific, be honest, check the review, and offer constructive criticism when writing a negative report. Journalysis collates submitted reviews and data for each journal and provides useful summary information (metrics). Authors wanting to find out more about specific journals can search its databases and find the best journal for their next manuscript submission. Journals can use these reviews and metrics to demonstrate high publishing standards, or to improve standards where reviews may be negative." .
SCR:014016 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciRev" ;
definition: "A database where researchers and editors can read and post reviews and ratings of scientific journals and their publishing processes. Efficient journals get credits for their efforts to improve their review process and the way they handle manuscripts, while less efficient journals are stimulated to put energy in better organization. Researchers can search for a journal with a speedy review procedure and have their papers published earlier. Editors get the opportunity to compare their journal's performance with that of others and to provide information about their journal at our website." .
SCR:014017 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Academic Karma" ;
definition: "A peer review management system which encourages timely and high quality peer review by using a credit system. Reviewers complete reviews using a general webform on academickarma.org, and if that review is submited to an editor within ten days, the reviewer is awarded a certain amount of points (karma credits). The author and editor both receive the review. Editors can use Academic Karma to identify specialized reviewers for future reference. A reviewer's personal profile, which includes the amount of karma credits they've received, is connected to their ORCID account and publication record for an overview of the reviewer's work." .
SCR:014018 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Libre" ;
definition: "A repository which hosts and archives original and edited scientific papers. Scientists can post their academic manuscripts on Libre, where they can find reviewers who will formally evaluate the manuscripts. Evaluated works are posted alongside the original manuscript with reviewers' identities disclosed and the work they edit given its own DOI. Users can post additional updated versions of their work to Libre or send their papers to journals. Papers and reviews are rated by other scientists, and from these Libre creates holistic indeces listing the best rated writers and reviewers." .
SCR:014019 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Paper Critic" ;
definition: "A database that archives publications and allows users to review and critique them. Users can write comments for and rate submitted publications for references, originality, argumentation, and reliability. Papercritic also collects tweets and blog posts about published papers to add as reviews and comments. Researchers who submit their published work to PaperCritic can keep track of multiple types of feedback. All reviews must be submitted with full identity disclosure." .
SCR:014020 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Publons" ;
definition: "A service resource which allows peer reviewers to record and showcase the peer reviews they have completed, both those that led to publication and to rejection. Peer reviews can be recorded on Publons by forwarding review receipts from journals to the site. The merit of reviewers is accrued by pre- and post-publication peer review, discussion papers in Publons, and comments on or endorsment of the contributions of other reviewers. Reviewers may publish their own reviews so long as the reviewed manuscript is published and the review policies of the journal allow for it. Users can choose what personal information is displayed and easily export their profile in a format suitable for inclusion in promotion and funding applications." .
SCR:014021 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pubmed Commons" ;
definition: "A forum where authors who have published in PubMed may comment on any publication in PubMed. Members of PubMed Commons are not anonymous and must agree to certain terms and guidelines concerning appropriate and inapproriate comments." .
SCR:014022 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PLOS Article-Level Metrics" ;
NIFRID:synonym "PLOS Article Level Metrics" ;
NIFRID:abbrev "PLOS ALMs" ;
definition: "A portal which provides access to article level metrics, PLOS news, and videos and presentations. PLOS ALMs provides altmetrics for every article published in PLOS. Researchers can stay up-to-date with their published work and share information about the impact of their publications with collaborators, funders, institutions, and the research community at large." .
SCR:014023 a "Commercial",
owl:NamedIndividual ;
rdfs:label "Plum Analytics" ;
definition: "A service resource which provides researchers with metrics around usage, captures, social media, citations, and mentions from various online research outlets. Plum Analytics pulls information from reserch outlets such as journal articles, books, videos, presentations, conference proceedings, datasets, and source code. Plum Analytics also collects metrics for labs, departments, and other research groups. PlumX is a product of Plum Analytics." .
SCR:014024 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rank Rank Hypergeometric Overlap" ;
NIFRID:abbrev "RRHO" ;
definition: "Software tool that compares two gene expression signatures. Each signature is processed as a ranked list based on expression differences between two classes of samples. The signatures can be input either as raw expression data and sample and class labels, or as a preranked gene list." .
SCR:014026 a owl:NamedIndividual ;
rdfs:label "partec flomax" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Partec uses FloMax software on most cytometers, which produces FCS 3.0 compliant files. FloMax rescales the fluorescent data on the acquisition display without changing the stored values." .
SCR:014041 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReNaBi" ;
NIFRID:synonym "Réseau National des plates-formes Bioinformatiques" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVCE, documented August 11, 2015. It has been replaced by the Institut Fran�ais de Bioinformatic (IFB). A network built upon different bioinformatics platforms located within France to support the structuration of bioinformatics.The network provides access to resources such as databases, proteomics, transcriptomics, and structural bioinformatics for the life science and bioinformatics communities." .
SCR:014042 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100010539" ;
rdfs:label "ChEMBL" ;
NIFRID:synonym "Chembl",
"ChEMBL Database",
"ChEMBLdb" ;
definition: "Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database." .
SCR:014043 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cytobank" ;
NIFRID:synonym "Cytobank Inc." ;
definition: "A cloud-based platform which allows users to analyze, visualize, and archive multiparamter cytometry data for single-cell biology. Multiple single-cell data sets can be analyzed and visualized simultaneously with a variety of graphics, inlcuding Sunburst, SPADE, and viSNE. Users can store and back up related data such as protocols, microscopy images, and presentations and collaborate and share analysis and data sets with other Cytobank users. Cytobank also provides a variety of services and training sessions to assist with experiment workflow." .
SCR:014044 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioPSE" ;
NIFRID:synonym "SCIRun/BioPSE" ;
definition: "A simulation software package which hosts a collection of algorithms used to run bioelectric field simulations inside of SCIRun. The software provided in the package may be used for geometric modeling, simulation, and visualization for solving bioelectric field problems." .
SCR:014045 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MediaWiki" ;
definition: "A server-based software wiki package written in PHP. It is a powerful, scalable software deigned for high-traffic websites. MediaWiki uses PHP to process and display data stored in a database such as MySQL. When a user submits an edit to a page, MediaWiki writes it to the database without deleting the previous versions, allowing easy reversions. MediaWiki is able to manage image and multimedia files, as well, which are stored in the filesystem." .
SCR:014046 a owl:NamedIndividual ;
rdfs:label "Vanderbilt University Medical Center; Tennessee; USA" ;
NIFRID:synonym "Vanderbilt University Medical Center",
"VU Medical Center" ;
definition: "A public health center and research institution affiliated with Vanderbilt University." .
SCR:014047 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CHAVI-ID" ;
NIFRID:synonym "Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery",
"Scripps CHAVI-ID" ;
definition: "A consortium whose goal is to further HIV research and accelerate the development of a preventative HIV vaccine. Its main research target is to define immunogens and immunization regimens that induce sustained HIV cross-protective B cell and CD4+ T cell responses." .
SCR:014048 a NIFSTD:birnlex_2085,
owl:NamedIndividual ;
rdfs:label "McGill University Health Centre; Quebec; Canada" ;
NIFRID:synonym "McGill University Health Centre" ;
NIFRID:abbrev "MUHC" ;
definition: "A public health center and research institution affiliated with McGill University." .
SCR:014049 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.240473.6",
"ISNI: 0000 0004 0543 9901",
"Wikidata: Q7163263" ;
rdfs:label "Penn State Milton S. Hershey Medical Center; Pennsylvania; USA" ;
NIFRID:synonym "Milton S. Hershey Medical Center",
"Penn State Hershey",
"Penn State Hershey Medical Center",
"Penn State Milton S. Hershey Medical Center" ;
definition: "A public health center and research institution affiliated with Penn State." .
SCR:014050 a NIFSTD:birnlex_2085,
owl:NamedIndividual ;
rdfs:label "Montefiore Medical Center; New York; USA" ;
NIFRID:synonym "Montefiore Medical Center" ;
definition: "A public health center and research institution affiliated with the Albert Einstein College of Medicine." .
SCR:014051 a owl:NamedIndividual ;
rdfs:label "University of Kansas Medical Center; Kansas; USA" ;
NIFRID:synonym "KU Medical Center",
"University of Kansas Medical Center" ;
definition: "A public health center and research institution affiliated with the University Kansas." .
SCR:014052 a NIFSTD:birnlex_2085,
owl:NamedIndividual ;
rdfs:label "University of Rochester School of Medicine and Dentistry; New York; USA" ;
NIFRID:synonym "University of Rochester School of Medicine and Dentistry",
"URMC School of Medicine and Dentistry" ;
definition: "A public health center and research institution affiliated with the University of Rochester." .
SCR:014053 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100007482",
"GRID grid.215654.1",
"ISNI 0000 0001 2151 2636",
"Wikidata Q670897" ;
rdfs:label "Arizona State University; Arizona; USA" ;
NIFRID:synonym "Arizona State University" ;
NIFRID:abbrev "ASU" ;
definition: "Public research university located in Tempe, Arizona, USA." .
SCR:014054 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.7719.8",
"ISNI: 0000 0000 8700 1153" ;
rdfs:label "Spanish National Cancer Research Center" ;
NIFRID:synonym "Centro Nacional de Investigaciones Oncologicos" ;
NIFRID:abbrev "CNIO" ;
definition: "A cancer research center whose goal is to offer innovative technoligies to spur the develpment of new methods of diagnosing and treating cancer. CNIO contains a variety of programs of investigation, including a biotechnology program, a clinical research program, and a molecular oncology program. CNIO also provides services that allow researchers to access and use technologies and tools such as cytogenetics and monoclonal antibodies, and hosts a biomedical biobank." .
SCR:014055 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ClaiMaker" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, docmented August 17, 2015. A web-based system for individuals or communities to publish and contest ideas and arguments. ClaiMaker provides tools for constructing argument maps, and a server on which they can then be published, navigated, filtered, and visualized." .
SCR:014056 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Sage Analytica" ;
definition: "A commercial organization which offers consultation services and performs research in the fields of global health and infectious disease epidemiology. Sage Analytica provides services to help design research or project programs, interpret data, and communicate reults. Ad hoc assistance is also offered." .
SCR:014057 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agropolis Foundation" ;
definition: "A funding resource which promotes and supports high-level research and higher education in agricultural sciences and sustainable development research. The scientific work supported by the Foundation covers all aspects of the plant, from its genes to its environments, and concerns temperate, Mediterranean, and tropical climates. It supports research initiatives in: genetics and genomics, plant breeding, eco-physiology; integrated crop protection, plant pests and diseases, symbiotes, population ecology; agro-ecosystems, agri-environmental innovations, and resource management; agri-food systems, processing, and quality of food and non-food material; and innovation processes and social management of innovation." .
SCR:014058 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HIrisPlex system" ;
definition: "An interactive software tool that predicts hair and eye color based on genetics. The website includes both the IrisPlex system and the HIrisPlex system." .
SCR:014059 a owl:NamedIndividual ;
rdfs:label "UCSD Human Milk Biorepository " ;
NIFRID:synonym "UCSD Breast Milk Research Bank" ;
definition: "A biorepository which collects and distributes human breast milk samples to the research community, as well as a research initiative which aims to learn more about the benefits of human milk, how it influences infant and child health and development, and the extent to which medications and other substances can be found in human milk. Nursing mothers who choose to donate are asked to provide around 2 ounces of breast milk to be used for future research projects. Breast milk, which include disease-specific and normal breast milk samples, is stored in the research bank for approved projects. " .
SCR:014061 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KWIPPED" ;
definition: "An online rental equipment marketplace which connects renters to instrument suppliers from various industries. Renters can rent directly from suppliers or request quotes from different suppliers." .
SCR:014070 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Peptide Synthesis" ;
definition: "A reagent manufacturer which provides custom peptide APIs and custom peptide synthesis services. These products and services include high throughput peptide library/array synthesis, high quality bulk API peptides, bioactive catalog peptides, and cosmetic peptides." .
SCR:014071 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mouse Phylogeny Viewer" ;
definition: "A custom genome browser which provides detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains of mice (both classical and wild-derived). Users can select a region of the genome and a set of laboratory strains and/or wild caught mice. The region is selected by specifying the start (e.g. 31200000 or 31200K or 31.2M), and end of the interval and the chromosome (i.e, autosome number and X chromosome). Samples can be selected by name or by entire set. Data sets include information on subspecific origin, heterozygosity regions, and haplotype coloring, among others." .
SCR:014072 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MUGA" ;
definition: "MUGA genotypes for 458 samples from the developing CC lines described in the February 2012 issue of Genetics. Genotypes for 168 reference strains that include biological and technical replicates for the the 8 CC founder strains and their F1 crosses are also provided. Genotype calls are those reported by Illumina. All results are provided as comma separated files with one row per marker. Each marker is identified by a probe name and its genomic position in NCBI Build 37." .
SCR:014074 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_017630" ;
rdfs:label "HED Tags" ;
NIFRID:synonym "HED",
"HED tags",
"Hierarchical Event Descriptor",
"Hierarchical Event Descriptor Tags" ;
definition: "Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging." .
SCR:014075 a owl:NamedIndividual ;
rdfs:label "Graph Theory GLM (GTG) MATLAB Toolbox" ;
NIFRID:synonym "Graph Theory GLM",
"GTG MATLAB Toolbox" ;
NIFRID:abbrev "GTG" ;
definition: "A software application that calculates and runs a GLM on graph theory properties derived from brain networks. The GLM accepts continuous and categorical between-participant predictors and categorical within-participant predictors. Significance is determined via non-parametric permutation tests. Both fully connected and thresholded networks are tested. The toolbox also provides a data processing path for resting state and (block design) task fMRI data. Options for partialing nuisance signals include local and total white matter signal and PCA of white matter/ventricular signal. For task fMRI, connectivity matrices are computed for each condition by dividing up the timeseries. To compensate for HDR-related delay, the timeseries is deconvolved, allowing for division at the actual onset/offset times." .
SCR:014077 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mpex" ;
rdfs:label "Membrane Protein Explorer" ;
NIFRID:synonym "Membrane Protein Explorer (MPEx)" ;
NIFRID:abbrev "MPEx" ;
definition: "Software which predicts topology and other features of membrane proteins through hydropathy plots based on thermodynamic and biological principles. This version of MPEx uses two types of hydropathy scales: Experiment-based whole-residue partitioning scales and experiment-based biological partitioning scales. The whole-residue partitioning scales predict the transmembrane (TM) segments of membrane proteins of known structure. The biological scale utilizes current knowledge of the code the Sec61 translocon to identify TM segments. MPEx is a Java program (not a Java applet) deployed using Java Web Start, which is part of the Java Runtime Environment." .
SCR:014078 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciLifeLab" ;
NIFRID:synonym "Science for Life Laboratory" ;
definition: "A Swedish national center of research for molecular biosciences with a focus on health and environmental research. Researchers from Sweden can use both the technology and the expertise provided by SciLifeLab. Swedish researchers typically pay only for reagents and other consumables. Users from commercial companies pay the actual costs of the analyses performed. SciLifeLab also provides educational courses, seminars, and programs for PhD students, postdocs, investigators and other employees within all Swedish universities." .
SCR:014079 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LabWorm" ;
NIFRID:synonym "The LabWORM" ;
NIFRID:abbrev "LW" ;
definition: "A comprehensive index for locating and compiling bioinformatics and online science tools. Users can browse, rate, share and save various tools listed in the LabWorm repository. Resources contain a short description, a list of related sites, comments, a list of users who have shared and rated the resource, and the main site URL. Resources may be saved to a personal toolbox collection. User news feeds can be customized to include new scientific literature from journals of choice. Users who want to utilize LabWorm tools to improve their own website can access the alternate Developer site." .
SCR:014080 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Skyline" ;
definition: "Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences." .
SCR:014082 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "APERTURE" ;
NIFRID:synonym "Analysis of Patterns in Electrophysiological Recordings Toolbox with Utilities for REsearch" ;
definition: "A MATLAB-based toolbox for analysis of EEG, MEG, and ECoG data. APERTURE allows flexible multivariate analysis of ERPs and oscillatory activity and supports mass-univariate analysis with advanced statistical tests. Computations are accelerated using parallel computing supported through the MATLAB distributed computing toolbox. Examination of large, high-dimensional datasets is made simple through data visualization tools, including advanced plotting routines and generation of PDF reports with many figures." .
SCR:014083 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3dsvm" ;
definition: "A command-line program and plugin for AFNI built around SVM-Light. It performs support vector machine (SVM) analysis on fMRI data and runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X." .
SCR:014084 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "7T Structural MRI scans ATAG" ;
definition: "Data sets from the atlasing of the basal ganglia (ATAG) consortium, which provides ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. They include whole-brain and reduced field-of-view MP2RAGE and T2 scans with ultra-high resolution at a sub millimeter scale. The data can be used to develop new algorithms that help building new high-resolution atlases both in the basic and clinical neurosciences. They can also be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinsons disease and neuropsychiatric diseases." .
SCR:014085 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atlases of amygdala and hippocampus for pediatric populations" ;
definition: "Anatomical atlases constructed by Computational Anatomy of Johns Hopkins University for analysis of shape vectors. The atlases were generated from segmented hippocampal and amygdala structures in acquired populations of children, adolescents and young adults in neuroimaging studies of major depression disorder (MDD) at Washington University at St Louis." .
SCR:014086 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BetA-Series COrrelation" ;
NIFRID:synonym "Beta Series Correlation",
"Beta-Series Correlation" ;
NIFRID:abbrev "BASCO" ;
definition: "A software tool (with GUI) for investigating inter-regional functional connectivity in event-related fMRI data and allows the user to assess the modulation of functional connectivity by an experimental condition." .
SCR:014087 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bic-mni-models" ;
definition: "Anatomical brain template library which includes models from ICBM 2009 template.Number of unbiased non-linear averages of MNI152 database have been generated that combines attractions of both high-spatial resolution and signal-to-noise while not being subject to vagaries of any single brain. Procedure involved multiple iterations of process where, at each iteration, individual native MRIs were non-linearly fitted to the average template from previous iteration, beginning with MNI152 linear template." .
SCR:014088 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BiofilmQuant" ;
definition: "A semi-automated software tool for dental plaque biofilm quantification in quantitative light-induced fluorescence (QLF) images." .
SCR:014089 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biomag Discussion Group on Yahoo" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented December 11, 2015. A discussion group for those actively involved in research into, or applications of, biomagnetism and magnetoencephalography (MEG)." .
SCR:014090 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Entropy in space and time (BEst)" ;
NIFRID:synonym "Brain Entropy in space and time" ;
NIFRID:abbrev "BEst" ;
definition: "A toolbox that implements several EEG/MEG source localization techniques within the Maximum Entropy on the Mean (MEM) framework. These methods are particularly dedicated to estimate accurately the source of EEG/MEG generators together with their spatial extent along the cortical surface." .
SCR:014091 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brainnetome Atlas Viewer" ;
definition: "Brainnetome Atlas Viewer shows the anatomical connectivity-based parcellation results, including the maximum probabilistic maps, probabilistic maps and both the anatomical and functional connectivity patterns, which have been developed in Brainnetome Center, CASIA. The atlas is based on the analysis of connectional architecture with in vivo multi-modal MRI data." .
SCR:014092 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brainnetome fMRI toolkit" ;
NIFRID:abbrev "brat" ;
definition: "An fMRI toolkit which contains a large selection of complex network measures in Matlab GUI. These measures are increasingly used to characterize structural and functional brain connectivity datasets." .
SCR:014093 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BROCCOLI" ;
definition: "A software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. If BROCCOLI is running on a GPU, it can perform non-linear spatial normalization to a 1 mm brain template in 4-6 s and run a second level permutation test with 10,000 permutations." .
SCR:014094 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "C-MIND Database" ;
NIFRID:synonym "CMIND Database" ;
definition: "A database that contains brain imaging data collected on 3T MRI scanners from over 200 normally developing healthy children from birth to 18 years. The imaging data stored in the C-MIND database are DTI, HARDI, 3DT1W, 3DT2W, concurrent ASL-BOLD scans during two language tasks (Stories and Sentence-Picture Matching), Resting State fMRI and Baseline ASL scans." .
SCR:014095 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CARLsim: a GPU-accelerated SNN Simulator" ;
NIFRID:synonym "CARLsim" ;
definition: "A GPU-accelerated library for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail. CARLsim allows execution of networks of Izhikevich spiking neurons with realistic synaptic dynamics on both generic x86 CPUs and standard off-the-shelf GPUs. The simulator provides a PyNN-like programming interface in C/C++, which allows for details and parameters to be specified at the synapse, neuron, and network level." .
SCR:014096 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clinical Toolbox for SPM" ;
definition: "A clinical toolbox useful for normalizing data from individuals with brain injury and/or modalities popular in the clinical environment (CT). It supports either enantiomorphic or lesion-masked normalization. It can be either scripted or used with SPM's simple graphical interface." .
SCR:014097 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CMIND PY" ;
NIFRID:synonym "CMIND-PY" ;
definition: "A python toolbox for analysis of MRI images. It relies on calls to a number of widely tested algorithms from the FMRIB software library (FSL) and the advanced normalization tools (ANTS) to provide analysis of simultaneously acquired ASL/BOLD fMRI data. It was developed for analyzing the datasets collected as part of the Cincinnati MR Imaging of NeuroDevelopment (C-MIND) project." .
SCR:014098 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COST" ;
NIFRID:synonym "Connectivity Orientation Spherical distribution Tool" ;
definition: "A tool that implements a graph-based connectivity assessment method. This method uses a multi-directional graph propagation method applied to sampled orientation distribution function (ODF), which can be computed directly from the original diffusion imaging data." .
SCR:014099 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dcm2nii" ;
definition: "A tool for converting images from the complicated formats used by scanner manufacturers (DICOM, PAR/REC) to the NIfTI format used by various scientific tools. dcm2nii works for all modalities (CT, MRI, PET, SPECT) and sequence types." .
SCR:014100 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DICOMConvert" ;
NIFRID:synonym "Dicom Converter" ;
definition: "A DICOM image converter based on the ITK IO mechanism for reading and writing images. The formats currently supported by the converter are DICOM to: Analyze (*.hdr); MetaImage (*.mhd); Nrrd (*.nhdr, *.nrrd)." .
SCR:014101 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Displacement Field Viewer" ;
NIFRID:synonym "DFViewer" ;
definition: "A tool for visualizing displacement fields estimated in association with image registration. Based on the displacement vector field, a mesh is generated for visualization. The mesh can be color mapped with the jacobian determinant at each point for better localization of regions that undergo compression or expansion. Other key features include: view synchronization, adjustable mesh resolution, and conversion from deformation and HAMMER displacement fields." .
SCR:014102 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DTI denoising" ;
NIFRID:synonym "DWI Denoising Package",
"DWIdenoisingPackage" ;
definition: "A Matlab package which contains six denoising filters and a noise estimation method for 4D DWI. The package includes nonlocal means, local PCA and Oracle DCT methods. Based on image redundancy and/or sparsity, the proposed filters provide efficient denoising while preserving fine structures." .
SCR:014103 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Efficient Longitudinal Upload of Depression in the Elderly (ELUDE)" ;
NIFRID:synonym "Efficient Longitudinal Upload of Depression in the Elderly" ;
NIFRID:abbrev "ELUDE" ;
definition: "A longitudinal study of late-life depression at Duke University. There are 281 depressed subjects and 154 controls included. An MR scan of each subject was obtained every 2 years for up to 8 years (total of 1093 scans). Clinical assessments occurred more frequently and consists of a battery of psychiatric tests, including several depression-specific tests." .
SCR:014104 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Efficient Permutation Testing" ;
NIFRID:synonym "Speeding Up Permutation Testing in Neuroimaging" ;
definition: "A Matlab implementation for efficient permutation testing by using matrix completion." .
SCR:014106 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ERPwavelab" ;
definition: "A toolbox developed for multi-channel time-frequency analysis of event related activity of EEG and MEG data. It provides tools for data analysis and visualization of the most commonly used measures of time-frequency transformed event related data as well as data decomposition through non-negative matrix and multi-way (tensor) factorization. The decompositions provided can accommodate additional dimensions like subjects, conditions or repeats and as such they are perfected for group analysis. The toolbox enables tracking of phase locked activity from one channel-time-frequency instance to another as well as tools for artifact rejection in the time-frequency domain." .
SCR:014107 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ExPosition Packages" ;
NIFRID:synonym "CRAN Package Exposition" ;
definition: "An R package for descriptive (i.e., fixed-effects) multivariate analysis with singular value decomposition." .
SCR:014108 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fast T2 relaxation data analysis with stimulated echo correction and non-local spatial regularisation" ;
definition: "A tool which offers a fast algorithm for computing myelin maps from multiecho T2 relaxation data using parallel computation with multicore CPUs and graphics processing units (GPUs). The tool also provides non-local spatial regularization to produce more accurate and reliable myelin maps for noisy T2 relaxation data." .
SCR:014109 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Forward: Accurate finite element electromagnetic head models" ;
NIFRID:synonym "Forward" ;
definition: "A project which aims to simplify the preparation of accurate electromagnetic head models for EEG forward modeling. It builds off of the seminal SimNIBS tool for electromagnetic field modelling of transcranial magnetic stimulation and transcranial direct current stimulation. Human skin, skull, cerebrospinal fluid, and brain meshing pipelines have been rewritten with Nipype to ease access parallel processing and to allow users to start/stop the workflows. Conductivity tensor mapping from diffusion-weighted imaging is also included." .
SCR:014110 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "freesurfR" ;
definition: "A software package which contains tools for doing group analysis of FreeSurfer surface data using the general linear model in R (lm). Results can be rendered in FreeSurfer freeview or AFNI SUMA. Plots for selected vertices can be rendered in R with ggplot2." .
SCR:014111 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Functional Connectivity Analysis Tool for near-infrared spectroscopy data" ;
NIFRID:abbrev "FC-NIRS" ;
definition: "A functional connectivity analysis tool for near-infrared spectroscopy data. Its functions include preprocessing, quality control, FC calculation and network analysis." .
SCR:014112 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GazeReader" ;
definition: "A toolbox for a point-process derived GLM analysis of eye tracking data in Matlab. Data loading, model specification, fitting and review are organized into a sequence of events, each of which is handled by a separate module in the toolbox. The graphical interface was created using the Matlab graphical user interface development environment." .
SCR:014113 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gCCA" ;
definition: "A multivariate method for fMRI data analysis based on generalized canonical correlation analysis (gCCA) to maximize SPM reproducibility without adopting any model for the hemodynamic response or other temporal brain responses. For multiple subjects, gCCA explores a broad range of temporal responses in fMRI time-series space while maximizing the mean of correlation coefficients between the pair-wise spatial maps of the subjects." .
SCR:014114 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Generation R Pediatric MRI Resources" ;
definition: "An MRI resource which provides age-appropriate images of children. It includes an average, age-appropriate T1-weighted image, constructed from 130 typically developing children ages 6-to-10 and a set of 32 resting-state ICA components. These components were generated from 494 typically developing children, ages 6-to-10 years old, using the MELODIC ICA tool, bootstrapped with 1000 resamples. Both of these resources are described in detail in a manuscript submitted for publication." .
SCR:014115 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GIMME" ;
NIFRID:synonym "Group Iterative Multiple Model Estimation" ;
definition: "Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels." .
SCR:014116 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GLMdenoise: a fast, automated technique for denoising task-based fMRI data" ;
NIFRID:synonym "GLMdenoise" ;
definition: "A MATLAB toolbox for denoising task-based fMRI data. It derives noise regressors from voxels unrelated to the experimental paradigm and uses these regressors in a general linear model (GLM) analysis of the data. The technique only requires a design matrix indicating the experimental design and an fMRI dataset." .
SCR:014117 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity" ;
NIFRID:synonym "GraphVar" ;
definition: "A user-friendly graphical-user-interface (GUI)-based toolbox (MATLAB) for comprehensive graph-theoretical analyses of brain connectivity, including network construction and characterization, statistical analysis on network topological measures, and interactive exploration of results." .
SCR:014118 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HAMMER: Deformable Registration" ;
definition: "A software package which 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." .
SCR:014119 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HBM Hackathon" ;
NIFRID:synonym "OHBM Annual Meeting" ;
definition: "A multi-day event hosted by the Organization for Human Brain Mapping which features collaborative and open neuroscience projects in data analysis and methods development. Locations change annually." .
SCR:014120 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HDBIG" ;
NIFRID:synonym "High Dimensional Brain Imaging Genomics Toolkit" ;
definition: "A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association." .
SCR:014121 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "High-quality diffusion-weighted imaging of Parkinsons disease" ;
NIFRID:synonym "High quality DWI of Parkinsons Disease",
"High quality DWI of PD" ;
definition: "A project which contains data and analysis pipelines for a set of 53 subjects in a cross-sectional Parkinsons disease (PD) study. The dataset contains diffusion-weighted images (DWI) of 27 PD patients and 26 age, sex, and education-matched control subjects. The DWIs were acquired with 120 unique gradient directions, b=1000 and b=2500 s/mm2, and isotropic 2.4 mm3 voxels. The acquisition used a twice-refocused spin echo sequence in order to avoid distortions induced by eddy currents." .
SCR:014122 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MGA - Multimodal Glioma Analysis" ;
NIFRID:synonym "Multimodal Glioma Analysis" ;
NIFRID:abbrev "MGA" ;
definition: "An MRI preprocessing pipeline built with HOF (Heterogeneous Optimization Framework) methodology. MGA prepares neuro-oncology clinical imaging studies for scientific analysis in both longitudinal and cross-sectional studies. It works on DICOM images from a single MRI study and includes perfusion (DSC sequence based) analysis and DTI analysis. MGA spatially co-registers all study images to an atlas template and to a template image within the study." .
SCR:014123 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Image Synthesis Tools" ;
definition: "A collection of software tools developed for medical image synthesis of typically magnetic resonance (MR) brain images. The approaches have been used to create computed tomography (CT) images from MR input. The goal of image synthesis is to recover MR images with a desired optimal contrast for further processing by either registration or segmentation." .
SCR:014124 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Imeka Tractography Service" ;
definition: "A diffusion MRI service that handles the processing of diffusion data from raw data to structural connectivity. They provide high angular resolution (HARDI) reconstruction from DTI data with at least 20 gradient directions acquisitions." .
SCR:014125 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "International Imaging Genetics Conference" ;
definition: "An international symposium held initially to assess the new technology and innovation in the various established fields of genetics and imaging, and to facilitate the transdisciplinary fusion needed to optimize the development of the emerging field of Imaging Genetics. This annual conference features presentations from investigators world-wide and places emphasis on facilitating in-depth discussions among the participants and presenters." .
SCR:014127 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0" ;
NIFRID:synonym "Intrinsic Unscented Kalman Filter Tractography Software",
"Intrinsic Unscented Kalman Filter Tractography Software v1.0",
"IUKF Tractography Software",
"IUKF Tractography Software v1.0" ;
definition: "A tractography algorithm for HARDI which provides a relatively accurate and efficient fiber tracking mechanism by reconstructing a bi-tensor model for underlying signals and exploiting intrinsic operations on the space of diffusion tensors. Given HARDI data sets, IUKF is capable of tracking in the presence of complex local geometries, such as crossing and kissing fibers. Reconstruction is only performed at the voxels along estimated fibers." .
SCR:014128 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Iterative dual-regression with sparse prior" ;
definition: "Software which aims to better estimate the neuronal activation of an individual using the results of an independent component analysis (ICA) method applied to a temporally concatenated group of functional magnetic resonance imaging (fMRI) data (i.e., Tc-GICA method). This approach employs iterative LS solutions to refine both the individual SPs and TCs with an additional a priori assumption of sparseness in the SPs (i.e., minimally overlapping SPs) based on L(1)-norm minimization." .
SCR:014131 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KWScene: MRML-based Atlas and Scene Builder/Reader/Writer" ;
NIFRID:synonym "KWScene",
"KWScene: MRML-based Atlas and Scene Builder/Reader/Writer collaboration with Kitware" ;
definition: "ITK-based processing and 3D Slicer scene management in ParaView. It is meant to broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The effort is focused on developing ParaView plug-ins for managing VTK structures from 3D Slicer MRML scenes and encapsulating ITK filters for deployment in ParaView." .
SCR:014132 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "L-Neuron" ;
NIFRID:synonym "L Neuron" ;
definition: "A program which creates anatomically realistic virtual neurons using the formalism of the Lyndenmayer systems to implement sets of neuroanatomical rules discovered by several research groups. The program algorithms read in experimental data - in the form of statistical distributions - to generate virtual structures. L-Neuron samples the values of the parameters within these statistical distributions in a stochastic (random) fashion during dendritic growth." .
SCR:014133 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Laplace Beltrami Filter on QuadEdge Meshes" ;
NIFRID:synonym "Laplace-Beltrami Filter on QuadEdge Meshes" ;
definition: "A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface." .
SCR:014134 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "libSBML" ;
NIFRID:synonym "Library for Systems Biology Markup Language",
"Systems Biology Markup Language Library" ;
definition: "A programming library to help users read, write, manipulate, translate, and validate SBML files and data streams. Specifically, it is a library that users may embed into their own applications." .
SCR:014135 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lightweight Data Pipeline" ;
definition: "A lightweight framework for setting up dependency-driven processing pipelines. The tool is essentially a configurable shell script (sh/bash), which can be included in other scripts and primarily provides a small number of utility functions for dependency checking and NFS-safe file locking for cluster processing." .
SCR:014136 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Longitudinal MS Lesion Imaging Archive" ;
NIFRID:synonym "Longitudinal MS Lesion Segmentation Challenge" ;
definition: "The Longitudinal MS Lesion Imaging Archive provides Training data consisting of longitudinal images from five patients and Testing data consisting of 15 patients. Each longitudinal dataset includes T1-weighted, T2-weighted, PD-weighted, and T2-weighted FLAIR MRI with 3-5 time points acquired on a 3T MR scanner. T1-weighted images have approximately a 1mm cubic voxel resolution, while the other scans are 1mm in plane with 3mm sections. Accounting for the multiple time points, this constitutes approximately 80 individual data sets. The Training data contains manual segmentations of the MS lesions from two different raters for each of the time points provided." .
SCR:014137 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MARS (Multi-Atlas Robust Segmentation)" ;
definition: "Software which provides the automatic solutions for efficent segmentation/labeling anatomcial structures from medical images. It has integrated several multi-atlas based segmentation methods such as majority voting, local weighted voting, and non-local patch based segmentation methods." .
SCR:014138 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "minc-toolkit" ;
NIFRID:synonym "MINC Tool Kit" ;
definition: "A set of MINC-based image processing tools packaged together. It includes MINC, N3, BICPL, EBKTS, ANIMAL, INSECT, BEaST, Register, Display, and xdisp." .
SCR:014139 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "minc-toolkit-testsuite" ;
definition: "Sample data in MINC format and collection of scripts to verify correct installation of minc-toolkit." .
SCR:014140 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MISST - Microstructure Imaging Sequence Simulation ToolBox" ;
NIFRID:synonym "Microstructure Imaging Sequence Simulation Toolbox" ;
NIFRID:abbrev "MISST" ;
definition: "A practical diffusion MRI simulator for development, testing, and optimisation of novel MR pulse sequences for microstructure imaging. MISST is based on a matrix method approach and simulates the signal for a large variety of pulse sequences and tissue models. It is designed for diffusion MRI researchers who are interested in understanding and developing diffusion pulse sequences for imaging microstructure." .
SCR:014142 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRIcroS" ;
definition: "A Matlab-based tool for computational neuroscience-based analysis and data visualization. Its features include: surface mesh visualization in PLY, PIAL, NV, STL,VTK, and GIFTI formats; conversion of NIfTI voxel images to surface meshes and saving as PLY or VTK; track (TRK files) visualization; connectome data (BrainNet Viewer .node and .edge files) visualization; intuitive GUI; that availability of all functions available in the GUI through scripting (automated scripts can be created); and exporting of rendered image as bitmap." .
SCR:014143 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multivariate General Linear Models (MGLM) on Riemannian Manifolds" ;
NIFRID:synonym "MGLM on Riemannian Manifolds",
"Multivariate General Linear Models on Riemannian Manifolds" ;
definition: "A statistical analysis tool for manifold-valued data. The SPD manifold for diffusion tensor images (DTI) and the Hilbert unit sphere for square root representation of orientation distribution functions (ODF) can be used." .
SCR:014144 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neoseg" ;
definition: "A tool which computes an automatic segmentation of neonatal brain MRI. It uses a registered probabilistic brain atlas to select training samples and to be used as a spatial prior." .
SCR:014145 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeoSegPipeline" ;
definition: "This tool allows segmenting neonate brain MRI using a subject-specific atlas. It generates a subject-specific atlas based on an atlas population and some diffusion images of the subject to segment. Then a single atlas method is run with this atlas to obtain results." .
SCR:014146 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuriteTracer" ;
definition: "A set of ImageJ plugins for fully automated measurement of neurite outgrowth in fluorescence microscopy images of cultured neurons. The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length. NeuriteTracer accurately measures neurite outgrowth from cerebellar, DRG and hippocampal neurons." .
SCR:014147 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroElf" ;
definition: "A Matlab-based toolbox initially created for reading, writing, and processing of BrainVoyager (QX) files in Matlab." .
SCR:014148 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuron-C" ;
NIFRID:synonym "Neuron C Neural Simulation Language",
"NeuronC",
"NeuronC Neural Simulation Language" ;
definition: "A simulation language for modeling biophysically realistic neural circuits (1 to 10,000 neurons) and simulating physiology experiments on it. Programs for plotting and displaying data are included." .
SCR:014149 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH Pediatric MRI Data Repository" ;
NIFRID:synonym "NIH MRI Study of Normal Brain Development Pediatric MRI Data Repository",
"Pediatric MRI Data Repository" ;
NIFRID:abbrev "NIHPD" ;
definition: "A database which contains longitudinal structural MRIs, spectroscopy, DTI and correlated clinical/behavioral data from approximately 500 healthy, normally developing children, ages newborn to young adult." .
SCR:014150 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH-CIDI Lung Segmentation Tool" ;
NIFRID:synonym "CIDI Lung Seg",
"CIDI-lung-seg" ;
definition: "A segmentation tool for the segmentation of a lung from CT images. The sofware can be run in two modes: fully automatic and semi-automatic with manual seeding by the user. The software also allows the user to perform basic filtering operations and manual correction to the segmentation. The VTK-based rendering implementation, along with option to view in axial, coronal, and sagittal, provides the user with better visualization of the segmented lung." .
SCR:014151 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering" ;
definition: "A MATLAB GUI for segmenting and quantifying PET images with multi-focal and diffuse uptakes. It imports a PET image and allows the user to draw region of interests (ROIs) in 2D or 3D to roughly separate the object of interest from the background. The areas are then segmented using a PET image segmentation method based on Affinity Propagation clustering to cluster the image intensities into meaningful groups. For quantification, the Standardized Uptake Value measurements of the binary or the user defined ROI are SUVmax, SUVmean, and Volume (mm^3) and can be exported into an excel sheet." .
SCR:014152 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NiiStat" ;
definition: "A set of Matlab scripts for analyzing neuroimaging data from clinical populations. The NiiStat tools are designed to correlate behavioral data (task performance) with brain imaging data." .
SCR:014153 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Northwestern University Schizophrenia Data and Software Tool (NUSDAST)" ;
NIFRID:synonym "Northwestern University Schizophrenia Data and Software Tool" ;
NIFRID:abbrev "NUSDAT" ;
definition: "A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data." .
SCR:014154 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Notion ResearchPACS" ;
definition: "Standalone software designed to be used by radiology researchers for storage and anonymization of research images." .
SCR:014155 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NTU-DSI-122: a DSI template in ICBM-152 space" ;
definition: "A diffusion spectrum imaging (DSI) template constructed in the standard ICBM-152 space from 122 healthy adults. The template was built through incorporating the macroscopic anatomical information using high-resolution T1-weighted images and the microscopic structural information obtained from DSI datasets, rendering it to achieve a high anatomical matching to the ICBM-152 space. This template can serve as a representative DSI dataset for a healthy adult population. It is released in its original DWI format." .
SCR:014156 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenViBE" ;
definition: "A multi-platform software dedicated to designing, testing and using brain-computer interfaces (BCI). OpenViBE is a software for real-time neurosciences that can be used to acquire, filter, process, classify and visualize brain signals in real time." .
SCR:014157 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenWalnut" ;
definition: "Open source tool for multi-modal medical and brain data visualization. It is a tool for the scientific user and a powerful framework for the visualization researcher. It is written in Standard C++ and uses a number of portable libraries (e.g. Qt, Boost and OpenSceneGraph). It runs on common GNU/Linux operating systems, Mac OSX and Windows." .
SCR:014158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Orientation Distribution Function in Constant Solid Angle (CSA-ODF)" ;
NIFRID:synonym "Orientation Distribution Function in Constant Solid Angle" ;
NIFRID:abbrev "CSA ODF" ;
definition: "A Matlab toolbox that computes the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) for diffusion-weighted MRI." .
SCR:014159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Parallel Stochastic Ion Channel Simulator" ;
NIFRID:abbrev "PSICS" ;
definition: "Software for efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes. It computes the behavior of neurons taking account of the stochastic nature of ion channel gating and the detailed positions of the channels themselves. It is designed as a complement for existing tools." .
SCR:014160 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Parkinsons Disease Discovery Database" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented Jan. 5, 2016. Tools will be available for biomedical data mining and visualization as well as linkages to Google Maps and other online resources." .
SCR:014161 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Prediction and Diagnosis for Depression and Schizophrenia" ;
NIFRID:synonym "UAIS Lab of Lanzhou University" ;
definition: "A topical portal for the UAIS Lab of Lanzhou University which researches predicting depression and schizophrenia based on demographics and physiological information (EEG, ERPs, Genetics, MRI, fMRI, etc.). It also researches wearable bio-signal sensors and antennas, bio-signal processing, speech analysis, pervasive mental health, psycho-physiological computing, bioinformatics and multimodal data fusion and modeling." .
SCR:014162 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Preprocessed Connectomes Project" ;
NIFRID:abbrev "PCP" ;
definition: "A project which systematically preprocess the data from the 1000 Functional Connectomes Project (FCP) and International Neuroimaging Data-sharing Initiative (INDI) and openly share the results. Data is currently hosted in an Amazon Web Services Public S3 Bucket and at NITRC." .
SCR:014163 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data" ;
definition: "An implementation of standard PCA algorithms for use on scalar or vector data sets. Kernel PCA is implemented in this class, where the data sets are scalar or vector valued functions assigned at each of the points in a PointSet. A Gaussian Distance Kernel class is provided with the PCA class." .
SCR:014164 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ruby NIfTI" ;
definition: "A library for handling NIfTI data in the Ruby programming language. Ruby NIfTI supports basic read and write access to NIfTI files, including basic and extended header information and image information. It doesn't attempt to touch the image data but it does provide access to qform and sform orientation matrices. It also provides a nice interface to get at NIfTI info from within Ruby." .
SCR:014165 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCORE" ;
definition: "A collection of methods for comparing the performance of different image algorithms. These methods generate quantitative scores that measure divergences to a standard." .
SCR:014166 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SFMProject" ;
definition: "Structure from motion algorithms repository. Common interface for various sfm algorithms." .
SCR:014167 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ShapePopulationViewer" ;
definition: "Software that allows users to dynamically interact with multiple surfaces simultaneously. It is very useful for visualisation and comparison of 3D surfaces by also displaying their scalars or vectors attributes stored in the points, and allowing the user to simply modify the colormap. ShapePopulationViewer is available as an extension of 3D Slicer." .
SCR:014168 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Simulated DW-MRI Brain Data Sets for Quantitative Evaluation of Estimated Fiber Orientations" ;
definition: "This resource provides simulated DW-MRI brain images and quantitative tools for evaluating the performance of diffusion analysis methods in terms of fiber orientation estimation and false-positive/-negative fiber rates, which are of fundamental importance to tractography based studies. DW data was generated using a multi-tensor model at SNRs of 9, 18 and 36, for sets of 20, 30, 40, 60, 90 and 120 gradient directions. For each combination of SNR and gradient direction set, 10 realizations of data are provided. All data is simulated with a diffusion-weighting of b=1000, as is common for clinical acquisitions." .
SCR:014169 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPIKECOR: fMRI tool for automated correction of head motion spikes" ;
definition: "This algorithm corrects for spikes in fMRI data, typically caused by abrupt head motion during scanning. It identifies outliers using Principal Component Analysis (PCA) in a sliding time-window; it is sensitive to global motion artifact, and stable against non-stationary signal changes." .
SCR:014170 a owl:NamedIndividual ;
rdfs:label "Spinal Cord Toolbox" ;
definition: "A comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord. The toolbox includes a template and several atlases, along with state-of-the-art methods to register any data to the template. It also includes useful scripts for data preprocessing: extraction of centerline, automatic segmentation, slice-wise motion correction, etc." .
SCR:014171 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stark Cross-Sectional Aging" ;
definition: "Behavioral and imaging data from about 120 participants aged 18-89. Data were collected as part of a grant to use high-resolution imaging and advanced behavioral tasks to understand how aging affects the hippocampus and how this is related to age-related cognitive decline. The full dataset includes traditional neuropsycholgical measures, hippocampal-specific behavioral measures, whole-brain DTI, high-resolution DTI of the medial temporal lobes, and structural MRI including segmentation of grey/white/CSF, of cortical regions and of hippocampal subfields." .
SCR:014172 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Coactivation Map" ;
definition: "The Brain Coactivation Map describes all the coactivation networks in the human brain based on the meta-analysis of more than 5,400 neuroimaging articles (from NeuroSynth) containing more than 16,000 individual experiments. The map can be browsed interactively (CoactivationMap.app on GitHub) or queried from a shell using a command line tool (cmtool on GitHub)." .
SCR:014173 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Striatal Subregional VOImap" ;
definition: "An atlas intended to provide accurate data in terms of specific uptake location to make the BP quantitation. The VOIs were manually drawn with software Analyze 9.0 (Mayo Clinic) in 18F-DOPA brain image after spatial normalization with a 18F-DOPA Template. Each striatum was divided into 6 sub-regions: ventral caudate, anterior dorsal caudate, posterior dorsal caudate, ventral putamen, anterior dorsal putamen and posterior dorsal putamen." .
SCR:014174 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Topographica" ;
definition: "A software package for computational modeling of neural maps developed as part of the NIMH Human Brain Project. Topographica focuses on the large-scale structure and function that is visible only when many thousands of such neurons are connected into topographic maps containing millions of connections. The software package provides a general-purpose framework for building models at this level, at an appropriate level of detail and complexity, as determined by the available computing power, phenomena of interest, and amount of biological data available for validation. It is intended to complement low-level neuron simulators that are available, such as General Neural Simulation System and NEURON." .
SCR:014175 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Turbo-BrainVoyager" ;
definition: "A software package for the real-time analysis and dynamic visualization of functional magnetic resonance imaging data sets. It allows users to observe the working brain \"online\" by incrementally computing statistical maps as contrasts of a General Linear Model (GLM). The program also performs real-time pre-processing, including 3D motion correction, spatial Gaussian smoothing and temporal filtering (drift removal)." .
SCR:014176 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CRL Unbiased and Deformable Spatiotemporal Atlas of the Fetal Brain" ;
NIFRID:synonym "Computational Radiology Laboratory Unbiased and Deformable Spatiotemporal Atlas of the Fetal Brain" ;
definition: "An atlas of of the fetal brain from MRI of normal fetuses scanned prenatally generated using a mathematical framework. The atlas shows the inter-subject anatomic variability of the fetal brain over the fetal brain growth period and is currently available between 27 weeks gestational age to 35 weeks. It has been constructed following an unbiased minimum distance template estimation approach which utilizes symmetric diffeomorphic deformation and the cross-correlation (CC) similarity metric integrated with kernel regression in age." .
SCR:014177 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UNC-Wisconsin Neurodevelopment Rhesus MRI Database" ;
definition: "A macaque brain MRI database characterizing the normal postnatal macaque brain development. This longitudinal primate database was acquired from a cohort of healthy macaque monkeys ranging from a few week olds up to 3-year-old adolescents. Each scan consists of structural (both T1 and T2) and diffusion MRI." .
SCR:014178 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX)" ;
NIFRID:synonym "Virtual Electrode Recording Tool for EXtracellular potentials" ;
NIFRID:abbrev "VERTEX" ;
definition: "A Matlab tool for simulating extracellular potential recordings in spiking neural network (SNN) models. VERTEX is designed to facilitate the simulation of extracellular potentials generated by activity in SNNs; in particular, spatially-organised networks containing thousands or hundreds of thousands of neurons. It has a limited scope but has a simpler user interface so that a simulation can be specified simply by setting some parameters and run using a few function calls." .
SCR:014180 a owl:NamedIndividual ;
rdfs:label "Wisconsin Cortical Thickness Analysis (CTA) Toolbox" ;
definition: "A Matlab tool to perform statistical analysis on cortical thickness signals on brain surfaces obtained from Freesurfer. It is used for multi-resolutional analysis of such cortical thickness signals and detecting group differences. It is based on the Spectral Graph Wavelet Transform (SGWT) toolbox and provides plug and play methods for deriving Wavelet Multiscale Descriptor (WMD), cortical thickness smoothing using SGWT, Multivariate General Linear Model (MGLM), and False Discovery Rate (FDR)." .
SCR:014181 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XFSL: An FSL toolbox" ;
NIFRID:abbrev "XFSL" ;
definition: "A set of many useful automation scripts to facilitate the neuroimaging data analysis process. It contains BASH scripts for MRI data management, FSL automation and web application." .
SCR:014182 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XNBC" ;
definition: "A full featured and extensible application which simulates biological neural networks using graphic tools which edit neurons and networks, run the simulation and analyze results. It is written in C and runs on Unix and Windows. It is specifically targeted for neuroscientists who are less experienced with computer programming." .
SCR:014183 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "YMDTI: Diffusion Tensor Images of Healthy Young Males" ;
NIFRID:synonym "Diffusion Tensor Images of Healthy Young Males" ;
NIFRID:abbrev "YMDTI" ;
definition: "A dataset which contains diffusion tensor images of 93 healthy, young male subjects." .
SCR:014184 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BraTumIA (Brain Tumor Image Analysis)" ;
NIFRID:synonym "BraTumIA" ;
definition: "Segmentation software for multimodal image analysis of brain tumor studies. It performs volumetric segmentation of healthy and tumor tissues by employing multispectral MRI sequences. Segmented tissues include Gray Matter, White Matter, Cerebrospinal Fluid, necrotic core, edema, non-enhancing tumor and enhancing tumor." .
SCR:014185 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CAWorks" ;
NIFRID:synonym "Computational Anatomy Works" ;
definition: "A software application developed to support computational anatomy and shape analysis. The capabilities of CAWorks include: interactive landmark placement to create segmentation (mask) of desired region of interest; specialized landmark placement plugins for subcortical structures such as hippocampus and amygdala; support for multiple Medical Imaging data formats, such as Nifti, Analyze, Freesurfer, DICOM and landmark data; Quadra Planar view visualization; and shape analysis plugin modules, such as Large Deformation Diffeomorphic Metric Mapping (LDDMM). Specific plugins are available for landmark placement of the hippocampus, amygdala and entorhinal cortex regions, as well as a browser plugin module for the Extensible Neuroimaging Archive Toolkit." .
SCR:014186 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND)" ;
NIFRID:abbrev "FRIEND" ;
definition: "A GUI-based software for real-time fMRI processing, multivoxel pattern decoding and neurofeedback. The package integrates routines for image preprocessing in real-time, ROI-based feedback and brain decoding-based feedback using the FSL and libSVM libraries. Users can create or employ pre-specified visual stimuli for neurofeedback experiments. FRIEND can be used as Windows standalone software or as a multiplatform toolbox (called FRIEND Engine)." .
SCR:014187 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Functional Mixed Processes Models" ;
NIFRID:abbrev "FMPM" ;
definition: "A tool which implements a functional analysis pipeline for the joint analysis of longitudinally measured functional data and clinical data (for example age, gender and disease status). FMPM consists of a functional mixed effects model for characterizing the association of functional response with covariates of interest by incorporating complex spatial–temporal correlation structure, an efficient method for spatially smoothing varying coefficient functions, an estimation method for estimating the spatial– temporal correlation structure, a test procedure with local and global test statistics for testing hypotheses of interest associated with functional response, and a simultaneous confidence band for quantifying the uncertainty in the estimated coefficient functions." .
SCR:014188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Papaya" ;
definition: "A pure JavaScript medical research image viewer, compatible across a range of popular web browsers. The orthogonal viewer supports NIFTI and DICOM files, overlays and atlas labels. It requires Firefox (7+), Chrome (7+), Safari (6+), MobileSafari (iOS 6+), or IE (10+)." .
SCR:014189 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sperm Stem Cell Libraries for Biological Research" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 18,2023. Stock center of Knockout and Transgenic Rats at UT Southwestern in Dallas." .
SCR:014191 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioXpress" ;
definition: "BioXpress is a gene expression and cancer association database in which the expression levels are mapped to genes using RNA-seq data obtained from The Cancer Genome Atlas, International Cancer Genome Consortium, Expression Atlas and publications. BioXpress can be searched by gene name or cancer type. To search the database by gene name, select the appropriate identifier type from the dropdown menu and type in the corresponding identifier in the adjacent text box. The results are computed and presented to the user with information such as variable expression levels and tumor expression. To search by cancer type, select the desired type from the dropdown menu, such as \"Cancer Type\", \"Significant\", \"Expression\", \"Adjusted p-value\" and \"p-value\". Results are shown in a graph displaying the top 10 differentially expressed genes for the specified cancer type in terms of the frequency of significant altered expression between the tumor and normal pairs." .
SCR:014193 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Primary Antibodies" ;
NIFRID:synonym "Primary Antibodies - Creative Diagnostics" ;
definition: "An antibody manufacture service from the commercial organization Creative Diagnostics which provides monoclonal and polyclonal matched antibody pairs, tag antibodies, phospho-specific antibodies, anti-idiotypic antibodies, cardiac markers antibodies, and blood group antibodies." .
SCR:014194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IonChannelGenealogy" ;
NIFRID:synonym "ICGenealogy" ;
NIFRID:abbrev "ICG" ;
definition: "A database that provides a comprehensive and quantitative assay of ion channel models currently available in the neuroscientific modeling community. Specifically, it contains analyses of the ion channel models from NEURON. The database quantifies the similarity in kinetics between models using a series of standardized voltage clamp simulation protocols and subsequent cluster analysis. Citation links and duplications of channels, along with similarity of kinetics between channel models, are combined into genealogical trees and dendrograms that are searchable through the ICG web interface. ICG also experimentally recorded current traces and provides tools for uploading new channel models." .
SCR:014195 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Advanced Connectivity Analysis (ACA)" ;
NIFRID:synonym "Advanced Connectivity Analysis",
"Advanced Connectivity Analysis (ACA): a large scale functional connectivity data mining environment" ;
NIFRID:abbrev "ACA" ;
definition: "A large scale functional connectivity data mining software package which enables large-scale seed-based analysis and brain-behavior analysis. It can examine a large number of seed regions with minimal user input. ACA has a brain-behavior analysis component to delineate associations among imaging biomarkers and one or more behavioral variables." .
SCR:014196 a owl:NamedIndividual ;
NIFRID:synonym "Voxel Based Morphometry Toolbox" .
SCR:014199 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SciRes_000161",
"SCR_002078",
"SCR_014234",
"SCR_014298" ;
rdfs:label "Adobe Photoshop" ;
NIFRID:synonym "Adobe Photoshop CC",
"Adobe Photoshop CS",
"Photoshop" ;
definition: "Software for image processing, analysis, and editing. The software includes features such as touch capabilities, a customizable toolbar, 2D and 3D image merging, and Cloud access and options." .
SCR:014201 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hFigures" ;
definition: "A Javascript library that aims to deliver a starting point for interactive health data visualization. Examples and demos are available on the site. hFigures was built with d3.js and a copy of the library is included in this repository. All rights and license terms apply to the d3.js library accordingly." .
SCR:014206 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CCHIPS" ;
NIFRID:synonym "Cincinnati Childrens Hospital Image Processing Software" ;
definition: "Research software used for post-processing of functional MRI, diffusion MRI, spectroscopy, and perfusion MRI data. It is written in Interactive Data Language." .
SCR:014209 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CWRU In Vivo Animal Facilities" ;
NIFRID:synonym "Case Western Reserve University In Vivo Animal Core Facilities",
"CWRU In Vivo Animal Core Facilities" ;
definition: "A set of core facilities of Case Western Reserve University School of Medicine which allows users to create and analyze in vivo animal models. The various facilities provide animal care, transgenic models, imaging, irradiation, and phenotyping for research concerning such topics as cancer, metabolic processes, and behavior. In vivo animals provided include mice, zebrafish, and rodents." .
SCR:014210 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Image Lab Software" ;
definition: "Imaging software used to acquire and analyze images from specific Bio-Rad imaging systems. Users can analyze gel or blot features, capture optimized image data, and generate a report of the data. Image Lab software exclusively runs on the Gel Doc EZ imager, Gel Doc XR+ imaging system, ChemiDo MP, ChemiDoc XRS+ imaging systems, Criterion Stain Free imager, and the GS-900calibrated densitometer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014212 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_015636" ;
rdfs:label "Origin" ;
NIFRID:synonym "OriginPro" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing." .
SCR:014213 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "STATISTICA " ;
NIFRID:synonym "Statistica",
"Statistica 10",
"STATISTICS Product Index" ;
definition: "Analytics platform with various sub platforms, each with specific performance capabilities for tasks such as data analysis, data management, data visualization, and data mining procedures." .
SCR:014214 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Thalamus in 3D Stereotactic Coordinates" ;
NIFRID:synonym "human motor thalamus" ;
definition: "A research tool for clinical and experimental neuroscience, which provides images of human thalamus in the stereotactic planes of the coordinate system based on intercommissural line. Images include histological sagittal sections, sagittal maps, coronal maps, horizontal maps, and MRI images all from the same brain. The website also provides materials and methods section, references to the articles and presentations describing research data (on which the maps are based), and a bibliography on the synaptic relationships of subcortical and cortical afferents with projection and local circuit neurons in the motor thalamus." .
SCR:014215 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FluoView FV10-ASW software" ;
NIFRID:synonym "FV10-ASW 3.0 Software",
"Olympus Fluoview FV10-ASW 3.0" ;
definition: "Image processing software used to modify and clarify sample images for FluoView FV1000 range of confocal laser scanning microscopes and Fluoview FV1000MPE multiphoton excitation systems. The software incorporates high-dynamic-range imaging, minimized signal-to-noise ratios, partial stitching with multiarea time-lapse imaging, and channel unmixing. The software also allows users to select specific areas of the whole sample, which can stitched together." .
SCR:014217 a owl:NamedIndividual ;
rdfs:label "iMosflm " ;
definition: "Software which processes diffraction data/images and produces an MTZ file of reflection indices with their intensities, standard deviations, and other parameters. The MTZ file is passed onto other programs of the CCP4 program suite for further data reduction. iMosflm processes data from CCD and pixel detectors. It is available for Windows, Mac OSX and Linux platforms. Tutorials are available at the website." .
SCR:014218 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pointless" ;
definition: "Pointless scores all the possible Laue groups consistent with the crystal class, which is based on cell dimension restraints, by matching potential symmetry equivalent reflections. For chiral systems, the Laue group uniquely implies the point group then checks sets of reflections which may be systematically absent to suggest a possible spacegroup. There is also a check for lattice centering, i.e., a check for whole classes of reflections having essentially zero intensity, including a check for obverse/inverse twinning in rhombohedral systems. Pointless is also capable of converting XDS, Scalepack, SHELX or SAINT formats to MTZ." .
SCR:014219 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phaser" ;
definition: "Crystallographic software which solves structures using algorithms and automated rapid search calculations to perform molecular replacement and experimental phasing methods." .
SCR:014220 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:shelx" ;
rdfs:label "SHELX " ;
definition: "A set of software programs that utilizes dual spaces algorithms for the determination of small and macromolecular crystal structures by single crystal X-ray and neutron diffraction. Libraries, extra files and environment variables are not required for the executables. SHELX is intended to be run on a command prompt but may be called from GUIs such as shelXle, Olex2, Oscail or WinGX, or hkl2map., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014221 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:buccaneer" ;
rdfs:label "Buccaneer" ;
NIFRID:synonym "buccaneer - Statistical protein chain tracing" ;
definition: "Software which performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target. The target distributions are generated by a simulation calculation using a known reference structure for which calculated phases are available. The success of the method is dependent on the features of the reference structure matching those of the unsolved work structure. For almost all cases, a single reference structure can be used, with modifications automatically applied to the reference structure to match its features to the work structure." .
SCR:014222 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:coot" ;
rdfs:label "Coot" ;
NIFRID:synonym "Crystallographic Object-Oriented Toolkit" ;
NIFRID:abbrev "COOT" ;
definition: "Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available." .
SCR:014223 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:cnssolve" ;
rdfs:label "Crystallography and NMR System (CNS)" ;
NIFRID:synonym "Crystallography and NMR System" ;
NIFRID:abbrev "CNS" ;
definition: "Software designed to provide a multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Features include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data. Modules, libraries, utility programs, tutorials, and a syntax manual are available on the website." .
SCR:014224 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phenix" ;
NIFRID:synonym "Python-based Hierarchical ENvironment for Integrated Xtallography" ;
definition: "A Python-based software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Phenix includes programs for assessing data quality, experimental phasing, molecular replacement, model building, structure refinement, and validation. It also includes tools for reflection data and creating maps and models. Phenix can also be used for neutron crystallography. Tutorials and examples are available in the documentation tab." .
SCR:014225 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Refmac" ;
definition: "A molecular refinement program with two main modes: REVIEW, which checks and updates the input model to establish that the geometric restraints can be properly set up, and REFINE mode, which is the standard mode and documented in keywords. In REVIEW users can: check model coordinates and write an extended output set of coordinates, find disulphide bonds and other covalent links, cis-peptides, output the sequence and REMARK records. In REFINEMENT mode users can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. Also in REFINEMENT mode, Refmac produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps. The program is supported by CCP4." .
SCR:014226 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MolProbity" ;
definition: "A structure-validation web application which provides an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. MolProbity works best as an active validation tool (used as soon as a model is available and during each rebuild/refine loop) and when used for protein and RNA crystal structures, but it may also work well for DNA, ligands and NMR ensembles. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot." .
SCR:014227 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TopSpin" ;
definition: "Software package for NMR spectra acquisition, processing, and data analysis. Features include: deconvolution/spectrum simulation/iteration; comprehensive functionalities for processing, displaying and analyzing one and multi-dimensional spectra; and user customization. A full list of features is available on the website." .
SCR:014228 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sparky " ;
definition: "A graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers. Sparky displays NMR spectra, the peaks of which users may pick, assign, and integrate using a graphical interface. Users can work with any number of 2, 3 or 4 dimensional spectra simultaneously. Spectra for input to Sparky can be produced with processing programs NMRPipe, Felix, VNMR, XWinNMR or UXNMR. Output consists of text peak lists showing assignments, chemical shifts, volumes, line widths, etc." .
SCR:014229 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:cyana",
"SCR_021949" ;
rdfs:label "CYANA" ;
definition: "Software for automated structure calculation of biological macromolecules on basis of conformational constraints from nuclear magnetic resonance. Program for automated NMR protein structure calculation. CYANA requires a sufficient list of assigned chemical shifts and lists of cross-peak positions and columns from 2D, 3D, or4D NOESY spectra in order to calculate the assignment of the NOESY cross-peaks and the 3D structure of the protein in solution." .
SCR:014230 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:amber" ;
rdfs:label "Assisted Model Building with Energy Refinement (AMBER)" ;
NIFRID:synonym "Assisted Model Building with Energy Refinement" ;
NIFRID:abbrev "AMBER" ;
definition: "Software package of molecular simulation programs. It is distributed into AmberTools15 and Amber14. AmberTools15 is a software package which can carry out complete molecular dynamics simulations with either explicit water or generalized Born solvent models. It is distributed in source code format and must be compiled in order to be used. Amber14 builds on AmberTools15 by adding the pmemd program, which provides better performance on multiple CPUs and dramatic speed improvements on GPUs compared to sander (molecular dynamics). GPU info, manuals, and tutorials are available on the website." .
SCR:014231 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SlideWrite Plus" ;
NIFRID:synonym "SlideWrite Plus v.7.0" ;
definition: "Software used to create presentation quality charts, graphs and slides for technical presentations, publications and reports. It can create complex drawings and 2D and 3D graphs with advanced scientific features." .
SCR:014235 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CorelDRAW Graphics Suite" ;
definition: "Graphic design software which can be used for vector illustration and page layout, web design, and photo editing. Features include: search, preview, application and transformation capabilities for both vector pattern and bitmap pattern fills; a fill engine with complete control over fountain, bitmap pattern and vector pattern fills; templates for website design; and vector shaping and page layout tools." .
SCR:014237 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Huygens Software" ;
definition: "A set of fluorescence microscope image processing packages which perform image restoration, interactive analysis, and volume visualization of 2D and 3D multi channel microscopy images or time series. The restoration is based on different deconvolution algorithms, that permit the recovery of objects from images that are degraded by blurring and noise. Tutorials and documentation are available on the website." .
SCR:014238 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Heinrich Heine University Dusseldorf; North Rhine-Westphalia; Germany" ;
NIFRID:synonym "Heinrich Heine University Düsseldorf",
"University of Dusseldorf",
"University of Düsseldorf" ;
definition: "University in Germany." .
SCR:014239 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nanoparticle Tracking Analysis" ;
NIFRID:synonym "Nanoparticle Tracking Analysis (NTA)" ;
NIFRID:abbrev "NTA" ;
definition: "Software which utilizes the properties of both light scattering and Brownian motion to obtain the particle size distribution of samples in liquid suspension. The Nanoparticle Tracking Analysis software tracks many particles individually and calculates their hydrodynamic diameters using the Stokes Einstein equation." .
SCR:014240 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SoftMax Pro Data Acquisition and Analysis Software" ;
NIFRID:synonym "SoftMax Pro Software" ;
definition: "A software package for microplate reader control and microplate data analysis. It includes analysis templates for a variety of assays run on Molecular Devices microplate readers." .
SCR:014241 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Opticon Monitor Software" ;
definition: "Software which controls all operations in the experimental setup, data acquisition and monitoring, and data analysis stages of the Bio-Rad Opticon 2 system. In the experimental setup stage, setup and programming operations are accessed from the Master File window. The master file consists of a plate file, which specifies the parameters of the plate, and a protocol file, which specifies the experimental conditions. After a plate and a protocol setup have been created or selected, a run can be initiated, which begins the data acquisition and monitoring stage. Data collection can be monitored during the run by viewing a plot of fluorescence intensity vs. cycle number. In the data analysis stage, data can be analyzed using the Quantitation, Melting Curve, and/or Analysis windows. The window used depends on the type of data being collected." .
SCR:014242 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JMP" ;
definition: "Statistical software that uses dynamic graphics rather than tables or graphs to visualize raw data. More specific versions of JMP are available for statistical analyses, clinical work, and genomics. Features include statistical modeling, data cleanup, automation and scripting, and experimental design." .
SCR:014243 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CrimeStat" ;
definition: "A spatial statistics program which provides tools for crime mapping and analyzing crime incident locations. CrimeStat is organized into five sections: data setup, which arranges and organizes the location data; spatial description, which performs analyses such spatial distribution, spatial autocorrelation, and distance and hot spot analysis; spatial modeling, which performs a number of analyses such as Bayesian journey to crime analysis and space-time analysis; crime travel demand modeling, which detects crime patterns and correlations over time and space; and CrimeStat libraries, which are component objects that include all of the routines that were developed through version 2.0 of the regular CrimeStat program." .
SCR:014244 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Braincon Platform Software" ;
NIFRID:synonym "BCI Braincon Platform Software" ;
definition: "Software that processes neural data at run-time to control the implant's electrical stimulation functionality for the Braincon brain-computer interface (BCI). Braincon Platform Software is a general, flexible and verifiable BCI software architecture with a filter pipeline for low-latency multi-threaded processing of neuronal signals." .
SCR:014245 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoAlign Head " ;
definition: "Software designed to automatically realign brain images for easier cross patient examination regardless of age, disease or head position. It positions and aligns anatomy-related sagittal, coronal and axial slices using anatomical landmarks." .
SCR:014246 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "ImageQuant" ;
NIFRID:synonym "ImageQuant TL" ;
NIFRID:abbrev "IQTL" ;
definition: "Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014247 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Living Image software" ;
definition: "In vivo imaging software which facilitates workflow for in vivo optical, X-ray and microCT image acquisition, analysis and data organization., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014249 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneSnap" ;
definition: "A software program used to control G:BOX hardware, specifically to capture and process images. While viewing images in real time, GeneSnap controls the illumination and exposure length of the lens, as well as the focussing, zooming and iris setting of a motorized lens." .
SCR:014251 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3ds Max" ;
NIFRID:synonym "3DS MAX" ;
definition: "3D modeling, animation, and rendering software which allows users to create custom tools and share design projects. 3ds Max contains various tools and templates for rendering and and editing, including tools for graph construction, project collaboration, and complex topography creation." .
SCR:014252 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AnimatLab" ;
definition: "A software tool that combines biomechanical simulation and biologically realistic neural networks to create realistic models of, and perform tests on, biomechanical workings. AnimatLab was primarily designed to model and test the operation of neural circuits that might produce behavior patterns observed in an intact animal. Users can create an animalistic or robotic body and place it in a virtual environment with physics that are accurate and realistic. Users can then design a nervous system that controls the behavior of the body within the physically realistic environment. Various models for different types of actions, builds, and movements are available." .
SCR:014253 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HomeCageScan " ;
definition: "Software used for automatic high throughput analysis of unconstrained rodent behaviors in a home cage. HomeCageScan is ideal for longitudinal studies where several animals are studied and tested over long periods. Its features include twenty-four-hour recording capabilities, statistical analysis, automatic adaptation to environmental changes (including day and night changes), and a batch‐mode which allows user to run multiple videos successively without human intervention. The software can detect various behaviors ranging from feeding and urination to jumping and foraging." .
SCR:014254 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Limelight " ;
definition: "A video tracking system designed for high-throughput behavioral experiments. LimeLight can track up to 4 arenas at once and can collect images at up to 30 frames per second for one animal or up to 8 frames per second when tracking 4 arenas at once. The tracking system has 2 different hardware configurations: the 1-camera system can be used to record 1 to 4 animals at once, while for multiple animals, each one is placed in a separate arena in one quadrant of the image. The software contains productivity features such as flexible arena setup, user-defined behavior scoring, stimulus control, and various analytical functions for quantifying behavior. The program is designed for experiments such as Open Field, Plus Maze, Radial Arm Maze, Zero Maze, Novel Object Recognition, Conditioned Place Preference, and Barnes Maze." .
SCR:014255 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LCG command line electrophysiology" ;
definition: "Software toolbox able to perform electrophysiological experiments using simple stimulation protocols and more complex paradigms, such as dynamic clamp or hybrid networks." .
SCR:014256 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CSIM" ;
NIFRID:synonym "Circuit SIMulator",
"CSIM: A neural Circuit SIMulator" ;
definition: "Software tool for simulating heterogeneous networks composed of different model neurons and synapses. CSIM simulates networks containing up to a few thousand neurons and up to the order of 1.000.000 synapses. It is capable of supporting different levels of modeling and has an object oriented design. A user manual is available on the site." .
SCR:014257 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeoCortical Simulator" ;
NIFRID:abbrev "NCS" ;
definition: "A neural simulator which models integrate-and-fire neurons with conductance-based synapses. NCS supports simulations for larger models and also supports real-time neurorobotics applications. Two versions of NCS are available: NCS 5, which is based on CPU cluster; and NCS 6, a multi-box, multi-GPU version. NCS 5 models integrate-and-fire neurons with conductance-based synapses using two clusters: four SUN 4600 machines and 208 Opteron cores. NCS 6 is a neural simulator for heterogeneous clusters of both CPUs and GPUS." .
SCR:014258 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scilab" ;
definition: "A software package for numerical computation providing a powerful computing environment for engineering and scientific applications. It includes hundreds of mathematical functions and has a high level programming language allowing access to advanced data structures, 2D and 3D graphical functions." .
SCR:014259 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CalC" ;
NIFRID:synonym "Calcium Calculator" ;
definition: "A modeling tool for simulating intracellular calcium diffusion and buffering. CalC solves continuous reaction-diffusion PDEs describing the entry of calcium into a volume through point-like channels, and its diffusion, buffering and binding to calcium receptors. Its features include: being platform-independent; being operated by simple script; combinable with MATLAB; and providing real-time views. Demos and manuals are provided on the website." .
SCR:014260 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:copasi" ;
rdfs:label "COPASI" ;
NIFRID:synonym "COPASI: Biochemical System Simulator" ;
definition: "Software application for simulation and analysis of biochemical network models and their dynamics. COPASI supports models in the SBML standard and can simulate their behavior using ODEs or Gillespies stochastic simulation algorithm. Arbitrary discrete events can be included in such simulations. Models in COPASI are based on reactions that convert a set of species into another set of species. Simulation can be performed either with stochastic kinetics or with differential equations. COPASI also includes various methods of analysis and data visualization." .
SCR:014261 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EDLUT" ;
NIFRID:synonym "EDLUT: Event-Driven simulator based on Look-Up-Tables",
"Event-Driven simulator based on Look-Up-Tables" ;
definition: "Simulation software which creates spiking cell models using either a time-driven strategy or an event-driven strategy based on look-up tables. EDLUT serves as a tool for studying the computational principles of neural systems to reveal how different functionalities of the brain and central nervous system are based on cell and topology properties." .
SCR:014262 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ERNST" ;
NIFRID:synonym "ERNST: Event Related Neuronal Simulation Tool",
"Event Related Neuronal Simulation Tool" ;
definition: "An event-based neuronal network simulator designed to handle large, complicated neuronal networks. The software is capable of creating realistic and accurate neuronal models in terms of neuronal dynamics and spike timing. ERNST is written in Java." .
SCR:014263 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KInNeSS" ;
NIFRID:synonym "KDE Integrated NeuroSimulation Software",
"KInNeSS: KDE Integrated NeuroSimulation Software" ;
definition: "Neurosimulation software that links sophisticated model development with behavior. The software package provides a framework that can be expanded using standard KDE (K Desktop Environment) parts and plugins to incorporate a variety of different projects, like visual system, auditory system or memory system. KInNeSS contains two fully developed project environments: one for generic input and another for spatial navigation tasks. The option of creating a new project environment is provided for advanced users. A user manual and tutorials/examples are provided as part of documentation." .
SCR:014264 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "neurodata" ;
definition: "Project portal dedicated to understand animal and machine intelligence and repository of data and tools. Suite of tools to analyze and graph imaging data. Image and data repository for large, publicly available neuro-specific data files and images. Contains tools for analytics, databases, cloud computing, and Web-services applied to both big neuroimages and big neurographs." .
SCR:014265 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vector NTI" ;
NIFRID:synonym "Vector NTI Software" ;
definition: "Software suite of sequence analysis and design tools that help manage, view, analyze, transform, share, and publicize various types of molecular biology data within one analysis environment. Users can analyze and compare sequences, design cloning and other vector related experiments, and curate and organize data and collections. Different classes for different user and experimental focuses are available." .
SCR:014266 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "A plasmid Editor" ;
NIFRID:abbrev "ApE" ;
definition: "Software tool for plasmid and sequence editing, annotating and drawing plasmid sequences. Used to view circular or linear maps of DNA sequences. Users can perform virtual digests whereby they select predefined DNA ladder, or specify their own, and visualize theoretical DNA fragments. Used to highlight restriction sites in editing window, accurately reflect Dam/Dcm blocking of enzyme sites, highlighting and drawing graphic maps using feature annotations from genbank and embl files, highlighting text using pre-defined and custom feature libraries, and directly BLASTing selected sequence at NCBI or Wormbase. Runs across Windows, OS X, and Linux/Unix." .
SCR:014268 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fuzzy Logic Toolbox" ;
definition: "A software toolbox which provides MATLAB functions, apps, and a Simulink block for analyzing, designing, and simulating fuzzy logic systems. Fuzzy Logic Toolbox allows users to model complex system behaviors using simple logic rules, and then implement these rules in a user-designed fuzzy inference system. Functions are provided for many common methods, including fuzzy clustering and adaptive neurofuzzy learning. The toolbox can be used as a stand-alone fuzzy inference engine or in connection with Simulink. Different versions of the software are available for specific fuzzy inference systems." .
SCR:014269 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Time Series analyzer" ;
definition: "An ImageJ plugin used for analyzing 2D time-lapse images or stacks. The plugin can be used to add a predefined ROI (Auto ROI) through mouse clicks. After selecting the object to be defined, an ROI is added on the image and in ROI Manager." .
SCR:014270 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Strathclyde Electrophysiology Suite" ;
definition: "A suite of programs for recording and analyzing signals from intracellular electrophysiology experiments. A list of the latest software is available from the website. The programs work with common electrophysiological laboratory interface units, including: Cambridge Electronic Design 1401 / 1401plus / Micro1401 / Power 1401; Axon Instruments Digidata 1200 or 1320/22, 1440, 1550, 1550A; Instrutech ITC16 or ITC-18; National Instruments multifunction interface cards; Biologic VP500; Tecella patch clamps; and Heka EPC-9, EPC-10." .
SCR:014271 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MassLynx " ;
NIFRID:synonym "MassLynx MS Software" ;
definition: "Software which can acquire, analyze, manage, and share mass spectrometry data. MassLynx controls any Waters mass spectrometry system, from sample and solvent management components to mass spectrometer and auxiliary detectors. The software can acquire nominal mass, exact mass, MS/MS and exact mass MS/MS data. The software system also maintains and consolidates all user sample data. Optional Application Manager programs provide additional information for specific MS analyses and data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014272 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PaDEL-Descriptor" ;
definition: "A software to calculate molecular descriptors and fingerprints. The descriptors and fingerprints are calculated using The Chemistry Development Kit with additional descriptors and fingerprints such as atom type electrotopological state descriptors, Crippen's logP and MR, extended topochemical atom (ETA) descriptors, and McGowan volume." .
SCR:014273 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Avalon Cheminformatics Toolkit" ;
definition: "Software toolkit containing tools to render and canonicalize SMILES and manipulate MOL file and related formats, as well as structure fingerprinting." .
SCR:014274 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14853" ;
rdfs:label "RDKit: Open-Source Cheminformatics Software" ;
NIFRID:synonym "RDKit",
"RDKit Open-Source Cheminformatics and Machine Learning" ;
definition: "An open-source cheminformatics and machine-learning toolkit that is useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc., as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. Documentation is available on the main website." .
SCR:014275 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CDK Descriptor Calculator GUI" ;
definition: "Software which can automatically detect descriptor classes defined in the CDK QSAR descriptor dictionary. Groups of descriptors and individual descriptors can be selected for evaluation. Input can be SDF or SMI formats, while output can be a variety of delimited text formats, annotated SDF or ARFF. The software can also evaluate fingerprints. A summary overview of the available descriptors and their names are available on the website." .
SCR:014276 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Signal" ;
definition: "A sweep-based data acquisition and analysis software package. Its uses range from a simple storage oscilloscope to complex applications requiring stimulus generation, data capture, control of external equipment and custom analysis. A built-in script language automates tasks and provides additional tools for custom analyses and applications. Signal includes functions for specific application areas, including dynamic clamp, whole cell and patch clamp electrophysiology, and evoked response including control of magnetic and other stimulus devices. Video tutorials and a demo version of Signal is available on the main page." .
SCR:014277 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EZ-C1 FreeViewer" ;
definition: "Software for browsing the image data acquired by Nikon C1 and a Nikon C1si system." .
SCR:014278 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCID Analysis" ;
definition: "Software designed to provide an image analysis software solution for offline analysis of images, ideally for the analysis of images where image capture is not required. Available applications for MCID Analysis include gel/blot analysis, fluorescence microscopy, and stereology." .
SCR:014279 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AcqKnowledge Software" ;
definition: "A software program that allows the user to perform data acquistion, stimulation and analyses. Users do not need to know the programming language or a new protocol view. AcqKnowledge Software is compatible with MP150 Research Systems, MP36R Research Systems, and MRI and fMRI Setups. A variety of offline and online analysis tools allows users to customize data recordings and targeted analyses. The software can perform automated analysis routines, output a range of stimulus paradigms, and allows users to record from multiple hardware devices simultaneously." .
SCR:014280 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016622" ;
rdfs:label "Quantity One 1-D Analysis Software" ;
definition: "Software used for Bio-Rad imaging systems to acquire, quantitate, and analyze a variety of data. The software allows automatic configuration of imaging systems with appropriate filters, lasers, LEDs, and other illumination sources. It also contains tools for automated analysis of tests and assays such as 1-D electrophoretic gels, western blots, and colony counts." .
SCR:014281 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StepOne Software" ;
definition: "A software program for the Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems. StepOne software allows the user to open and analyze experiments generated from either the StepOne or the StepOnePlus system. Users can set up experiments, send experiments to the instrument, control the instrument settings, and collect and analyze data." .
SCR:014282 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tscratch " ;
definition: "Software tool for automated analysis of monolayer wound healing assays. Available as a stand alone application for Macintosh and Windows and as a source code. Offers a graphical user interface for inspection of analysis results and manual modification of analysis parameters., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014283 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Definiens Developer XD" ;
definition: "A development environment designed to create automated image analysis solutions for segmentation and classification tasks. It delivers quantitative and consistent data for any type of image (e.g., IHC, ISH, IF images in different formats). Developer XD also contains a large library of image analysis algorithms, which users can add to, for whole slide images and tissue microarrays (TMAs). It can be integrated with an existing Tissue Studio installation." .
SCR:014284 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Axograph " ;
definition: "A software tool which provides a means to acquire and analyze time-series data, as well as a direct route to publication quality graphics. It provides a variety of graph styles and automated, extended, and/or customizable analyses." .
SCR:014285 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Monkey Motion" ;
definition: "A graphical source code file used for an automated motion detection and reward system for animal training (see comment for full paper title). It was designed on the LabVIEW programming system. Running the program requires the appropriate LabVIEW runtime software from National Instruments Corporation." .
SCR:014286 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GPCR Network" ;
definition: "A protein family specific platform that works closely with the GPCR community to determine the high resolution structure and function of GPCRs. Structures are available in the glutamate, secretin, frizzled/TAS2, adhesion, and rhodopsin branches of the protein phylogenetic tree. Users can access a list of protein structure targets and completed protein structures." .
SCR:014287 a owl:NamedIndividual ;
rdfs:label "Maya 3D animation" ;
definition: "Software used for modeling, simulation, and rendering of 3-D models. The tool is designed to provide a starting point to model, animate, work with lighting, and create VFX." .
SCR:014288 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Canvas X" ;
definition: "Illustration and communication software for engineers and technical graphics professionals that combines the ability to make 3D images while also applying filters and duatone images. The software has minimum precision levels and object illustration and image editing tools to keep data accurate throughout the authoring process. Users can accelerate and streamline the technical illustration workflow from initial import and design to final presentation, facilitate collaboration, and improve the overall productivity. Tutorials and technical documents are available on the website." .
SCR:014289 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ANY-maze" ;
NIFRID:synonym "any maze",
"ANY-MAZE",
"ANY-Maze" ;
definition: "Video tracking system used to automate testing in a variety of behavioral apparatus. ANY-maze can automatically track the tail, head, or body of a test animal in up to 16 pieces of apparatus. The software can record live images or digital files with different camera types and save the data in multiple formats. ANY-maze contains built in statistical tests and standard measures for distance, speed, mobility, duration, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014290 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneMapper " ;
NIFRID:synonym "GeneMapper Software",
"GeneMapper Software 5",
"GeneMapper Software 6" ;
definition: "Genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. GeneMapper specializes in multiapplication functionality, including amplified fragment length polymorphism, loss of heterozygosity, microsatellite, and SNP genotyping analysis. The software provides remote auto-analysis and command line operation, and allows for multiuser, client-server deployment." .
SCR:014291 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:scratch" ;
rdfs:label "SCRATCH" ;
NIFRID:synonym "Scratch Protein Predictor" ;
definition: "Web protein structure and structural feature prediction server.Software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. User provides amino acid sequence and selects desired predictions, then submits to the server." .
SCR:014292 a owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:nncon" ;
rdfs:label "NNcon" ;
definition: "Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008." .
SCR:014293 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SAP Visual Enterprise Author" ;
NIFRID:synonym "SAP 3D Visual Enterprise Author" ;
definition: "A desktop application used to create and manage 2D and 3D animation and video and audio assets. SAP Visual Enterprise Author can be used to render visual content into common desktop documents, file formats, and business applications for secure downstream use. A variety of tools allows users to view, transform, optimize, animate, and publish in different formats." .
SCR:014294 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaFluor Fluorescence Ratio Imaging Software" ;
definition: "Software designed for single or multi-wavelength intracellular ion measurements. It provides simultaneous display of raw data, ratio image, graphs of intensities, ratios, ion concentrations, and a non-ratiometric image such as a brightfield or phase-contrast image. Two different ratiometric indicators can be imaged and measured simultaneously to provide greater insight to ion exchange and intracellular function regardless of dye loading concentrations, conditions, or emission intensities." .
SCR:014295 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Transfer Entropy Toolbox" ;
NIFRID:synonym "TE Toolbox" ;
definition: "A suite of MATLAB/C and C++ tools for computing standard and extended versions of transfer entropy (as recorded by Thomas Schreiber) on sparse, binary time series. Delay 1, delayed, and higher-order transfer entropy are available in the toolbox. The speed of the program is dependent upon the number of delays, the length of the data set, the number of neurons, and the message length/order. Documentation and examples are provided on the website." .
SCR:014296 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MED Associates Activity Monitor software" ;
NIFRID:synonym "Activity Monitor",
"MED Associates Activity Monitor" ;
definition: "Software designed to record and organize data. All experiments and subject data are entered into a database, with all subject data linked together allowing the software to track everything, and save it based on the assigned Subject ID. All standard data is displayed in real time along with a cumulative plot of the subject’s activity for all chambers. Users may choose the specific chamber size allowing for distance traveled to be measured in real units instead of beams broken. A rotational analysis option allows examination of large or small rotations, allowing for rotational measures to be obtained on staggering, ataxic, lesioned, or other loco-motor impaired mice or rats. Zonal analysis allows the user to change boundaries around the animal in post analysis. Up to eight systems can be connected to one computer." .
SCR:014297 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FEI" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software used for a variety of functions including image automation frameworks and advanced 3D data quantification, and simulation technologies." .
SCR:014299 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multi Gauge" ;
NIFRID:synonym "MultiGuage" ;
definition: "A software application for one-dimensional electrophoretic analysis of multi-labeled fluorophores. It was designed to analyze multi-channel fluorescence data from Fujifilm FLA-5000 and FLA-8000 scanning systems. The software also works with other scanners in the BAS/FLA series and with the LAS series." .
SCR:014300 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SlideBook " ;
NIFRID:synonym "SlideBook 6" ;
definition: "Digital microscopy software for research microscopy. It comes standard with drivers to control numerous instruments in and around the microscope. When online, data is acquired in a native-3D format over time, color and specimen locations in customizable experiment protocols. Data can be analyzed by a wide variety of tools for image processing including mathematical operations, statistics functions, analysis scripting and import to/export from MATLAB. Additional modules are available for special applications ranging from deconvolution to photomanipulation to multiphoton." .
SCR:014301 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:niftyfit",
"biotools:niftyfit" ;
rdfs:label "NiftyFit" ;
definition: "Software package for multi-parametric model-fitting of 4D Magnetic Resonance Imaging data. Software library to facilitate voxel wise fitting on a number of datatypes including T1 and T2 relaxometry, Arterial Spin Labeled MRI, Diffusion Weighted Imaging and Dynamic Contrast Enhanced MRI. T" .
SCR:014302 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Janelia Workstation" ;
definition: "A discovery platform used to analyze and annotate imagery for individual projects, while assembling shared data resources. It was originally applied to Drosophila neuronal anatomy and neuroblast lineage analysis and is currently being extended to support mouse whole-brain projection tracing. The Workstation is both a pipeline management system that extracts entities from 3D imagery and a suite of tools that enable scientists to annotate large imagery datasets. A Entity-Attribute-Value (EAV) graph permits any element to be annotated by users with custom ontologies. By allowing any entity to have multiple parents, the graph can be re-arranged by each user without copying the underlying image data." .
SCR:014303 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:fluorender" ;
rdfs:label "FluoRender" ;
NIFRID:synonym "FluoRender Visualization" ;
definition: "Interactive rendering tool for confocal microscopy data visualization. Combines rendering of multi-channel volume data and polygon mesh data, where properties of each dataset can be adjusted independently and quickly. Designed for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples. Features include feature tracking, 3D measurement tools, multiple render modes for multi-channel confocal data, and volume paint selection and segmentation." .
SCR:014304 a owl:NamedIndividual ;
rdfs:label "ResearchIQ" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented March 14, 2016. Research Integrative Query (ResearchIQ) tool, a semantically anchored resource discovery platform that facilitates semantic discovery of local and publicly available data through a single web portal designed for researchers in the biomedical informatics domain within The Ohio State University." .
SCR:014306 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Brain Project Cell Morphology" ;
definition: "Data set about mapping information provided as text files. The text files contain 3D representations of neuronal morphologies reconstructed using Neurolucida." .
SCR:014307 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ScanImage" ;
NIFRID:synonym "Scan Image" ;
definition: "Open source software application for laser scanning microscopy, electrophysiology, laser scanning photostimulation, and other physiological methods focused on neurobiology. Used to control laser scanning microscopes without need for custom data acquisition hardware. Standard data acquisition boards are used to acquire data and control laser scanning. The tasks of signal integration and image processing are placed on the computer CPU. Multiple versions of ScanImage are available, each with their own features." .
SCR:014308 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TurboReg" ;
definition: "An ImageJ plugin for the automatic alignment of a source image (or a stack) to a target image. Manual, automatic, and batch alignment modes are available. Users may specify some landmarks to establish the initial correspondence between images. In automatic and batch modes, the landmarks are automatically refined to match the landmarks of the target image. After registration, the plugin creates a warped image using the final position of the source image and the target landmarks. The plugin can be called by a macro or by another plugin. Technical guidance is available on the website." .
SCR:014309 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clocklab" ;
definition: "Point and click program used to quickly analyse circadian activity data using algorithms and embedded controls to make every graph interactive and useful for data analysis. The analysis program has been used for a variety of species including mice, hamsters, rats, sheep, Drosophila, and humans. This program has three separate applications: one for data collection, one for analysis, and a chamber control program." .
SCR:014310 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "InfoStat" ;
NIFRID:synonym "Software Estadistico" ;
definition: "A general stastical software for Windows which can perform basic statistical analysis, statistical modeling, multivariate analysis, and produce of graphs. InfoStat also has facilities that could be useful in teaching statistics. It can connect to R through the interpreter, which can run R scripts without leaving the InfoStat working environment, and through the implemented menu-driven procedures, which make use of the R calculation engine." .
SCR:014311 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ImageScope" ;
definition: "Slide image modification software that allows the user to adjust the magnification, compare slides, pan and zoom, annotate specific areas, and perform image analysis of digital slides. Users can create macros and algorithms to automate analysis and create plots, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014313 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPOT Basic" ;
NIFRID:synonym "SPOT Basic software" ;
definition: "Image capture software which creates publication quality images. SPOT allows users to view the live image and a preview of the captured image side by side, enabling image editing before capture. Enhancements such as calibration marks and measurements can be applied after image capture. An advanced version is also available." .
SCR:014314 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BlueBrain Bluima Connectivity" ;
definition: "A dataset of brain region connectivity statements mined from neuroscientific literature. Users can search for brain regions and explore region connectivity." .
SCR:014315 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AttoVision software" ;
NIFRID:synonym "BD AttoVision",
"BD AttoVision software" ;
definition: "Software used to analyze cellular image data obtained from BD Pathway bioimaging systems. Its features include object splitting for small spots or objects, band segmentation outputs, image preprocessing, and segmentation filters." .
SCR:014320 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gene Designer" ;
NIFRID:synonym "Gene Designer 2.0" ;
definition: "Software used to design, clone, and validate genetic sequences de novo. Users can remove or add sequence motifs, recode open reading frames, design oligonucleotides for sequencing primers, and more. Once the gene is designed, users can order the synthetic DNA fragments with Gene Designer files. Sequences can be imported and exported in GeneDesigner, Genbank, and FASTA formats. Demos and support are available on the main site." .
SCR:014321 a owl:NamedIndividual ;
rdfs:label "Scaffold" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Visualize and validate complex MS/MS proteomics experiments" .
SCR:014322 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:MASCOT" ;
rdfs:label "Mascot" ;
NIFRID:synonym "Mascot Server" ;
definition: "A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters." .
SCR:014323 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nanoprobes.com" ;
NIFRID:synonym "Nanoprobes" ;
definition: "A nanoparticle research collaborative which engineers nanoparticle products in order to find cures for cancer and other diseases. The gold labels produced are uncharged molecules which are cross-linked to specific sites on biomolecules. Labels can be attached to any molecule with a reactive group (proteins, peptides, oligonucleotides, small molecules and lipids) for detection and localization. New probes can be engineered based on any fragment of a naturally occurring biomolecule, and the label can be positioned away from the binding site so it does not interfere with binding." .
SCR:014325 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LabView " ;
NIFRID:synonym "LabVIEW",
"LabVIEW System Design Software",
"LabView System Design Software",
"NI LabVIEW software" ;
definition: "A development environment for engineers and scientists to visualize, create, and code engineering systems. The system design software is integrated with all measurement hardware and contains signal processing IP. Other features include multithreaded execution, software deployment to hardware, and program integration into a single environment." .
SCR:014326 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Primer Express" ;
definition: "Software that allows users to manually or automatically design custom primers and probes for gene quantitation and allelic discrimination (SNP) real-time PCR applications. It supports assays based on TaqMan and SYBR Green I dye chemistries." .
SCR:014328 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Canvas X Draw" ;
definition: "Software for professional vector graphics and rich photo-editing tool. Used for digital drawing." .
SCR:014329 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIS-Elements" ;
NIFRID:synonym "Nikon Instruments Software",
"Nikon Instruments Software Elements",
"NIS Elements" ;
definition: "Microscope imaging software suite used with Nikon products. NIS-Elements includes software applications for advanced and standard research, documentation, confocal microscopy, and high-content analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014330 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bioplex Manager Software" ;
NIFRID:synonym "Bio-Plex Manager Software" ;
definition: "Software for Bio-Plex systems which automates data optimization, operates Bio-Plex instruments, and analyzes data." .
SCR:014331 a owl:NamedIndividual ;
rdfs:label "MetaFluor Fluorescence Ratio Imaging Software" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software designed to take single or multi-wavelength intracellular ion measurements an provide simultaneous display of the raw data, ratio image, graphs of intensities, ratios, ion concentrations, and a non-ratiometric image for microscope techniques such as a brightfield or phase-contrast image. Two different ratiometric indicators can be imaged and measured simultaneously to provide greater insight to ion exchange and intracellular function regardless of dye loading concentrations, conditions, or emission intensities." .
SCR:014332 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Illumina Real Time Analysis" ;
NIFRID:synonym "Illumina RTA" ;
definition: "Software used with Illumina sequencing instruments to control PC acivity and perform base call and quality scoring. The primary analysis is performed during the chemistry and imaging cycles of a sequencing run, giving users the option to view data and decide how to proceed in the run." .
SCR:014333 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AMT Image Capture Software" ;
definition: "AMT camera system software that performs digital image acquisition, processing, and storage. An operations manual and software specifications are available on the main site." .
SCR:014334 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VideoMot2" ;
NIFRID:synonym "TSE VideoMot2" ;
definition: "A video tracking system that takes automated recordings and analyzes animal activity through various arena and maze systems. It can track multiple arenas using one camera, and an unlimited number of zones of interest can be generated for performing spatial analyses or controlling data acquisition. Features include 3-point detection, 3D measurements, access to raw data, and reanalysis of tracking data." .
SCR:014335 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Startle Monitor Software" ;
definition: "Software designed for use in tandem with the Startle Monitor system. It is Windows NT based software with a single input screen for all processes. The user can input session parameters, order a trial list, input subject information, edit trials, and edit sessions." .
SCR:014336 a "resource",
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011126" ;
rdfs:label "Integrated Digitized Biocollections" ;
NIFRID:abbrev "iDigBio" ;
definition: "iDigBio is the National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation. Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public." .
SCR:014337 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biobserve Viewer" ;
NIFRID:synonym "Bio Observe Viewer" ;
definition: "Software that provides subject tracking with body axis alignment and angle of view, which is then used to track body, nose and tail movements without marking the animal. Users may create the scoring system used by the software, as well as zones to observe, quantify, and compare the behavior of an animal in one or more areas. The software features several data acquisition and analysis tools to gather and interpret the data." .
SCR:014338 a owl:NamedIndividual ;
rdfs:label "Pixera" ;
NIFRID:synonym "Pixera Corporation" ;
definition: "A commercial provider of imaging software that works in tandem with Pixera camera and imaging systems." .
SCR:014339 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rhinoceros" ;
NIFRID:synonym "Rhino" ;
definition: "3D modeling software used to create, edit, analyze, document, render, animate, and translate surfaces, solids, point clouds, and polygon meshes. It can also be used to analyze and manufacture a variety of products." .
SCR:014340 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss LSM software" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. The LSM Image Browser comes with many functions from the Zeiss LSM software package, however, it is not used only for the Zeiss image database. This browser is an ideal tool for general image archiving, handling and interactive measurement in labs and workgroups. Features include orthogonal sectioning, 3D cut function, 3D view with calculation of single projections, interactive measurement functions in the overlay dialog, such as scale bar, distance, area etc." .
SCR:014341 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ClinProTools" ;
definition: "Biomarker detection and evaluation software which provides an advanced basis for mining unknown potential biomarkers in complex protein profiles. Visualization tools such as stack plots and box-and-whiskers plots can be used to interactively inspect and compare large data sets originating from samples that contain different clinical diagnoses. ClinProTools also supplies sophisticated mathematical algorithms for the discovery of complex biomarker pattern models. Besides validation, class-prediction tools are also integrated to allow the implementation of the whole biomarker detection and evaluation process." .
SCR:014342 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus Cell Software" ;
definition: "A collection of 7 individual software packages that all control the Olympus Imaging systems while also providing different individual features including (but not limited to): basic measurement functions, process automation, ratio analysis, and real time image acquisition." .
SCR:014344 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LSM Image Examiner" ;
NIFRID:synonym "LSM Image Browser" ;
definition: "Software used to compile images obtained from the Zeiss LSM 510 confocal microscope. The browser can be used for general image archiving and handling and interactive measurement in labs and workgroups. Features include orthogonal sectioning, 3D cut function, 3D view with calculation of single projections, and interactive measurement functions in the overlay dialog, such as scale bar, distance, and area." .
SCR:014345 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scaffold Proteome Software" ;
NIFRID:synonym "Scaffold" ;
definition: "Software for MS/MS proteomic experiments to compare samples, identify biological relevance, and identify isoforms and protein PTMs. These proteins can be classified based on molecular function or organelle. Users can investigate spectrum details and counts, as well as use high through-put batch processing. Tutorials and a free trial are available through the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014346 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Visualizing Continuous Health Usability Test Results Dataset" ;
NIFRID:synonym "Health Visualization Dashboard Usability Results" ;
definition: "A dataset containing the results of three usability studies conducted on a modeled patient using a software tool that visualized the health situation of the patient over time. The modeled patient was diagnosed with Type 2 Diabetes and had begun a coaching program. The study followed the progress of the patient as he/she progressed through the coaching program. An after scenario questionnaire, computer system usability questionnaire, and Nielsens Heuristic Evaluation were used to evaluate the patient. Separate CSV files, available on the website, contain the answers to the questionnaires and the laboratory details." .
SCR:014351 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.5281/zenodo.1303822" ;
rdfs:label "SimThyr" ;
definition: "Open source simulation software for thyroid homeostasis, based on published nonlinear model of pituitary thyroid feedback control. Simulates pituitary thyroid feedback control, which allows users to study relationship between structure and behaviour of thyroid homeostasis." .
SCR:014352 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPINA Thyr" ;
NIFRID:synonym "Structure Parameter Inference Approach",
"Structure Parameter Inference Approach Thyroid" ;
NIFRID:abbrev "SPINA" ;
definition: "Software tool to deliver estimated structure parameters of endocrine feedback control systems in vivo from serum or plasma hormone levels. Used for evaluation of thyroid function. Allows for calculating thyroid maximum secretory capacity (GT or SPINA-GT) and sum activity of peripheral 5'-deiodinases (GD or SPINA-GD) from levels of TSH, (F)T4 and (F)T3 that have been determined once only (SPINA Thyr). Binaries are available for Mac OS, Mac OS X, Palm OS, Garnet OS and Windows. For other operating systems, including Linux, Solaris and BSD, SPINA Thyr is available as sourcecode. Building from source requires THINK Pascal (for Mac OS Classic), winsoft PocketStudio (for Palm OS / Garnet OS) or Lazarus/Free Pascal (for Mac OS X, Windows, Linux, BSD and Solaris). Special version of calculation engine is available for modern S implementation, e.g. R." .
SCR:014353 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MSstats" ;
NIFRID:synonym "MSStats" ;
definition: "A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations." .
SCR:014354 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Xenopus laevis Research Resource for Immunobiology (XLRR)" ;
NIFRID:synonym "Xenopus laevis Research Resource",
"Xenopus laevis Research Resource for Immunobiology" ;
NIFRID:abbrev "XLRR" ;
definition: "A comprehensive resource specializing in the use of the amphibian Xenopus laevis (the African clawed frog) for biomedical and immunological research. Several genetically-defined inbred strains and clones are available for study. The facility also maintains and develops research tools such as transgenic animals, monoclonal antibodies, cell lines, DNA libraries, and molecular probes. XLRR includes a satellite facility devoted to study infectious diseases caused by iridovirus. Technical assistance, education, and training are also provided." .
SCR:014356 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VDJ Server" ;
NIFRID:synonym "VDJServer" ;
definition: "A web application immune repertoire management, analysis, and archiving. Users can collaborate and share data either privately or publicly. Users can perform a variety of tasks, such as create and share projects with other users, conduct pre-processing tasks on single end reads, run IgBlast, and obtain basic repertoire characterization results for B cell receptor and T cell receptor repertoires." .
SCR:014357 a "Commercial",
owl:NamedIndividual ;
rdfs:label "PCI Geomatica" ;
definition: "A commercial geospatial tool typically used for orthorectification and mosaicking of aerial and satellite imagery; however, it can also be used for biomedical imaging and modeling purposes. The developer software contains image processing tools and functions to edit images and design custom applications." .
SCR:014358 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CyberUnits" ;
definition: "A cross-platform class library for development of high-performance life science computer simulations. It supports modelling for biomedical cybernetics and systems biology with Object Pascal. It contains a set of Pascal units for rapid programming of high-performance computer simulations called the Brick collection." .
SCR:014359 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ICEPO" ;
NIFRID:synonym "Ion Channel ElectroPhysiology Ontology",
"Ion Channel ElectroPhysiology Ontology (ICEPO)" ;
definition: "An ontology distributed in OWL format which contains comprehensive terms describing ion channel electrophysiology. Terms from related ontologies, such as Cell Physiology Ontology (CPO), Cardiac Electrophysiology Ontology (CEPO), and Unit Ontology, were integrated into ICEPO." .
SCR:014360 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Free Pascal Compiler" ;
NIFRID:abbrev "FPC",
"FPK" ;
definition: "Free Pascal is a 32, 64 and 16 bit professional Object Pascal compiler targeting multiple processor architectures and operating systems. Documentation, including guides and manuals, are available on the website." .
SCR:014361 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "monoclonal antibody-based chemiluminescence immunoassay for 3,5-diiodothyronine (3,5-T2)" ;
NIFRID:abbrev "5-T2 CLIA" ;
definition: "Specific, sensitive, precise and accurate CLIA for 3,5-T2 detection in human serum." .
SCR:014362 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lazarus IDE" ;
NIFRID:synonym "Lazarus",
"Lazarus integrated development environment" ;
NIFRID:abbrev "Laz" ;
definition: "A cross-platform integrated development environment (IDE) for Free Pascal. It contains a class library (LCL) that supports rapid application development for native code on numerous platforms, processor architectures and operating systems." .
SCR:014363 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_005976" ;
rdfs:label "Optseq" ;
NIFRID:synonym "Optseq2",
"Optseq - fMRI Event Scheduler" ;
definition: "Software tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events). Events in RPER are presented closely enough in time that their hemodynamic responses will overlap. This requires that the onset times of the events be jittered in order to remove the overlap from the estimate of the hemodynamic response. RPER is highly resistant to habituation, expectation, and set because the subject does not know when the next stimulus will appear or which stimulus type it will be." .
SCR:014364 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rexplore" ;
definition: "An application which provides an environment to explore and organize scholarly data. Rexplore leverages solutions in large-scale data mining, semantic technologies and visual analytics, which allows users to detect and follow research trends, identify and map relationships between authors, perform expert searches, and analyze research performance." .
SCR:014365 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Isolectin GS-IB4 From Griffonia simplicifolia, Alexa Fluor 647 Conjugate" ;
definition: "A conjugated form of isolectin B4 for fluorescence identification of non-peptidergic nociceptors in mouse dorsal root ganglia and spinal cord." .
SCR:014367 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lysosome Enrichment Kit for Tissues and Cultured Cells" ;
definition: "A kit which enables isolation and enrichment for intact lysosomes from crude cell and tissue extracts. The kit provides sufficient reagents for preparing 25 extracts and uses OptiPrep Cell Separation Media for the density-based separation of lysosomes from contaminating cell structures." .
SCR:014368 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cytokine Registry" ;
NIFRID:synonym "ImmPort Cytokine Registry" ;
definition: "A registry of cytokines, chemokines, and receptors generated for the purpose of collecting, integrating, and mapping between entity names and synonyms from several resources. These resources include MeSH, the Protein Ontology, EntrezGene, HGNC, MGI, UniProt and others." .
SCR:014372 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIDDK Research Resources" ;
NIFRID:synonym "National Institute of Diabetes and Digestive and Kidney Diseases Research Resources" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Registry listing NIDDK resources, such as reagents, data, and protocols. They are derived from publicly available information provided by NIDDK-funded investigators, projects, and publications." .
SCR:014373 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Action to Control Cardiovascular Disease Risk in Diabetes Follow-up Study (ACCORDION)" ;
NIFRID:synonym "Action to Control Cardiovascular Disease Risk in Diabetes Follow-up Study" ;
NIFRID:abbrev "ACCORDION" ;
definition: "A prospective, observational follow-up study of at least 8000 participants who were treated and followed in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) Trial. Treatment in ACCORD ended in 2009 and ACCORDION is designed to further elucidate the long-term effects of the ACCORD treatment strategies and provide additional data on the relationships among various cardiovascular and diabetic risk factors." .
SCR:014374 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT) " ;
NIFRID:synonym "Predicting Response to Standardized Pediatric Colitis Therapy" ;
NIFRID:abbrev "PROTECT" ;
definition: "A study of how children newly diagnosed with ulcerative colitis (UC) respond to mesalamine and prednisone (corticosteroid), the standard initial therapies used to treat this disorder. Over a period of 5 years PROTECT will prospectively study the course of 430 children newly diagnosed with UC who are treated with standardized care. Biospecimens (blood, stool, colonic biopsy tissue) will be obtained and used to better understand the effects of genetics, mechanisms of inflammation, Vitamin D, and the bacteria contained in the stool (microbiome) on clinical outcomes." .
SCR:014376 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Lifestyle Interventions for Expectant Moms (LIFE-Moms) " ;
NIFRID:synonym "Lifestyle Interventions for Expectant Moms" ;
NIFRID:abbrev "LIFE-Moms" ;
definition: "A consortium whose overall goal is to identify effective behavioral and lifestyle interventions that will improve weight, glycemic control and other pregnancy-related outcomes in obese and overweight pregnant women, and determine whether these interventions reduce obesity and metabolic abnormalities in their children. The study/consortium is comprised of seven clinical centers, with each clinical center conducting its own trial. Additional information on the consortium and individual trials is located in the Consortium Summaries tab." .
SCR:014377 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hyperglycemia and Pregnancy Outcomes Follow-Up Study Consortium (HAPO-FUS)" ;
NIFRID:synonym "Hyperglycemia and Pregnancy Outcomes Follow-Up Study Consortium" ;
NIFRID:abbrev "HAPO-FUS" ;
definition: "The goal of this follow-up study of mothers who participated in the Hyperglycemia and Adverse Pregnancy Outcomes (HAPO) study is to determine the levels of blood sugar during pregnancy that are linked to increased body fat in the child, as well as to determine the chances of a mother developing diabetes 8-12 years after the pregnancy. The original study examined 23,316 mother-child pairs, and researchers determined that the hyperglycemia of a mother was linked to newborn birth weight and body fat. HAPO-FUS will enroll 7,000 or the original HAPO mother-child pairs for one follow-up visit to assess body composition, blucose metabolism, medical history, and other metabolic parameters." .
SCR:014378 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Symptoms of Lower Urinary Tract Dysfunction Research Network (LURN) " ;
NIFRID:synonym "Symptoms of Lower Urinary Tract Dysfunction Research Network" ;
NIFRID:abbrev "LURN" ;
definition: "A research consortium with the long term goal of developing and testing measurement tools to describe symptoms of lower urinary tract dysfunction (LUTD) in women and men. The group plans to study targeted populations of patients with LUTD in order to expand our understanding of the causes of symptoms and common ways that symptoms change over time. The researchers will also collect biosamples from patients for current and future study of LUTD." .
SCR:014379 a owl:NamedIndividual ;
rdfs:label "Porphyria Consortium" ;
NIFRID:synonym "Porphyrias Consortium",
"The Porphyria Consortium" ;
definition: "A consortium which includes five of the leading porphyria centers in the United States that provide expertise and experience in the diagnosis and treatment of patients with porphyria. The staff in each Center includes porphyria physicians, researchers, research coordinators, and technical/laboratory staff. Together with the American Porphyria Foundation, the Porphyrias Consortium enables a large scale collaborative effort to develop strategies and methods for diagnosis, treatment, and prevention of illness and disability resulting from these rare disorders." .
SCR:014380 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nephrotic Syndrome Study Network (NEPTUNE)" ;
NIFRID:synonym "Nephrotic Syndrome Study Network" ;
NIFRID:abbrev "NEPTUNE" ;
definition: "A consortium of researchers conducting a cohort study that investigates the underlying disease mechanisms of pro non-inflammatory glomerular diseases. The aim is to elucidate pathogenesis and identify therapeutic targets for clinical trials. The study participants will be classified according to the kidney biopsy results into one of three subcohorts, including Minimal change disease/Focal segmental glomerulosclerosis; Membranous nephropathy; and other conditions." .
SCR:014381 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "CKD Biomarkers Consortium" ;
NIFRID:synonym "BioCon" ;
definition: "A consortium which aims to promote the discovery and validation of biomarkers to advance the field of CKD research. The NIDDK CKD Biomarkers Consortium brings together investigators whose expertise includes clinical nephrology, epidemiology, molecular biology, genomics, proteomics, metabolomics, systems biology, laboratory medicine, biostatistics, and laboratory test verification and qualification." .
SCR:014382 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vitamin D to Prevent Type 2 Diabetes (D2d) " ;
NIFRID:synonym "Vitamin D to Prevent Type 2 Diabetes" ;
NIFRID:abbrev "D2d" ;
definition: "A study to determine whether vitamin D supplementation is safe and effective in delaying the onset of type 2 diabetes in people at risk for the disease and to gain a better understanding of how vitamin D affects glucose metabolism." .
SCR:014383 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Restoring Insulin Secretion Consortium (RISE)" ;
NIFRID:synonym "Restoring Insulin Secretion Consortium" ;
NIFRID:abbrev "RISE" ;
definition: "Consortium which includes 3 studies, each assessing the hypothesis that aggressive glucose lowering will lead to recovery of beta-cell function that will be sustained after treatment in those with prediabetes and early type 2 diabetes." .
SCR:014384 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Glycemic Reduction Approaches in Diabetes: A Comparative Effectiveness Study (GRADE) " ;
NIFRID:synonym "Glycemic Reduction Approaches in Diabetes: A Comparative Effectiveness Study" ;
NIFRID:abbrev "GRADE\\\\t" ;
definition: "A comparative study that aims to determine which combination of two medications is best for glycemic control in Type 2 Diabetes, has the fewest side effects, and is the most beneficial for overall health. GRADE is a randomized clinical trial of participants diagnosed with type 2 diabetes within the past 10 years who are already on metformin. Participants will be randomly assigned to 1 of 4 commonly-used glucose-lowering drugs (glimepiride, sitagliptin, liraglutide, and basal insulin glargine), plus metformin, and will be followed for up to 7 years." .
SCR:014385 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Clinical Islet Transplantation Consortium (CITC)" ;
NIFRID:synonym "Clinical Islet Transplantation Consortium" ;
NIFRID:abbrev "CIT",
"CITC" ;
definition: "Network of clinical centers and a data coordinating center established to conduct studies of islet transplantation in patients with type 1 diabetes." .
SCR:014386 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Assessment Serial Evaluation and Subsequent Sequelae in Acute Kidney Injury (ASSESS-AKI) " ;
NIFRID:synonym "Assessment Serial Evaluation and Subsequent Sequelae in Acute Kidney Injury" ;
NIFRID:abbrev "ASSESS-AKI" ;
definition: "A study which recruits patients with and without an episode of acute kidney injury during a hospitalization, and follows them longitudinally for major cardiac, renal and mortality events. An important aspect of the study is the prospective evaluation of potential biomarkers for renal and cardiac outcomes." .
SCR:014387 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Integrated Islet Distribution Program (IIDP) " ;
NIFRID:synonym "Integrated Islet Distribution Program" ;
NIFRID:abbrev "IIDP" ;
definition: "The goal of the Integrated Islet Distribution Program (IIDP) is to work with the leading islet isolation centers in the U.S. to distribute high quality human islets to the diabetes research community, in order to advance scientific discoveries and translational medicine." .
SCR:014389 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ambergpumdsimulation" ;
rdfs:label "Molecular Dynamics Workflow (BioKepler) " ;
NIFRID:synonym "Amber GPUMD Simulation",
"AmberGPUMDSimulation",
"Molecular Dynamics Workflow",
"Molecular Dynamics Workflow Software" ;
definition: "A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like." .
SCR:014392 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dcGO" ;
definition: "A database of domain-centric ontologies on functions, phenotypes, diseases and more. As a biomedical ontology resource, dcGO integrates functional, phenotypic, disease, and drug information. As a protein domain resource, it includes annotations to both the individual domains and supra-domains. Domain classifications and ontologies are organized in hierarchies, and dcGO includes the facility to browse the hierarchies: SCOP Hierarchy for browsing domains, GO Hierarchy for browsing GO terms, and BO Hierarchy for browsing other terms (mostly phenotypes). Users can mine and browse through resources." .
SCR:014393 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Human Islet Research Network (HIRN) " ;
NIFRID:synonym "Human Islet Research Network" ;
NIFRID:abbrev "HIRN" ;
definition: "Network helps to organize and support collaborative research related to loss of functional beta cell mass in Type 1 Diabetes (T1D). Project consists of four independent research initiatives: Consortium on Beta Cell Death and Survival (CBDS), Consortium on Human Islet Biomimetics (CHIB), Consortium on Modeling Autoimmune Interactions (CMAI), Consortium on Targeting and Regeneration (CTAR), and Human Pancreas Analysis Program (HPAP)." .
SCR:014396 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GDAL - Geospatial Data Abstraction Library " ;
NIFRID:synonym "GDAL: Geospatial Data Abstraction Library",
"Geospatial Data Abstraction Library" ;
NIFRID:abbrev "GDAL" ;
definition: "A translator library for raster and vector geospatial data formats that presents a single raster abstract data model and vector abstract data model to the calling application for all supported formats. It includes formats such as GeoTIFF, Erdas Imagine, Arc/Info Binary, CEOS, DTED, GXF, and SDTS. It is intended to provide efficient access suitable for use in viewer applications, and also attempts to preserve coordinate systems and metadata. Python, C, and C++ interfaces are available." .
SCR:014397 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AnimalTracker" ;
NIFRID:synonym "Animal Tracker" ;
definition: "A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation." .
SCR:014398 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GNU Octave" ;
NIFRID:synonym "Octave" ;
definition: "A high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments. It may also be used as a batch-oriented language. Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, functions written in the Octave language, or by using dynamically loaded modules written in C, C++, Fortran, or other languages., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014399 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mastrave modelling library" ;
NIFRID:synonym "Mastrave",
"Mastrave modeling library" ;
definition: "A software library written to perform vectorized scientific computing and oriented to ease complex modelling tasks such as those typically needed within environmental models, even when involving irregular and heterogeneous data series. The Mastrave project attempts to allow a more effective, quick interoperability between GNU Octave and Matlab users by using a well documented wrap around the main incompatibilities between those computing environments and by promoting a general idiom based on their common, stable syntagms." .
SCR:014401 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eutherian comparative genomic analysis protocol" ;
definition: "Eutherian comparative genomic analysis protocol as one framework of eutherian gene data set revisions. Protocol integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis with 3 new tests including test of reliability of public eutherian genomic sequences using genomic sequence redundancies, test of contiguity of public eutherian genomic sequences using multiple pairwise genomic sequence alignments and test of protein molecular evolution using relative synonymous codon usage statistics. Public eutherian reference genomic sequence data sets." .
SCR:014402 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:sortmerna",
"OMICS_02619" ;
rdfs:label "SortMeRNA" ;
definition: "Sequence analysis software for filtering, mapping and OTU-picking NGS reads. SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014403 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HiSpOD" ;
NIFRID:synonym "High Specific Oligonucleotide Design",
"High Specific Oligonucleotide Design (HiSpOD)" ;
definition: "A software dedicated to microbial ecology and environmental studies which uses individual nucleic sequences or consensus sequences produced by multiple alignments to design degenerate probes in order to target gene families covering many sequence variants. Probe specificity is assessed by similarity search against an exhaustive formatted database dedicated to microbial ecology containing coding sequences (CDS) and their putative 5-prime and 3-prime unstranslated regions (UTR). Potential cross-hybridizations identified by the program are clustered and results are organized in order to simplify user interpretation." .
SCR:014404 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GlycoEpitope" ;
NIFRID:synonym "GlycoEpitope Index",
"GlycoEpitope: Index" ;
definition: "A database of carbohydrate antigens and matching antibodies. Epitopes and antibodies are listed within the database. Users may also search for epitopes and antibodies by keyword, epitope ID, tissue, receptor, enzyme, and other fields." .
SCR:014405 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CollecTF" ;
definition: "A database of experimentally-validate transcription factor binding sites (TFBS) in the Bacteria domain. CollecTF places special emphasis on providing a curation process that captures the experimental support for sites as reported by authors in peer-reviewed publications. Reported binding sites are mapped to NCBI RefSeq complete genome records. The database can be browsed by transcription factor families, NCBI taxonomy or experimental support, or through customized searches integrating these three elements." .
SCR:014406 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:psygenet2r" ;
rdfs:label "PsyGeNET" ;
NIFRID:synonym "Psychiatric disorders Gene association NETwork",
"Psychiatric disorders Gene association Network" ;
definition: "Knowledge platform on psychiatric disorders and their genes. Resource for exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of database and set of analysis tools and is the result of the integration of information from DisGeNET and data extracted from the literature by text mining, followed by curation by domain experts." .
SCR:014407 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:unicarb-db" ;
rdfs:label "UniCarb-DB" ;
NIFRID:synonym "UniCarb-DB structural- MS spectral library database" ;
definition: "An experimental glycomic MS database initially created to meet the in-house need to store structural and MS-glycomic data. Users can search by taxonomy and tissue, mass and composition, and MS/MS." .
SCR:014409 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SuBLIME" ;
definition: "Software used for detection of lesions in patients with multiple sclerosis. It provides an automated method for segmenting incident lesion voxels and allows for sensitive and specific detection of lesion incidence that can be applied to large collections of images. Using the explicit form of the statistical model, SuBLIME can be adapted to cases when more or fewer imaging sequences are available." .
SCR:014410 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:unicarbkb" ;
rdfs:label "UniCarbKB" ;
definition: "International effort which has created a glycomics knowledgebase with access to a database of information on the glycan structures of glycoproteins. It serves as and promotes an online information storage and search platform for glycomics and glycobiology research. Open access knowledgebase offers resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data." .
SCR:014411 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Planteome" ;
definition: "An international collaborative effort to develop and enrich new and existing reference ontologies for plants, improve ontology use and cross-references, and to develop data annotation standards. Users can search for ontology terms and bioentities and submit the ontology-related term requests by visiting the following GitHub request trackers." .
SCR:014412 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AgreementMakerLight" ;
NIFRID:synonym "AgreementMakerLight (AML-Jar)" ;
NIFRID:abbrev "AML-Jar" ;
definition: "AML is a lightweight ontology matching system specialized on the biomedical domain but applicable to any ontology. It can be used to generate alignments automatically, as a platform for reviewing alignments, or as an alignment repair system (both automatically and interactively)." .
SCR:014413 a owl:NamedIndividual ;
rdfs:label "Rare Kidney Stone Consortium (RKSC)" ;
NIFRID:synonym "Rare Kidney Stone Consortium" ;
NIFRID:abbrev "RKSC" ;
definition: "An organization of various participants and independent efforts representing four major diseases of hereditary nephrolithiasis. The Consortium facilitates cooperative exchange of information and resources among investigators, clinicians, patients, and researchers in order to improve care and outcomes for patients with rare stone diseases. The consortium promotes ready availability of diagnostic testing, pooling of clinical experiences, and availability of tissue banks in order to advance the science." .
SCR:014414 a owl:NamedIndividual ;
rdfs:label "International Cell Line Authentication Committee" ;
NIFRID:synonym "International Cell Line Authentication Committee (ICLAC)" ;
NIFRID:abbrev "ICLAC" ;
definition: "An independent committee established to improve visibility of cell lines and promote awareness and authentication testing to combat false or misidentified cell lines. It contains a databases of cross-contaminated or otherwise misidentified cell lines, as well as resources to familiarize users of cell lines and the problem of misidentification. Their Terms of Reference defines false or misidentified cell lines and other commonly used terms, as well as sets out the committee goals and ground rules." .
SCR:014415 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Undiagnosed Diseases Network" ;
NIFRID:synonym "NIH Undiagnosed Diseases Network" ;
definition: "A network of clinical sites and core laboratories to accelerate discovery and innovate the way medical professionals diagnose and treat patients with previously undiagnosed diseases. It will serve to test whether this type of cross-disciplinary approach to disease diagnosis is feasible to implement in academic medical centers. It also provides clinical training of contemporary genomic approaches in diagnosing disease." .
SCR:014416 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iPTMnet" ;
definition: "A protein database which connects multiple disparate bioinformatics tools and systems text mining, data mining, analysis and visualization tools, and databases and ontologies." .
SCR:014417 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pediatrics Annotation and Medicine" ;
NIFRID:synonym "PAM System" ;
NIFRID:abbrev "PAM" ;
definition: "A standardized database for childrens disease classification and annotation. It is also an information exchange platform." .
SCR:014418 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Muse | Portable Scalp EEG Device (Muse S Athena)" ;
NIFRID:synonym "Muse 2",
"Muse: the brain sensing headband" ;
definition: "It is a portable scalp electroencephalography (EEG) system that can be used to measure brain activity. It is battery powered and has four active electrodes located at 10-20 coordinates TP9, AF7, AF8, and TP10, a common mode reference, and a driven right leg. It includes an accelerometer and gyroscope, and works with desktop and mobile EEG acquisition and visualization software. Muse 2 expands upon the first model with increasingly robust hardware." .
SCR:014419 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCID Core " ;
definition: "A complete imaging software that accepts image files in various formats and serves as a host for phosphor imagers, laser scanners, scanning densitometers and similar devices. Camera support is via compatible digital cameras such as the CoolSNAP or Qimaging range. MCID Core is available as an off the shelf software solution or as part of a number of software/hardware packages optimized for specific applications." .
SCR:014420 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FlexField Software" ;
definition: "Transformation software designed to help model and change Oracle account charts. This can be used to reorganize Oracle accounts due to events such as mergers, acquisitions, regulatory requirements and the need for more ranges when the data outgrows the range of the current chart of accounts. FlexField transforms an existing accounting flexfield segment structure, values, code combinations, and CCIDs according to user mappings, and applies the new code combinations and CCIDs. It propagates the change throughout an existing E-Business Suite data, everywhere the accounting flexfield is used. It removes the old code combinations and CCIDs, and aligns the new Chart of Accounts (COA) so that all balances belonging to a single CCID are summarized into a single line." .
SCR:014421 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Navios Software" ;
NIFRID:synonym "Navios Tetra Software" ;
definition: "Used in tandem with the Navios Flow Cytometer in order to acquire data for use in analyzing cellular characteristics." .
SCR:014422 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BD Accuri C6 Plus" ;
definition: "Software used for collecting and analyzing flow cytometry data. Files can be exported in FCS 3.1 format for import into other flow cytometry analysis programs such as FCS Express™ software and FlowJo™ software." .
SCR:014423 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SlideBook" ;
definition: "Digital microscopy software for research microscopy. It comes standard with drivers to control numerous instruments in and around the microscope. When online, data is acquired in a native-3D format over time, color and specimen locations in customizable experiment protocols. Data can be analyzed by a wide variety of tools for image processing including mathematical operations, statistics functions, analysis scripting and import to/export from MATLAB. Additional modules are available for special applications ranging from deconvolution to photomanipulation to multiphoton." .
SCR:014424 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pannoramic Viewer" ;
definition: "Software tool as a digital virtual microscope for viewing and moving scanned histological slides and for making annotations and measurements on them. Used in digital pathology. Helps to simplify the areas of the pathology workflow where imaging, slide digitization, storage, archivation, visualization and analysis are performed." .
SCR:014425 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus MicroSuite Five" ;
definition: "Imaging software for monochrome and color image acquisition and processing. It is fully integrated with Olympus microscopes, as well as third party stages and other devices, and supports various CCD and video cameras and TWAIN devices." .
SCR:014426 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCiLS Lab" ;
NIFRID:synonym "SCiLS Lab 2015a" ;
NIFRID:abbrev "SCiLS" ;
definition: "Statistical software for visualization, analysis and interpretation of MALDI imaging data. Its features are tailored to mining MALDI imaging data and include univariate analysis, unsupervised and supervised multivariate analysis, and preprocessing of data. Tutorials, software trainings, and example data sets can be accessed from the website." .
SCR:014427 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PreSurgMapp" ;
definition: """A MATLAB toolbox for processing the functional areas of the brain using multi-modal fMRI data for pre-surgical mapping.
It is composed of three types of individual-level ICA analyses for user use. Traditional ICA (task) can be used for task fMRI. Either Traditional ICA (rest) or ICA with DICI (rest) can be used for rs-fMRI. Traditional ICA (rest) is designed for users who already have a hypothesis of the pattern of the target component and want to have manually set components by themselves. ICA with DICI (rest) is completely automatic, given that the user provides a template (provided). The software utilizes an automatic component identification method that is based on the discriminatory-index. All the components from multiple ICA runs with multiple component settings are ranked and compiled.""" .
SCR:014429 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FreezeFrame" ;
NIFRID:synonym "FreezeView" ;
definition: "A video-based system to detect animal movement in fear conditioning experiments, as well as movements in learned helplessness experiments. FreezeFrame can detect animal movements (as small as 1mm) and actions, including grooming, sniffing, turning, and rearing. It can also collect and process data for learned helplessness experiments, such as Tail Suspension and the Porsolt Forced Swim Test. This software can monitor animals for up to 15 times per second." .
SCR:014430 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AnalySIS FIVE software" ;
NIFRID:synonym "AnalySIS 5" ;
definition: "Image analysis software designed to process, measure, and analyze images on a personal computer. It is used with either an Olympus brand microscope or an Olympus brand digital camera. The AnalySiS FIVE software can be used to directly control an Olympus brand microscope or camera, take measurements, store results, and analyze the resulting images up to the particle level." .
SCR:014431 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Avizo 3D Software" ;
definition: "A 3D analysis software for scientific and industrial data. Avizo is used for image data processing, exploration, and analysis. This software is designed to mainly be used commercially in industries including but not limited to: material sciences, life sciences, geo-sciences, and engineering." .
SCR:014432 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Q Capture software" ;
NIFRID:synonym "QCapture Pro" ;
definition: "A microscopic image capturing software that is meant to be used in conjunction with Q-imaging cameras. Image workflow is managed using a multiple document interface (MDI). There is also a publish image feature to capture high quality images of what is on the screen, including the overlay, the region of interest, and capture of single frames in time lapses or movies." .
SCR:014433 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Surveyor with Turboscan" ;
definition: "Automated scanning software used in conjunction with the Leica DM6000B microscope to obtain whole-slide image mosaics of histological slides. When performing a scan, Turboscan or the standard scan may be used." .
SCR:014434 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phylo_win" ;
definition: "Software used to create phylogenetic trees through neighbor-joining, parsimony, maximum likelihood methods and bootstrap confidence tests. Specific taxonomic species groups as well as conserved regions can be defined using a mouse standard and then stored into sequence files. Reconstructed trees can be drawn, edited, printed, stored and evaluated according to numerous criteria." .
SCR:014435 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Palm RoboSoftware" ;
definition: "Software used to control and calibrate the Palm Robo Microbeam microscope according to user specified parameters. Processes such as system calibrations and correct laser settings are fully automated." .
SCR:014436 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Avisoft-RECORDER" ;
definition: "A multi-channel triggering hard-disk recording system designed specifically for bio-acoustics, although it can be used for other audio signals. This software uses real-time spectrographic and spectrum display and posesses a customizable metadata input tool for embedding user-defined data directly into the resulting .wav files. The maximum sampling rate for real-time display and streaming to disk depends on the type of acquisition board and computer performance. These embedded records can later be accessed from SASLab Pro and integrated into another metadata base." .
SCR:014437 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FloMax" ;
definition: "Software for acquisition and analysis of flow cytometry data. FloMax data analysis works with data from flow cytometers that support the flow cytometry file standard (FCS). FloMax operates on computers with Windows 95, 98, and 2000., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014438 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Avisoft SASLabPro" ;
definition: "Sound analysis software used to process and analyze animal acoustic communications. Its features include digital filtering, real-time spectrogram display, and advanced metadata management. Avisoft SASLabPro is designed to accommodate large numbers of sound files and includes organizational features, including labeling options for single point data and time section labels." .
SCR:014439 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProTools LE software" ;
NIFRID:synonym "Avid ProTools",
"Avid ProTools LE software",
"Avid ProTools software" ;
definition: "Audio recording and editing software. ProTools LE software allows sound mixing, batch fades, and other audio mixing techniques." .
SCR:014440 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Advanced Image Data Analyzer" ;
NIFRID:synonym "AIDA",
"AIDA BioPackage" ;
definition: "Bioimaging analysis software used to acquire quantitative and qualitative data from various types of biological samples. The software provides a variety of image modification features, including contrast optimizing, image printing, 1-dimensional densitometry, fragment length and molecular weight determination, and 2-D densitometry." .
SCR:014442 a NLX:152328,
owl:NamedIndividual ;
rdfs:label " ReBuilding a Kidney " ;
NIFRID:synonym "(Re)Building a Kidney" ;
NIFRID:abbrev "RBK" ;
definition: "A consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. Their goal is to coordinate and integrate research to support the development and implementation of strategies such as de novo repair of nephrons, the re-generation of nephrons, and the in vitro engineering of a biological kidney to enhance renal repair and promote the generation of new nephrons in the postnatal organ. Investigators may apply for funding of a kidney-related project through the RBK Partnership Project. Funded projects would join the consortium." .
SCR:014445 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xFITOM" ;
definition: "A fully customizable program that uses a graphical user interface to locate transcription factor-binding sites in genomic sequences. xFITOM scans DNA or RNA sequences for putative binding sites as defined by a collection of aligned known sites, a consensus sequence in IUPAC degenerate-base format, or a combination of the two." .
SCR:014446 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ventana Image Viewer" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 12,2024. A digital slide image software that is used with the VENTANA iScan Coreo Au slide scanner. This software helps facilitate viewing high quality images with little latency. The image view software can also support the viewing of multiple images simultaneously." .
SCR:014447 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IMAGIC" ;
definition: "An image analysis software that can process spectra and other multi-dimensional data-sets. The software package is aimed at processing large data sets from (cryo-) electron microscopy, especially in the field of single particle analyses. This software can be used with light and raster-tunneling microscopes, computer tomographs, FT-IR spectrometers and other signal collecting devices. This resource provides three-dimensional data processing and angular reconstitution modules that allow the three-dimensional reconstruction with point-group symmetry from the two dimensional electron microscopy projections. These models aid in the analysis of the macromolecules." .
SCR:014448 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Wolfram Mathematica" ;
definition: "A technical computing software and computing environment that provides users with algorithms and mathematical functions for various projects and purposes. The resource incorporates other Wolfram products such as Wolfram Algorithmbase, Wolfram Language, and Wolfram Knowledgebase." .
SCR:014449 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Maple" ;
NIFRID:synonym "Maple Soft",
"Maple Software",
"MapleSoft",
"Maplesoft" ;
definition: "Mathematical software that can compute both numeric and symbolic solutions. It can be used to analyze, explore, visualize, and solve mathematical problems." .
SCR:014450 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Online Application for Survival Analysis (OASIS)" ;
NIFRID:synonym "Online Application for Survival Analysis" ;
NIFRID:abbrev "OASIS" ;
definition: "A tool for various statistical tasks involved in analyzing survival data which provides a uniform platform to facilitate efficient statistical analyses of survival data in the aging field. The statistical features of OASIS include the calculation of Kaplan-Meier estimates, mean/median lifespan, mortality rate, Mantel-Cox Log-Rank test, Fishers exact test, weighted Log-Rank test, Kolmogorov-Smirnov test and Neymans smooth test. Moreover, OASIS generates survival and mortality curves that can be easily exported and modified by using common graphic softwares." .
SCR:014454 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Macrogen" ;
NIFRID:synonym "Macrogen Inc." ;
definition: "A company that provides a variety of next generation sequencing services. The company provides researchers with whole genome resequencing, exome sequencing, targeted sequencing, transcriptomics, and epigenome sequencing." .
SCR:014455 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LCModel" ;
definition: "Software for automatic quantification of in vivo proton MR spectra. Though it is mainly used for brain analysis, it can be used for a variety of analyses in different areas of the body. It receives time-domain data as input and gives a one page summary output. It is fully automatic, non-interactive, and operator-independent., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014456 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuriteOrientation" ;
definition: "A method to automatically extract the neurite centerline and compute orientation properties at multiple scales using source code. Code is dependent on standard Python-based scientific packages and presegmentation of images." .
SCR:014457 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011591" ;
rdfs:label "Brain Transcriptome Database" ;
NIFRID:synonym "BrainTX",
"Cerebellar Development Transcriptome Database CDT-DB" ;
definition: "A platform that allow users to visualize and analyze transcriptome data related to the genetics that underlie the development, function, and dysfunction stages and states of the brain. Users can search for cerebellar development genes by name, ID, keyword, expression, and tissue specificity. Search results include general information, links, temporal, spatial, and tissue information, and gene category." .
SCR:014461 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Andor iQ" ;
definition: "A live cell imaging software that allows for control of iXon EMCCD and sCMOS cameras in synchronized combination with a number of additional imaging hardware devices. iQ can be used to run experiments to investigate dynamic processes in both single cells and multicellular systems, image fixed samples, and generate 3 dimensional image volumes for analysis." .
SCR:014462 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Helicon Focus" ;
definition: "A software designed to aid in macro or micro photography using the focus-stacking technique. It takes multiple shots at many different focus distances and combines the images to a fully focused image." .
SCR:014464 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Grapher" ;
definition: "A technical graphing software that can be used to create various graph types including 2D or 3D plots, statistical graphs, pie charts, contour plots, and surface plots. The user can customize the graph, axes, legend, and plots." .
SCR:014465 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AmplifX" ;
definition: "A software for managing, testing, and drawing primers. The software can locate primers for target sequences, calculate the quality score, predict amplified fragments and dimers, and create graphic representations of the primers." .
SCR:014466 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "2100 Expert Software" ;
definition: "A software for analyzing digital assay data. The software performs RNA quality control, comparison between multiple chips, smear analysis, and data export in multiple formats." .
SCR:014467 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:funrich" ;
rdfs:label "FunRich: Functional Enrichment analysis tool" ;
definition: "A software tool used for functional enrichment and interaction network analysis of genes and proteins. Users can search against a default background database or load customized database. The results can be depicted as venn, bar, column, pie and doughnut charts." .
SCR:014468 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Demon Voltammetry and Analysis Software" ;
definition: "A software for performing fast scan cyclic voltammetry recordings in brain tissue for detection of neurotransmitters. It was written in the LabView programming language and can be used to provide command voltage to equipment and record the resulting waveforms. The analysis portion of the software can view and export data, apply noise filters, perform chemometric and waveform kinetic analysis, and create figures." .
SCR:014469 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MaxIm DL " ;
NIFRID:synonym "Cyanogen Imaging MaxIm DL" ;
definition: "An imaging software for collecting and analyzing astronomical image data. This software includes observatory integration, and control of astronomical equipment to integrate the researcher's camera, autoguider, filter wheels, focuser, camera rotator, telescope mount, observatory webcam, remote switches, weather station and dome." .
SCR:014470 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Entropy Mapping Toolbox" ;
NIFRID:synonym "Brain Entropy Mapping Toolbox: BENtbx" ;
NIFRID:abbrev "BENtbx" ;
definition: "A toolkit for mapping brain entropy using fMRI. It uses several functions from ASLtbx. At its core, the toolkit is a collection of batch scripts that implement a pipeline for processing fMRI data in order to get Sample entropy for each voxel." .
SCR:014475 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vector Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. A full service viral vector core facility located at the University of Pennsylvania. This facility provides technological resources for investigators in their use of viral based vectors for gene transfer. The main objective of this core is to provide investigators with state-of-the-art vector technology for preclinical studies and other basic research applications, that will then increase understanding of gene function and the further development of therapeutic vectors." .
SCR:014477 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Proteome Discoverer" ;
definition: "Software for identifying, characterizing, and quantifying proteins in biological samples. Can be used for range of proteomics workflows such as protein and peptide identification, PTM analysis, and isobaric mass tagging for quantification. Supports multiple database search algorithms and multiple dissociation techniques., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014478 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpikeSort 3D" ;
definition: "A software for spike waveform-to-cell classification which can be used both online and offline. The user can identify and isolate clusters/cells using 3D manipulation, as well as calculate waveform parameters like peak, valley, area, and energy." .
SCR:014479 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Inkscape" ;
definition: "A vector graphics software which runs on Windows, Mac OS X and GNU/Linux. It can import and export various file formats, including SVG, AI, EPS, PDF, PS and PNG. Features include object creation, object manipulation, color editing, and text editing." .
SCR:014480 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KlustaKwik" ;
definition: "A program for cluster analysis by fitting a mixture of Gaussians. KlustaKwik works by implementing a hard EM algorithm with unconstrained covariance matrices. It was designed for the specific problem of spike sorting of multi-electrode arrays, but can be used for any application." .
SCR:014481 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WIS-NeuroMath" ;
definition: "A software tool for automated analysis and quantification of fluorescent microscopy images of nerve cells in vivo and in vitro. The tool also can be used for analysis of cell morphology, neurite length analysis for sections with no cell body, and ganglion explant analysis." .
SCR:014482 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clickjoint" ;
definition: "A software for analyzing animal movement on videos and images. The user can define the animal's joints so the software can analyze using a tracking algorithm." .
SCR:014483 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Minitab" ;
definition: "A statistical software package that allows the user to import data, create graphs, and perform statistical analysis. It can perform basic statistical tests like descriptive statistics, hypothesis tests, confidence intervals, and normality tests as well as regression and ANOVA and quality assessment." .
SCR:014484 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Plot Digitizer" ;
definition: "An application for extracting numerical data from pictures. It can be used to view the original data values (x,y) from printed graphs. The user can perform basic operations like cut, copy, paste as well as select axes colors, zoom in or out, remove noise, re-calibrate the y-axis, and insert, edit or move points. It offers support for GIF, JPEG, and PNG files." .
SCR:014485 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MaxQuant" ;
definition: "A quantitative proteomics software package for analyzing large-scale mass-spectrometric data sets. It is a set of algorithms that include peak detection and scoring of peptides, mass calibration, database searches for protein identification, protein quantification, and provides summary statistics." .
SCR:014486 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CopyCaller" ;
definition: "A software for analyzing real-time PCR data and quantifying DNA targets. It can perform copy number analysis, report confidence in copy number, display data in table and graphic format, change analysis parameters, and view data analysis information for multiple experiments at once." .
SCR:014487 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BayesTraits" ;
definition: "A computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. It incorporates earlier programs including Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a discrete number of states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, ancestral states and correlations among pairs of traits., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014488 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DNASIS" ;
definition: "A bioinformatics software for editing, annotating, and analyzing DNA, RNA, and amino acid sequences. It includes analytical tools and can be expanded with homology search, multiple alignment and base calling, and sequence assembly (Phred/Phrap) modules." .
SCR:014489 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BD CellQuest Pro" ;
definition: "A software for acquiring and analyzing flow cytometry data. The user can create plots with elements like regions, gates, statistics, markers, and annotated text. The software can also be used for batch analysis or quality control of analysis. Results can be exported and saved., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014490 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProbeFinder " ;
definition: "A software for primer design. The user can choose the target sequence or gene and design primers for the real-time PCR. After, the user can examine the results and choose from the recommended probes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014491 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ImageMagick" ;
definition: "Software suite for creating, editing, composing, and converting bitmap images. It can read and write images in over 200 formats including PNG, JPEG, JPEG-2000, GIF, TIFF, DPX, EXR, WebP, Postscript, PDF, and SVG. The user can use this software to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves." .
SCR:014492 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gatan Microscopy Suite" ;
definition: "A software for (scanning) transmission electron microscope experimental control and analysis." .
SCR:014493 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mercator" ;
definition: "A software package for quantification of histological sections. This software performs functions including: management and analysis of regions of interest, annotations, statistical analysis, and 3D visualization. These results are edited in an Excel-compatible spreadsheet." .
SCR:014494 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TopScan Lite" ;
definition: "A single point video tracking system. It uses the center of the mass of the animal and tracks it over the course of the experiment to determine location, distance traveled, velocity etc. Examples of applications include: Open Field, Novel Object Recognition, Maze Analysis, Morris Water Maze, Barnes Maze, Place Preference, etc." .
SCR:014495 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FreezeScan" ;
definition: "Software for detecting the onset and completion of freezing behavior of a rodent. It outputs the freezing behaviors as a sequential list, allowing for further statistical analysis. Freezescan detects freezing behaviors, random intervals, interval freezing, and activity levels. It also detects animal activity during the experiment and can output in quantitative and graphical form." .
SCR:014496 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QI Macros" ;
definition: "A statistical process control (SPC) add-in for Microsoft Excel. The user can select their data and the program will draw the desired chart or run the desired statistical test." .
SCR:014497 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VitalView Software" ;
definition: "A data acquisition and analysis software program. The program collects data from sensors and receivers and displays graphical data analysis as well as descriptive statistics." .
SCR:014498 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Predicting Language Outcome and Recovery After Stroke (PLORAS)" ;
definition: "A research project investigating the difficulties of recovering language after stroke (aphasia). The overall aim of the study is to give future stroke survivors accurate predictions of their aphasia recovery by creating clinical tools and discerning why some patients recover from aphasia better than others." .
SCR:014501 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuroscience Information Toolbox" ;
NIFRID:synonym "Neuroscience Information Toolbox (NIT)" ;
NIFRID:abbrev "NIT" ;
definition: "A toolkit for EEG-fMRI multimodal fusion and fMRI data preprocessing and analysis. NIT allows users to perform batch processing of fMRI data analysis and data preprocessing based on SPM8, as well as parallel computing for data preprocessing, nuisance signals removal, and FCD and FOCA calculating. Users can also use NIT to calculate functional connectivity density and four dimensional (spatio-temporal) consistency of local neural activities." .
SCR:014504 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Line Authentication Testing" ;
NIFRID:synonym "cell line identification testing; cell authentication",
"Genetica DNA Laboratories Cell Line Authentication" ;
NIFRID:abbrev "CLA" ;
definition: "A material analysis service of the commercial organization Genetica DNA Laboratories which provides authentication of human cancer cell lines, stem cell lines and xenografts utilizing STR DNA technology." .
SCR:014505 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "International Geo Sample Number" ;
NIFRID:synonym "International Geo Sample Number (IGSN)",
"International GeoSample Number" ;
NIFRID:abbrev "IGSN" ;
definition: "A persistent unique identifier for samples and specimens collected from the natural environment. IGSNs are created by the user and are case sensitive. They should be concise, machine readable, and non-derivable to ensure originality. IGSNs were created and are organized by the IGSN e.V., whose goal is to implement and promote standard methods for locating, identifying, and citing physical samples with confidence by operating an international IGSN registration service with a distributed infrastructure for use by and benefit to its members." .
SCR:014507 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rapid Novor Inc" ;
NIFRID:synonym "Rapid Novor" ;
definition: "A commercial biomaterial analysis service dedicated to developing antibody protein sequencing and characterization technologies. The main service it offers is antibody de novo sequencing. Both heavy and light chains are directly sequenced using multiple enzyme digestion and high resolution LC-MS/MS. The sequencing process does not require hybridoma, mRNA, or other sequence information. Rapid Novor also offers to make recombinant versions of antibody proteins sent in for sequencing." .
SCR:014508 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012052" ;
rdfs:label "The Cancer Immunome Database" ;
NIFRID:synonym "The Cancer Immunome Database (TCIA)" ;
NIFRID:abbrev "TCIA" ;
definition: "A database which provides results of comprehensive immunogenomic analyses of next generation sequencing data for 19 solid cancers from The Cancer Genome Atlas and other datasources. The database can be queried for the gene expression of specific immune-related gene sets, cellular composition of immune infiltrates (characterized using gene set enrichment analyses and deconvolution), neoantigens and cancer-germline antigens, HLA types, and tumor heterogeneity (estimated from cancer cell fractions). It also provides survival analyses for different types immunological parameters." .
SCR:014511 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Py3DN" ;
definition: "A set of software tools used for morphometric analysis and visualization of the 3D structure of neurons. Py3DN works exclusively with data collected with the commercial system Neurolucida." .
SCR:014512 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PrePubMed" ;
definition: "A database which indexes preprints from arXiv q-bio, PeerJ Preprints, Figshare, bioRxiv, F1000Research, and The Winnower." .
SCR:014513 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Serial Cloner" ;
NIFRID:synonym "Serial Cloner 2.6" ;
definition: "Molecular biology software for DNA cloning and analysis and construct preparation. Serial Cloner provides tools for analyzing and manipulating sequences and assists in setting up new sub-cloning projects and in preparing electronic versions of these constructs. The software reads and writes DNA Strider-compatible files and imports and exports files in the universal FASTA format." .
SCR:014514 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012061" ;
rdfs:label "Genomic Data Commons Data Portal (GDC Data Portal)" ;
NIFRID:synonym "GDC Data Portal",
"Genomic Data Commons Data Portal" ;
definition: "A unified data repository of the National Cancer Institute (NCI)'s Genomic Data Commons (GDC) that enables data sharing across cancer genomic studies in support of precision medicine. The GDC supports several cancer genome programs at the NCI Center for Cancer Genomics (CCG), including The Cancer Genome Atlas (TCGA), Therapeutically Applicable Research to Generate Effective Treatments (TARGET), and the Cancer Genome Characterization Initiative (CGCI). The GDC Data Portal provides a platform for efficiently querying and downloading high quality and complete data. The GDC also provides a GDC Data Transfer Tool and a GDC API for programmatic access." .
SCR:014515 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nuclear Receptor Cistrome" ;
NIFRID:synonym "NR Cistrome" ;
definition: "A web-interface that enables users to access and download the processed ChIP chip/seq data of nuclear receptors, co-regulators and histone modifications. The web resources also includes processed differential expression data under ligand induction in conditions matched to ChIP_chip/seq data whenever possible. All the ChIP chip/seq peak regions are annotated with enriched HRE and co-regulator motifs. A list of predicted hormone response genes from integration of nuclear receptor ChIP chip/seq data and differential expression data is also readily available to the users." .
SCR:014516 a owl:NamedIndividual ;
rdfs:label "EuReGene" ;
definition: "A European organization primarily concerned with the study of renal disorders. The organization is working towards discovering the genes responsible for renal development, renal disease and the related proteins and their actions. EuReGene consists of a consortium of scientists, clinicians, and SME partners that study functional genomics and their application in kidney research." .
SCR:014517 a owl:NamedIndividual ;
rdfs:label "Stem Cell Genome Anatomy Projects " ;
NIFRID:synonym "SCGAP Urologic Epithelial Stem Cells Project" ;
NIFRID:abbrev "SCGAP" ;
definition: "A research organization which aims to conduct a variety of stem cell research projects. These projects include: to CD phenotype the human prostate and bladder using a confocal microscopy, to CD the phenotype of the mouse prostate and bladder, to profile samples of basal and stromal cells using uncultured cells, to confirm cell-type specific expression of genes that were identified by array analysis, and to create a database with the resulting database." .
SCR:014518 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GATACA GUDMAP Gene Explorer " ;
definition: "A database which can be used to search for genes critical for a variety of Genito-Urinary system functions and diseases." .
SCR:014519 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CoSMoMVPA" ;
definition: "A multi-modal multivariate pattern analysis of neuroimaging data in Matlab / GNU Octave. Links to examples, exercises, and information for developers are available on the main page." .
SCR:014520 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TDTPy" ;
NIFRID:synonym "tdtpy" ;
definition: "Software for interfacing with Tucker-Davis System 3 hardware. It is a Python wrapper around Tucker-Davis Technologies ActiveX library. Along with standard operations, the software can conduct type conversions between analog and digital units, handle robust errors, and has a remote procedure call server that allows multiple processes and/or programs to communicate with the hardware across the same connection." .
SCR:014521 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clone Manager Software" ;
definition: "A software system to assist with cloning simulation, enzyme operations, and graphic map drawing. Clone Manager can also be used as a way to view or edit sequence files, find open reading frames, translate genes, or find genes or text in files. Clone Manager Professional is an upgraded version of Clone Manager Basic., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014522 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cornell Heart Lung Blood Resource for Optogenetic Mouse Signaling (CHROMus)" ;
NIFRID:synonym "Cornell Heart Lung Blood Resource for Optogenetic Mouse Signaling" ;
NIFRID:abbrev "CHROMus" ;
definition: "A transgenic mouse supplier which develops mouse lines expressing genetically encoded calcium indicators (GECIs) and optogenetic effectors in lineages relevant to cardiac, vascular, lung and blood diseases. The mouse strains created are designed to allow for inter crossing resulting in co-expression of sensors with discrete emission wavelengths in interacting lineages (e.g. endothelial and smooth muscle cells), as well as optically compatible effector/detector pairs." .
SCR:014525 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyLMM" ;
definition: "A Python package for doing linear mixed model associations in genome wide association studies (GWAS). The software corrects for population structure using EMMA." .
SCR:014526 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Seahorse Wave" ;
definition: "Software to manage Seahorse XFe24 Analyzer, which measures OCR and ECAR of live cells in a 24-well plate format. Users can create and modify assay templates and analyze and manage data." .
SCR:014527 a owl:NamedIndividual ;
rdfs:label "Brain.io" ;
NIFRID:synonym "Brain.io The Path to Paradigm Shift" ;
definition: """A startup research, development and innovation company based in The Grand Duchy of Luxembourg working on four major areas:
Open Research, as Information Hub; Information Technology, as The Common Brain; Collective Awareness, as Manifesto; and Biophysics, as Human Extensibility. The Information Hub researches a methodology to conduct open research using a collaborative approach designed for multi-disciplinary interventions, multi-scope goal alignment, advanced analytics and a unified research experience for international cooperation. The Common Brain researches an open source intelligent architecture for future internet, one that is deeply sustainable over a highly distributed hybrid network, self-governed, heterogenous, and logical. Manifesto researches a methodology for a collaborative approach for policy making, open standardization, accreditation, verification and compliance. Human Extensibility researches the establishment of the scientific ground for a field of science concerned with the study of the physics and physiology of the human being, to provide techniques and genetic algorithms for human extensibility.""" .
SCR:014528 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciUnit" ;
definition: "A test-driven framework for formally validating scientific models against data." .
SCR:014529 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford CNI" ;
NIFRID:synonym "Stanford Center for Cognitive and Neurobiological Imaging",
"Stanford Center for Cognitive and Neurobiological Imaging (CNI)" ;
definition: "A shared facility at Stanford University dedicated to research and teaching for researchers and students in cognitive and neurobiological sciences. The core instrumentation provided by the CNI is a research-dedicated 3T MRI scanner, a GE Discovery MR750. The CNI has an array of MRI Coils, including Nova Medical 32-channel and 16-channel head coils and a GE 8-channel head coil. For stimulus delivery they provide a custom large-screen flat-panel display as well as a goggle system with eye tracker and audio. Other equipment includes an MR-compatible 256-channel EEG system, a Polhemus 3D digitizer used for EEG electrode localization, Fiber Optic Response Devices (FORP), as well as a MRI Simulator (Mock Scanner)." .
SCR:014530 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GUID Tool" ;
definition: "A customized software application that generates a Global Unique Identifier for each study participant. The GUID is a universal subject ID that allows researchers to share data specific to a study participant without exposing personally identifiable information (PII). The GUID has been approved by the NIH Office of General Counsel." .
SCR:014531 a owl:NamedIndividual ;
rdfs:label "CyVerse" ;
NIFRID:synonym "iPlant" ;
definition: """A google drive interface for scientific big data. CyVerse cyberinfrastructure is applicable to all life sciences disciplines and works equally well on data from plants, animals, or microbes.
It provides life scientists with computational infrastructure to handle large datasets and complex analyses. Its extensible platforms provide data storage, bioinformatics tools, image analyses, cloud services, and APIs.""" .
SCR:014532 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.461811.b" ;
rdfs:label "T1D Exchange" ;
NIFRID:synonym "T1D Exchange Inc." ;
definition: "Provides access to resources T1D researchers need to conduct clinical studies. Data sets from their clinic registry is openly available, as are new study results. They also offer use of T1D Discovery Tool, which allows users to search different fields from registry data, and T1D Exchange Biobank, which offers specimen types such as serum, plasma, white blood cells, DNA, and RNA." .
SCR:014534 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LANDMark BioBanks" ;
definition: "A repository of human tissue samples collected during the LANDMark study (Longitudinal Assessment of Neuropathy in Diabetes using novel ophthalmic markers). The LANDMark Biobank longitudinal dataset contains blood and tissue (skin) samples and matching detailed phenotypic data of three microvascluar complications of type 1 diabetes: neuropathy, nephropathy and retinopathy." .
SCR:014535 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Diabetes Research Centers " ;
definition: "Diabetes Research Centers (DRC) is an integrated program of diabetes, endocrinology and metabolism research." .
SCR:014536 a owl:NamedIndividual ;
rdfs:label "FlashX" ;
definition: "A collection of big data analytics tools. FlashX performs data analytics in the form of graphs and matrices and utilize solid-state drives (SSDs) to scale to large datasets in a single machine. It has three main components: FlashGraph, FlashMatrix, and FlashR. FlashGraph is a general-purpose programming framework with a vertex-centric programming interface for large-scale graph analysis. FlashMatrix is a matrix computation engine that provides a small set of generalized matrix operations to express varieties of data mining and machine learning algorithms. FlashR is an extension of the R programming framework to process datasets at a scale of terabytes with the speed of optimized parallel C code." .
SCR:014538 a owl:NamedIndividual ;
rdfs:label "pubatlas.org" ;
NIFRID:synonym "PubAtlas",
"PubAtlas: Association Explorer" ;
definition: "A program that searches PubMed to generate a heat map using a user's search terms. It also allows you to see over the years how many publications there are with the user's search term(s)." .
SCR:014539 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KnowledgeSpace" ;
NIFRID:synonym "Knowledge Space",
"Neuroscience Knowledge Space" ;
NIFRID:abbrev "KS" ;
definition: "A community encyclopaedia that links brain research concepts with data, models and literature from around the world. It is an open project where users can participate and contribute to the global research community." .
SCR:014540 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIRStar" ;
NIFRID:synonym "NIRS Acquisition Software by NIRx",
"NIRStar - NIRS Acquisition Software by NIRx" ;
definition: "Commercial software tool designed to function as a multiplatform instrument controlling environment for NIRx products. Its features include the ability to run full or partial sensing configurations, montage views and viewing options, and a real-time system status reporting display." .
SCR:014541 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIRSPORT" ;
definition: "A commercial cap product that records fNIR signals from the participant. NIRSport integrates for concurrent measurements with EEG, fMRI, eye-tracking, cochlear implants, TMS, tDCS, EMG, pulse oximetry, and other modalities for concurrent measurements. Researchers can conduct tandem studies with two separate systems synchronized to operate simultaneously." .
SCR:014542 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mobidb" ;
rdfs:label "MobiDB" ;
definition: "A database of protein disorder and mobility annotations. The database features three levels of annotation: manually curated data (which are extracted from the DisProt database), indirect data, and predicted data. Additional annotations are included from external sources, including UniProt, Pfam, PDB, and STRING." .
SCR:014543 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DataJoint" ;
NIFRID:synonym "DataJoint: Data management for science labs" ;
definition: "MATLAB and Python 3 high-level programming interface for MySQL databases to support data processing chains in science labs. Specifically designed to provide robust and intuitive data model for scientific data processing chains.Used for scientific data pipelines and workflow management." .
SCR:014544 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AbMiner" ;
definition: "A tool that allows users to search for appropriate, commercially available antibodies for research purposes, and to match each antibody to its respective genomic identifiers. The antibodies are screened by Western blot and the results are listed on AbMiner. AbMiner also includes the diluitons used and vendor information for all antibodies. Users can conduct general or advanced searches and browse antibodies by gene." .
SCR:014545 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Preclinical Data Forum Network" ;
NIFRID:synonym "European College of Neuropsychopharmacology - Preclinical Data Forum Network",
"Preclinical Data Forum Network of the ECNP",
"Preclinical Data Forum Network of the European College of Neuropsychopharmacology" ;
definition: "A forum for preclinical data sharing and interpretation to enhance its utility for clinical research and development. The forum allows researchers to communicate and collaborate on modern preclinical issues and data sharing." .
SCR:014546 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AFQ: Automated Fiber Quatification" ;
NIFRID:abbrev "AFQ" ;
definition: "A framework for generating Tract Profiles of tissue properties for major fiber tracts in healthy and diseased brains. Online documentation can be found at: https://github.com/yeatmanlab/AFQ/wiki. AFQ has been tested for MATLAB r2009b through MATLAB r2014b. It requires functions from the MATLAB stats toolbox, vistasoft and SPM." .
SCR:014547 a owl:NamedIndividual ;
rdfs:label "ASIPro" ;
NIFRID:synonym "ASIPro VM" ;
definition: "An image analysis software." .
SCR:014548 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pixel-Wise Modeling Tool" ;
NIFRID:synonym "Pixelwise Modeling Tool" ;
NIFRID:abbrev "PXMOD" ;
definition: "A software to apply modeling techniques directly to individual pixels within an image and create a parametric map from it. The resulting outcomes show the values within the model parameter in each image pixel. This is used to make quantitative tissue properties easier to visualize and compare with information from other sources. Furthermore, the quantitative maps can then be statistically analyzed within the software using a step-by step method. This tool is designed to be used with the PKIN tool." .
SCR:014549 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FluorChem Q Imager" ;
definition: "A software used for quantitative Western blot imaging and analysis. This software is compatible with several dyes and kits, providing extra flexibility for application. This software is designed to be able to look at multiple proteins simultaneously on a single assay. This software is sensitive enough to distinguish co-migrating proteins, such as phosphorylated and unphosphorylated isoforms." .
SCR:014550 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dotSlide Software" ;
definition: "An imaging system that can be used in lieu of conventional light microscopy. The specimen, rather than being viewed through the eyepiece of the microscope, is displayed a monitor after the system has scanned it at the desired resolution. This is done by a series of scans of single images acquired through the scanning process being automatically stitched together to make the ultimate seamless overview image through the \"virtual slide\". The digital images can be saved to a web-based database so that it can be accessible for online conferences." .
SCR:014551 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016238",
"SCR_018869" ;
rdfs:label "Olympus cellSens Software" ;
NIFRID:synonym "Olympus cellSens Dimension",
"Olympus CellSens Imaging software" ;
definition: "Software suite for image acquisition and analysis. The software can be paired with high-quality cameras to maximize output quality and export it for sharing and research applications." .
SCR:014552 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID: 100005191",
"grid.428355.d" ;
rdfs:label "CRAIG H. NEILSEN FOUNDATION" ;
NIFRID:synonym "CRAIG NEILSEN FOUNDATION",
"NEILSEN FOUNDATION" ;
NIFRID:abbrev "CHN" ;
definition: "A non-profit organization that awards grants to a broad spectrum of charities, including those that benefit spinal cord injury efforts. The Foundation is primarily dedicated to funding extensive research, education and quality of life programs for improving the lives of people affected by spinal cord injury." .
SCR:014553 a NLX:152328,
owl:NamedIndividual .
SCR:014554 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aging Dementia and Traumatic Brain Injury Study" ;
NIFRID:synonym "Aging Dementia and TBI Study" ;
definition: "The Aging, Dementia and Traumatic Brain Injury Study is a detailed neuropathologic, molecular and transcriptomic characterization of brains of control and TBI exposure cases from a unique aged population-based cohort from the Adult Changes in Thought (ACT) study. The study contains six data sets: histology and immunohistochemistry, in situ hybridization, rna-seq, protein quantification by luminex, isoprostane quantification, and specimen metadata." .
SCR:014555 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cBioPortal" ;
NIFRID:synonym "cBioPortal for Cancer Genomics" ;
definition: "A portal that provides visualization, analysis and download of large-scale cancer genomics data sets." .
SCR:014556 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ELIXIR Tools and Data Services Registry" ;
NIFRID:synonym "European Infrastructure for Biological Information Tools" ;
definition: "Elixir Interoperability Platform to help people and machines to discover, access, integrate and analyse biological data. Encourages life science community to adopt standardized file formats, metadata, vocabularies and identifiers and works internationally to achieve its goals. Bioinformatics resource registry that provides scientific and technical information about analytical tools and data services for bioinformatics. Gateway to databases and tools for life science data analysis.Provides comprehensive and up-to-date catalogue of resources that are interactive and downloadable, and that offer programmatic access. The registry also allows the community to upload their own resources to the registry following a simple log in procedure." .
SCR:014557 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioBlend Library" ;
NIFRID:synonym "BioBlend" ;
definition: "A Python library which provides Python access to and interaction with Galaxy's API and CloudMan. The library allows users to create a CloudMan compute cluster via an API and directly from a local machine, reconnect to an existing CloudMan instance and manipulate it, and interact with Galaxy via a straightforward API and an object-oriented API. The library itself can be used with either service irrespective of the other." .
SCR:014558 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:proteinprospector" ;
rdfs:label "Protein Prospector" ;
NIFRID:synonym "ProteinProspector" ;
definition: "A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass." .
SCR:014559 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DynaMine" ;
definition: "An NMR based method for protein folding prediction. Users can enter a UniProt identifier, FASTA sequences, or upload a file containing FASTA sequences and results are returned., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014560 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Transgenic Huntington's Disease Monkey Resources" ;
NIFRID:synonym "Transgenic Huntington's Disease Monkey Resources (THDMR)" ;
NIFRID:abbrev "THDMR" ;
definition: "Center for resources to facilitate basic and preclinical applications of the transgenic Huntington's disease (HD) monkey model to advance scientific knowledge and the discovery of a cure for HD. Their resources include longitudinal biomaterials and MRI data, postmortem biomaterials, and research proposal assistance." .
SCR:014561 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FRAGFOLD" ;
NIFRID:synonym "GPGPUFRAGFOLD",
"GPUFRAGFOLD" ;
definition: "A structural folding computational tool. The method is based on the assembly of supersecondary structural fragments taken from highly resolved protein structures using a simulated annealing algorithm." .
SCR:014562 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "linkRbrain" ;
NIFRID:synonym "LinkRBrain",
"linkRbrain: online tool for neuroscience" ;
definition: "An online tool for managing and viewing datasets. Data can be viewed in 2D or 3D with activation points as points clouds or projections on the cortex surface. Data can be imported as a NIfTI file or a list of activation peaks and results can be exported as a PDF file." .
SCR:014564 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Extensible Simulation Package for Research on Soft matter (ESPResSo)" ;
NIFRID:synonym "Extensible Simulation Package for Research on Soft matter" ;
NIFRID:abbrev "ESPResSo" ;
definition: "A highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, ferrofluids and biological systems like DNA and lipid membranes." .
SCR:014565 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:gromacs",
"OMICS_05081" ;
rdfs:label "GROMACS" ;
NIFRID:synonym "Gromacs" ;
definition: "Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers." .
SCR:014566 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Comstat" ;
definition: "A software that is used to analyze image stacks of biofilms that were recorded by confocal microscopes. While this program does not have any statistical calculation methods, it can extract a number of quantitative parameters from the images. This software was initially developed by Arne Heydorn and Bjarne Ersboll as a MatLab script until it was expanded into an independent software in 2008." .
SCR:014567 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CombineZP" ;
definition: "A software used to process stacks of digital images. All of the resulting images are processed to have the same dimensions and then are consolidated into a single image." .
SCR:014568 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:cummerbund",
"OMICS_07349" ;
rdfs:label " CummeRbund" ;
definition: "Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions." .
SCR:014569 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VolView" ;
definition: "A software for volume visualization that can be used by researchers to explore and analyze medical and scientific data. This software uses a variety of tools to load and visualize the data on either a 2D or 3D display. Theses tools include volume rendering, maximum intensity projections and oblique reformatting. Visualizations can be saved mid-session and be reopened at a later time." .
SCR:014570 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NewCAST" ;
NIFRID:synonym "Visiopharm NewCAST" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 18, 2018; A software which provides unbiased stereological estimates of numbers, lengths, areas, and volumes present in images that were captured by microscopes or virtual slides. This software is intended to estimate structural information in a 3D format from 2D tissue sections.
There are other software tools at this company, but they have either changed names or are simply different software tools." .
SCR:014571 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Swedish Information Centre for Rare Diseases" ;
NIFRID:synonym "Swedish Information Center for Rare Diseases" ;
definition: "A database which contains detailed information rare diseases. The information is produced in collaboration with leading medical specialists and patient associations. New disease descriptions are added continuously and the texts are updated on a regular basis. Both the common names and the technical names for diseases are provided." .
SCR:014572 a owl:NamedIndividual ;
rdfs:label "National Organization for Rare Disorders (NORD)" ;
NIFRID:synonym "National Organization for Rare Disorders" ;
NIFRID:abbrev "NORD" ;
definition: "An organization which supports those with rare diseases and those researching rare diseases." .
SCR:014573 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NORD Rare Disease Database" ;
definition: "A database which provides brief introductions of rare diseases. New topics and diseases are added with the help of rare disease medical experts. This is mainly targeted at patients and their families but has useful information for professionals." .
SCR:014574 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Med Associates Video Freeze Software" ;
definition: "Automation software used to analyze fear behavior in rodents. Freezing is represented in the data file in several different ways, including the total time the subject spends motionless during the session, the percent of time motionless, the number of freezing episodes or occurrences, or as an average index of motion." .
SCR:014575 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Desmond" ;
definition: "Software designed to perform high-speed molecular dynamic simulations of biological systems on conventional commodity clusters, supercomputers and GPUs. This code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms with a large number of processors. It can be used with a single computer." .
SCR:014576 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BRAINS Imagebank" ;
NIFRID:synonym "Brain Images of Normal Subjects (BRAINS) Imagebank",
"Brain Images of Normal Subjects Imagebank" ;
definition: "A searchable collection of anonymised images and associated clinical data. It includes normal individuals at all ages (from prenatal to old age). The image bank contains integrated data sets already collected as part of research studies which include control subjects. New data is added as they become available." .
SCR:014577 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MicrocircuitDB" ;
definition: "A database for storing and efficiently retrieving realistic computational models of brain microcircuits and networks. The focus is on microcircuits that are based on experimentally demonstrated properties of neurons and their connectivity." .
SCR:014578 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ORModelDB" ;
NIFRID:synonym "Olfactory Receptors Model Database" ;
definition: "A repository of the results of the efforts of the scientific community in computationally elucidating the structure of the olfactory receptor with a view to establishing a mechanistic basis for OR-odorant binding." .
SCR:014579 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Odyssey CLx" ;
NIFRID:synonym "Odyssey CLx Imaging System" ;
definition: "A data analysis software developed to simplify and record data from fluorescent related assays such as Western Blots, EMSAs, and Western Assays. This software will consolidate all of the resulting data into one easy-to-track image, and thus removes the need for multiple exposures, as well as standardizing the resulting fluorescent bands without image saturation, blowout, or removed sensitivity. Odyssey CLx is capable of scanning multiple mini-blots, microplates, or slides at the same time." .
SCR:014580 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MC DataTool" ;
NIFRID:synonym "MC_DataTool" ;
definition: "An add-on tool used to export data retrieved with the MC_Rack program. This software is used to convert MC_Rack data files into other file formats." .
SCR:014581 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "nif-0000-33434" ;
rdfs:label "HDD Access" ;
NIFRID:synonym "3M HDD Access",
"3M Healthcare Data Dictionary" ;
NIFRID:abbrev "HDD" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Database built up with software and services that maintains multiple versions of terminologies, map sets, and values sets concurrently. HDD Access has superseded Concept Hub." .
SCR:014582 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TIDA" ;
definition: "A software which is used to acquire physiological data from the HEKA Patch Clamp Amplifiers and HEKA interfaces." .
SCR:014583 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:fastqc",
"OMICS_01043",
"SCR_005539" ;
rdfs:label "FastQC" ;
NIFRID:synonym "FastQC v0.11.5" ;
definition: "Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis." .
SCR:014584 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:qmrlfs-finder" ;
rdfs:label "QmRLFS-finder" ;
NIFRID:synonym "QmRLFS finder" ;
definition: "A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis." .
SCR:014585 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Image Reader LAS-1000" ;
definition: "A software which is used to control the LAS-1000plus luminescent image analyzer. This software adjusts the focus, exposure time, sensitivity, and cooling temperature, and will record the data after the sample is scanned." .
SCR:014586 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Extraction Tool" ;
NIFRID:synonym "Brain Extraction Tool (BET2)",
"Brain Extraction Tool (BET)" ;
NIFRID:abbrev "BET",
"BET2" ;
definition: "Software tool which deletes non-brain tissue from image of the whole head and estimates both internal and external skull surfaces." .
SCR:014587 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss Axioskop Software" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVCE, documented January 19, 2022. Software used to control the Zeiss Axioskop microscope." .
SCR:014588 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PowerChrom" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. A software which collects, displays, and analyzes chromatographic signals. This software doesn't require any programming, and collects signals from one or two detectors. PowerChrom is supplied as part of the PowerChrom system, or separately for use with e-corder recording systems." .
SCR:014589 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vision Egg" ;
definition: "A programming library that uses standard graphics cards to produce 2D and 3D visual stimuli for vision research experiments." .
SCR:014590 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSigRP" ;
definition: "Software used to automate the process of presenting stimulus signals and acquiring signal data. The software is designed to work with System 3 hardware and files generated by TDT's signal design software SigGenRP." .
SCR:014591 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stopwatch+" ;
NIFRID:synonym "Stopwatch Plus",
"Stopwatch plus",
"Stopwatch-plus" ;
definition: "A software which tracks the number of occurrences and duration of up to 16 defined events. The user can group events together so that turning on one event in a group will automatically turn off other active events in the group. Sessions can end after a fixed length of time, or the sessions can be ended manually, At the end of the session, the data can be saved in a comma-delimited file which can be easily imported into a spreadsheet application." .
SCR:014592 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeCyder 2D" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 24, 2016. A software which is used with gel electrophoresis analysis and is used with the Ettan DIGE system. This system allows the option of reference to the internal standard for each spot, which ultimately eliminates gel-to-gel variation, and gives quantitation. This gel comparison method introduces nearly zero statistical error." .
SCR:014593 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Xcalibur" ;
definition: "A software which acquires and processes data sets, primarily through the Xcalibur system." .
SCR:014594 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioWorks" ;
definition: "A a configurable software package for peptide and protein mass spectrometry analyses. It includes the SEQUEST search algorithm to identify separate proteins in complex mixtures, interactive navigation tools to filter and sort protein summaries, customized spectral plots, and chromatograms using the PEPMATCH and PEPMAP tools. This software also has batch processing capabilities to improve throughput by queuing up several files, and custom-build proprietary databases, index databases, and retrieve databases through a public server." .
SCR:014595 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenStat" ;
definition: "A statistical software which can be used for basic statistics, experimental design, sample size calculations, and analysis of linear mixed models, time series, and spatial analysis." .
SCR:014596 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "7500 Real-Time PCR Software" ;
NIFRID:synonym "7500 Real Time PCR Software",
"Applied Biosystems 7500 Real-Time PCR Software" ;
definition: "A software used to control and operate the Applied Biosystems 7500 Real-Time PCR system." .
SCR:014597 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:cufflinks",
"OMICS_01304",
"SCR_013307" ;
rdfs:label "Cufflinks" ;
definition: "Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality." .
SCR:014598 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SigmaGel Software" ;
NIFRID:synonym "SigmaGel" ;
definition: "Gel analysis software which can be used on a PC with TWAIN-compatible scanners without specialty equipment. Users scan or load an image which can then be calibrated. SigmaGel allows users to make lane measurements, spot measurements, and molecular weight measurements. After data analysis was completed, users can print or copy and paste data and images." .
SCR:014599 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Schizo-Pi" ;
NIFRID:synonym "Schizo Pi",
"Schizophrenia Protein Interactome" ;
definition: "An interactome of protein-protein interactions related to schizophrenia, it contains novel PPIs predicted with the HiPPIP model. Schizophrenia associated genes are gathered from GWAS genes, historical candidates, and OMIM. Members of the scientific community can also suggest genes to add to the interactome." .
SCR:014600 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Animal Germplasm Program (NAGP)" ;
NIFRID:synonym "National Animal Germplasm Program",
"US Animal Germplasm Program" ;
NIFRID:abbrev "NAGP" ;
definition: "A national germplasm database where users can donate or request germplasms from a variety of non-human animals, including fish, invertebrates, bison, elk, pig, turkey, and yak. Germ plasm types include white blood cells, embryo, heart, larvae, liver, muscle, oocyte, ovarian tissue, DNA, red blood cells, semen, skin, sperm, spleen, testicular tissue, and blood." .
SCR:014601 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ggplot2" ;
rdfs:label "ggplot2" ;
NIFRID:synonym "grammar of graphics plot2" ;
definition: "Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers." .
SCR:014602 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FactoMineR" ;
NIFRID:synonym "factominer" ;
definition: "Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables." .
SCR:014604 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Core Gene Evaluation Script" ;
definition: "A tool used to screen for core gene sets as an indicator of completeness of draft genomes. The download includes a Perl script and required archaeal and bacterial core genes fasta and cluster files." .
SCR:014606 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:theseed" ;
rdfs:label "RAST Server" ;
NIFRID:synonym "Rapid Annotation using Subsystem Technology",
"Rapid Annotation using Subsystem Technology Server" ;
NIFRID:abbrev "RAST" ;
definition: "A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes." .
SCR:014607 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GINGKO" ;
definition: "A GUI software package to help non-expert statisticians conduct multivariate analysis methods. Various multivariate analysis methods are available, including correspondance analysis, aglomerative hierarchical clustering, related multidimensional scaling, and discriminant analysis (linear, quadratic or distance-based)." .
SCR:014608 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "inVUE" ;
definition: "An API and software suite for large scale data visualization and analysis." .
SCR:014609 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_07818" ;
rdfs:label "LEfSe" ;
NIFRID:synonym "LDA Effect Size" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014610 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:metastats" ;
rdfs:label "Metastats" ;
definition: "A statistical software package for comparing metagenomic datasets and clinical data sets comprised of two treatment populations, with each treatment population being made up of multiple samples. It relies on a non-parametric t-test." .
SCR:014611 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_16932" ;
rdfs:label "MicrobiomeUtilities" ;
NIFRID:synonym "Microbiome Utilities Portal of the Broad Institute" ;
definition: "A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology." .
SCR:014612 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP" ;
definition: "An R-package which uses Dirichlet-Multinomial distribution to perform formal hypothesis testing on the species abundance distribution of human microbiome data, and to calculate power and sample size requirements for human microbiome experiments." .
SCR:014613 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HMPTrees" ;
NIFRID:synonym "HMPTrees - Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data",
"Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data" ;
definition: "An R-package which uses Object Oriented Data Analysis (OODA) methods to analyze taxonomic trees directly, providing tools to model, compare, and visualize populations of taxonomic tree objects." .
SCR:014614 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Simrank" ;
definition: "A rapid and sensitive general-purpose k-mer search tool." .
SCR:014615 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "speciateIT" ;
definition: "A software package for speciation of 16S sequence data." .
SCR:014616 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Unifrac" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. A suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample." .
SCR:014617 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fast-Unifrac" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. Provides a suite of tools for the comparison of microbial communities using phylogenetic information." .
SCR:014618 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SitePainter" ;
definition: "An interactive data visualization tool which allows users to create and upload pictures of their study site, load diversity analyses, and display both diversity and taxonomy results in a spatial context." .
SCR:014619 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BMTagger" ;
NIFRID:synonym "Best Match Tagger" ;
definition: "A tool that discriminates between human reads and microbial reads without performing an alignment of all reads to the human genome." .
SCR:014620 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HUMAnN" ;
NIFRID:synonym "HMP Unified Metabolic Analysis Network",
"HMP Unified Metabolic Analysis Network (HUMAnN)" ;
definition: "A pipeline which takes short DNA/RNA reads as inputs and produces gene and pathway summaries as outputs. The pipeline converts sequence reads into coverage and abundance tables summarizing the gene families and pathways in one or more microbial communities." .
SCR:014621 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Metapath" ;
definition: "A statistical package for comparing metagenomic data-sets at the pathway level. It relies on a combination of metagenomic sequence data and prior metabolic pathway knowledge, which is pulled from KEGG." .
SCR:014622 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Targets" ;
NIFRID:synonym "Center for Therapeutic Target Validation",
"Centre for Therapeutic Target Validation" ;
definition: "A public–private initiative that supports research that provides evidence on the biological validity of therapeutic targets and that gain insight into the effectiveness of pharmacological intervention. It aims to provide a research and development framework that applies human disease. It shares its information openly." .
SCR:014623 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProtVista" ;
definition: "A BioJS viewer for protein sequence features." .
SCR:014624 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Big Data Bag" ;
definition: "Software package with tools which assemble, identify, and provide access to subsets of data in a large and complex data collection workflow. The software utilities work primarily with BagIt packages that conform the BDDS Bagit and BDDS Bagit/RO profiles. JSON-LD is used to provide a standard way for linking metadata with existing ontologies and vocabularies." .
SCR:014625 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "International Human Epigenome Consortium Data Portal" ;
NIFRID:synonym "IHEC Data Portal",
"International Human Epigenome Consortium (IHEC) Data Portal" ;
definition: "A data portal of the International Human Epigenome Consortium which provides access to comprehensive data sets of reference epigenomes relevant to health and disease. The IHEC Data Portal can be used to view, search and download data already released by different IHEC-associated projects. Data are organized by consortium, by tissue, and by assay category. Users can visualize data sets using the data grid provided or the UCSC Genome Browser." .
SCR:014626 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "clValid " ;
NIFRID:synonym "clValid - Validation of Clustering Results",
"clValid: Validation of Clustering Results" ;
definition: "An R package which contains functions for validating the results of a clustering analysis." .
SCR:014627 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:i-tasser",
"SCR_018803" ;
rdfs:label "I-TASSER" ;
NIFRID:synonym "Iterative Threading ASSEmbly Refinement",
"Iterative Threading Assembly Refinement" ;
definition: "Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation." .
SCR:014628 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:prottest",
"OMICS_11547" ;
rdfs:label "ProtTest" ;
definition: "Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014629 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:phyml",
"OMICS_04241" ;
rdfs:label "PhyML" ;
definition: "Web phylogeny server based on the maximum-likelihood principle." .
SCR:014630 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:composition_profiler" ;
rdfs:label "Composition Profiler" ;
definition: "Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output." .
SCR:014631 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:fatcat" ;
rdfs:label "FATCAT" ;
NIFRID:synonym "(Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists",
"(Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT)" ;
definition: "Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014632 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IUPRED" ;
NIFRID:synonym "Prediction of Intrinsically Unstructured Proteins",
"Prediction of Intrinsically Unstructured Proteins (IUPRED)" ;
definition: "A web server which recognizes tertiary structures from an amino acid sequence based on estimated pairwise energy content. Users can input SWISS-PROT/TrEMBL identifier or accession number, or paste the amino acid sequence." .
SCR:014633 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Metabolomics Workbench Metabolite Database" ;
NIFRID:synonym "Metabolomics Workbench Database",
"UCSD Metabolomics Workbench Metabolite Database" ;
definition: "A database which contains structures and annotations of biologically relevant metabolites from public repositories such as LIPID MAPS, ChEBI, HMDB, PubChem, and KEGG. Users can search for molecular structure based on substructure, text, or mass." .
SCR:014634 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "NIH Metabolomics program" ;
NIFRID:synonym "National Institutes of Health (NIH) Common Fund Metabolomics",
"NIH Common Fund Metabolomics program" ;
definition: "A US national program which supoorts the development of technologies in order to enhance the metabolomics field. It specifically increases the national metabolomics research capacity by supporting five core programs: Training in Metabolomics, Metabolomics Technology Development, Metabolomics Reference Standard Synthesis, Metabolomics Data Sharing and International Collaboration, and Comprehensive Metabolomics Resource Cores." .
SCR:014635 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StatPlus Mac" ;
NIFRID:synonym "StatPlus" ;
definition: "A statistical data analysis tool that works with Microsoft Excel and is designed especially for use in IOS systems. Tutorials and examples are provided within the program." .
SCR:014637 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Truncation Thresholds Software" ;
definition: "Software used to compute truncation thresholds, pair of spike detection thresholds that are used for separating extracellular neural recordings into two segments consisting of signal and noise, using truncated probability distributions." .
SCR:014638 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Teaching Commons" ;
definition: "A library of open source teaching and educational resources for professors and students. It includes resources such as textbooks, lesson plans, multimedia, and lectures from participating universities and institutions. Subject areas include the life sciences, the arts and humanities, law, social and behavioral sciences, medicine and health, engineering, education, the physical sciences, and mathematics. Users can share their own work and adopt others' on the platform." .
SCR:014639 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ir-tweak" ;
NIFRID:synonym "ir-tweak" ;
definition: "Interactive software application used for manual image registration (e.g., aligning, scaling, warping) of ssLM and ssTEM images. Users place control points in one image, and these points' locations are predicted on a moving or warped second image. Transform parameters are updated once the user adjusts and corrects the predicted points on the second image." .
SCR:014641 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Network for Pancreatic Organ Donors with Diabetes" ;
NIFRID:synonym "Network for Pancreatic Organ Donors with Diabetes (nPOD)",
"The Network for Pancreatic Organ Donors with Diabetes" ;
NIFRID:abbrev "nPOD" ;
definition: "A collaborative research project that supports nPOD approved diabetes investigators by freely providing rare and difficult-to-obtain tissues from type 1 and type 2 diabetes donors. Interested researchers are encouraged to apply to obtain nPOD tissues, or to request access to analyze cases in the nPOD Online Pathology site. Interested donors can contact nPOD directly for more information." .
SCR:014642 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ImmunoBase" ;
definition: "Web based resource focused on the genetics and genomics of immunologically related human diseases. Their mission is to provide a curated and integrated set of datasets and tools to support and promote research in this area. The current focus of the site is to integrate and curate summary case/control association statistics from the consortium of 12 diseases originally targeted by the ImmunoChip consortium." .
SCR:014643 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciDAVis" ;
NIFRID:synonym "Scientific Data Analysis and Visualization (SciDAVis)" ;
definition: "Interactive application for data analysis and visualization in the form of plots. Its main feature is its usability and its simple graphical user interface. SciDAVis runs on GNU/Linux, Windows and MacOS X." .
SCR:014644 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KLayout" ;
NIFRID:synonym "KLayout - High Performance Layout Viewer And Editor" ;
definition: "A GDS and OASIS file viewer editor that has file overlay and file creation capabilities. It features include: layer grouping, flexible rulers, image overlay, partial editing functions, and external library support." .
SCR:014645 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UM High Content Screening Core Facility" ;
NIFRID:synonym "HCS Core" ;
definition: "Core facility that utilizes a ThermoFisher Cellomics ArrayScan VTI instruments and associated automated cellular analysis software. The High Content Screening (HCS) Core provides a multiplexed functional screening and imaging platform to perform multi-well cell-based assays." .
SCR:014646 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRC Psycholinguistic Database" ;
definition: "A machine usable dictionary containing thousands of words, each with linguistic and psycholinguistic attributes (psychological measures are recorded for a small percentage of words). The dictionary may be of use to researchers in psychology or linguistics to develop sets of experimental stimuli, or those in artificial intelligence and computer science who require psychological and linguistic descriptions of words." .
SCR:014647 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "State Space Models" ;
NIFRID:synonym "State Space Models (SSM)",
"S|S|M" ;
NIFRID:abbrev "SSM" ;
definition: "An open source library built to reduce technical friction and help modelers share their work. Models within SSM can be used for inference of time-series analysis." .
SCR:014648 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH StrokeNet" ;
NIFRID:synonym "NIH Strokenet",
"StrokeNet",
"Strokenet" ;
definition: "NIH network designed to follow and help conduct clinical trials and research studies investigating acute stroke treatment, stroke prevention, and stroke recovery and rehabilitation. Clinical trials are listed once they are reviewed, approved, and ready for volunteer recruitment." .
SCR:014649 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ENIGMA-DTI Pipeline" ;
NIFRID:synonym "ENIGMA DTI pipeline",
"ENIGMA DTI protocol",
"ENIGMA-DTI protocol" ;
definition: "Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols." .
SCR:014650 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:OpenWorm",
"SCR_014984" ;
rdfs:label "OpenWorm" ;
NIFRID:synonym "Open Worm",
"OpenWorm Browser" ;
definition: "3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders." .
SCR:014651 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HIPPIE" ;
NIFRID:synonym "Human Integrated Protein Protein Interaction Reference",
"Human Integrated Protein-Protein Interaction rEference",
"Human Integrated Protein-Protein Interaction rEference (HIPPIE)" ;
definition: "Web tool used to generate confidence scored and functionally annotated human protein-protein interaction networks. Users can run a protein query using a UniProt identifier (ID or accession), gene symbol or Entrez gene id, or a network query using set fields." .
SCR:014652 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Taller Peaks" ;
definition: "Spike detection algorithm that is improvement to native spike detection algorithm of Wave_clus spike sorting software. Software patch that incorporates Taller Peaks algorithm into Wave_clus as optional spike detection algorithm for single wire data." .
SCR:014653 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:RepeatScout",
"biotools:RepeatScout" ;
rdfs:label "RepeatScout" ;
definition: "Algorithm used to identify de novo repeat families in newly sequenced genomes. Repeat libraries for C. briggsae, M. muscles (X chromosome), R. novegicus (X chromosome), armadillo, H. sapiens (X chromosome), and various other mammals created using RepeatScout are available on the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014654 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "REPCLASS" ;
definition: "Tool for the classification of known transposable elements in eukaryotic genomes. It can be combined with ab initio repeat finding in order to recover contrasting transposable element landscapes between species." .
SCR:014655 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Taxonomer" ;
definition: "Genome sequence classification tool based on kmer. The code allows users to build nucleotide databases and protein databases, classify reads, construct binner databases, and create taxonomic relationship files. The website provides information on how to perform these actions with code, though users can access a web-based Taxonomer if they need/want to." .
SCR:014656 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:PASA" ;
rdfs:label "PASA" ;
NIFRID:synonym "Program to Assemble Spliced Alignments",
"Program to Assemble Spliced Alignments (PASA)" ;
definition: "Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute." .
SCR:014657 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genezilla" ;
definition: "Reconfigurable eukaryotic gene finder based on the Generalized Hidden Markov Model framework. The run time and memory requirements are linear in the sequence length. Genezilla utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, and CAP sites." .
SCR:014658 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Analysis and Annotation Tool (AAT) Package" ;
NIFRID:synonym "AAT Package",
"Analysis and Annotation Tool Package" ;
definition: "Genome tool for analyzing and annotating large genomic sequences containing introns. It includes a program for comparing the query sequence with a protein database and another for comparing the query with a cDNA database. The database search program identifies regions of the query sequence that are similar to a database sequence. Then the alignment program constructs an optimal alignment for each region and the database sequence, as well as reports the coordinates of exons in the query sequence. Pairwise alignments of the query sequence with protein and cDNA database sequences are combined into multiple sequence alignments, which provide a view of all protein and cDNA sequences matching a query region." .
SCR:014659 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_017649" ;
rdfs:label "EVidenceModeler" ;
NIFRID:abbrev "EVM" ;
definition: "Software tool for automated eukaryotic gene structure annotation that reports eukaryotic gene structures as weighted consensus of all available evidence. Used to combine ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. Inputs include genome sequence, gene predictions, and alignment data (in GFF3 format)." .
SCR:014660 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zero Mode Waveguide Imaging and Analysis package tools" ;
definition: "MATLAB software tool collection for data acquisition and image analysis from zero mode waveguides." .
SCR:014661 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eelbrain" ;
definition: "Statistical analysis toolbox for MEG and EEG. There are three primary data-objects: Factor for categorical variables, Var for scalar variables, and NDVar for multidimensional data. Factor is a container for one-dimensional, categorial data – each case is described by a string label. Var is a container to associate one-dimensional numpy.ndarray objects with a name. NDVars offer numpy functionality that takes into account the dimensions. There is also a Dataset class which acts as a vessel for variable objects (Factor, Var and NDVar) describing the same cases." .
SCR:014662 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Coordination of Standards in Metabolomics" ;
NIFRID:synonym "COordination of Standards in MetabOlomicS",
"COordination of Standards in MetabOlomicS (COSMOS)" ;
NIFRID:abbrev "COSMOS" ;
definition: "A group which aims to create open standards for metabolomics data shsaring and analysis." .
SCR:014663 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011556" ;
rdfs:label "MetaboLights" ;
definition: "A cross-species, cross-technique database for metabolomics experiments, data, and derived information. It includes metabolite structures and their reference spectra, their biological roles, locations and concentrations, and experimental data from metabolic experiments." .
SCR:014664 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013740" ;
rdfs:label "MetabolomeXchange" ;
definition: "International effort whose objective is to improve and encourage the exchange of Metabolomics data. Datasets are stored in external data repositories independent of MetabolomeXchange; however, MetabolomeXchange allows users to browse datasets directly then proceed to the external repository for more information." .
SCR:014665 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Metabolomics Society" ;
NIFRID:synonym "Metabolomics Society Inc",
"The Metabolomics Society Inc" ;
definition: "An independent, non-profit organization whose main goal is to promote the growth and development of the field of metabolomics internationally. They also aim to provide collaborative opportunities among scientists in metabolomics, create connections between academia, government and industry in the field of metabolomics, provide opportunities for presentation of research achievements and creation of workshops, and promote the publication of meritorious research in the field." .
SCR:014666 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Birmingham Metabolite Library" ;
definition: "A collection of experimental 1D and 2D J-resolved NMR spectra of 208 metabolite standards." .
SCR:014667 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Glycan Mass Spectral Database (GMDB)" ;
NIFRID:synonym "Glycan Mass Spectral Database" ;
NIFRID:abbrev "GMDB" ;
definition: "A multistage tandem mass spectral database using a variety of structurally defined glycans. It provides tools for glycomics research that enable users to identify glycans by spectral matching. The database stores MS2, MS3, and MS4 spectra of N-and O-linked glycans, and glycolipid glycans as well as the partial structures of these glycans." .
SCR:014668 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mass Spectral Library" ;
definition: "A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals. " .
SCR:014669 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012313" ;
rdfs:label "mzCloud" ;
NIFRID:synonym "mzCloud - Advanced Mass Spectral Database" ;
definition: "A mass spectral database that assists in identifying compunds in life sciences, matabolomics, pharmaceutical research, toxicology, forensic investigations, environemnta analysis, food control, and industry." .
SCR:014670 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetabolomeExpress" ;
NIFRID:synonym "Metabolome Express (Mx)",
"metabolomexpress.org" ;
NIFRID:abbrev "Mx" ;
definition: "A metabolomics database which contains GC/MS metabolomics datasets. General users can search a curated annotated metabolite database, a metabolite response statistics database, experimental datasets, and uncurated repositories. Registered users can use Metabolome Express for data processing and management. " .
SCR:014671 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100010822" ;
rdfs:label "Spectral Database System (SDBS)" ;
NIFRID:synonym "Spectral Database for Organic Compounds",
"Spectral Database System" ;
NIFRID:abbrev "SDBS" ;
definition: "A mass spectral database for organic compounds. The spectra included in the database are: electron impact Mass spectrum (EI-MS), Fourier transform infrared spectrum (FT-IR), 1H nuclear magnetic resonance (NMR) spectrum, 13C NMR spectrum, laser Raman spectrum, and electron spin resonance (ESR) spectrum." .
SCR:014672 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CTSgetR" ;
definition: "R interface to Chemical Translation Service which provides translation between chemical and biological database identifiers." .
SCR:014673 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hierarchical Clustering" ;
NIFRID:synonym "R - Hierarchical Clustering",
"R: Hierarchical Clustering" ;
definition: "R documentation for hierarchical cluster analysis on a set of dissimilarities for n objects. Each object is assigned to its own cluster, which an algorithm proceeds through iteratively. Two of the most similar clusters are joined at each stage until there is a single cluster. Distances between clusters are recomputed at each stage by the Lance–Williams dissimilarity update formula according to the particular clustering method being used. Clustering methods include: Ward's minimum variance method, complete linkage method, and single linkage method." .
SCR:014674 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:imdev" ;
rdfs:label "imDEV" ;
NIFRID:synonym "Interactive modules for Data Exploration and Visualization",
"Interactive modules for Data Exploration and Visualization (imDEV)" ;
definition: "A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data." .
SCR:014675 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Linear Discriminant Analysis" ;
definition: "R documentation for a function to perform linear discriminant analysis; specifically, to detect if the within-class covariance matrix is singular." .
SCR:014676 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Principal Components Analysis" ;
definition: "R documentation for a function that performs a principal components analysis on a given data matrix and returns the results as an object of class prcomp." .
SCR:014677 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mwtabR" ;
NIFRID:synonym "R Package for downloading and parsing mwTab files from the Metabolomics Workbench" ;
definition: "An R package that downloads and parses mwtab data from Metabolomics Workbench studies. Downloaded files are converted into R lists." .
SCR:014678 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3Omics" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented October 19, 2016. A web tool for visualizing and integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data. 3Omics generates inter-omic correlation networks to visualize relationships in data with respect to time or experimental conditions for transcripts, proteins and metabolites." .
SCR:014679 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ACD/ NMR Processor" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented September 27, 2016. A software package that provides 1D and 2D NMR tools as well as processing and interpretation for all other major analytical techniques (LC/MS, IR, Raman, and more) in one package. It also has support for structure verification and multiplet reports." .
SCR:014680 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIST Mass Spectrometry Data Center" ;
NIFRID:synonym "Mass Spectrometry Data Center",
"MS Data Center",
"NIST MS Data Center" ;
definition: "A data center that develops evaluated mass spectral libraries and provides related software tools that assist compound identification by providing reference mass spectra for GC/MS (by electron ionization) and LC-MS/MS (by tandem mass spectrometry). It also provides gas phase retention indices for GC. Resources include the mass spectral library, the peptide library, and a standard refernece material guide." .
SCR:014681 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chemical Translation Service" ;
NIFRID:synonym "Chemical Translation Service (CTS)" ;
NIFRID:abbrev "CTS" ;
definition: "A translation service which contains a registry of pubicly available chemical information such as structures, chemical names, chemical synonyms, database identifiers, molecular masses, XlogP and proton-donor/acceptor data for compound-specific, structure-based cross references. It offers single ID conversion, batch ID conversion, InChI code conversion, and other services." .
SCR:014682 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chenomx NMR Suite" ;
NIFRID:synonym "Chenomx" ;
definition: "A software suite for identifying and quanitfying compounds in NMR spectra. Features include a compound profiler, tools to process data, a compound builder, spin simulator and library manager. More information can be requested, and installation instructions are available on the website." .
SCR:014683 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeviumWeb" ;
definition: "A software suite for data wrangling, creating interactive data visualization, performing statistical analyses, cluster analyses, exploratory data analysis and visualization (such as principal component analysis), predictive modeling and biochemical pathway analysis. " .
SCR:014684 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MBRole" ;
definition: "Software program for overrepresentation (enrichment) analysis of categorical annotations for a set of compounds. These categorical annotations correspond to biological and chemical information found in public databases and software. Annotations can be biological (pathways, enzyme interactions, pharmacological action) or chemical (taxonomy and chemical groups). " .
SCR:014685 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:metamapr" ;
rdfs:label "MetaMapR" ;
definition: "An open-source software program for integrating enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate connected metabolic networks and display results using data visualization techniques." .
SCR:014686 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:metap" ;
rdfs:label "MetaP" ;
NIFRID:synonym "metap",
"MetaP Server" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 5,2023. Software tool for processing in metabolomics experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014687 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Metscape " ;
definition: "A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data." .
SCR:014688 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SIMCA" ;
definition: "A company that provides data analysis software with features such as multivariate tools, data mining, process modeling and interactive graphics." .
SCR:014689 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TeachingDemos" ;
definition: "A portal and resource for tutorials on a variety of data analysis techniques, the use of tools such as MetaMapR, workshops on data visualization, and R code manuals." .
SCR:014690 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CLIK" ;
NIFRID:synonym "Cutoff Linked to Interaction Knowledge",
"Cutoff Linked to Interaction Knowledge (CLIK)" ;
definition: "Statistical method that uses previously annotated interaction data to automatically determine biologically informed statistical significance cutoffs for genome-wide screens." .
SCR:014691 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iBRAIN" ;
NIFRID:synonym "Intelligence BRain Analysis through Images and Networks",
"Intelligence Brain Analysis Through Images and Networks",
"Intelligence BRain Analysis through Images and Networks (iBRAIN)" ;
definition: "Brain research group affiliated with the Nanjing University of Aeronautics and Astronautics (NUAA) in China. The main research interests of iBRAIN include developing methods in machine learning, data mining, neural computation, and related areas for decoding brain functions or recognizing brain disease. Research related code and datasets can be found on the main site." .
SCR:014693 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "InVesalius 3" ;
definition: "Software for magnetic resonance image reconstruction and computed tomography reconstruction. Its main application geared towards rapid prototyping, teaching, forensics, and medicine. Its features include the ability to import DICOM or Analyze files, to export files to the STL, OBJ, and PLY formats, volume rendering, and manual or semiautomatic image segmentation." .
SCR:014694 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ultimate Rough Aggregation of Metabolic Map" ;
NIFRID:synonym "An Ultimate Rough Aggregation of Metabolic Map" ;
definition: "Metabolic pathway map that collects metabolic data gathered from multiple public databases and organizes them in one central location." .
SCR:014695 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bio.tools",
"r3d100013668" ;
rdfs:label "bio.tools" ;
definition: "Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information." .
SCR:014696 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CVODE" ;
NIFRID:synonym "SUNDIALS CVODE" ;
definition: "Solver for stiff and nonstiff ordinary differential equation (ODE) systems (initial value problem), given in explicit form y' = f(t,y), based on Adams and BDF methods. It is one of the programs that makes up the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014697 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011903" ;
rdfs:label "RepOD" ;
NIFRID:synonym "Repository for Open Data",
"Repository for Open Data (RepOD)" ;
definition: "An online platform for open source data/datasets created, collected or annotated for scientific research of all fields and disciplines. Registered users can share data relating to their research project and view data from other projects. Groups can combine datasets into collections associated with the group, in contrast to individual members of the group hosting their own data." .
SCR:014698 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PeerJ Article Repository" ;
NIFRID:synonym "PeerJ" ;
definition: "An article repository which archives peer-reviewed papers and non-peer-reviewed preprints in PeerJ. It includes papers and preprints from the biological and medical sciences PeerJ journal and from the computer science PeerJ journal." .
SCR:014699 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thieme Chemistry" ;
definition: "Publishing company which provides access to its four journals SYNTHESIS, SYNLETT, SynOpen, and SYNFACTS; their reference works Science of Synthesis and Pharmaceutical Substances; and the paired encyclopedia ROEMPP." .
SCR:014700 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tool for Tumor Progression" ;
NIFRID:synonym "Tool for Tumor Progression (TTP)" ;
NIFRID:abbrev "TTP" ;
definition: "Software used to simulate tumor progression in various stages of growth in order to study the process' dynamics. The input can be fitness landscape, mutation rate, and cell division time. The output is growth dynamics and other relevant statistics, such as expected tumor detection time and expected appearance time of surviving mutants. The tool is implemented in Java and runs on all operating systems which run a Java Virtual Machine (JVM) of version 1.7 or above." .
SCR:014701 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Emovera" ;
definition: "Data collection and self-expression/-discovery/-management software tool that separates conscious cognition, subconscious emotion, and unconscious motivation. Tests are given depending on the topic chosen and results are analyzed to give the user information concerning their subconscious motivators." .
SCR:014702 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "N2A" ;
NIFRID:synonym "Neurons to Algorithms",
"Neurons to Algorithms (N2A)" ;
definition: "An object-oriented language for modeling large-scale neural systems, along with an IDE for writing and simulating models. N2A represents neural systems in a parts-relations framework combined with dynamics where each part has as set of equations that define its state variables and how they evolve over time. Each part is a pattern for a population of instances, and each instance has its own unique copy of the state variables." .
SCR:014703 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Measures of Effect Size Toolbox" ;
NIFRID:synonym "MES Toolbox" ;
NIFRID:abbrev "MES" ;
definition: "Matlab statistics toolbox allowing the computation of a wide range of measures of effect size. Four main toolbox functions cover common analysis designs, including two-sample-, oneway- and twoway- data sets as well as categorical data. Data may be repeated-measures." .
SCR:014706 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R3DS3K",
"DOI:10.25504/FAIRsharing.sN8d9i",
"DOI:10.26193" ;
rdfs:label "Australian Data Archive" ;
definition: "A consortium of leading national Australian universities which collects and preserves digital research data and makes these data available for secondary analysis. The consortium provides a data catalogue comprised of seven sub-archives: Social Science, HIstorical, Indigenous, Longitudinal, Qualitative, Crime and Justice, and International. All users can browse and search the catalogue, view study and variable documentation, and download related material. Registered users can also analyze and visualize most data online and users who have completed the relevant undertaking form(s) can download entire studies or subsets of variables. Deposited data are processed, reviewed, and published for research use." .
SCR:014707 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Cambridge Crystallographic Data Centre (CCDC)" ;
NIFRID:synonym "Cambridge Crystallographic Data Center",
"CCDC" ;
definition: "Institution which compiles and distributes small molecule crystallography data from the Cambridge Structural Database (CSD), a repository of experimentally determined organic and metal-organic crystal structures. CCDC also produces associated knowledge-based application software for structural chemists. Structures deposited with CCDC are made publically available for download at the point of publication or at consent from the depositor." .
SCR:014708 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.5255",
"DOI:10.17616/R3088K",
"DOI:10.25504/FAIRsharing.qtm44s",
"grid.438826.3",
"ISNI: 0000 0001 0377 8000",
"Wikidata: Q17039301" ;
rdfs:label "UK Data Archive" ;
definition: "Organization which acquires, curates, and provides access to a collection of digital data in the social sciences and humanities in the United Kingdom." .
SCR:014709 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Adaptive Biotechnologies" ;
definition: "Commercial organization which combines high-throughput sequencing and bioinformatics to profile T-cell and B-cell receptors." .
SCR:014710 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MIT Laboratory for Computational Physiology" ;
definition: "A group which conducts research on improving health care through new and refined approaches to interpreting data. LCP research incorporates physiology, computer science, engineering, and applied mathematics." .
SCR:014711 a NIFSTD:birnlex_2085,
owl:NamedIndividual ;
rdfs:label "UCSF Clinical and Translational Science Institute" ;
NIFRID:synonym "UCSF Clinical and Translational Science Institute (CTSI)" ;
NIFRID:abbrev "UCSF CTSI" ;
definition: "An institute which provides infrastructure, services, and training to support clinical and translational research. It develops broad coalitions and partnerships at the local and national levels to enable a transformation of the research environment." .
SCR:014712 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Xperiment" ;
definition: "Mobile software application for behavioral social science experiments on an online platform. It can be used on computers, tablets, and smartphones. It is hardware independent, does not require online connectivity to perform a test, and has the option of interfacing with outside sensors, such as heart rate or weighting scales." .
SCR:014713 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WinWCP" ;
NIFRID:synonym "Windows Whole Cell Program" ;
definition: "Windows software program for recording and analyzing signals from whole cell voltage and current clamp experiments. Its features include automatic waveform measurement, quantal content analysis, command voltage pulse generation, and spontaneous event detection." .
SCR:014714 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Research Data Centre of the German Centre of Gerontology" ;
NIFRID:synonym "Forschungsdatenzentrum Deutsches Zentrum fur Altersfragen",
"Forschungsdatenzentrum DZA",
"Research Data Center of the German Center of Gerontology" ;
NIFRID:abbrev "FDZ-DZA" ;
definition: "A facility for data housing and research on gerontology in Germany. It focuses on making data of the German Ageing Survey DEAS and the German Survey on Volunteering (FWS) accessible to researchers by providing user-friendly Scientific Use Files (SUF), documentation of the contents and instruments as well support for scholars using the data." .
SCR:014715 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "German Medical Science" ;
definition: "A portal for online journals, meetings and research reports. It offers open access to scientific articles to scientists from the field of medicine along with the option to publish their research results online." .
SCR:014716 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Association of the Scientific Medical Societies in Germany" ;
NIFRID:synonym "Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften" ;
NIFRID:abbrev "AWMF" ;
definition: "An association of various medical entities in Germany. The organization advises on matters and tasks of fundamental and interdisciplinary interest in medicine, develops recommendations and resolutions and represents them at the institutions occupied with such tasks, such as research strategies, education, and postgraduate training." .
SCR:014722 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.11577",
"r3d100011554" ;
rdfs:label "Coherent X-Ray Imaging Data Bank (CXIDB)" ;
NIFRID:synonym "Coherent X-ray Imaging Data Bank",
"Coherent X-ray Imaging Data Bank (CXIDB)",
"CXIDB" ;
definition: "Database of Coherent X-ray Imaging (CXI) experiments. This data is widely accessible to researchers worldwide." .
SCR:014723 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bioinformatics Infrastructure for Life Sciences" ;
NIFRID:synonym "Bioinformatics Infrastructure for Life Sciences (BILS)" ;
NIFRID:abbrev "BILS" ;
definition: "A national research infrastructure that provides bioinformatics support to life science researchers in Sweden. Their work is supported by the Swedish Research Council." .
SCR:014725 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID:100010046",
"grid.8356.8",
"ISNI:0000 0001 0942 6946",
"Wikidata:Q1075104" ;
rdfs:label "University of Essex; England; United Kingdom" ;
definition: "A public research university in Colchester, Essex, England. The institution has degree programs that span the humanities, social sciences, and health." .
SCR:014728 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011836" ;
rdfs:label "Johns Hopkins Research Data Repository" ;
definition: """Open access repository for Johns Hopkins University researchers to share their research data.
Data repository is administered by professional curators at JHU Data Services, who will work with depositors to enable future discovery and reuse of your data, and ensure your data is Findable, Accessible, Interoperable and Reusable (FAIR). Each dataset has citation and DOI, facilitating attribution, and connection to research publications.""" .
SCR:014731 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pilon",
"OMICS_14553" ;
rdfs:label "Pilon " ;
definition: "Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome." .
SCR:014732 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:prokka",
"OMICS_04220" ;
rdfs:label "Prokka" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014733 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TranslatorX" ;
definition: "Nucleotide sequence alignment and alignment cleaning based on amino acid information. Users can paste nt-sequences into the application and select the desired protein alignment method and the genetic code, and the option for alignment cleaning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014734 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SplitsTree" ;
NIFRID:synonym "SplitsTree3",
"SplitsTree4" ;
definition: "Application that uses molecular sequence data to compute unrooted phylogenetic networks. Given an alignment of sequences, a distance matrix, or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014735 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SimTracker" ;
definition: "MATLAB-based tool for use with NEURON network models. It supports the modeler with model design, organization, execution (including on supercomputers), analysis, and reproducibility." .
SCR:014736 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SparseTracer" ;
definition: "Software used to automatically trace single neurons. It supports VTK 3D visualization." .
SCR:014740 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PePPER Prokaryote Promoter Prediction" ;
NIFRID:abbrev "PePPER" ;
definition: "A webserver for the prediction of prokaryote promoter elements and regulons. DNA in FASTA or plain format serve as input. A gene table can be included with the run." .
SCR:014741 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCAM" ;
NIFRID:synonym "Symbolic Circuit Analysis in Matlab",
"Symbolic Circuit Analysis in Matlab (SCAM)" ;
definition: "Software toolbox for deriving and solving circuit equations symbolically in MATLAB." .
SCR:014742 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SLiCAP" ;
NIFRID:synonym "Symbolic Linear Circuit Analysis" ;
definition: "A software toolbox containing a symbolic linear circuit analysis program. It is a MATLAB application that helps set up and solve design equations of electronic circuits." .
SCR:014743 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Symbolic SPICE" ;
definition: "Analog circuit analyzer and approximator used as a pre-processor to find design formulas or as a post-processor to approximate design formulas. The program performs the .AC analysis in SPICE symbolically with optional numeric evaluation and user selected threshold approximation." .
SCR:014744 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Simulink" ;
definition: "Block diagram environment that contains a graphical editor, customizable block libraries, and solvers for multidomain simulation and model-based design in MATLAB. It supports simulation, automatic code generation, and continuous test and verification of embedded systems." .
SCR:014745 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "PSpice" ;
definition: "Commercial software company that offers simulation technology for both simulation and PCB design. PSpice has integrated analog and event-driven digital circuit simulation and a focus on bringing the tools needed for simulation that will help bring customer products to market. The website contains resources, libraries, and a user forum to support use of PSpice technology." .
SCR:014746 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PGENESIS" ;
NIFRID:synonym "Parallel Genesis" ;
definition: "A software add-on that builds upon GENESIS by adding a library to installed versions of GENESIS. It is useful for simulations that must be run many times independently and for large-scale network models." .
SCR:014748 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MicroDraw" ;
definition: "Web application used to visualise and annotate collaboratively high resolution histology data. In short, it uses public ontologies to create collaborative, community-curated atlases. Annotations are vectorial, and users can use boolean operations to combine, subtract and split regions." .
SCR:014749 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Neuroimaging Laboratory" ;
NIFRID:synonym "OpenNeuroLab" ;
definition: "Web framework for collaborative applications for neuroimaging. It hosts various web applications for curation, editing, and analysis in conjunction with neuroimaging data available publicly online." .
SCR:014750 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BrainBox" ;
definition: "Web application which allows users to visualise and collaboratively segment and annotate any brain MRI dataset available online via URL. A list of brains are available for use on the main site. Segmentations are automatically saved and can be downloaded as Nifti files or triangular meshes. Users can point BrainBox to their own Nifti data, or try data catalogues created by the community." .
SCR:014751 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaSearch" ;
definition: "Web application search tool intended to help users find MRI data shared publicly on the Web, particularly from projects organized under the 1000 Functional Connectomes Project (FCP) and International Neuroimaging Data-sharing Initiative (INDI). Users can perform queries visually to select a cohort of participants with brain imaging data based on their demographics and phenotypic information and then link out to imaging measures." .
SCR:014752 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Umea Brain Arteries" ;
definition: """Stereotactic atlases with probabilistic values describing the location of the main cerebral arteries. The data collected are from the COBRA study as described in "COBRA: A prospective multimodal imaging
study of dopamine, brain structure and function, and cognition" by Nevalainen et al.""" .
SCR:014753 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BluePyOpt" ;
NIFRID:synonym "Blue Brain Python Optimisation Library",
"Blue Brain Python Optimisation Library (BluePyOpt)",
"Blue Brain Python Optimization Library" ;
definition: "An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms." .
SCR:014754 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "phiSite" ;
definition: "Database of bacteriophage gene regulation elements, genes, and genomes. Data are collected from scientific papers and cross-referenced with other database resources. The database can be searched using keywords or browsed by phage genome. Sets of regulatory sequences can browsed and exported in various formats." .
SCR:014755 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuronify" ;
definition: "Neuron education application for smart phones which provides an introduction to neural simulations at a low entry point." .
SCR:014756 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "499 fROI atlas" ;
NIFRID:synonym "Willard atlas" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Atlas of functional ROIs (fROIs) containing 499 regions, with extensive gray matter coverage. Atlases are available for download directly from the website." .
SCR:014757 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "90 fROI atlas" ;
definition: "Atlas of functional ROI's, including individual networks (auditory network, sensorimotor network, etc.). Atlases of individual networks and combined networks are available for download directly from the website." .
SCR:014758 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NetPyNE" ;
NIFRID:synonym "Network development Python package for NEURON" ;
definition: "Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks." .
SCR:014759 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroExperimenter" ;
NIFRID:synonym "NeuroExperimenter (NEx)" ;
NIFRID:abbrev "NEx" ;
definition: "Software which provides an interface for MindWave Mobile hardware, allowing users to view and listen to brainwave output of different \"mind states\". Users can: view any or all brainwaves, specify a combination of brainwaves via a formula, compare a base line session to a performance session, and create a log and run it through the application to view different graphical outputs. NeuroExperimenter only runs on Windows" .
SCR:014760 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mvaspike" ;
definition: "Tool for modeling and simulating large, complex biological neural networks, particularly pulse-coupled, spiking neural networks. Its main features include modular or hierarchical modeling strategy of networks, phase-coded neurons, event-driven simulation, and integration of standard file formats." .
SCR:014761 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CNrun" ;
definition: "Neuronal network model simulator for both individual neurons and networks of neurons. It uses NeuroML for network description. Various neuron and synapse model types are supported. CNN features include: an integration cycle which uses a Runge–Kutta 6-5-order method, extensive scripting capabilities, individual unit state introspection from scripts, and neuroplastic processes identified by label or regexp." .
SCR:014762 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IonChannelLab" ;
definition: "Software for kinetic modeling of ion channels which operates on Windows XP or Windows Vista." .
SCR:014763 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_09368" ;
rdfs:label "libRoadRunner" ;
definition: "Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support." .
SCR:014764 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RoadRunner" ;
definition: "Environment for carrying out deterministic simulation Systems Biology Markup Language models. It relies on libraries for SBML support, conservation analysis, integration and steady state analysis and a .NET core." .
SCR:014765 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "madsim" ;
definition: "A function which allows users to generate two biological conditions synthetic microarray datasets. The user provides a subset of parameters, but default parameter settings can be modified." .
SCR:014766 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neural Field Simulator" ;
definition: "Simulation software which computes activity numerically in 2-dimensional neural fields by solving integral-differential equations involving transmission delays and visualizes the spatio-temporal activity. Installation and simulation documentation are provided on the homepage." .
SCR:014767 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COMSOL Multiphysics" ;
definition: "General-purpose software platform for modeling and simulating physics-based problems which accounts for coupled or multiphysics phenomena. The platform includes a set of core physics interfaces for common physics application areas such as structural analysis, laminar flow, pressure acoustics, transport of diluted species, electrostatics, electric currents, heat transfer, and Joule heating." .
SCR:014768 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "neuronPM" ;
definition: "Client/server application that makes parameter maps for neural simulations written in NEURON." .
SCR:014769 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroRD" ;
definition: "Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways." .
SCR:014770 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PCSIM" ;
NIFRID:synonym "Parallel Neural Circuit Simulator",
"Parallel neural Circuit SIMulator",
"Parallel Neural Circuit Simulator (PCSIM)" ;
definition: "Software tool for simulating heterogeneous networks composed of different model neurons and synapses. It is intended to simulate networks containing up to millions of neurons and on the order of billions of synapses by distributing the network over different nodes of a computing cluster by using MPI." .
SCR:014771 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyDSTool" ;
definition: "Integrated simulation and analysis environment for dynamic systems models of physical systems. It supports symbolic math, optimization, phase plane analysis, continuation and bifurcation analysis, data analysis, and other tools for modeling. It is written in Python with some underlying C and Fortran legacy code." .
SCR:014772 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Radiometer" ;
definition: "Commercial organizations which develops, manufactures, and sells solutions and equipment for blood sampling, blood gas analysis, transcutaneous monitoring, and IT management systems under certain brand names." .
SCR:014773 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "EcoCyte Bioscience" ;
definition: "Supplier and servicer of products for expression studies in Xenopus laevis oocytes. Products include overnight delivery of freshly prepared Xenopus laevis oocytes, Cell & Tissue Media necessary during preparation, maintenance, and recording of Xenopus oocytes and lab chemicals. Services for pharmacological studies include heterologous expression and in vitro electrophysiology." .
SCR:014774 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Zeitz" ;
NIFRID:synonym "Zeitz Instruments",
"Zeitz-Instruments" ;
definition: "Manufacturer and supplier of the DMZ Universal electrode pullers which produce pipettes and electrodes with a tip diameter down to 0.2 micrometers." .
SCR:014775 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "King Precision Glass" ;
NIFRID:synonym "King Precision Glass Inc" ;
definition: "American manufacturer of premium specialty glass tubing products that meet the needs of hermetic seal production, electronics assembly, commercial applications, medical device manufacture, and various research fields. Products include hermetic seal glass, capillary tubing, glass spacers, insulator beads, and custom-made tubing." .
SCR:014776 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "word2vec" ;
definition: "Software tool which provides implementation of the continuous bag-of-words and skip-gram architectures for computing vector representations of words. These representations can be used in many natural language processing applications and for further research. It takes a text corpus as input and produces the word vectors as output. It first constructs a vocabulary from the training text data and then learns vector representation of words. The resulting word vector file can be used as features in natural language processing and machine learning applications." .
SCR:014777 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioC Java Library" ;
definition: "An interchange format to represent, store and exchange data and annotations in a standardized manner." .
SCR:014778 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford CoreNLP" ;
definition: "A Java suite of core natural language analysis tools. It can take raw human language text input and give multiple outputs, including the base forms of words, their parts of speech, and marked up structure of sentences in terms of phrases or word dependencies. Supported languages include English, Arabic, Chinese, French, German, and Spanish." .
SCR:014779 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biocemid" ;
NIFRID:synonym "BioC Experimental Molecular Interaction Detection" ;
definition: "A manually annotated data set of full text articles and a tool for identifying passages describing experimental methods for physical protein-protein interactions." .
SCR:014782 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OncoKB" ;
definition: "Precision oncology knowledge base which contains information about the effects and treatment implications of specific cancer gene alterations. OncoKB contains detailed information about specific alterations in 418 cancer genes. Each variant entry contains biological effect, prevalence, prognostic information, and treatment implications. Information is curated from various sources, such as guidelines from the FDA, ClinicalTrials.gov, and scientific literature by a network of clinical fellows, research fellows, and faculty members at Memorial Sloan Kettering Cancer Center." .
SCR:014783 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Digimizer" ;
definition: "Image analysis software package that allows precise manual measurements and automatic object detection with measurements of object characteristics. Pictures may be X-rays, micrographs, and the like. Supported file formats include JPG, GIF, TIFF, BMP, PNG, WMF, EMF and DICOM files. Image rotation and light can be edited." .
SCR:014784 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Silfradent" ;
definition: "Commercial supplier of dental and medical laboratory equipment." .
SCR:014785 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Optogenetics and Transgenic Technology Core" ;
NIFRID:synonym "NIDA Trangenic Rat Project" ;
definition: "Core facility and data repository which creates and characterizes transgenic rats for use in models of neurological diseases, such as addiction and neurodegeneration. Researchers can request strain(s) from RRRC or go to the Transgenic Rat Request page." .
SCR:014786 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iVision" ;
definition: "Microscopy imaging software for image acquisition, processing, measurement, and analysis. iVision‐Mac directly supports the acquisition of images and time-lapse series." .
SCR:014788 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Networks Toolbox" ;
definition: "Software repository containing code for measuring brain networks from structural and functional MRI data. Several programs require MATLAB to run." .
SCR:014789 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multi-Mode Analysis Software" ;
definition: "Software that configures and controls the measurement protocols and actions performed by the FilterMax Multi-Mode Microplate Readers and the SpectraMax Paradigm Multi-Mode Detection Platform, which are commercially available microplate readers from Molecular Devices." .
SCR:014790 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AlleleID" ;
definition: "Desktop software application for bacterial identification, pathogen detection, or species identification. It can be used for cross-species identification for microarrays and real time PCR primers. It uses ClustalW to align sequences then analyzes conserved and species specific regions within those sequences." .
SCR:014791 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeitzeiger" ;
NIFRID:synonym "ZeitZeiger" ;
definition: "R package for regularized supervised learning on high-dimensional data from an oscillatory system. Zeitzeiger can quantify rhythmic behavior, make accurate predictions, identify major patterns and important features, and detect when the oscillator is perturbed." .
SCR:014793 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "neMESYS UserInterface" ;
NIFRID:synonym "nemesys User Interface",
"nemesys UserInterface" ;
definition: "Software used to configure and control up to 32 neMESYS syringe pumps. Its features include automatic detection of connected dosing units, graphical display of syringe size, syringe level and valve position, configurable SI units for volumes and flow rates, and real-time display of all current values like flow rate, syringe fill level or dispensed volume." .
SCR:014794 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Psychology Experiment Building Language (PEBL)" ;
NIFRID:synonym "Psychology Experiment Building Language" ;
NIFRID:abbrev "PEBL" ;
definition: "A programming language made for creating and conducting standard psychology experiments. The site also serves as a portal for experimental software, design, and exchange." .
SCR:014795 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SMIA-CUKIE" ;
NIFRID:synonym "Simultaneous Multichannel Immunofluorescence Analysis",
"Simultaneous Multichannel Immunofluorescence Digital Imaging Analyzer" ;
NIFRID:abbrev "SMIA" ;
definition: "Software used to analyze and quantify images stained with multiple fluorophores in vitro or in vivo. It can output both image and value outputs." .
SCR:014796 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OrientationJ" ;
NIFRID:synonym "Orientation J" ;
definition: "Software used to automatically characterize the orientation and isotropy properties of a region of interest in an image based on the evaluation of the structure tensor in a local neighborhood. OrientationJ has four functionalities: visual representation of the orientation, quantitative orientation measurement, making distribution of orientations, and corner detection." .
SCR:014798 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:topgo" ;
rdfs:label "topGO" ;
definition: "Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied." .
SCR:014799 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PsycINFO" ;
definition: "Database for published, indexed resources pertaining to psychological, psychiatric and other behavioral and social science research. Users can search for resources by document type, research methodology, and funding source." .
SCR:014800 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Philips DVT2700 Voice Tracer Digital Recorder with Dragon NaturallySpeaking software" ;
definition: "Software and accompanying hardware for transcription and voice recording. Software is Windows-compatible only and comes in a physical CD." .
SCR:014802 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NVivo" ;
definition: "Software suite for qualitative data analysis for text-based data and higher-order forms of data. Various packages are available and are dependent on the system used and the type of data analysis needed." .
SCR:014803 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OmniPlex Software" ;
definition: "Neural data acquisition software for signal visualization in neuron recordings along with spike wave-form classification methods. It is made up of the PlexControl software program and the OmniPlex Server." .
SCR:014804 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BatchTINT" ;
NIFRID:synonym "BatchTINTV2",
"BatchTINTV3" ;
definition: "GUI created by the Taub Institute in order to create an end-user friendly batch processing solution to complement Axona's new command line modification of TINT. This GUI allows the user to define a directory. Within this directory it will be continuously (unless closed) searching for new files to analyze via TINT." .
SCR:014805 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LFPy" ;
definition: "Python package for calculation of extracellular potentials from multicompartment neuron models. LFPy can be used to set up a model, run simulations, and calculate the extracellular potentials arising from activity in the given model neuron. It relies on the Python interface provided by the NEURON simulator." .
SCR:014806 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_015719" ;
rdfs:label "Allen Cell Types Database" ;
NIFRID:synonym "Allen Brain Atlas",
"Allen Brain Atlas Cell Types",
"Allen Brain Atlas Data Portal" ;
definition: "Database of neuronal cell types based on multimodal characterization of single cells to enable data-driven approaches to classification. It includes data such as electrophysiology recordings, imaging data, morphological reconstructions, and RNA and DNA sequencing data." .
SCR:014807 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Diagenode" ;
definition: "Commercial provider of equipment and resources for epigenetics research, biological sample preparation, and diagnostic assays. The products Diagenode provides include automation and semi-automation software, antibodies, reagents, kits, and shearing technologies." .
SCR:014808 a NLX:152342,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.470425.0" ;
rdfs:label "Sage Science" ;
NIFRID:synonym "Sage Science Inc" ;
definition: "Biotechnology company that develops products for genomics research and molecular diagnostics, such as systems for DNA and protein analysis, DNA and protein fractionation technologies, and other sequencing equipment." .
SCR:014809 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HBio: Multichallel Systems | MEA2100 System" ;
definition: "In vitro recording system for electrophysiology research with integrated amplifier and stimulus generator, temperature control, and the option for real-time signal detection and feedback. The system can record up to 4 MEAs in parallel at a sampling rate of 50 kHz per channel." .
SCR:014810 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neural Signal Archive" ;
definition: "Public archive of neural signals recorded from various types of cells and sites in neural systems. Any data can be publicly accessed and downloaded, and users can submit their data." .
SCR:014811 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iModel" ;
definition: "Database of interactive neural computation computer models at levels ranging from simple linear filters to large-scale networks of spiking units. Interface tools are provided while browsing and exploring models." .
SCR:014813 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PixyTrackingSystem" ;
definition: "Software for automated optical tracking for freely moving and head-fixed animals. It provides real-time and post-hoc tracking methods." .
SCR:014814 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MultiXplore" ;
definition: "Graphical user interface that has been implemented as a 3D Slicer plugin (scripted module). It serves to display a corresponding set of cortical regions from functional connectivity matrix in an explorable 3D scene that represents brain anatomical environment. In addition to grey matter regions, MultiXplore automatically finds and extracts deterministic fiber bundles which exist between selected region(s) and adds them to the 3D environment. This feature helps in generating region-based fiber bundles given a desired whole-brain tractography data." .
SCR:014815 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ,
;
rdfs:label "Automatic Tractography-based Parcellation Pipeline" ;
NIFRID:synonym "Automatic Tractography-based Parcellation Pipeline (ATPP)" ;
NIFRID:abbrev "ATPP" ;
definition: """Integrated pipeline for tractography-based brain parcellation with automatic processing and massive parallel computing. ATPP offers a CLI version for parcellating multiple brain regions and a GUI version for parcellating a specific brain region.
" ATPP completely follows the scientific cultural shift to open science, which aims at making scientific research including journal papers, lab notes, data, and, of course, workflow tools, accessible and transparent to all levels of society. ATPP is publicly accessible in Neuroimaging Informatics Tools and Resources Clearinghouse8 (NITRC) (https://www.nitrc.org/projects/atpp). Its source codes are hosted in GitHub9 (https://github.com/haililihai/ATPP_CLI; https://github.com/haililihai/ATPP_GUI), under the GNU generic purpose license version 310 (GPLv3), and are welcome to download and fork. The Digital Object Identifiers (DOIs) providing a persistent way to make digital data easily and uniquely citable was created from Zenodo11 platform with those GitHub repositories (ATPP CLI v2.0.0, doi: https://doi.org/10.5281/zenodo.239702; ATPP GUI v2.0.0, doi: https://doi.org/10.5281/zenodo.239705). \"""" .
SCR:014816 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Single Cell Portal" ;
NIFRID:synonym "Single-Cell RNA-Seq Portal for Brain Research" ;
NIFRID:abbrev "SCP" ;
definition: "Portal specializes in visualizing and disseminating single cell data. Allows you to use natural language and faceted search to discover other scientists’ research and share your own findings. Each study includes information on cell types, singular or multiple gene expression, and spatial transcriptomics. Interactive visualizations allow to explore cell clusters and search for related genes." .
SCR:014817 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FRET Ratio Imaging Module" ;
NIFRID:synonym "FRET",
"FRET and RatioTool Software Module",
"RatioTool" ;
definition: "Full featured, excitation and emission, FRET and ratio-imaging software module which allows users to view and change setup parameters as images are being acquired. It is a standard component of ISee Analytical Imaging Software." .
SCR:014818 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NovoAlign" ;
definition: "Software tool designed for mapping short reads onto a reference genome generated from Illumina, Ion Torrent, and 454 NGS platforms. Its features include paired end alignment, methylation status analysis, automatic base quality calibration, and in built adapter trimming and base quality trimming." .
SCR:014819 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:gemini" ;
rdfs:label "GEMINI" ;
NIFRID:synonym "GEMINI - a flexible framework for exploring genome variation",
"GEnome MINIng",
"Genome Mining",
"GEnome MINIng (GEMINI)" ;
definition: "Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD." .
SCR:014820 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSigRZ" ;
NIFRID:synonym "BioSigRZ - ABR and DPOAE Screening" ;
definition: "RZ6 processor tool designed for rapid animal screening. It automates the process of presenting stimulus signals and averaging response signal data. It automates the process of presenting stimulus signals and averaging response signal data by giving users control over the stimulus signal parameters used to generate stimuli that vary across successive presentations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014821 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RTCA Software" ;
NIFRID:synonym "Real Time Cell Analysis (RTCA) Software",
"Real Time Cell Analysis Software",
"RTCA 2.0 Software" ;
definition: "Data acquisition and analysis software used for xCELLigence Real Time Cell Analysis SP, DP and MP instruments. The software is used to program and execute experiments and analyze data." .
SCR:014822 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TissueQuest Analysis Software" ;
definition: "Image analysis software for cells and stained areas in samples stained with immunofluorescent markers." .
SCR:014823 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HistoQuest Analysis Software" ;
NIFRID:synonym "HistoQuest" ;
definition: "Brightfield image analysis software for the FACS-like analysis of samples stained with immunohistochemical or other stains." .
SCR:014824 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Imaging Analysis Kit" ;
NIFRID:synonym "Brain Imaging Analysis Kit (BrainIAK)",
"BrainIAK" ;
definition: "Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data." .
SCR:014825 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Webulous" ;
definition: "Server used to create spreadsheets with ontology based data validations. Webulous can process populated templates and transform them into OWL/RDF using design patterns expressed in OPPL. It also has an add-on with Google spreadsheets which supports loading templates from a Webulous server and allows users to submit populated spreadsheets back to the Webulous server for transformation into OWL." .
SCR:014826 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SEARCHBreast" ;
definition: "Database and repository of tissues relating to mouse models of breast cancer. Users can search and share models, and members can enter details of available material to share on a collaborative basis." .
SCR:014827 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NMRbox" ;
NIFRID:synonym "NMRbox.org",
"Nuclear Magnetic Resonance box" ;
definition: "Computing platform for biomolecular NMR available to not-for-profit or government users. It consists of a virtual machine (VM) provisioned with dozens of widely-used NMR software packages, and is available as a cloud-based Platform-as-a-Service (PaaS) or as a downloadable VM for local execution." .
SCR:014828 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellOrganizer" ;
NIFRID:synonym "Cell Organizer" ;
definition: "Image analysis software that learns modular models of things such as cell shape, nuclear shape, vesicular organelle distribution and microtubule distribution directly from 2D or 3D images and can produce specific instances of cell geometries without the need to create them by hand or to segment microscope images. These geometries can be combined with biochemical models to perform spatially realistic cell simulations if used in conjunction with MCell." .
SCR:014829 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Biopac Systems Inc" ;
NIFRID:synonym "BIOPAC",
"Biopac" ;
definition: "Commercial organization which provides hardware and software products for life science research and teaching." .
SCR:014830 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Psykinematix" ;
definition: "Standalone solution dedicated to Visual Psychophysics running on Mac OS X. Psykinematix runs standard psychophysical protocols, presents complex stimuli, collects subject's responses, and analyzes results on the fly. It consists of a unique OpenGL-based software package that does not require any programming skill to create and run complex experiments." .
SCR:014831 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "La Jolla Institute for Immunology Bioinformatics Core Facility" ;
NIFRID:synonym "Institute for Immunology",
"La Jolla Institute; La Jolla Institute for Allergy and Immunology Bioinformatics Core;La Jolla Institute for Allergy and Immunology Bioinformatics Core Facility" ;
definition: "Core Facility provides support for short or long-term projects requiring expertise the analysis of biological datasets. The services provided include the analysis of large-scale datasets (e.g. next-gen sequencing data, microarrays, etc.), the development of customized databases and reusable analysis pipelines, guidance on experimental design, support with technical sections of manuscripts and grants, and training on analysis software packages. All services are charged at our hourly rate." .
SCR:014832 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5678" ;
rdfs:label "La Jolla Institute for Immunology Flow Cytometry Core Facility" ;
NIFRID:synonym "La Jolla Institute for Allergy and Immunology Flow Cytometry Core Facility" ;
definition: "Flow cytometry core which offers a wide range of routine and custom flow cytometry, mass cytometry, cell sorting services, data analysis, strategic planning for novel assays, user training, and full scale research collaborations." .
SCR:014833 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "La Jolla Institute for Immunology Clinical Studies Core Facility" ;
NIFRID:synonym "La Jolla Institute for Allergy and Immunology Clinical Studies Core",
"La Jolla Institute for Allergy and Immunology Clinical Studies Core Facility" ;
definition: "Core facility for clinical studies carried out by the La Jolla Institute of Allergy and Immunology. It is also a non-profit research organization that focuses on studying topics lthat include pollen allergies, HIV, food allergies and tuberculosis." .
SCR:014834 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "La Jolla Institute for Allergy and Immunology Department of Laboratory Animal Care" ;
NIFRID:synonym "La Jolla Institute for Allergy and Immunology Department of Laboratory Animal Care (DLAC)",
"La Jolla Institute for Allergy and Immunology DLAC" ;
NIFRID:abbrev "LJI DLAC; DLAC" ;
definition: "The department of laboratory animal care at the La Jolla Institute for Allergy and Immunology." .
SCR:014835 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5688" ;
rdfs:label "La Jolla Institute for Immunology Microscopy and Histology Core Facility" ;
definition: "Core facility dedicated to providing a static or dynamic (in vitro/in vivo) imaging services by offering histology and microscopy services and providing support and training to interested researchers. The facility offers a range of light microscopes, related imaging systems and image analysis resources for assisted or independent use (upon training). It also can provide advice on proper sample fixation, processing, embedding of tissues with attention to desired orientation, decalcification of bone tissue, cutting of paraffin blocks, cryosectioning, routine and special stains as well as training in histological techniques." .
SCR:014836 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "La Jolla Institute for Allergy and Immunology Functional Genomics Core Facility" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5, 2024. Core facility that combines large-scale automation and high-throughput capabilities with gene disruption techniques to pinpoint the function of individual genes and find new ways to disrupt genetic triggers of disease. The research capabilities are aimed towards finding new treatments for immune-related diseases." .
SCR:014837 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "La Jolla Institute for Immunology" ;
NIFRID:synonym "Institute for immunology",
"la jolla",
"La Jolla Institute for Allergy and Immunology",
"LJI" ;
definition: "Non profit collaborative research organization located in La Jolla, California, UCSD Research Park. Institute researches immunology and immune system diseases to pinpoint specific genes involved, accelerate progress toward development of new treatments and vaccines to prevent and cure type 1 diabetes, cancer and infectious disease. Developer of Immune Epitope Database (IEDB). Provides core facilities with access to equipment, technologies, training and expertise to support innovative research." .
SCR:014838 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1640" ;
rdfs:label "Salk Institute Biophotonics Core Facility" ;
definition: "Core facility equipped with commercial imaging and data analysis technologies. The facility will provide technical assistance to the Salk Institute faculty through access to confocal microscopy (both fixed and live cell), TIRF microscopy, two-photon microscopy, electron microscopy and super-resolution microscopy as well as in vivo imaging modalities." .
SCR:014839 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1643" ;
rdfs:label "Salk Institute Flow Cytometry Core Facility" ;
NIFRID:synonym "Salk Institute Flow Cytometry Core Facility (FACS)" ;
definition: "Core facility dedicated to advancing research projects requiring cell sorting and/or analysis of cell populations by flow cytometry. The core offers training on and access to shared use instrumentation for analytical flow cytometry, services for fluorescence activated cell sorting (FACS) as well as technical consultation and support on experimental design, execution, and data analysis." .
SCR:014840 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Salk Institute Behavior Testing Core Facility" ;
NIFRID:abbrev "BTC" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2024. Core facility that provides the resources to investigate sensory, motor and complex behavioral testing in rat and mouse models. The facility offers standard neurobehavioral tests, customized test batteries, training for independent use of the equipment, data interpretation and anlaysis." .
SCR:014841 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Salk Institute Functional Genomics Core Facility" ;
NIFRID:abbrev "FGL" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5,2024.Core facility that provides Salk researchers access to gene expression analysis services such as whole-genome expression and genotyping using Affymetrix GeneChip technology, high-throughput qPCR and SNP services using Fluidigm Biomark System and Applied Biosystems 7900HT System, and DNA miniprep extraction using Qiagen BioRobot." .
SCR:014842 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC)" ;
NIFRID:synonym "Bioinformatics",
"Core Facility",
"Institute",
"Integrative Genomics",
"Razavi Newman",
"Salk",
"UCSD" ;
NIFRID:abbrev "IGC",
"SALK IGC" ;
definition: "Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications." .
SCR:014843 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1637" ;
rdfs:label "Salk Institute Mass Spectrometry Core Facility" ;
NIFRID:synonym "Salk Institute Mass Spectrometry Core",
"Salk Institute Mass Spectrometry Core (MASS)" ;
NIFRID:abbrev "MASS" ;
definition: "Core facilty that provides access and services for analyzing targeted and complex mixtures of protein and small molecules, like metabolites. By utilizing these tools, research on disease states can be augmented by proteomic and metabolomic study." .
SCR:014844 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Salk Institute Media Preparation Core Facility (MPRP)" ;
NIFRID:synonym "Salk Institute Media Preparation Core Facility" ;
NIFRID:abbrev "MPRP" ;
definition: "Core facility that provides media, plates, and commonly used buffers for molecular biology applications and culturing mammalian cells, C. elegans, yeast, and bacteria. The Media Preparation Core Facility is equipped with 3 automatic plate pourers supported by 2 programmable media kettles capable of producing up to 9 liters of agar or nutrient media per run under gentle and reproducible conditions. Plates are available in 6 cm or 10 cm formats." .
SCR:014845 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.185006.a",
"ISNI 0000 0004 0461 3162",
"Wikidata Q6463245" ;
rdfs:label "La Jolla Institute for Immunology" ;
definition: "Institute dedicated to research in immunology by utilizing the academic and research communities in the La Jolla area as well as technological advances in biomedical research, imaging and analysis. Specific topics include autoimmune disease, cancer, allergies, infectious diseases and inflammation." .
SCR:014846 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1641" ;
rdfs:label "Salk Institute Next Generation Sequencing Core (NGS)" ;
NIFRID:synonym "Salk Institute Next Generation Sequencing Core" ;
NIFRID:abbrev "NGS" ;
definition: "Core houses state-of-the-art equipment in sequencing and genomics, including high-throughput sequencing systems such as Illumina NovaSeq 6000, NextSeq 2000, MiniSeq, and PacBio Sequel IIe system (long-read sequencing), as well as 10x Genomics Chromium Controller single-cell solution, NanoString nCounter MAX Analyzer, and GeoMx Digital Spatial Profiler instrument, along with QuantStudio Real-Time PCR instruments." .
SCR:014847 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1642" ;
rdfs:label "Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core Facility" ;
NIFRID:synonym "Salk Institute Gene Transfer Targeting and Therapeutics Core",
"Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core (GT3)" ;
NIFRID:abbrev "GT3" ;
definition: "Core facility that provides consultation on the use of viral vector technologies as well as custom design and production services for multiple vector types. The GT3 facilitates the use of these research tools by Salk researchers and others across diverse fields of study such as systems neuroscience, stem cell biology, metabolism, ageing, cancer biology and gene therapy. The GT3 core is a designated Cancer Center Council (C3) core facility. Cancer Center members from participating C3 institutes have preferential rates." .
SCR:014848 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Salk Institute Peptide Synthesis Core Facility" ;
definition: "Core facility that provides services such as peptide synthesis, incorporation of non-conventional and/or modified amino acids, HPCL characterization and purification, and Mass spec analysis." .
SCR:014849 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Animal Facility" ;
NIFRID:synonym "SBP Animal Facility",
"SBP Medical Discovery Institute Animal Facility" ;
definition: "Animal facility that provides housing for specific pathogen free rodents, frogs, and zebrafish. The facility also has trained animal care technicians provide expertise in animal husbandry, transgenic and knockout mouse breeding colony maintenance and assistance with routine technical procedures." .
SCR:014850 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Salk Institute Stem Cell Core Facility" ;
NIFRID:synonym "Salk Institute Stem Cell Core (STEM)",
"Salk Institute Stem Cell Core; STEM Core" ;
NIFRID:abbrev "STEM" ;
definition: "Core facility that provides services to support stem cell research for Salk Institute researchers and their direct collaborators. The STEM Core provides well-characterized human embryonic stem (hES) cell lines and human induced pluripotent stem (iPS) cell lines, space and equipment for research, as well as training and consultation." .
SCR:014851 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Animal Imaging and Analysis" ;
NIFRID:synonym "SBP Animal Imaging and Analysis",
"SBP Medical Discovery Institute Animal Imaging and Analysis" ;
definition: "Animal imaging and analysis lab that provides imaging and analytical services for SBP investigators. The facility can perform in vivo non-invasive luminescence and fluorescence imaging for xenograft tumor growth and metastasis studies. Analytical equipment supports complete blood cell counts (CBC) and analysis of serum components revealing metabolic or organ stress from small samples of mouse blood." .
SCR:014852 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Salk Institute Scientific Core Facilities Senior Director's Office" ;
definition: "The central leadership office of the Salk Institute's scientific core facilities. This office provides general management and oversight for administrative, scientific, budgetary and personnel matters for all the scientific core research facilities at the Salk Institute." .
SCR:014853 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Model Organisms" ;
NIFRID:synonym "SBP Medical Discovery Institute Model Organisms",
"SBP Model Organisms" ;
definition: "Facility that provides Drosophila melanogaster and Caenorhabditis elegans as model systems. It also provides training in how to manipulate the organisms and use equipment and provides technician assistance." .
SCR:014854 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_446" ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Flow Cytometry Core Facility" ;
NIFRID:synonym "SBP Flow Cytometry Facility",
"SBP Medical Discovery Institute Flow Cytometry Facility" ;
definition: "Facility that provides access to high-speed cell sorting and analytical flow cytometry. Core allows investigators to have 24-hr/day access to variety of analytical flow cytometers available for independent use. Core staff provide technical expertise and hardware and software training, operate the facility cell sorters, and are available to assist with analysis experiments for those who prefer to have their samples run by an expert cytometrist." .
SCR:014855 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Cellular Imaging Facillity" ;
NIFRID:synonym "SBP Cellular Imaging Facillity",
"SBP Medical Discovery Institute Cellular Imaging Facillity" ;
definition: "Medical research facility that supports research programs by providing access to sophisticated microscopes for digital imaging, as well as training, assistance and guidance. The core facility offers expertise, training and assistance in advanced biological microscopic imaging techniques and use of complex image processing software, use of well-maintained, aligned, and calibrated microscopic equipment, and troubleshooting of equipment and experimental problems." .
SCR:014856 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core" ;
NIFRID:synonym "SBP Medical Discovery Institute Stem Cell Core",
"SBP Stem Cell Core" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The former functions of this facility are split into two separate operations. The first is the generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators with the Snyder lab. The second is a shared laboratory dedicated to the culture and analysis of stem cells that is available to SBP investigators." .
SCR:014857 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Histology Core Facility" ;
NIFRID:synonym "SBP Histology Core Facility",
"SBP Medical Discovery Institute Histology Core Facility" ;
definition: "Facility that provides standard and customized research specific histology services including tissue processing, fixed and frozen sectioning. It also offers routine and special histological stains as well as immunohistochemistry and immunofluorescence. Other services include training for several pieces of common use equipment, such as, paraffin microtome, cryostat, and a cytospin. Training is also provided for basic histological techniques such as perfusion and tissue collection. The tissue acquisition service assists investigators with regulatory/legal compliance, as well as obtains and stores human tissue samples and associated clinical data." .
SCR:014858 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Tumor Analysis" ;
NIFRID:synonym "SBP Medical Discovery Institute Tumor Analysis",
"SBP Tumor Analysis" ;
definition: "Facility that provides analysis of animal models of human cancer and other diseases. It provides investigators access to a wide variety of human cancer cell lines for xenograft studies, some primary human xenograft models and additional transgenic mouse solid tumors and leukemia models. The core also offers serial passaging of tumors and derivation of 2D and 3D cultures from xenograft tumors, including patient-derived xenograft (PDX) models. These short-term cell cultures established from PDXs enable in vitro analysis including high throughput screening with compounds or RNAi for functional characterization." .
SCR:014859 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Functional Genomics Core Facility" ;
NIFRID:synonym "SBP Functional Genomics Core Facility",
"SBP Medical Discovery Institute Functional Genomics Core Facility" ;
definition: "Facility that provides infrastructure for RNAi-based Target Discovery services, from initial feasibility assessment to verification of identified targets. It also serves as a repository for reagents and assays, expertise and other technical information, and works towards technical improvements when necessary. Other available services include consultation, libraries for cloning and screening, and access to equipment such as High-Throughput Microscopes and Plate Readers." .
SCR:014860 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute X-ray Crystallography Facility" ;
NIFRID:synonym "SBP Medical Discovery Institute X-ray Crystallography Facility",
"SBP X-ray Crystallography Facility" ;
definition: "Facility equipped with X-ray crystallography equipment, such as the Rigaku FR-E SuperBright Ultra high-intensity rotating anode generator. The instrument is inteded for self-usage by trained users. It utilizes both ports with two independent diffraction stations that can run simultaneously. Each station is equipped with an X-stream cryogenic system for standard low temperature (~100 K) data collection. The system is used to collect high resolution diffraction data from native and inhibitor-bound crystals or to test and optimize diffraction quality (cryo-protectant conditions, etc.) and screen for further data collection at synchrotron sources." .
SCR:014861 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute NMR Facility" ;
NIFRID:synonym "SBP Medical Discovery Institute NMR Facility",
"SBP NMR Facility" ;
definition: "Facility that acts as a centralized shared resource for NMR studies on proteins, peptides, small molecules, and carbohydrates in solution or in solid state. It provides instrumentation and expertise for NMR data collection. It also provides consultation with investigators on the feasibility of NMR for structural studies of protein candidates, as well as the optimal method to obtain solution structures and binding information by multi-dimensional NMR techniques. It can also train users in basic spectrometer operations, trouble-shoot for instrumental and operational problems, and set up NMR experiments for users as requested." .
SCR:014862 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Protein Analysis Core" ;
NIFRID:synonym "SBP Medical Discovery Institute Protein Analysis Core",
"SBP Protein Analysis Core" ;
definition: "Facility that provides a variety of analytical services focused on biophysical characterization of structural and functional properties of proteins in solution, under native, non-denaturing conditions. Examples of services include quality control of protein samples (folding, stability, aggregation); measuring molecular weight of proteins, protein complexes, oligomers and assemblies; charcaterizing protein conformation and shape in solution; determining oligomeric state of protein (including stoichiometry and Kd for self-association) and measuring protein binding to proteins, peptides, small molecules, compounds, metals, nucleotides and other ligands (including determination of equilibrium (Kd) and kinetic rate (kon, koff) constants, stoichiometry, binding enthalpy and entropy)." .
SCR:014863 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Genomics Microarray/Q-PCR Facility" ;
NIFRID:synonym "SBP Genomics Microarray/Q-PCR Facility",
"SBP Medical Discovery Institute Genomics Microarray/Q-PCR Facility" ;
definition: "Facility that provides full-service microarray-based global analysis of gene expression in RNA samples from humans or mice using an Illumina platform. Services include RNA sample quality and quantity analysis, microarray analysis, and Q-PCR service and analysis, as well as special services such as RNA purification and Copy Number Variation analysis." .
SCR:014864 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Viral Vector Core Facility" ;
NIFRID:synonym "SBP Medical Discovery Institute Viral Vector Core Facility",
"SBP Viral Vector Core Facility" ;
definition: "Facility that provides cost-effective production of high-quality, high-titer lentiviral, retroviral and adenoviral vectors. Services include production of ready-to-transduce lentiviral and adenoviral particles, custom lentiviral, retroviral, and adenoviral production and titrations. Other activities of the facility include packaging, concentrating, and titration of user-supplied lentiviral constructs. Specialized services include custom lentiviral vector construction for constitutive or inducible cDNA/shRNA expression as well as promoter/enhancer reporter, viral packaging, and titration (ready-to-transduce control particles provided)." .
SCR:014865 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Proteomics Facility" ;
NIFRID:synonym "SBP Medical Discovery Institute Proteomics Facility",
"SBP Proteomics Facility" ;
definition: "Facility that provides mass spectrometry-based proteomics services with methods tailored to the needs of scientific investigators for routine mass spectrometric analysis of peptides and proteins, identification of novel proteins, characterization of post-translational modifications, and quantitative proteomics analysis of simple to complex biological samples. The facility identifies, validates and develops new methods designed for the characterization and identification of biologically important proteins. It also supports users with software applications and development, data analysis and experimental design of proteomics studies." .
SCR:014866 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Genomics DNA Analysis Facility" ;
NIFRID:synonym "DNA Analysis Facility",
"Genomics Core",
"Medical Discovery Institute",
"SBP" ;
NIFRID:abbrev "Genomics Core at SBP" ;
definition: "Core facility that provides sequencing services, access to equipment and consultation on experimental design and data analysis. Available instruments include the Life Technologies Ion Torrent PGM and Ion Proton sequencers. Core also provides amplification-free analysis of RNA expression using the NanoString nCounter, and additionally provides sequencing and analysis services to investigators outside of SBP. Included in the cost of sequencing is basic bioinformatic analysis (SNP/InDel calling, transcript abundance). Lastly, the core also provides advice on experimental design, and guidance on the capabilities of next-generation sequencing." .
SCR:014867 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Assay Development Core Facility" ;
NIFRID:synonym "SBP Assay Development Core Facility",
"SBP Medical Discovery Institute Assay Development Core Facility" ;
definition: "Core facility that performs design, development, validation and pilot screening of biological high-throughput assays. It provides services such as designing and developing de-novo assays, converting low-throughput lab protocols (e.g. cuvette- or gel-based) into plate-based HTS assays, and access to major robotic equipment and resources. The facility also provides direct assistance with preparing screening-related grants, guidance through assay development stages, help in designing testing funnels, and generation of preliminary data." .
SCR:014868 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility" ;
NIFRID:synonym "Bioinformatics",
"Data Management Facility",
"MDI",
"Medical Discovery Institute",
"Sanford Burnham Prebys",
"SBP" ;
NIFRID:abbrev "SBP MDI Bioinformatics and Data Management Facility",
"SBP Medical Discovery Institute Bioinformatics and Data Management Facility" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 11132025. Facility that provides database development and management and bioinformatic network building services by utilizing on-site hardware and software. Three members of the facility are available to assist researchers with advanced bioinformatics and biostatistics analysis to help put data into biological context across various disease areas to create testable hypotheses and understand biology of the process. The bulk of support includes connecting functional genomic data with pathways and networks, connecting gene/protein expression and disease state and consultations on statistical aspects of the research with the team statistician." .
SCR:014869 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute High-content Screening Core Facility" ;
NIFRID:synonym "SBP High-content Screening Core Facility",
"SBP Medical Discovery Institute High-content Screening Core Facility" ;
NIFRID:abbrev "HCS" ;
definition: "Core facility that provides access to the HTS plate and liquid handling infrastructure of the screening center, as well as the screening center�s cell culture facility. Other services include assay development, screening, and data analysis/mining expertise and services for high content screens. Consultation from the team is available for high content image-based screens including sample preparation, image acquisition, image analysis, image data management, and algorithm development." .
SCR:014870 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Cell-based Disease Modeling and Screening Core" ;
NIFRID:synonym "SBP Cell-based Disease Modeling and Screening Core",
"SBP Medical Discovery Institute Cell-based Disease Modeling and Screening Core" ;
definition: "Core facility that aims to develop cell based disease models for screening and testing small molecules and drugs, and specializes in culture, scaling, and directed differentiation of human embryonic and induced pluripotent stem cells. It provides resources and expertise to researchers at the Institute and to their external partners to facilitate development of stem cell based assays and patient-specific disease models in screenable formats." .
SCR:014871 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute High-Throughput Screening Facility" ;
NIFRID:synonym "SBP High-Throughput Screening Facility",
"SBP Medical Discovery Institute High-Throughput Screening Facility" ;
NIFRID:abbrev "HTS" ;
definition: "Core facility that provides diverse screening instrumentation, compound libraries and expertise on high throughput screens and automation in support of collaborative, and user- or facility-driven screening projects. The facility collaborates with a number of partners to develop molecular therapies. Services available include consultation for high throughput screening approaches, conversion of assays to automation compatible formats and data analysis." .
SCR:014872 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Medicinal Chemistry Facility" ;
NIFRID:synonym "SBP Medical Discovery Institute Medicinal Chemistry Facility",
"SBP Medicinal Chemistry Facility" ;
definition: "Core facility that provides general synthetic and medicinal chemistry resources and expertise to the biomedical research community. Services include chemistry consulting for projects, grant applications, synthetic chemistry, medicinal chemistry, and analytical chemistry, as well as access to equipment for synthesis, purification, and analysis." .
SCR:014873 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_565" ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core Facility" ;
NIFRID:synonym "Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core",
"SBP Cancer Metabolism Core",
"SBP Medical Discovery Institute Cancer Metabolism Core" ;
definition: "Facility that aims to investigate role of metabolism in cancer on cellular and organismal level, combining in vitro and in vivo analysis. Comprehensive metabolic facility, including stable isotope tracing and flux analysis. Provides analysis of metabolism using specialist instruments and methodologies, together with advice on planning experiments and analyzing data. All instruments and approaches are available on fee-for-service basis to Cancer Center scientists, but alsoto outside users. Samples for most services can be shipped, but Seahorse analyzer users need to be local so they can bring live cells for analysis." .
SCR:014874 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Scripps Research Institute Center for Antibody Development and Production" ;
NIFRID:synonym "TSRI Center for Antibody Development and Production" ;
definition: "Producer of antibodies for investigators to use as diagnostic tools and therapeutic reagents in their research studies. The center works in conjunction with the Department of Animal Resources, and is able to assist in all stages of both polyclonal and monoclonal antibody development." .
SCR:014875 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Cheminformatics Core" ;
NIFRID:synonym "SBP Cheminformatics Core",
"SBP Medical Discovery Institute Cheminformatics Core" ;
definition: "Core facility that supports assay development, high throughput (HTS), ultra-high throughput (uHTS), and high-content screening (HCS) activities performed at the Conrad Prebys Center for Chemical Genomics by providing databases and tools for compound registration and inventory, HTS plate formatting and tracking, HTS and HCS bioassay data processing as well as related data and information handling. Data mining and reporting are also facilitated with a user-friendly database interface. The Cheminformatics core also supports the design and obtaining of appropriate compound collections, as well as SAR follow-up of hits, hit-to-lead optimization and in silico screening through docking and other molecular modeling approaches." .
SCR:014876 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.479509.6",
"ISNI: 0000 0001 0163 8573",
"Wikidata: Q7417591" ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute" ;
NIFRID:synonym "ABP Medical Discovery Institute" ;
NIFRID:abbrev "SBP" ;
definition: "Non-profit dedicated to conducting collaborative research to find cures for human disease, improve quality of life, and educate and train the next-generation of scientists. It is the overarching organization of more than a dozen core facilities that provide various resources in biomedical research." .
SCR:014877 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_618",
"SCR_017832" ;
rdfs:label "Scripps Research Institute Florida Cell Based High Throughput Screening Core Facility" ;
NIFRID:synonym "Cell-Based High-Throughput Screening Core",
"Scripps Research Institute Cell-Based Screening Core",
"The Scripps Research Institute (CBS) Core",
"The Scripps Research Institute Cell-Based Screening (CBS) Core" ;
NIFRID:abbrev "TSRI CBS" ;
definition: "Core facility that provides access to genome-wide collections of cDNAs and siRNAs that can be used to interrogate cellular models of signal transduction pathways and phenotypes. Services include cell lines, hit-picking clones and various screening sets, and access to equipment.Provides instruments:Analyst Molecular Devices,Embla Molecular Devices, Envision Perkin Elmer, Platemate Matrix, Tecan M200, Wellmate Matrix." .
SCR:014878 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ICM Browser" ;
NIFRID:synonym "ICM-Browser" ;
definition: "Molecular graphics environment which provides biologists and chemists with representations of proteins, DNA, RNA, and multiple sequence alignments. Users can build, annotate, and edit interactive views and slides of molecules. Users can also superimpose protein structures, search PDB, measure distanaces and angles, and view and make high resolution images of alignments." .
SCR:014879 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.421925.9",
"ISNI: 0000 0001 0903 5603",
"Wikidata: Q7432923" ;
rdfs:label "Schrodinger" ;
NIFRID:synonym "Schrodinger Inc." ;
definition: "Commercial ogranization which provides molecular and drug discovery software and services to researchers. American software company that develops chemical simulation software for use in pharmaceutical, biotechnology, and materials science research. Provides products ranging from general molecular modeling programs to a full suite of chemical simulation and drug design software, including ligand- and structure-based methods." .
SCR:014880 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "OpenEye" ;
NIFRID:synonym "OpenEye Scientific" ;
definition: "Commercial organization which provides molecular modelling and cheminformatics software to the pharmaceutical industry." .
SCR:014881 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LeadIT" ;
definition: "Drug discovery platform for medicinal and computational researchers. Users can assess the binding affinity and contributions to binding of a complex, find new scaffolds, grow molecules towards pharmacophore points, link fragments, and investigate possible dock binding conformations." .
SCR:014882 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MOE" ;
definition: "Drug discovery software package which can be used in structure-based design, fragment-based design, pharmacophore discovery, medicinal chemistry, protein and antibody modelling, and molecular modeling and simulations. Each aspect of the software package has its own unique features: for example, features for structure-based design include active site detection, scaffold replacement, multi fragment search, and solvent analysis." .
SCR:014883 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SYBYL-X Suite" ;
definition: "Drug and molecular design environment with tools for molecular modeling. It includes tools for small molecule and macromolecular modeling and simulation, cheminformatics, lead identification and lead optimization. Users can: perform multi-criteria drug design; predict safety issues and/or off-target pharmacology; identify leads using ligand-based or structure-based virtual screening, and chemical library design; and perform lead optimization using various QSAR methods." .
SCR:014884 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phase" ;
definition: "Pharmacophore modeling software to create 3D structure activity relationships, screen databases, and generate hits through establishing a chemical space occupied by active ligands. Used in drug design." .
SCR:014885 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FRED - Fast exhaustive docking" ;
NIFRID:synonym "Fast exhaustive docking",
"Fast exhaustive docking (FRED)" ;
NIFRID:abbrev "FRED" ;
definition: "Complementary OEDocking tool for virtual screening, it performs a systematic and non-stochastic examination of all possible protein-ligand poses. The software also filters for shape complementarity and chemical feature alignment before selecting and optimizing protein-ligand poses." .
SCR:014886 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open National Cancer Institute Database" ;
definition: "Public web server that provides structures, data, tools, programs and other useful information to the public for computer-aided drug design. It is the official database of the Computer-Aided Drug Design (CADD) Group." .
SCR:014887 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Prime" ;
definition: "Software package that uses homology modeling and fold recognition to make protein structure predictions." .
SCR:014888 a owl:NamedIndividual ;
rdfs:label "Relibase" .
SCR:014889 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LigandScout" ;
definition: "Software that takes a macromolecular structure containing a bound ligand and identifies the key features on the ligand which are interacting with points on a protein. Its features include: automatic interpretation of PDB ligands using geometry, dictionaries and rule; advanced handling of co-factors, ions, water molecules and covalently bound ligands; pharmacophore export to Catalyst(tm), MOE(tm) and PHASE(tm) for virtual screening; and the ability to treat co-factors and water molecules as part of the ligand or part of the macromolecule." .
SCR:014890 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iResearch Library" ;
definition: "Database of commercially accessible screening compounds from international chemistry suppliers. iResearchLibrary is updated on a weeky basis and offers support for creating internal screening libraries containing commercially accessible compounds, developing exploratory and targeted libraries, selecting commercially accessible compounds for SAR, lead expansion, and hit follow-up projects, and using structures for pharmacophore searching, virtual screening and other computational work." .
SCR:014891 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "World Drug Index" ;
definition: "Database of marketed and developed drugs indexed with internationally-recognized drug names, synonyms, trade names, trivial names and trial preparation codes in one source, plus compound structures and activity data. Each record has chemical structure and is classified by drug activity, mechanism of action, treatment, manufacturer, synonyms, medical nformation and literature references." .
SCR:014892 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CHARMM" ;
definition: "Software program that simulates molecular interactions. It has features that allow broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques, and a range of implicit solvent models. It also primarily targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. CHARMM can also be applied to inorganic materials with applications in materials design and has a comprehensive set of analysis and model builiding tools." .
SCR:014893 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GVKBIO databases" ;
NIFRID:synonym "GVK BIO",
"GVK Biosciences" ;
definition: "Collection of databases with standalone databases, which gives opportunity for customers to integrate the data into their internal tools and databases, as well as online databases, that are available to the customers from a dedicated website where an individual can query and export the data in the selected format. The standalone database topics include medicinal chemistry, drugs and target class based compounds. The online databases are comprised of three major compilations: GVK BIO Online Structure Activity Relation Database (GOSTAR), GVK BIO Biomarker Database (GOBIOM), and Clinical Trial Outcome Database (CTOD)." .
SCR:014894 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NAMD" ;
definition: "Parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR." .
SCR:014895 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Jaguar" ;
definition: "Ab initio molecular modeling software program that computes an array of molecular properties such as multipole moments, polarizabilities, and electrostatic potential. It can also map reaction coordinates between reactants, products, and transition states." .
SCR:014896 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gamess" ;
NIFRID:synonym "The General Atomic and Molecular Electronic Structure System" ;
definition: "Software program for ab initio molecular quantum chemistry. GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Capabilities include using nuclear gradients for automatic geometry optimization, modeling of solvent effects, computation of the energy hessian for prediction of vibrational frequencies, as well as computation of nuclear wavefunctions. The program can also compute variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities." .
SCR:014897 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gaussian" ;
definition: "Software program for electronic structure modeling that enables researchers to study and predict the properties of molecules and reactions under a wide range of conditions, especially those that are difficult or impossible to observe experimentally." .
SCR:014898 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MOPAC" ;
definition: "Software program for semiempirical quantum chemistry for handling of biomolecules." .
SCR:014899 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21304" ;
rdfs:label "Ghemical" ;
definition: "Molecular modelling software package with 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). It contains geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms." .
SCR:014900 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NWChem" ;
definition: "Software toolkit of computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software is designed to work with biomolecules, nanostructures, and solid-state, from quantum to classical, and all combinations, ground and excited-states, Gaussian basis functions or plane-waves, scaling from one to thousands of processors, and the properties and relativistic effects of computational chemistry problems." .
SCR:014901 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPARTAN" ;
definition: "Software program for determining molecular structure and calculating chemical properties. It has a graphical interface and accurate computational models that are compatible with the iPad, iPhone and iPod Touch. When combined with the Spartan'16 Parallel Suite, this enables the first fully-functional open-ended molecular modeling environment on popular mobile technology." .
SCR:014902 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StarDrop" ;
definition: "Software toolkit for drug design and discovery, including plugins for in silico compound optimization, compound selection and integration into other databases." .
SCR:014903 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ADMET Predictor" ;
definition: "Software program for advanced predictive modeling of Absorption, Distribution, Metabolism, Elimination, and Toxicity (ADMET) properties of chemical substances in the human body. ADMET Predictor can estimate a number of vital ADMET properties (listed below) from molecular structures and build predictive models of new properties from user's data." .
SCR:014904 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Leadscope" ;
definition: "Commercial developer of database and predictive model software tools used in chemical toxicity assessment." .
SCR:014905 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ADMEWORKS Predictor" ;
definition: "Software program for high-speed virtual screening intended for simultaneous evaluation of ADMET properties of compounds. ADMEWORKS Predictor employs a number of models to predict ADMET properties using models based on values of topological, geometric, physicochemical and substructure descriptors derived from the molecular structures." .
SCR:014906 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QikProp" ;
definition: "Software program for ADME property prediction for drug development. The program uses properties such as octanol/water and water/gas log Ps and 3D molecular structure. It is capable of screening compound libraries using computed properties to filter out unlikely drug candidates." .
SCR:014907 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ToxAlert" ;
definition: "Software tool for high-throughput toxicity prediction; it assists in the early and quick identification of toxic drug candidates. ToxAlert provides probability percentages for different toxicity endpoints such as oncogenicity, mutagenicity, teratogenicity, neurotoxicity or cell toxicity." .
SCR:014908 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetabolExpert" ;
definition: "Software tool for initial estimation of the structural formula of metabolites, which might be formed by a substance in humans, animals or in plants. MetabolExpert is also capable of predicting the most common metabolic pathways in animals, exporting results to SDF and RDF format and graphical highlighting that empasizes the essence of metabolic reactions that occurred." .
SCR:014909 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HazardExpert Pro" ;
definition: "Software tool for initial estimation of toxic symptoms of organic compounds in humans and in animals and estimating the bioavailability of the compounds by a simple but powerful model. HazardExpert Pro is capable of bioaccumulation calculation, histogram representation of the results including toxicity classification, graphical interface for editing toxic fragments and has open knowledge bases in which a user can add their own fragments." .
SCR:014910 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MEXAlert" ;
definition: "Software tool for quick and sensitive prediction of the common first-pass metabolic routes. It supports high throughput screening, a graphical interface for editing transformation rules and open knowledge bases where users can add own rules." .
SCR:014911 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VolSurf" ;
definition: "Software package for molecular descriptors, ADME prediction and membrane permeability prediction. These can then be used with provided chemometric tools to build statistical models." .
SCR:014912 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Meteor Derek Nexus" ;
definition: "Software for accurate toxicity predictions in silico to identify potentially toxic chemicals during the drug development process." .
SCR:014913 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RetroMex" ;
definition: "Software design tool in retro-metabolic drug design that considers a variety of conepts such as prodrugs, soft drugs, and chemical drug-delivery systems. RetroMex predicts the structure of the retro-metabolites, collects them in compound databases, and presents the results in tree format." .
SCR:014914 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bioclipse" ;
definition: "Open source downloadable application which contains a framework for managing and analyzing chemical compounds, as well as supports editing in 2D, processing large collections of molecules in tables, calculate various types of properties, and more cheminformatics functionality. This software also is used for the management and analysis of biological sequences (DNA, RNA, and protein), and relates the chemical structures and a target and then describes them using mathematical descriptors and models them using statistical methods. Bioclipse is equipped with a scripting language (Bioclipse Scripting Language or BSL) which can be used to automate tasks or create reusable snippets that can be shared with others," .
SCR:014915 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaSite" ;
definition: "Software which predicts metabolic transformations related to cytochrome and flavin-containing monooxygenase mediated reactions in phase I metabolism. MetaSite uses both enzyme-substrate recognition and the chemical transformations induced by the enzyme. MetaSite provides the structure of the metabolites formed with rankings derived from the site of metabolism predictions. This software is not training set dependent, and can predict �hot spots� as well as suggest the regions that contribute most towards each one." .
SCR:014916 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "METAPC" ;
definition: "Software program to predict metabolic and degradation products of chemicals. METAPC has dictionaries on mammalian metabolism, aerobic microbial degredation, anerobic microbial degredation, and photo degredation." .
SCR:014917 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pipeline Pilot" ;
definition: "Software used to automate the process of accessing, analyzing and reporting scientific data. This software can be used by a person with little or no software development experience can create scientific protocols that can be executed through a variety of interfaces including: BIOVIA Web Port, other BIOVIA solutions such as BIOVIA Electronic Lab Notebook, Isentris, Chemical Registration and third-party applications such as Microsoft SharePoint. The protocols aggregate and provide immediate access to volumes of research data, they automate the scientific analysis of data and allow researchers to explore, visualize and report results." .
SCR:014918 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TIMES" ;
definition: "Heuristic algorithm used to generate plausible metabolic maps from a comprehensive library of biotransformations and abiotic reactions, and prioritizes the transformations based on estimated system-specific probabilities occurrence of the transformations. The reliability of generated pathways, metabolites and maps can be assessed according to the extent that they have been supported by observed metabolic data." .
SCR:014919 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CACTVS System" ;
definition: "Computational chemistry related-software used for the computation management, analysis and visualisation of chemical information of any defined type. This software uses a worldwide network of databases with property descriptions, computational modules, data analysis tools, visualization servers, data type handlers and I/O modules to increase the software�s capacity extensibility." .
SCR:014920 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:open_babel" ;
rdfs:label "Open Babel" ;
definition: "Software toolbox that is used to convert, analyze, or store data from molecular modeling, chemistry, biochemistry and other related areas. This software is used to read, write, and convert into over 110 chemical file formats." .
SCR:014921 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GingerALE" ;
definition: "Software available from brainmap.org to perform meta-analyses via the activation likelihood estimation (ALE) method. It also includes the transforms for icbm2tal conversions." .
SCR:014922 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pennsylvania State University SLEIC" ;
NIFRID:synonym "Penn State SLEIC",
"Pennsylvania State University Social Life and Engineering Imaging Center" ;
NIFRID:abbrev "PSU SLEIC" ;
definition: "Imaging center dedicated to fostering research in the social, behavioral, biological, engineering, and materials sciences where imaging methodologies play a central role. The SLEIC provides the Penn State research community with instrumentation, technological and substantive expertise, educational opportunities, and financial support for conducting magnetic resonance imaging (MRI) and electrophysiology (EEG, ERP) experiments." .
SCR:014923 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:spex2" ;
rdfs:label "SPEX2" ;
definition: "Automatic software program for profiling spatial gene expression patterns from Fly embryo ISH images. It utilizes image-based genome-scale profiling of whole-body mRNA patterns." .
SCR:014924 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XenMARK" ;
NIFRID:synonym "BioInfo",
"Xenopus Image Annotator" ;
definition: "Database of Xenopus gene expression patterns, queryable by specific location or region in the embryo. Each entry includes information such as images, species, and gene name." .
SCR:014926 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Epilepsy T1 and Hippocampal Segmentation Datasets" ;
definition: "Shared dataset which consists of skull-stripped T1 MRI images and segmented hippocampi of 163 Temporal Lobe Epilepsy (TLE) patients. The T1 and hippocampal segmentation data of TLE patients are uploaded in three separate datasets which can be accessed from the main site." .
SCR:014927 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Accelerating Medicines Partnership" ;
NIFRID:synonym "Accelerating Medicines Partnership (AMP)" ;
NIFRID:abbrev "AMP" ;
definition: "Partnership between the National Institutes of Health (NIH), the U.S. Food and Drug Administration (FDA), and multiple biopharmaceutical companies and non-profit organizations whose goal is to increase the number of new diagnostics and therapies for patients and reduce the time and cost of developing them. The group explores three major areas of disease: diabetes, Alzheimer's disease, and rheumatoid arthritis and lupus." .
SCR:014928 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_014925" ;
rdfs:label "Alfa Chemicals" ;
NIFRID:synonym "Alfa Chemistry" ;
definition: "Commercial organization which offers a catalog of building blocks, reagents, catalysts, reference materials, and research chemicals for various applications. Analytical services and laboratory services are also provided." .
SCR:014929 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "National Association of Science Writers" ;
NIFRID:synonym "National Association of Science Writers (NASW)" ;
NIFRID:abbrev "NASW" ;
definition: "Association whose goal is to foster the spread of accurate scientific information." .
SCR:014930 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open MEG Archive" ;
NIFRID:synonym "OMEGA:Open MEG Archive" ;
NIFRID:abbrev "OMEGA" ;
definition: """Open data repository fully dedicated to MEG data in raw and processed form. The archive also contains anatomical MRI volumes and demographic and questionnaire information.
Organized and stored as the Brain Imaging Data Structure (BIDS) with the integration of multimodal electrophysiology data.
Directly readable by data-analysis software with Brainstorm.
OMEGA will continue to expand, with contributions from the scientific community.""" .
SCR:014931 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PAUP" ;
NIFRID:synonym "Phylogenetic Analysis Using Parsimony" ;
definition: "Software which creates phylogenetic trees from molecular, morphological and/or behavioral data through high speed computer analysis." .
SCR:014932 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:paml",
"OMICS_04238" ;
rdfs:label "PAML" ;
NIFRID:synonym "Phylogenetic Analysis by Maximum Likelihood",
"Phylogenetic Analysis by Maximum Likelihood (PAML)" ;
definition: "Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML estimates parameters and tests hypotheses to study the evolutionary process from a phylogenetic tree., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014933 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hypermut" ;
NIFRID:synonym "Hypermut 2.0" ;
definition: "Web application for the analysis and detection of APOBEC-induced hypermutations. The first sequence in the input alignment will be used as the reference sequence, and each of the other sequences will be used as a query sequence." .
SCR:014934 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_15373" ;
rdfs:label "Seq-Gen" ;
definition: "Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree." .
SCR:014935 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TMHMM Server" ;
NIFRID:synonym "TMHMM Server v 2.0" ;
definition: "Web application for the prediction of transmembrane helices in proteins using Hidden Markov Models. FASTA formatted sequences can be uploaded via file or copy-paste, and output can be formatted as extensive with graphics, extensive without graphics, or one line per protein. Submissions are limited to 10,000 sequences and 4,000,000 amino acids - each sequence is limited to no more than 8,000 amino acids." .
SCR:014936 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:prop",
"biotools:prop" ;
rdfs:label "ProP Server" ;
NIFRID:synonym "ProP",
"ProP 1.0",
"ProP 1.0 Server" ;
definition: "Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction." .
SCR:014937 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DRIFTER" ;
NIFRID:synonym "DRIFTER Toolbox" ;
definition: "Model based Bayesian method for eliminating physiological noise from fMRI data. This algorithm uses image voxel analysis to isolate the cardiac and respiratory noise from the relevant data." .
SCR:014938 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rpkmforgenes.py" ;
definition: "Python script which calculates gene expression for RNA-Sequencing data. It analyzes files in formats such as BED, BAM, and SAM to output data about RNA." .
SCR:014939 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LINCS Data Portal" ;
definition: "Portal which provides a unified interface for searching LINCS dataset packages and reagents. Users can use the portal to access datasets, small molecules, cells, genes, proteins and peptides, and antibodies." .
SCR:014941 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:chicago" ;
rdfs:label "CHiCAGO" ;
NIFRID:synonym "Capture HiC Analysis of Genomic Organisation",
"Capture HiC Analysis of Genomic Organization",
"CHiCAGO: Capture HiC Analysis of Genomic Organisation" ;
definition: "Statistical pipeline for detecting significant chromosomal interactions in Capture Hi-C data. CHiCAGO uses a convolution background model accounting for both random Brownian collisions between chromatin fragments and technical noise. CHiCAGO then performs a p-value weighting procedure based on the expected true positive rates at different distance ranges, with scores representing soft-thresholded -log weighted p-values., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014942 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016468" ;
rdfs:label "Algal Resources Collection" ;
NIFRID:synonym "Algal Resource Collection (ARC)" ;
NIFRID:abbrev "ARC" ;
definition: "Supplier of algae strains that aims to be a resource to both the HAB research community and biotechnological applications. Researchers can order and deposit strains with the ARC." .
SCR:014943 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aloha Medicinals" ;
NIFRID:synonym "Aloha Medicinals Culture Bank",
"Aloha Medicinals Inc" ;
definition: "Producer and supplier of organic medicinal mushrooms and medicinal mushroom products. Its product line includes raw materials and private label products for pharmaceutical and nutraceutical use, as well as its own branded line of \"Condition Specific\" dietary supplements available to the public." .
SCR:014944 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Animal Biotech Industries" ;
NIFRID:synonym "Animal Biotech Industries Inc",
"Animal Biotech Industries Inc." ;
NIFRID:abbrev "ABI" ;
definition: "Supplier of live porcine models and post mortem tissues, organs, glands, and glandular secretions." .
SCR:014945 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Northern Spalting - Applied Mycology Lab" ;
NIFRID:synonym "Applied Mycology Lab",
"Northern Spalting" ;
definition: "Supplier of non-toxic, pure-culture fungi through Oregon State University which are kept active in the lab. All organisms arrive in an aggressive, pigmenting state. It's website also features scientific information on spalting, DIY guides, lists of upcoming spalting events, and a menagerie of other spalting resources." .
SCR:014946 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aquatic Research Organisms" ;
NIFRID:synonym "Aquatic Research Organisms (ARO)",
"Aquatic Research Organisms Inc",
"Aquatic Research Organisms Inc." ;
NIFRID:abbrev "ARO" ;
definition: "Supplier of laboratory-reared and field-collected freshwater, marine, and estuarine organisms. Invertebrates and vertebrates are available, and seasonal and unlisted organisms can be requested. Its test organisms are available for environmental and biomedical research." .
SCR:014947 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Aquatica BioTech" ;
NIFRID:synonym "Aquatica" ;
definition: "Company developing spawning techniques to allow increased reproduction of tropical fish for the research industry." .
SCR:014948 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Archer Farms" ;
NIFRID:synonym "Archer Farms Inc." ;
definition: "Producer and supplier of swine and sheep for research purposes. Archer Farms delivers its specimens directly to research facilities throughout the East Coast." .
SCR:014949 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ascidian Stock Center (ASC)" ;
NIFRID:synonym "Ascidian Stock Center" ;
NIFRID:abbrev "ASC" ;
definition: "Supplier of Ciona (C. robusta and C. savignyi) adults and stable transgenic animals expressing tissue-specific fluorescent proteins for research laboratories. This ascidian culturing facility is located at the marine laboratory of the University of California at Santa Barbara (UCSB)." .
SCR:014950 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bacillus Genetic Stock Center (BGSC)" ;
NIFRID:synonym "Bacillus Genetic Stock Center" ;
NIFRID:abbrev "BGSC" ;
definition: "Supplier of genetically characterized strains, cloning vectors, and bacteriophages for the genus Bacillus and related organisms. The BGSC can distribute these materials to qualified scientists and educators throughout the world." .
SCR:014951 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Bio Breeders" ;
NIFRID:synonym "Bio Breeders Inc",
"Bio Breeders Inc." ;
definition: "Developer of specialized and appropriate hamster models for research on human diseases. These specialized hamsters have features similar to those seen in certain human diseases. Bio Breeders provides these specialized hamsters to the biomedical community worldwide." .
SCR:014952 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Botanic Gardens Conservation International PlantSearch Database" ;
NIFRID:synonym "Botanic Gardens Conservation International (BGCI) PlantSearch database",
"PlantSearch database" ;
definition: "Global database of living plant, seed, and tissue collections. Users can search by genus, species, infraspecific epithet, and conservation status." .
SCR:014953 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brown Family Enterprises" ;
NIFRID:synonym "Brown Family Enterprises LLC" ;
definition: "Research facility and licensed commercial research animal breeder that specializes in custom polyclonal antibody production, contract research, animal models for research, and animal tissue procurement. Brown Family Enterprises can make and distribute custom polyclonal antibodies using rabbits, goats, sheep, and horses." .
SCR:014954 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "C.M. Rick Tomato Genetic Resources Center" ;
NIFRID:synonym "C.M. Rick Tomato Genetic Resources Center (TGRC)",
"Tomato Genetic Resources Center" ;
NIFRID:abbrev "TGRC" ;
definition: "Genebank of wild relatives, monogenic mutants and miscellaneous genetic stocks of tomato. TGRC offers seed samples for free to researchers worldwide." .
SCR:014955 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MC Rack" ;
NIFRID:synonym "MC_Rack" ;
definition: "Commercial data acquisition and analysis software that forms a data acquisition system for measuring extracellular activities of excitable cells in vitro and in vivo. It has been developed especially for use with the data acquisition systems from Multi Channel Systems MCS, but the software can also be used with other experimental setups." .
SCR:014956 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:MeroX",
"biotools:MeroX" ;
rdfs:label "MeroX" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Software tool for the analysis of cross-linking/mass spectrometry datasets using MS-cleavable cross-linkers. MeroX is specialized for MS/MS-cleavable cross linking reagents and identifies the specific fragmentation products of the cleavable cross links." .
SCR:014957 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StavroX" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Software tool for analyzing cross-linking/mass spectrometry datasets using any bifunctional cross-linker. It can be used to identify cross links of peptides – such as DSS, BS3, Disulfides, and zero-length – in complex mixtures." .
SCR:014958 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Caenorhabditis elegans Natural Diversity Resource (CeNDR)" ;
NIFRID:synonym "Caenorhabditis elegans Natural Diversity Resource" ;
NIFRID:abbrev "CeNDR" ;
definition: "Supplier and researcher of wild C. elegans strains. CeNDR supplies organisms, analyzes whole-genome sequences, and facilitates genetic mappings to aid researchers in gene discovery." .
SCR:014959 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Center for Forest Mycology Research" ;
NIFRID:synonym "Center for Forest Mycology Research Culture Collection",
"The Center for Forest Mycology Research (CFMR)" ;
NIFRID:abbrev "CFMR" ;
definition: "Climate-controlled mycological herbarium housing preserved specimens of forest fungi. CFMR scientists and other researchers use the CFMR collections to test hypotheses of distribution, relatedness, and biological activity of forest fungi." .
SCR:014960 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chlamydomonas Resource Center" ;
NIFRID:synonym "Chlamydomonas Resource Center (CRC)" ;
NIFRID:abbrev "CRC" ;
definition: "Central repository that receives, catalogs, preserves, and distributes wild type and mutant cultures of the green alga Chlamydomonas reinhardtii, as well as useful molecular reagents and kits for education and research." .
SCR:014961 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Saccharomyces Genome Deletion Project" ;
definition: "Database and project to reveal open reading frames (ORFs) in the yeast genome in order to discover their functions. A PCR-based gene deletion strategy is used to assign functions through phenotypic analysis of mutants." .
SCR:014962 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GUSSI" ;
definition: "Software program that can illustrate the output of SEDFIT and SEDPHAT programs and can perform simple calculations with the data. It is designed to work with sedimentation velocity, sedimentation equilibrium, ITC, DLS, and isotherm data." .
SCR:014963 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent Feature Extraction Software" ;
definition: "Software that automatically reads and processes up to 100 raw microarray image files. The software finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences." .
SCR:014964 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:gnomad" ;
rdfs:label "Genome Aggregation Database" ;
NIFRID:synonym "Exome Aggregation Consortium",
"gnomAD 2.0",
"gnomAD Browser",
"gnomAD version 2.0" ;
NIFRID:abbrev "gnomAD" ;
definition: "Database that aggregates exome and genome sequencing data from large-scale sequencing projects. The gnomAD data set contains individuals sequenced using multiple exome capture methods and sequencing chemistries. Raw data from the projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects." .
SCR:014965 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Jackson Laboratory Clinical Knowledgebase" ;
NIFRID:synonym "Jackson CKB" ;
NIFRID:abbrev "CKB" ;
definition: "Semi-automated and manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and oncology clinical trials. Users can search CKB via gene, gene variants, drug, drug class, indication, and clinical trials." .
SCR:014966 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:GENCODE" ;
rdfs:label "GENCODE" ;
NIFRID:synonym "ENCODE" ;
definition: "Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation." .
SCR:014967 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenomeSpace" ;
definition: "Interoperability framework which supports integrative genomics analysis via access to various bioinformatics tools. Rather than performing analyses itself, GenomeSpace acts as a hub for data from supported bioinformatics tools and reformats data and results when necessary." .
SCR:014968 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ClinGen" ;
NIFRID:synonym "Clinical Genome Resource",
"Clinical Genome Resource (ClinGen)" ;
NIFRID:abbrev "CGR" ;
definition: "Genomics knowledgebase for clinical relevance of genes and variants for use in research. ClinGen's primary function is to store and share information for the benefit of the scientific community. Laboratory scientists, clinicians, and patients can share and access data." .
SCR:014969 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DataAssist" ;
NIFRID:synonym "DataAssist Software" ;
definition: "Data analysis tool that utilizes the Comparative CT (ddCT) method to rapidly and accurately quantitate relative gene expression across a large number of genes and samples. Raw input from plates or arrays can be analyzed according to user-determined settings." .
SCR:014975 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:morpheus-framework" ;
rdfs:label "Morpheus" ;
definition: """Modeling and simulation environment for study of multi scale and multicellular systems.
Users can construct and simulate models of gene regulation, signaling pathways, tissue patterning and morphogenesis and explore the effects of multiscale feedbacks between these processes. Morpheus can render 2D and 3D models using graphical user interface.""" .
SCR:014976 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Drososhare" ;
NIFRID:synonym "Drososhare GmbH" ;
definition: "Website resource for researchers to order and send Drosophilia specimens to each other. This community-driven supplier also works with the FlyBase Drosophilia database to search for synonyms for fly species." .
SCR:014977 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Group Sparse Canonical Correlation Analysis" ;
NIFRID:abbrev "GSCCA" ;
definition: "Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data." .
SCR:014978 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Nectagen" ;
NIFRID:synonym "Nectagen Inc",
"Nectagen Inc." ;
definition: "Commercial antibody supplier which provides a web-accessible database of reference and applications data with their reagents." .
SCR:014979 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Elsevier Pathway Studio Software Package" ;
NIFRID:synonym "Elsevier Pathway Studio",
"Elsevier Pathway Studio software package version 10.0",
"Elsevier's Pathway Studio software package version 10.0" ;
definition: "Text mining software that searches curated molecular pathway and cell interaction libraries." .
SCR:014980 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KaleidaGraph" ;
definition: "Data analysis, graphing, and management application that allows users to import, manipulate, analyze data, and create customized plots. Plots include x-y probability, histogram, box, percentile, horizontal bar, stack bar, column, stack column, polar, and pie. Binned data can be exported to a histogram, step plot, or spike plot. KaleidaGraph works with Windows and Macintosh systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:014981 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ICASSO" ;
NIFRID:synonym "Icasso",
"Icasso 1.2" ;
definition: "Software implementing a method for assessing both the algorithmic and statistical reliability of estimated independent components developed by Himburg et al in their 2004 paper. The method is based on running the ICA algorithm many times with slightly different conditions and visualizing the clustering structure of the obtained components in the signal space. In experiments with magnetoencephalographic (MEG) and functional magnetic resonance imaging (fMRI) data, the method was able to show that expected components are reliable; furthermore, it pointed out components whose interpretation was not obvious but whose reliability should incite the experimenter to investigate the underlying technical or physical phenomena." .
SCR:014982 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:multiqc",
"OMICS_12426" ;
rdfs:label "MultiQC" ;
definition: "Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python." .
SCR:014983 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Illumina | NextSeq 500" ;
definition: "High-throughput sequencing machine which enables sequencing of exomes, whole genomes, and transcriptomes. It also provides flow cell types, real-time analysis, and integration with Illumina's BaseSpace computing environment." .
SCR:014985 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RD-CONNECT" ;
definition: "Integrated platform that serves as a central resource for rare disease research databases, registries, biobanks and clinical bioinformatics. The RD-CONNECT project utilizes researcher cooperation and data sharing to improve research methods and further scientific understanding of rare diseases." .
SCR:014987 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lancelet Genome Sequence and Annotation Project Database" ;
definition: "Database project to document the genome sequence of the Lancelet, a basal extant chordate. Information provided includes reference haploid genome sequence and annotation data, gene models and function, and integrated information from diploid genome sequence and annotation data." .
SCR:014988 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Japanese Lamprey Genome Project" ;
definition: "Online database documenting the genome of the Japanese lamprey. The project uses the genome to gain insight into the evolution of vertebrate organisms." .
SCR:014989 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:orcae" ;
rdfs:label "Online Resource for Community Annotation of Eukaryotes" ;
NIFRID:synonym "Online Resource for Community Annotation of Eukaryotes (OrcAE)" ;
NIFRID:abbrev "ORCAE",
"OrcAE" ;
definition: "Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community." .
SCR:014990 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FIESTA" ;
NIFRID:synonym "Fluorescence Image Evaluation Software for Tracking and Analysis",
"Fluorescence Image Evaluation Software for Tracking and Analysis (FIESTA)" ;
definition: "Fully automated software program which can detect point-like and elongated objects with nanometer precision. Also included are analysis tools such as drift correction, color offset calculation, path statistics and mean-square-calculation." .
SCR:014991 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HeteroAnalysis" ;
NIFRID:synonym "HeteroAnalysis Version 1.1.0.58" ;
definition: "Software for analyzing sedimentation equilibrium (SE) data from analytical ultracentrifugation experiments. It uses a model-dependent simulation of data for matching data in order to determine when equilibrium has been achieved." .
SCR:014992 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LTQ-Orbitrap Fusion Tribrid Mass Spectrometer" ;
NIFRID:synonym "Orbitrap Fusion Tribrid Mass Spectrometer" ;
definition: "Mass spectrometer that combines quadrupole, ion trap, and Orbitrap mass analysis." .
SCR:014993 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | EASY-nLC 1000 Liquid Chromatograph" ;
NIFRID:synonym "EASY-nLC 1000" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented April 10, 2017. It has been succeeded by the Thermo Scientific EASY-nLC 1200 Liquid Chromatography system." .
SCR:014994 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | 2200 TapeStation Instrument" ;
NIFRID:synonym "Agilent 2200 TapeStation",
"Agilent 2200 TapeStation system" ;
definition: "Hardware system which automates RNA, DNA, and protein sample QC, including sample loading, separation, and imaging." .
SCR:014995 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nikon | Eclipse FN1 Microscope" ;
NIFRID:synonym "Eclipse FN1" ;
definition: "Fixed-stage microscope for electrophysiological research. Features include open design, noise reduction, 16x objective lens, and water dipping objective with depth induced aberration correction." .
SCR:014996 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Puerto Rico Open Data Interconnection Portal" ;
definition: "Portal for datasets relating to all aspects of Puerto Rican life, including health, education, economy, and environment among others. The datasets available range in quality and amount of information provided, and some offer only limited information. Several of the health ones relate to methadone and methadone clinic usage." .
SCR:014997 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NYC Health and Nutrition Examination Survey" ;
NIFRID:synonym "New York City Health and Nutrition Examination Survey",
"NYC Health and Nutrition Examination Survey (NYC HANES)" ;
NIFRID:abbrev "NYC HANES" ;
definition: "Large scale, population-based, cross-sectional study containing interviews, physical exams, and biological samples. Data is prepared for analysis with SAS and SUDAAN, and is weighted in order to be representative of the New York population." .
SCR:014998 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Economic Commission for Latin America and the Caribbean" ;
NIFRID:synonym "Comision Economica para America Latina y el Caribe",
"Economic Commission for Latin America and the Caribbean (ECLAC)" ;
NIFRID:abbrev "CEPAL",
"ECLAC" ;
definition: "Regional commission of the United Nations with the purpose of contributing to the economic development of Latin America, coordinating actions directed towards this end, reinforcing economic ties among countries and with other nations, and promoting social development." .
SCR:014999 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CEPALSTAT" ;
NIFRID:synonym "CEPALSTAT - Bases de Datos y Publicaciones Estadisticas" ;
definition: "Data repository for statistical information of Latin America and the Caribbean countries collected, systematized and published by CEPAL. CEPALSTAT provides access to statistics and indicators produced by separate ECLAC Divisions which can be used for socio-economic and environmental analysis, as well as various decision-making processes related to Central and South America. Users can export data and cross-tabulate indicators to produce tables combining data from different series, countries and/or periods." .
SCR:015000 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CDC Laboratory Quality Assurance and Standardization Programs" ;
definition: "Standardization program which helps assure the quality of laboratory test data and results so patients, healthcare providers, researchers, and public health officials can be confident that laboratory test results they receive are accurate. CDC services include reference materials, proficiency testing, training, guideline creation, and consultations. Quality assurance and standardization programs can be can be customized by and for users and laboratories." .
SCR:015001 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nexus" ;
NIFRID:synonym "Nexus 1.8.5",
"Nexus 2",
"Nexus 2.4.0",
"Nexus 2.5.0" ;
definition: "Data capture software for use with Vicon motion capture system. Its features include MATLAB integration, Python pre-installed, customized workflow, and automated quality assessment." .
SCR:015002 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bodybuilder" ;
NIFRID:synonym "Bodybuilder 3.6.3",
"Bodybuilder 3.6.4",
"Bodybuilder Software" ;
definition: "Software package for modeling body biomechanics for use with the Vicon motion capture system. Bodybuilder allows users to, among other things, edit and modify trajectories and interpolate broken trajectories, model body segments and joints, create kinematic and kinetic models, and output results to text or file." .
SCR:015004 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pCASL Analysis" ;
definition: "Collection of analysis scripts for pCASL (pseudo-Continuous ASL) data." .
SCR:015005 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genome Resources for Yeast Chromosomes" ;
NIFRID:synonym "Genome Resources for Yeast Chromosomes (GRYC)" ;
NIFRID:abbrev "GRYC" ;
definition: "Database which provides annotated sequence data for the genomes of basidio and ascomycete yeasts. The resources provided include genetic element pages, data sets for downloading, quick and advanced searches, facilities for BLAST comparisons, and a genome browser powered by JBrowse from GMOD." .
SCR:015006 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pituitary Network Association" ;
NIFRID:synonym "Pituitary Network Association (PNA)" ;
NIFRID:abbrev "PNA" ;
definition: "International non-profit organization for patients, relatives, and physicians with pituitary tumors and disorders." .
SCR:015007 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Adrenal Diseases Foundation" ;
NIFRID:abbrev "NADF" ;
definition: "Foundation to support research in and diagnosis of adrenal diseases. The portal provides basic information about adrenal diseases as well as a community for patients." .
SCR:015008 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:busco" ;
rdfs:label "BUSCO" ;
NIFRID:synonym "Benchmarking Universal Single-Copy Orthologs",
"Benchmarking Universal Single-Copy Orthologs (BUSCO)",
"BUSCO v1",
"BUSCO v2" ;
definition: "Software tool to quantitatively measure genome assembly and annotation completeness based on evolutionarily informed expectations of gene content." .
SCR:015009 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Reefgenomics" ;
NIFRID:synonym "reefgenomics.org" ;
definition: "Database for marine genomics data. Users can access genomics datasets from various organisms as well as carry out BLAST and submit genomics information of their own. Data sets include coral, aiptasia, sponges, and sybiodinium." .
SCR:015010 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID: 100002608",
"grid.478451.b",
"ISNI: 0000 0001 0943 2860" ;
rdfs:label "American Thyroid Association" ;
NIFRID:synonym "American Thyroid Association (ATA)" ;
NIFRID:abbrev "ATA" ;
definition: "Organization studying thyroid biology and the prevention and treatment of thyroid disease and cancer. It offers professionals access to thyroid research resources and offers patients general thyroid information, clinical trial information, and patient support links." .
SCR:015011 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Endotext" ;
NIFRID:synonym "endotext.org" ;
definition: "Information portal for practicing endocrinology physicians, trainees, fellows, and other health professionals. Essentially a regularly updated web textbook, it contains endocrinological information written by physicians for other practicing endocrinologists." .
SCR:015012 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " AnaMorph" ;
definition: "Framework for creating 3D neuronal morphologies from point/diameter descriptions." .
SCR:015013 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VTK" ;
NIFRID:synonym "Visualization Toolkit",
"VTK 7.0.0",
"VTK 7.1" ;
definition: "Cross-platform visualization software system for 3D computer graphics, image processing, and data visualization. Various visualization algorithms and advanced modeling techniques are supported within VTK, as well as parallel processing and interoperability with select databases." .
SCR:015014 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenMinTeD" ;
NIFRID:synonym "Open Mining Structure for Text and Data",
"Open Minted",
"OPENM1N7ED" ;
definition: "Text mining consortium and hub for code and resources. Its ultimate goal is to create an infrastructure that encourages the use, incorporation, and interoperability of existing text mining technologies in scientific publications." .
SCR:015015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciLite" ;
NIFRID:synonym "SciLite Annotations" ;
definition: "Text mining tool from Europe PMC that allows biological terms or concepts to be highlighted for readers on full text articles. These terms and concepts are identified by text mining algorithms, which are developed by a variety of text mining groups. However, it is up to the reader to control which selection of highlighted concepts they see. Once concepts of interest have been identified within the text, they are formatted according to the W3C Web Annotation Data Model and stored in a triple store via the EMBL-EBI RDF Platform. As a reader views an article in a web browser, any annotations in the triple store associated with the article are made available in a menu alongside the article." .
SCR:015016 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DrInventor" ;
NIFRID:synonym "Dr Inventor" ;
definition: "Text mining tool that finds similarity between documents based on sentences and tokens such as ontology terms, instead of simple similarity based on lexical terms." .
SCR:015017 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bioz" ;
NIFRID:synonym "bioz" ;
definition: "Search engine that mines life sciences papers using Natural Language Processing and Machine Learning to clean, tag and structure the data. Insights focus on experimentation and include objective recommendations, ratings and insights for reagents, lab equipment, assays, protocols and researchers." .
SCR:015018 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018408" ;
rdfs:label "SourceData" ;
NIFRID:synonym "Source Data",
"source data",
"sourcedata" ;
definition: """Software semantic platform for curating and searching figures. Allows to share scientific figures and underlying data in way that is machine readable and findable. Platform for researchers and publishers to make their papers discoverable based on their data content.
Used to make scientific papers discoverable based on data content, to enable researchers to find specific data, to test or generate new hypotheses, and to share and connect data. Openly accessible and easily applicable data discovery tool as initiative by EMBO.""" .
SCR:015019 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UNSILO" ;
definition: "Text mining tool for publishers and researchers. UNSILO modules possess functions such as searching, recommending articles with similar topics, mapping article relationships, and providing insights into article trends and metrics." .
SCR:015020 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olelo" ;
definition: "Question answering platform for integration of various Natural Language Processing tasks for the biomedical domain. It is built on top of the SAP HANA database and uses MeSH to navigate sentences extracted from papers. Olelo processes three types of questions based on the type of answer a user desires. Answers can be returned as MeSH ontological terms, short answers or facts, and summaries. Document abstracts associated with the search topic are also available for reference." .
SCR:015021 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BeCalm" ;
NIFRID:synonym "Be Calm",
"Biomedical Annotation Metaserver" ;
definition: "Server that contains a registry of text mining tools primarily within the biomedical field. It includes resources for biomedical text annotation visualization, biomedical text annotation prediction, and benchmarking biomedical entity recognition between independent automatic prediction systems." .
SCR:015022 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MicrobiomeAnalyst" ;
NIFRID:synonym "Microbiome Analyst" ;
definition: "Web based data analysis tool for microbiome statistical analysis, visual explortation, and data integration. It supports compositional profiling, functional profiling, comparative analysis, and meta analysis of microbiome datasets." .
SCR:015023 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HKL 3000" ;
NIFRID:synonym "HKL3000R",
"HKL 3000R",
"HKL-3000",
"HKL-3000R",
"HLK3000" ;
definition: "Semi-automatic crystallographic data collection software that integrates data collection, data reduction, phasing and model building in a single software package." .
SCR:015025 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:soapnuke" ;
rdfs:label "SOAPnuke" ;
definition: "Multi-threaded software for rapid quality control and preprocessing of high throughput sequencing data specified for different experiments. It consists of four modules that speed up the report on statistics graphs of raw datasets, preprocessed datasets and preprocessing status." .
SCR:015026 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GapCloser" ;
definition: "Module of SOAPdenovo2 commonly used independently to close gaps in genome assemblies." .
SCR:015027 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:repeatmodeler" ;
rdfs:label "RepeatModeler" ;
definition: "Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015028 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH Brics" ;
NIFRID:synonym "Biomedical Research Informatics Computing System",
"Biomedical Research Informatics Computing System (BRICS)" ;
NIFRID:abbrev "BRICS" ;
definition: "Modular, web-based bioinformatics system for research studies and clinical trials data collection. Tools include a data dictionary, data repository, meta study, global unique identifiers for studies, protocol management and data capture, and query and exportation of data." .
SCR:015029 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "International Image Interoperability Framework" ;
NIFRID:synonym "International Image Interoperability Framework (IIIF)" ;
NIFRID:abbrev "IIIF" ;
definition: "Set of shared application programming interface specifications for interoperable functionality in digital image repositories. It utilizes JSON-LD, linked data, and standard W3C web protocols to parse and share digital image data, migrate across technology systems, and provide enhanced image access." .
SCR:015030 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenStax" ;
NIFRID:synonym "Open Stax",
"Open Stax Textbooks",
"OpenStax Textbooks" ;
definition: "Group that provides open source, college-level textbooks to instructors and their students. Educators can use the textbooks in class and access faculty-specific resources and content online." .
SCR:015031 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaMap" ;
NIFRID:synonym "MetaMap 2016",
"MetaMap 2016v2" ;
definition: "Program to map biomedical text to the UMLS Metathesaurus and to discover Metathesaurus concepts referred to in text based on symbolic, natural-language processing and computational-linguistic techniques." .
SCR:015033 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Astrocyte Reactivity RNA-Seq Browser" ;
definition: "Database containing information about RNA-sequencing and astrocyte reactivity. Searching a gene through this engine provides differential expression data for various experimental conditions." .
SCR:015034 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID: 100003227",
"grid.423291.f",
"ISNI: 0000 0000 9148 0660" ;
rdfs:label "Osteogenesis Imperfecta Foundation" ;
NIFRID:synonym "Osteogenesis Imperfecta Foundation (OIF)" ;
NIFRID:abbrev "OIF" ;
definition: "Foundation for improving the quality of life for people affected by OI through treatment and cure research, education, awareness, and mutual support. OIF lists personal resources for individuals affected by osteogenesis imperfecta as well as professional and clinical resources for researchers." .
SCR:015035 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ALD Connect" ;
definition: "Group whose goal is to improve health outcomes for individuals with X-linked adrenoleukodystrophy by raising disease awareness, improving education, providing support for and information to patients, and performing clinical ALD research." .
SCR:015036 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:egsea" ;
rdfs:label "EGSEA" ;
NIFRID:synonym "Ensemble of Gene Set Enrichment Analyses",
"Ensemble of Gene Set Enrichment Analyses (EGSEA)" ;
definition: "Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets." .
SCR:015037 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100007856",
"GRID grid.39382.33",
"ISNI 0000 0001 2160 926X",
"Wikidata Q2892284" ;
rdfs:label "Baylor College of Medicine; Houston; Texas" ;
definition: "Health sciences university located in Texas Medical Center in Houston, Texas, US. It includes medical school, Baylor College of Medicine, graduate school of Biomedical Sciences, School of Allied Health Sciences, and National School of Tropical Medicine." .
SCR:015038 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013295" ;
rdfs:label "Complex Portal" ;
NIFRID:synonym "EBI Complex Portal" ;
definition: "Database and encyclopaedic resource of macromolecular complexes found in key model organisms from scientific literature. Data includes protein-only complexes, protein-small molecules, and protein-nucleic acid complexes. The information within the portal is manually curated and available for download." .
SCR:015039 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NaviCom" ;
definition: "Web application which allows users to create interactive molecular network portraits using high-throughput datasets." .
SCR:015040 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent Masshunter Quantitative Analysis software" ;
NIFRID:synonym "MassHunter",
"MassHunter Software" ;
definition: "This resource is not available. Documented on October 6, 2020.Software for the analysis of mass spectrometry data. MassHunter also works with software-specific packages to do more specialized analysis tasks." .
SCR:015041 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018818" ;
rdfs:label "HCImage" ;
NIFRID:synonym "HCImage Image Acquisition and Analysis Software" ;
definition: "Image acquisition and analysis software suite for Hamamatsu imaging devices. Hamamatsu Photonics imaging system for microscopy." .
SCR:015043 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Empirical Gramian Framework" ;
NIFRID:synonym "emgr - EMpirical GRamian framework",
"Empirical Gramian Framework (EMGR)" ;
NIFRID:abbrev "emgr" ;
definition: "Software for empirical gramians for model reduction of (nonlinear) input-output systems." .
SCR:015044 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MedCalc" ;
definition: "Statistical software for ROC curve analysis. MedCalc performs several statistical tests such as method comparison, method evaluation, reference intervals, and meta-analysis." .
SCR:015045 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:tomominer" ;
rdfs:label "TomoMiner" ;
definition: "Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging." .
SCR:015047 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.266685.9",
"ISNI:0000 0004 0386 3207",
"Wikidata:Q15144" ;
rdfs:label "University of Massachusetts Boston; Massachusetts; USA" ;
NIFRID:synonym "University of Massachusetts Boston" ;
definition: "Public university located in Boston, Massachusetts that offers degree programs in the social sciences, humanities, and sciences." .
SCR:015048 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "AddictionResources" ;
definition: "Private organization that offers resources and serves as a community for those recovering from addiction and to help patients find the highest quality care for a successful recovery." .
SCR:015051 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CMEIAS software" ;
NIFRID:synonym "CMEIAS Microscopy Image Analysis Software" ;
definition: "Collection of image analysis software developed for microbial ecology." .
SCR:015052 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SnapGene" ;
definition: "Molecular biology software for visualizing and documenting gene constructs for InFusion cloning, Gibson assembly, restriction cloning, PCR, and mutagenesis." .
SCR:015053 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SnapGene Viewer" ;
definition: "Visualization software that allows users to create, browse, and share annotated DNA sequence files from SnapGene." .
SCR:015054 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:wise" ;
rdfs:label "GeneWise" ;
definition: "Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool." .
SCR:015055 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CEGMA" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Tool to annotate core genes in eukaryotic genomes (that was replaced by BUSCO). Its resulting core gene dataset can be used to train a gene finder or to assess the completeness of the genome or annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015056 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MITObim " ;
definition: "Method for mitochondrial baiting and iterative mapping. MITObim assembles novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads." .
SCR:015057 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:paleomix",
"OMICS_03749" ;
rdfs:label "PALEOMIX " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software toolkit for the processing of ancient and modern HTS data. PALEOMIX also aids in metagenomic analysis of the extracts from the HTS processing." .
SCR:015058 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bcl2fastq " ;
NIFRID:synonym "bcl2fastq2",
"bcl2fastq2 Conversion Software v2.20" ;
definition: "Conversion software that both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis." .
SCR:015059 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:seaview",
"OMICS_08908" ;
rdfs:label "SeaView" ;
definition: "Graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees." .
SCR:015060 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:DOGMA" ;
rdfs:label "DOGMA" ;
NIFRID:synonym "Dual Organellar GenoMe Annotator",
"Dual Organellar GenoMe Annotator (DOGMA)" ;
definition: "Web-based annotation tool for plant chloroplasts and animal mitochondrial genomes. DOGMA allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes." .
SCR:015061 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RiceGE " ;
NIFRID:synonym "Rice Functional Genomic Express Database",
"RiceGE: Genome Express Database" ;
definition: "Gene database for Japonica rice. RiceGE is associated with SIGnAL at the Salk Institute." .
SCR:015064 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IbdNe" ;
definition: "Program that estimates the historical effective population size of a homogenous population. The input for the IBDNe program is the set of identity-by-descent (IBD) segments detected by the IBDseq program." .
SCR:015066 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2863" ;
rdfs:label "Einstein-Mount Sinai Diabetes Research Center Human Islet and Adenovirus Core Facility" ;
NIFRID:synonym "Einstein-Mount Sinai Diabetes Research Center Human Islet and Adenovirus Core" ;
definition: "Core which provides methodologies, technology and infrastructure to support investigators in the use of human islets for research studies for the Einstein-Mount Sinai Diabetes Research Center. It isolates and prepares human and rodent islets/beta cells and cell lines for investigator-initiated research and generates specific viral vectors (adenovirus and lentivirus) for gene delivery of cDNAs and shRNAs of interest to beta cells and other islet cell types." .
SCR:015067 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2862" ;
rdfs:label "Einstein-Mount Sinai Diabetes Research Center Biomarker Analytic Research Core Facility" ;
NIFRID:synonym "Einstein-Mount Sinai Diabetes Research Center Biomarker Analytic Research Core",
"Einstein-Mount Sinai Diabetes Research Center Biomarker and Analytical Research Core" ;
NIFRID:abbrev "BARC" ;
definition: """Core provides information and tools for Einstein and Montefiore investigators from initial study planning stage through analysis and data output. Facility services include: mass spectrometry analysis, including stable isotopes, as well as research-grade determination of lipids, and metabolic markers for human subjects and animal model projects; High-throughput robotics for semi-automated high-quality sample preparation and analysis by immunoassay and liquid chromatography–mass spectrometry (LC/MS); Support for novel developmental projects featuring applications of LC/MS and two-site bead-based assays;
Research quality analysis of metabolites for human and animal samples using Olympus AU400 autoanalyzer; Advanced training in analytical chemistry.""" .
SCR:015068 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2861" ;
rdfs:label "Einstein-Mount Sinai Diabetes Research Center Translational Research Core Facility" ;
NIFRID:synonym "Einstein-Mount Sinai Diabetes Research Center Translational Research Core" ;
definition: "Core services include consultation, technical support and training and mentoring in clinical and translational research methods that are specifically applicable to diabetes, its complications and related metabolic disorders. Personel provides expertise in first-in-human and mechanistic studies in integrative physiology, in clinical trials of diabetes and obesity, and in application of new technologies." .
SCR:015069 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2860" ;
rdfs:label "Boston Area Diabetes Endocrinology Research Center Cell Biology and Morphology Core Facility" ;
NIFRID:synonym "Boston Area Diabetes Endocrinology Research Center Cell Biology and Morphology" ;
definition: "Services provided include tissue preparation, embedding and sectioning for electron microscopy, use of electron microscope and photography of thin sections, immunogold staining for electron microscopy, preparation and incubation of samples (cells and tissues) for immunofluorescence microscopy, confocal microscopy and digital imaging." .
SCR:015070 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Einstein-Mount Sinai Diabetes Research Center " ;
definition: "Research center that facilitates the research of diabetes and related studies in obesity, metabolism and endocrinology" .
SCR:015071 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Einstein-Mount Sinai Diabetes Research Center Stable Isotope and Metabolomics Core Facility" ;
NIFRID:synonym "Einstein-Mount Sinai Diabetes Research Center Stable Isotope and Metabolomics Core" ;
definition: "Core which uses stable isotope flux and metabolite profiling to help formulate and test hypotheses about the metabolic consequences of various changes in gene expression and protein function, in order to guide further integrative systems biology analyses of the underlying mechanisms in diabetes, insulin resistance, obesity, and diabetic complications." .
SCR:015072 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Area Diabetes Endocrinology Research Center " ;
definition: "Consortium of laboratory-based and clinical investigators who research etiology, pathogenesis, treatment and cure of type 1 and type 2 diabetes, and their associated microvascular and atherosclerotic complications." .
SCR:015073 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Area Diabetes Endocrinology Research Center Pancreatic Islet " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 23,2024.Core which provides islets to the local diabetes research community in the Boston area. They collaborate with researchers nationally to provide nonhuman primate (NHP) islets for research." .
SCR:015074 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Area Diabetes Endocrinology Research Center Transgenic " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 23,2024.Transgenic core which generates transgenic and gene knockout mouse models relevant to obesity, diabetes and nutrition research. It also provides consultation on all aspects of making transgenic and gene knockout mice." .
SCR:015075 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Columbia Diabetes Research Center " ;
definition: "Research center which provides research support for investigators pursuing research on diabetes and metabolic disorders." .
SCR:015076 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Einstein-Mount Sinai Diabetes Research Center Animal Physiology Core Facility" ;
NIFRID:synonym "Einstein-Mount Sinai Diabetes Research Center Animal Physiology Core" ;
definition: "Core which assists with the in vivo assessment of glucose and fatty acid metabolism, insulin sensitivity and energy homeostasis in mice and rats. It provides tools to understand the behavior and physiology mediating the relationships among diabetes, nutrient sensing, obesity and diabetic cardiovascular complications in rodents." .
SCR:015077 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2859" ;
rdfs:label "Columbia Diabetes Research Center Translational Biomarker Analytical Core Facility" ;
NIFRID:synonym "Columbia Diabetes Research Center Translational Biomarker Analytical Core",
"Translational Biomarker Analytical Core (TBAC)" ;
NIFRID:abbrev "TBAC" ;
definition: "Core makes available to Diabetes Research Center investigators variety of high quality radio-immunoassay, ELISA, and other analytical methods, and facilitates access of DRC investigators to measurement of small molecules by targeted and untargeted metabolomics/lipidomics with the Irving Institute Biomarkers Core. TBAC also provides consultations and services for in vivo methods to measure insulin secretion and sensitivity." .
SCR:015078 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2857" ;
rdfs:label "Columbia Diabetes Research Center Flow Cytometry and Cell Sorting Core Facility" ;
NIFRID:synonym "Columbia Diabetes Research Center Flow Cytometry and Cell Sorting Core" ;
definition: "Core which assists investigators to quantify and phenotypically characterize cell populations that contribute to the metabolic, immunologic and developmental programs of diabetes and its complications; and to purify populations of cells of relevance to diabetes and its complications." .
SCR:015079 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Area Diabetes Endocrinology Research Center Molecular Biology " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 24,2024. Core that provides services for DNA sequencing and oligonucleotide synthesis, as well as support for projects that require research laboratory automation, such as siRNA screens and transcript abundance profiling. It also offers experimental design and advice for automation and high throughput screening of siRNA collections based on the Ambion siRNA collection." .
SCR:015080 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana Diabetes Research Center " ;
definition: "Center that includes over seventy investigators engaged in basic and translational research in diabetes and related metabolic disorders, and their complications. It contains four Research Cores that serve for innovative and translational research." .
SCR:015081 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2889" ;
rdfs:label "Indiana University School of Medicine Center for Diabetes and Metabolic Diseases Islet and Physiology Core Facility" ;
NIFRID:synonym "Indiana Diabetes Research Center Islet and Physiology Core",
"Indiana Diabetes Research Center Islet and Physiology Core Facility",
"Indiana University School of Medicine Center for Diabetes and Metabolic Diseases Islet and Physiology Core",
"Islet and Physiology Core" ;
definition: "Services include islet isolation services from mice and rats and access to porcine and human islets. The core is equipped with BioRep Perifusion Apparatus for measurement of insulin secretion and offers services for islet and beta cell calcium imaging. Provides services for islet transplantation and assists investigators who wish to perform immunohistochemistry, immunofluorescence and/or analysis of endocrine or beta cell mass on whole pancreata from mouse and rat models.Offers services for rodent metabolic characterization, including performance of insulin and glucose tolerance testing, analysis of body composition, and metabolic cage analysis using the TSE System cages. Recently added services include zebrafish characterization to screen genes and small molecules for their effects on islet development and function." .
SCR:015082 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2856" ;
rdfs:label "Columbia Diabetes Research Center Mouse Metabolic Function and Phenotyping Core Facility" ;
NIFRID:synonym "Columbia Diabetes Research Center Mouse Metabolic Function and Phenotyping Core",
"Mouse Metabolic Function and Phenotyping Core" ;
definition: "Core that provides services that facilitate the efficient characterization of mouse models of diabetes and its complications: NMR Body Composition Analysis, Whole Body Metabolic Assessment (chamber calorimetry with motion detection), Metabolic Clamps, Gastric Infusion/Feeding and Thermogenic Phenotyping." .
SCR:015083 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Indiana Diabetes Research Center Microscopy Core Facility" ;
NIFRID:synonym "Indiana Diabetes Research Center Microscopy Core" ;
definition: "Core that provides consultation and specialized services for intravital microscopy of pancreas and transplanted islets, FRET assays, and fluorescent biosensors for analysis of intracellular signaling cascades to serve the area diabetes investigators." .
SCR:015084 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Indiana Diabetes Research Center Translation Core Facility" ;
NIFRID:synonym "Indiana Diabetes Research Center Translation Core",
"Indiana Translation Core" ;
definition: "Core within Indiana Center for Diabetes and Metabolic Diseases that offers services that facilitate conduct of research involving human subjects, including providing low-cost, high quality analyte measurements for variety of hormones, cytokines, lipids and other analytes. Its human studies services include metabolic phenotyping (e.g. GTT, clamp studies, tracer studies), and access to a biobank of human tissues and serum." .
SCR:015085 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2854" ;
rdfs:label "Columbia Diabetes Research Center Advanced Tissue Pathology and Imaging Core Facility" ;
NIFRID:synonym "Advanced Tissue Pathology and Imaging Core",
"Columbia Diabetes Research Center Advanced Tissue Pathology and Imaging Core" ;
definition: "Core that provides spectrum of advanced cellular and tissue pathology and imaging services for diabetes researchers at Columbia University. It also has microscopy equipment and services such as confocal, live 2-photon and scanning and transmission electron microscopy." .
SCR:015086 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Johns Hopkins University - University of Maryland Diabetes Research Center " ;
definition: "Center whose goal is to understand the causes of both type 1 and 2 diabetes and promotes translational research that is aimed at reducing the burden of these diseases in the U.S. It has a specific focus on childhood diabetes and diabetes that affects minority populations." .
SCR:015087 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Johns Hopkins University - University of Maryland Diabetes Research Center Administrative Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 24,2024. Core that typically organizes a meeting with the investigator/user and relevant core directors to discuss the different services and tests that the Diabetes Research Center would recommend to the investigator. It also provides support letters for grant proposals submitted by investigators." .
SCR:015088 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Johns Hopkins University - University of Maryland Diabetes Research Center Integrated Physiology Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 24,2024. Core consisting of several subcores: Ligand Assay and Biomarker Subcore (offers services in Multiplex Assay Detection Systems, Comprehensive Laboratory Animal Monitoring System (CLAMS), and Body Composition), Rodent Physiology and Behavioral Analysis Subcore, and Glucose Metabolism Analysis Subcore (provides services in Dynamic Physiologic Testing)." .
SCR:015089 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana Diabetes Research Center Swine Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 14,2024. Core which utilizes a breeding colony of Ossabaw swine with metabolic syndrome and long-term complications, most notably cardiovascular disease. It provides swine maintenance (glucose tolerance tests, body composition, glucose clamp studies, and imaging studies), characterization of cardiovascular disease (intravascular ultrasound, blood flow velocity, microvascular studies), and tissues (both banked and fresh) for analysis ex vivo." .
SCR:015090 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Johns Hopkins University - University of Maryland Diabetes Research Center Cell Biology Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 9,2024. Core that provides services in tissue analysis and imaging, islet biology, liver biology, and adipocyte biology. It includes the indepedent cores Derivation of IPSC and Bioenergetics as well as the Specialty Animal Surgery Subcore and Bone Biology Subcore." .
SCR:015091 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Johns Hopkins University - University of Maryland Diabetes Research Center Gene Editing Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 9,2024. Core that provides services in Gene Editing Expertise Using CRISPR/CAS9, Conventional Transgenic Mouse Generation, Conventional Knockout, Knock-In Mouse Generation, and Cryopereservation of Sperm, Oocytes and Embryos." .
SCR:015092 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Joslin Diabetes Center Bioinformatics and Biostatistics Core" ;
NIFRID:synonym "Bioinformatics",
"Bioinformatics and Biostatistics Core",
"Biostatistics",
"JDC",
"Joslin Diabetes Center" ;
definition: "Core that offers support for data-driven projects related to basic, clinical and translational research, with a particular emphasis on diabetes. The core aims to ensure that researchers take advantage of the most modern and robust methods available in the field of Bioinformatics and Biostatistics." .
SCR:015093 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Johns Hopkins University - University of Maryland Diabetes Research Center Health and Populations Science Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 9,2024. Contains description of and contact information for multiple health and social science departments." .
SCR:015094 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Joslin Diabetes Center Enrichment Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 9,2024. Six component core which facilitates the exchange of research information and discussions among investigators, fellows and students within the Joslin Diabetes Center, as well as between Joslin Staff and outside researchers with similar interests." .
SCR:015095 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of California San Diego - University of California Los Angeles Diabetes Research Center Metabolic and Molecular Physiology Core Facility" ;
NIFRID:synonym "UCSD UCLA DRC Metabolic and Molecular Physiology",
"University of California San Diego - University of California Los Angeles Diabetes Research Center Metabolic and Molecular Physiology Core" ;
definition: "Provides DRC investigators with thorough scientific consultation and timely, accurate, and easily accessible mouse, tissue, and cellular phenotyping. Services include whole animal, tissue and cellular metabolism, insulin action, and inflammatory signaling as well as cardiac, vascular and renal phenotyping associated with diabetes complications research. It also administers drugs and other substances to mice by different routes in a well-controlled setting." .
SCR:015096 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2948" ;
rdfs:label "University of California San Diego - University of California Los Angeles Diabetes Research Center Transgenic and Knockout Mouse Core Facility" ;
NIFRID:synonym "UCSD UCLA DRC Transgenic and Knockout Mouse Core",
"University of California San Diego - University of California Los Angeles Diabetes Research Center Transgenic and Knockout Mouse Core" ;
definition: "Core that provides and produces transgenic mice. Services and methodologies include pronuclear microinjection and blastocyst microinjection for creation of new mouse cell lines as well as archival services like embryo and sperm freezing." .
SCR:015097 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2947" ;
rdfs:label "University of California San Diego - University of California Los Angeles Diabetes Research Center Genomics and Epigenetics Core Facility" ;
NIFRID:synonym "UCSD UCLA DRC Genomics and Epigenetics Core",
"University of California San Diego - University of California Los Angeles Diabetes Research Center Genomics and Epigenetics Core" ;
definition: "Core which provides Diabetes Research Center investigators access to high-throughput sequencing, data acquisition and analysis. Its main services include Sample QC and Processing, Illumina Platform Library Preparation and Sequencing, and Expression microarrays (RNA, microRNA)." .
SCR:015098 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of California San Diego - University of California Los Angeles Diabetes Research Center Targeted Pathway Analysis Core Facility" ;
NIFRID:synonym "UCSD-UCLA DRC Targeted Pathway Analysis Core",
"University of California San Diego - University of California Los Angeles Diabetes Research Center Targeted Pathway Analysis Core" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 8, 2024. Core with main goal to steer investigators through introductory discovery lipidomics and proteomics experiments toward statistically powered, targeted experiments aimed at measuring biological pathways relevant to diabetes and metabolism." .
SCR:015099 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2946" ;
rdfs:label "University of California San Diego - University of California Los Angeles Diabetes Research Center Human Genetics Core Facility" ;
NIFRID:synonym "UCSD-UCLA DRC Human Genetics Core",
"UCSD-UCLA Human Genetics Core" ;
definition: "Core provides services such as assistance in the development and successful completion of well-designed genetic studies, establishment and storage of EBV-transformed lymphoblastoid cell lines (LCLs), as well as PAXgene tubes, and specialized (e.g., the exome chip) single nucleotide polymorphism (SNP) testing, candidate gene sequencing, whole exome sequencing (WES), whole genome sequencing (WGS), and large-scale gene methylation analysis." .
SCR:015100 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of California San Diego - University of California Los Angeles Diabetes Research Center " ;
definition: "Research center across five institutions for clinical research in diabetes. Collaborators include UC San Diego's School of Medicine, Salk Institute, Cedars-Sinai Medical Center, UC Los Angeles' School of Medicine, and LA Biomedical Research Center." .
SCR:015101 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of California San Francisco Diabetes Research Center Mouse Metabolism Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 10,2024. Core which provides technical support for UCSF investigators to conduct metabolic studies using a 12-chambered Comprehensive Lab Animal Monitoring System (CLAMS), an EchoMRI, and Dual energy X-ray absorptiometry, which together allow measurement of food intake, water intake, motor activities, core temperature, and body composition in live mice. It also helps to identify emerging technologies that will enhance multiple research programs and coordinates the acquisition and maintenance of those facilities." .
SCR:015102 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of California San Francisco Diabetes Research Center " ;
definition: "One of sixteen research centers established by the National Institute of Diabetes and Digestive and Kidney Diseases that fosters research and training in the areas of diabetes and related endocrine and metabolic disorders." .
SCR:015103 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of California San Francisco Diabetes Research Center Microscopy Core Facility" ;
NIFRID:synonym "DRC Microscopy Core" ;
definition: "Core that consolidates, enhances and disseminates Diabetes Center resources and expertise in tissue and cell imaging technologies. Confocal fluorescence, widefield fluorescence, high throughput fluorescence and brightfield microscopes are available directly within the DRC Microscopy Core. Image quantification and analysis is performed at dedicated workstations." .
SCR:015104 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of California San Francisco Diabetes Research Center Lentiviral RNAi Core Facility" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 5,2024. Core that provides reagents, equipment, training, supervision, and monitoring of investigators wishing to ensure the proper compliance with biosafety containment required for lentiviral-based research, lentiviral preparation services for investigators, and education on RNAi experimentation, through the lentiviral core website, and through protocols available at the facility." .
SCR:015106 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of California San Francisco Diabetes Research Center Islet Production Core Facility" ;
definition: "Core that enables clinical and basic research that analyzes the function of isolated pancreatic islets. It coordinates and delivers purified human islets to investigators when research need matches the availability of a human pancreas." .
SCR:015107 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Alabama at Birmingham Diabetes Research Center " ;
definition: "Research center which operates in collaboration with the University of Alabama Birmingham Comprehensive Diabetes Center to promote excellence in diabetes research and patient care. The DRC supports the areas of animal physiology, human biology and intervention and translational research. It focuses on developing new methods to treat, prevent, and ultimately cure diabetes and its complications." .
SCR:015108 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2970" ;
rdfs:label "University of Alabama at Birmingham Diabetes Research Center Administrative Core Facility" ;
definition: "Core responsible for the scientific, education/enrichment, and fiscal operations of the DRC. Their goal is to assure the growing vitality of an intellectual community and a highly productive research program in diabetes by effective deployment of DRC resources for the benefit of our investigators, patients, and trainees." .
SCR:015109 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of California San Francisco Diabetes Research Center Mouse Genetics Core Facility" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 5,2024. Core that provides a shared resource for the establishment of mutant mouse models for DRC research. It coordinates DRC members with contacts to a number of UCSF-wide facilities for knock-out/knock-in and transgenic mouse generation." .
SCR:015110 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2971" ;
rdfs:label "University of Alabama at Birmingham Diabetes Research Center Animal Physiology Core Facility" ;
NIFRID:synonym "Animal Physiology Core" ;
definition: "Core that provides diabetes researches with diabetes related phenotyping in small animal models. Their services offered include the assessment of body composition, energy balance, glucose homeostasis, cardiovascular assessment, imaging, and transgenic animals models." .
SCR:015111 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2972" ;
rdfs:label "University of Alabama at Birmingham Diabetes Research Center Human Physiology Core Facility" ;
NIFRID:synonym "Human Physiology Core" ;
definition: "Core which incorporates and combines expertise and technology for assessment of hormones and other analytes in both humans and animal models; body composition and fat distribution; insulin sensitivity and substrate metabolism; energy expenditure; and cardiovascular function." .
SCR:015112 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Michigan Diabetes Research Center" ;
NIFRID:synonym "Michigan Diabetes Research Center (MDRC)" ;
NIFRID:abbrev "MDRC" ;
definition: "Multidisciplinary unit of the University of Michigan funded by the National Institute of Diabetes and Digestive and Kidney Diseases/National Institute of Health. Promotes new discoveries and enhance scientific progress through the support of basic and clinical research related to diabetes, its complications, and related disorders. Creates environment that supports innovative research; attracts and retains early stage investigators and investigators new to diabetes research; provides core services that leverage funding and unique expertise; fosters interdisciplinary collaborations; raises awareness and interest in fundamental and clinical diabetes research at their institutions, as well as locally, regionally, and nationally." .
SCR:015113 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2973" ;
rdfs:label "University of Alabama at Birmingham Diabetes Research Center Bioanalytical REDOX Biology Core Facility" ;
NIFRID:synonym "BARB Core",
"Bio-Analytical Redox Biology (BARB) Core" ;
definition: "Core which promotes redox biology in diabetes-related research. It promotes research in areas common to the metabolic and vascular aspects of diabetes and cardiovascular disease. The core provides services in mitochondrial damage, function, proteomics, and oxidative stress assessment support for investigators carrying out diabetes mellitus (DM) and cardiometabolic disease (CMD) research at UAB." .
SCR:015114 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Chicago Diabetes Research and Training Center " ;
definition: "Center which promotes multidisciplinary research in diabetes through raising awareness and interest in fundamental and clinical research, enhancing diabetes research, education and training opportunities, and providing core services that leverage funding and unique expertise." .
SCR:015115 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Michigan Diabetes Research Center Administrative Core Facility" ;
NIFRID:synonym "MDRC Administrative Core",
"Michigan Diabetes Research Center Administrative Core" ;
NIFRID:abbrev "MDRC" ;
definition: "Administration Core of the Michigan Diabetes Research Center (MDRC) provides leadership, infrastructure, and resources to support and enhance diabetes research, including the translation of scientific discoveries from bench to bedside. Establishes, promotes, and enhances multidisciplinary and collaborative basic biomedical and clinical research among member investigators studying diabetes, its complications, and related endocrine and metabolic disorders." .
SCR:015116 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Johns Hopkins University - University of Maryland Diabetes Research Center Molecular and Translational Genomics Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Core that provides services in genotyping, sequencing, biobanks, and genetic epidemiology. It also offers access to the Amish exome variant database, basic molecular services, and viral vector construction and development." .
SCR:015117 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Michigan Diabetes Research Center OMICS Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Core that supports the use of the OMICS technologies by MDRC members (specifically on projects relevant to diabetes and related endocrine and metabolic disorders, including their complications) by supporting pilot studies that utilize these technologies." .
SCR:015118 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Michigan Diabetes Research Center Microscopy and Image Analysis Core Facility" ;
NIFRID:synonym "MDRC Microscopy and Image Analysis Core",
"Michigan Diabetes Research Center Microscopy and Image Analysis Core" ;
definition: "Provides MDRC researchers with expert consultation, training and support for routine and advanced microscopy and image analysis techniques. Services include Consultation and Advice on Microscopy and Immunohistochemistry, Cryosection Service, Confocal Microscopy, Image Analysis, Widefield Light Microscopy,Live Cell Microscopy,Training and Education." .
SCR:015119 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Michigan Diabetes Research Center Molecular Genetics Core Facility" ;
definition: "Core that provides services related to the application of genetic methodologies to research related to diabetes. Services include generation of targeted genetic mouse models, using CRISPR/Cas9 system in mouse or rat embryos, generation of specialty viral vectors, specialty viral reagents, and specialty mouse models." .
SCR:015120 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Joslin Diabetes Center Induced Pluripotent Stem Cell Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Core that maintains a centralized facility for the generation and propagation of reprogrammed iPS cells for use in molecular and cellular pathologies underlying diabetes and its complications." .
SCR:015121 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Penn Diabetes Research Center Functional Genomics Core " ;
definition: "Core which offers experiment planning, sample preparation, quality assessment, library construction, DNA sequencing, and data analysis services to DRC members. Its services also include RNAseq, microRNAseq, GroSeq, CLIP-seq, nucleosome mapping, ATAC-Seq, ChIPseq, Exome sequencing, whole genome and targeted methylome analysis, hydroxymethyl DIP, and single cell RNAseq." .
SCR:015122 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Penn Diabetes Research Center Metabolomics Core " ;
definition: "Core which aims to develop and validate metabolomic methods and data analysis software and provide high quality routine metabolomic services. Its services include quantitation of selected water-soluble metabolites, fatty acids, and lipids, quantitation of metabolic fluxes using stable isotope tracers, and identification of novel metabolites involved in diabetes pathophysoiology." .
SCR:015123 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Penn Diabetes Research Center " ;
definition: "Diabetes research center created to address the prevalence of diabetes and obesity. The goal of the center is to support and develop successful approaches to the prevention, treatment, and cure of diabetes mellitus and obesity." .
SCR:015124 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Washington Diabetes Research Center Administrative Core " ;
definition: "Core facility that supports the Diabetes Research Center in its primary mission to enhance research, education and training in diabetes, obesity and related disorders at the University of Washington and in the Greater Seattle area. The Core coordinates and manages programs, evaluates Center activities, and performs other duties." .
SCR:015125 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Washington Diabetes Research Center Cellular and Molecular Imaging Core " ;
definition: "Core facility that provides Diabetes Research Center affiliates with access to specialized expertise and equipment required for high quality histochemical and morphological analyses in a cost-effective manner." .
SCR:015126 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Washington Diabetes Research Center " ;
definition: "University-affiliated center to support both basic and clinical research in diabetes and related metabolic disorders with the ultimate purpose of translating findings into opportunities to prevent these diseases and to improve clinical care and outcomes." .
SCR:015127 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Washington Diabetes Research Center Human Studies Core Facility" ;
NIFRID:synonym "Human Studies Core",
"University of Washington Diabetes Research Center Human Studies Core" ;
definition: "Core facility that provides specialized technical resources and expertise to enhance the efficiency, productivity and multidisciplinary nature of clinical research performed by Diabetes Research Center (DRC)-affiliated investigators." .
SCR:015128 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Washington Diabetes Research Center Cell Function Analysis Core Facility" ;
NIFRID:synonym "University of Washington Diabetes Research Center Cell Function Analysis Core" ;
definition: "Core facility that supports the Diabetes Research Center affiliates by offering precise real time functional analysis of intact cells and primary tissue. The Cell Function Analysis Core also provides an islet isolation service, which gives affiliates easy access to primary tissue/cells ex vivo." .
SCR:015129 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Chicago Diabetes Research and Training Center Molecular Biology and Genetics Core Laboratory " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Molecular biology and genetics core which helps independently funded investigators with an interest in diabetes mellitus and other metabolic disorders to clone, sequence and characterize cDNAs and genes of interest. It also provides research tools and expertise to enable investigators to discover how genetic variation in diabetes genes leads to hyperglycemia." .
SCR:015130 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Washington Diabetes Research Center Vector and Transgenic Mouse Core " ;
definition: "Core facility that provides Diabetes Research Center affiliates with vectors necessary to overexpress, knockdown, knockout, or alter expression of RNAs and proteins of interest in cultured cells, isolated tissues, and animals." .
SCR:015131 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Washington Diabetes Research Center Quantitative and Functional Proteomics Core Facility" ;
NIFRID:synonym "University of Washington Diabetes Research Center Quantitative and Functional Proteomics Core" ;
definition: "Core facility that provides the powerful tools of modern mass spectrometry and complex data set analysis to Diabetes Research Center investigators to permit structural identification and quantitation of proteins involved in diabetes and its complications." .
SCR:015132 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Chicago Diabetes Research and Training Center Islet Cell Biology Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core which provides services and hands-on training in the isolation and functional characterization of pancreatic islets from normal and diabetic humans and mice. It also maintains a repository of insulinoma cell lines for distribution. It puts emphasis on facilitating studies of primary islet cells and it has developed many unique tools and techniques for carrying such studies including novel animals models, biophysical methods and a library of adenovirus-based expression constructs for studying beta-cell function." .
SCR:015133 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Michigan Diabetes Research Center Animal Studies Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Fee-for-service laboratory that provides consultation and utilizes specialized skills and equipment to assess the metabolic state and related endocrine and behavioral phenotypes of rats and mice. The labs include Rat Metabolic Phenotyping Lab, Optogenetics and Behavioral Phenotyping Lab, Islet Laboratory, and Continuous Glucose Monitoring Lab." .
SCR:015134 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Chicago Diabetes Research and Training Center Animal Models and Physiology Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core whose goal is to facilitate the use of model organisms in diabetes and metabolism-related research. The Core provides access to resources, technology, equipment and services for the generation and study of genetically modified mice and other model organisms; consultation on experimental design and analysis; technology development; and opportunities for collaboration and training." .
SCR:015135 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Alabama at Birmingham Diabetes Research Center Interventions and Translation Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core which provides expertise and services that range from methods of intervention development, basic study design and data analysis, and cutting-edge methodologies in measurement, to subject recruitment and retention strategies with an emphasis on increasing minority participation." .
SCR:015136 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University School of Medicine Diabetes Research Center Morphology and Metabolic Analysis Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core facility with the goal of assisting Diabetes Research Core investigators in obtaining metabolic tissues and conducting functional and metabolic analysis of cells and tissues relevant to the pathogenesis of diabetes." .
SCR:015137 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University School of Medicine Diabetes Research Center Mass Spectrometry Core " ;
definition: "Core facility which provides mass spectrometry analyses to Diabetes Research Center investigators that includes quantification as well as structural characterization of diabetes-related biomolecules." .
SCR:015138 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University School of Medicine Diabetes Research Center " ;
definition: "University-affiliated center established to support and enhance research in diabetes and related metabolic diseases. Its long-term goal is the development of new preventive strategies and therapies aimed at improving the lives of Americans with or at risk for diabetes." .
SCR:015139 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Michigan Diabetes Research Center Clinical Core Facility" ;
NIFRID:synonym "Michigan Diabetes Research Center Clinical Core" ;
definition: "Clinical Core of the Michigan Diabetes Research Center (MDRC) provides expertise and services to support basic biomedical research, research focused on the translation of basic science findings into early phase clinical trials, and the testing of treatments related to diabetes in human subjects." .
SCR:015140 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University School of Medicine Diabetes Research Center Cell and Tissue Imaging Core " ;
definition: "Core facility which provides researchers access to and technological support for advanced cellular microscopy and tools." .
SCR:015141 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University School of Medicine Diabetes Research Center Transgenic and ES Cell Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core facility that provides services for efficient and cost-effective development of genetically altered mouse models to elucidate the pathogenesis of diabetes and related metabolic disorders." .
SCR:015142 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Yale Diabetes Research Center " ;
definition: "University-affiliated center that promotes research in diabetes and related metabolic and endocrine disorders at Yale University." .
SCR:015143 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University School of Medicine Diabetes Research Center Immunology of Type 1 Diabetes Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core facility that provides logistic support to investigators examining autoimmune or type 1 diabetes mellitus (T1DM) or other endocrine autoimmunities. Its main purpose is to foster fundamental studies on T1DM through support for acquisition and use of diabetogenic strains of mice, islet isolation, and distribution of cells and antibodies relevant for immunological studies of T1DM." .
SCR:015144 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Chicago Diabetes Research and Training Center Administrative Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core which coordinates and directs the research and training efforts in diabetes conducted at the University of Chicago. It administrates the Pilot and Feasibility Program that supports new investigators in diabetes research as well as established investigators in other fields to conduct novel research related to diabetes." .
SCR:015145 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Yale Diabetes Research Center Molecular Genetics Core " ;
definition: "Core facility which provides genetically modified mice and rodents, mainly transgenic and knockout mice and rodents in the NOD system. It also provides transgenic mice in F2 (usually B6/C3H) and rats on Sprague-Dawley, and chimeric mice using the 129 strain ES cells. It also provides training and management" .
SCR:015146 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for American Indian and Alaska Native Diabetes Translational Research " ;
definition: "Center dedicated to extending prevention and management research of proven efficacy to both clinical and community settings, with the goal of improving the diabetes-related health of Native Americans. The CAIANDTR provides core services and consultation locally, regionally, and nationally in areas relevant to NIDDK's translational research agenda." .
SCR:015147 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yale Diabetes Research Center Physiology Core Facility" ;
NIFRID:synonym "Yale Diabetes Research Center Physiology Core" ;
definition: """Fee-for-service core facility for DRC members to facilitate in vivo diabetes-related research dealing with biological outcomes in normal, diabetic, and genetically manipulated rodents and mice. Physiology Core is divided into two Sub-cores: the Animal Surgery and Experimental Procedure Sub-core, which provides assistance with in vivo rodent studies
the Analytical Sub-core, which assists with measurement of various analytes in rat and mouse samples.""" .
SCR:015148 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for American Indian and Alaska Native Diabetes Translational Research Administrative Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025. Administrative Core of the Center for American Indian and Alaska Native Diabetes Translational Research. The CAIANDTR is dedicated to extending prevention and management research of proven efficacy to both clinical and community settings, with the goal of improving the diabetes-related health of Native Americans." .
SCR:015149 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Centers for Diabetes Translation Research " ;
definition: "Centers that are part of an integrated program whose cores support and enhance diabetes type II translation research. The CDTRs aim to enhance the efficiency, productivity, effectiveness and multidisciplinary nature of diabetes translation research." .
SCR:015150 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Diabetes Research and Training Center Metabolic Physiology Shared Resource " ;
NIFRID:synonym "Human Metabolic Physiology and Genomics Core" ;
definition: "Core facility that provides a range of animal model systems to investigators working in the areas of diabetes and metabolism. It also offers surgical and experimental services, with limited analytical capacity in blood glucose and serology. The Human Metabolic Physiology and Genomics Core evolved from the Metabolic Physiology Shared Resource." .
SCR:015151 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Center for American Indian and Alaska Native Diabetes Translational Research National Resource" ;
definition: "Purpose is to assemble, focus, mobilize, provide, monitor, and evaluate resources necessary to stimulate, carry out, and translate the outcomes of diabetes prevention and management research." .
SCR:015152 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Center for American Indian and Alaska Native Diabetes Translational Research Resource" ;
definition: "Provides access to the CAIANDTR engagement core, technology core, sustainability core, and implementation, dissemination, and diffusion core." .
SCR:015153 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Diabetes Research and Training Center " ;
definition: "University-affiliated center that facilitates the discovery, application, and translation of scientific knowledge to improve the lives of people with diabetes." .
SCR:015154 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Diabetes Research and Training Center Transgenic Mouse and ES Cell Shared Resource " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025.Core facility that provides services, consultation and collaboration to enable the generation, storage and regeneration of genetically altered mice at Vanderbilt." .
SCR:015155 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Georgia Center for Diabetes Translation Research Engagement and Behavior Change Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025. Core which works to create more equitable health promotion and educational programs." .
SCR:015156 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Washington University School of Medicine Diabetes Research Center Diabetes Models Phenotyping Core Facility" ;
NIFRID:synonym "Diabetes Research Center Diabetes Models Phenotyping Core",
"Washington University School of Medicine Diabetes Research Center Diabetes Models Phenotyping Core" ;
definition: "Core facility that provides services to multiple funded research projects in the area of diabetes and its complications so that rigorous experiments performed in model systems have the potential to yield compelling results that can be translated to a clinical context." .
SCR:015157 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Georgia Center for Diabetes Translation Research Disparities Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025. Core which facilitate combined diabetes-disparities translation research that can identify ways to improve engagement in evidence-based diabetes prevention and management interventions among vulnerable populations. Their services include methodological expertise, sociocultural competencies, access to populations in community, and clinical settings, and relevant databases, tools, and technologies that help diabetes investigators." .
SCR:015158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " New York Regional Center for Diabetes Translation Research Population Health and Health Systems Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025. Core facility that supports research that promotes the health of populations with or at risk for diabetes. The Core addresses how to improve the uptake of type 2 diabetes research findings into practice and disseminate effective interventions across health care and community settings." .
SCR:015159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Health Delivery Systems Center for Diabetes Translational Research Diabetes and Obesity Prevention Core " ;
definition: "Research core for the prevention of diabetes and obesity in young women and children. The core works to collaborate on issues of translational interventions for diabetes and obesity prevention by research, evaluation and implementation studies." .
SCR:015160 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Health Delivery Systems Center for Diabetes Translational Research " ;
definition: "Research center for translation research on diabetes within the health care delivery systems affiliated with the HMO Research Network, University of California San Francisco, and the State of California. Their aims include improving health care disparities, diabetes and obesity prevention, and health information technology interventions." .
SCR:015161 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Washington University School of Medicine Diabetes Research Center Translational Diagnostics Core" ;
definition: "Core provides range of assays for human and animal hormones, peptides, and metabolites related to metabolic disorders." .
SCR:015162 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yale Diabetes Research Center Clinical Metabolism Core Facility" ;
NIFRID:synonym "Yale Diabetes Research Center Clinical Metabolism Core" ;
definition: "Core facility which provides personnel, methodology, and instrumentation for the centralized analysis of stable isotopic enrichment of biochemical compounds using Gas Chromatographic-Mass Spectrometric (GC-MS), Liquid Chromatographic-Mass Spectrometric-Mass Spectrometric (LC-MS-MS) and nuclear magnetic resonance spectroscopy (NMR) spectroscopic methods." .
SCR:015163 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yale Diabetes Research Center Molecular Core Facility" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30, 2025. Core facility whose goal is to facilitate the introduction and use of molecular genetic methods by potential DERC investigators at Yale. It provides services, training, consultation, and equipment and resources dedicated to support essential molecular techniques." .
SCR:015164 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Georgia Center for Diabetes Translation Research Design and Evaluation Core Facility" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025. Core which provides services such as translation research and data, especially in the areas of health services research, design, and evaluation, and uptaking of prevention programs to reduce morbidity, and by generating policy- and practice-oriented data to inform investments in diabetes interventions." .
SCR:015165 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Health Delivery Systems Center for Diabetes Translational Research Health Disparities Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30,2025. Research core dedicated to translational research for diabetes with a focus on interventions for closing the gap in health disparities among various underserved populations. The core works to increase awareness of and techniques to survey populations equitably and effectively, evaluate the implementation of various interventions, and identify mediators for health disparities." .
SCR:015166 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yale Diabetes Research Center Administrative Core Facility" ;
NIFRID:synonym "Yale Diabetes Research Center Administrative Core" ;
definition: "Core which is designed to provide centralized offices for the coordination of the Diabetes Research Center's research activities. The core manages grant and financial management, supervises other cores and programs, and provides informataional services." .
SCR:015167 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yale Diabetes Research Center Cell Biology Core Facility" ;
NIFRID:synonym "Yale Diabetes Research Center Cell Biology Core" ;
definition: "Core whose goal is to provide instrumentation, technical personnel, and expertise for the analysis of cell function to Yale Diabetes Research Center investigators. The Core focuses on molecular and cellular imaging techniques and on analysis of islet cell function. Imaging methods include light and electron microscopy, and quantitative infra-red imaging of gels and multiwell plates." .
SCR:015168 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yale Diabetes Research Center Diabetes Translational Core Facility" ;
NIFRID:synonym "Yale Diabetes Research Center Diabetes Translational Core" ;
definition: "Core facility whose goal is to provide training and education for the development of clinical researchers in diabetes." .
SCR:015169 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Michigan Center for Diabetes Translational Research Leveraging Community, Peer, and Family Support Core Facility" ;
NIFRID:synonym "and Family National Support Core",
"and Family Support Core",
"Leveraging Community",
"MCDTR Leveraging Community",
"Michigan Center for Diabetes Translational Research MCDTR and UNC-Chapel Hill Peer Support Core",
"Peer" ;
definition: "Core is outgrowth of Michigan-UNC Peer Support Core, funded through Michigan Center for Diabetes Translational Research, 2016-21. It continues the Peer Support Core’s emphasis on the variety of peers and peer support approaches and the processes that undergird them, while expanding on these to include families and communities. Services include individual consultation to researchers and on research projects, national outreach, and facilitation such as through webinars and annual research workshops of national Special Interest Group of researchers interested in contributions of and interactions among community, peer, and family supports for reducing inequity in diabetes prevention and management." .
SCR:015170 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Michigan Center for Diabetes Translational Research Intervention and Technology Research Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Core that provides assistance to the Michigan Center for Diabetes Translational Research. Its three main services are consultation on content development and technologies, consultation about evidence for translatable diabetes interventions, and providing access to patient-centered health platforms." .
SCR:015171 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Center for Diabetes Translation Research Translation Methods Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 30, 2025. Core which provides support for translational research methodological issues such as health literacy, risk communication, patient centered communication, and cultural communication." .
SCR:015172 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Center for Diabetes Translation Research " ;
definition: "Research center dedicated to providing services to investigators with externally funded, diabetes-related translational research in areas such as innovations in care, community engagement, and clinical trials." .
SCR:015173 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Center for Diabetes Translation Research Community Engagement Core " ;
definition: "Core facility which offers services such as consultation of study design for community-based research, development of IRB protocols, usage of community resources for recruitment efforts, and access to community charcateristics data and geographic information on the community." .
SCR:015174 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " New York Regional Center for Diabetes Translation Research " ;
definition: "Center designed to increase collaboration and enhance communication among diabetes researchers from multiple institutions and diverse disciplines" .
SCR:015175 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Center for Diabetes Translation Research Community Outreach and Heath Disparities Core " ;
definition: "Core facility whose goal is to encourage and facilitate effective diabetes translation research among vulnerable minority populations, especially African and Hispanic Americans. They have three sub-units which include the Community-Based Participatory Research Unit/Planning Unit, the Behavioral Intervention Unit, and the Assessment, Design, and Analysis Unit. Services include a variety of assessments (psychological, dietary, community health surveys, physical activity) as well as research and implementation." .
SCR:015176 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " New York Regional Center for Diabetes Translation Research Life Course Methodology Core " ;
definition: "Core facility that supports type II translational research in diabetes prevention and control. The life course perspective focuses on biopsychosocial and behavioral processes that individuals experience during particular periods in their life, and examines the interplay between these exposures in shaping disease risk." .
SCR:015177 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Center for Diabetes Translation Research Behavioral Intervention Technologies and Services Core " ;
definition: "Core facility whose goal is to incorporate and implement diabetes research outcomes into clinical settings. Services include data processing management and a software toolset and workflow methodology for electronic collection and management of research and clinical trial data." .
SCR:015178 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Chicago Center for Diabetes Translation Research Health Disparities and Community-Based Participatory Research Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 30,2023. Core facility that provide support for diabetes translation research aiming to reduce health disparities and support translation research in the community." .
SCR:015179 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Chicago Center for Diabetes Translation Research " ;
definition: "Center to improve the lives of people with diabetes and people at risk for diabetes through prevention, improved diabetes care, and community empowerment." .
SCR:015180 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " New York Regional Center for Diabetes Translation Research Translational Intervention Methodology Core " ;
definition: "Core facility that supports research that addresses the prevention and control of diabetes using a social-ecological approach to address the dynamic interrelations of biological, psychological and social factor at a personal and environmental level." .
SCR:015181 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Marion Bessin Liver Research Center Animal Models Stem Cells and Cell Therapy " ;
definition: "Core that provides resources, technologies and scientific expertise to advance translational applications of animal and human liver cells. It also provides bred animals for research, isolation and culture of animal and human liver cells, as well as provision of cell culture additives and materials." .
SCR:015182 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Marion Bessin Liver Research Center Imaging and Cell Structure " ;
definition: "Core that supports and assists with use of specialized instrumentation, including laser scanning confocal microscopy, deconvolution microscopy, multi-photon microscopy, cryo-electron microscopy (cryo-EM) and correlative light electron microscopy (CLEM). It also provides expertise in and assistance with specialized imaging techniques such as correlative microscopy, vesicle tracking, volumetric measurements, ultrastructural sample preparation, super resolution fluorescence microscopy (STORM/SIM), Fluorescence Recovery After Photobleaching (FRAP), Fluorescence Resonance Energy Transfer (FRET) and Total Internal Reflection Microscopy (TIRF)." .
SCR:015183 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Center for Diabetes Translation Research Research Partnerships with American Indian/Alaskan Native Communities Core " ;
definition: "Core facility whose services include consultation for community engagement strategies, communication with Native and non-Native American policy experts, and technical assitance in developing culturally appropriate study paradigms." .
SCR:015184 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Molecular Biology and Next Generation Technology " ;
definition: "Core that provides services ranging from classical qPCR and RT-qPCR plus specialized preparation of miRNA and development of targeted genotyping assays." .
SCR:015185 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Georgia Center for Diabetes Translation Research " ;
definition: "Research center for translational research on type 2 diabetes with a strong emphasis on translation into real world health care settings and communities." .
SCR:015186 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Marion Bessin Liver Research Center Genetic Engineering and Gene Therapy " ;
definition: "Core that provides Liver Research Center investigators an extensive array of customized viral and non-viral vectors, viral and non-viral vectors for reprogramming somatic cells, generating special non-viral vectors, consultation for study design and, if appropriate, data analysis." .
SCR:015187 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Michigan Center for Diabetes Translational Research " ;
NIFRID:abbrev "MCDTR" ;
definition: "Multidisciplinary unit of the University of Michigan funded by National Institute of Diabetes and Digestive and Kidney Diseases/National Institutes of Health. MCDTR is one of seven NIH Centers funded to focus on type 2 translational research in diabetes with mission to establish, promote, and enhance multidisciplinary collaboration among researchers directed at prevention and control of diabetes, its complications, and comorbidities, by providing access to specialized expertise and resources." .
SCR:015188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Michigan Center for Diabetes Translational Research Methods and Measurements Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Research core that works to assist investigators in designing studies, collecting data, and analyzing data to examine questions related to the causes, prevention, and control of diabetes, its complications, and comorbidities." .
SCR:015189 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " New York Regional Center for Diabetes Translation Research Latino Network for Diabetes Translational Research " ;
definition: "Research network dedicated to supporting translation research in diabetes prevention and control. The core has a strong emphasis on sociocultural adaption for Latinos in the U.S and can provide expertise in Latino biopsychosocial research." .
SCR:015190 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Marion Bessin Liver Research Center " ;
definition: "Center that conducts scientific investigation to understand fundamental mechanisms of normal liver function, alterations in these functions resulting from metabolic disorders, genetic diseases, acute and chronic liver injury, hepatitis virus infection, hepatic fibrosis and liver cancer, and ways to overcome these abnormalities through methods of genetic engineering, gene therapy and liver cell transplantation." .
SCR:015191 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Texas Medical Center Digestive Diseases Center " ;
definition: "Center designed to serve basic and clinical scientists at institutions within the Texas Medical Center, including Baylor College of Medicine, The University of Texas Health Science Center at Houston and the MD Anderson Cancer Center. It facilitates digestive diseases research, promotes translational collaborative research between basic and clinical areas, develops new projects, nurtures new investigators, and provides GI educational activities." .
SCR:015192 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Health Delivery Systems Center for Diabetes Translational Research California State Resource Program " ;
definition: "Program and partnership for supporting the California Diabetes Program. This partnership engages in various supportive activtes, including diabetes surveillance; the design, implementation, and evaluation of prevention and care strategies for diabetes; understanding the implications of policy change on diabetes care and prevention; and dissemination of new findings to diabetes stakeholders throughout the state." .
SCR:015193 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Health Delivery Systems Center for Diabetes Translational Research Health Information Technology Core " ;
definition: "Core dedicated to promoting and integrating health information technology into every day health care settings. These technologies include data networks, surveillance of patterns of diabetes care, and management tools for diabetic populations." .
SCR:015194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Michigan Center for Diabetes Translational Research Administrative Core Facility" ;
NIFRID:synonym "MCDTR Administrative Core" ;
definition: "Administrative core for the Michigan Center for Diabetes Translational Research. It works to raise awareness of and interest in type 2 diabetes research, manage its grant program, and support investigators working on both clinical and implementationl diabetes research." .
SCR:015195 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cincinnati Children's Hospital Digestive Health Center" ;
NIFRID:synonym "Cincinnati Children's",
"Cincinnati Children's Hospital",
"DHC" ;
NIFRID:abbrev "Cincinnati Children's DHC",
"Cincinnati Children's Hospital DHC" ;
definition: "Core that provides Digestive Health Center (DHC) investigators technologies for gene and protein expression. The services provided by the Core are grouped into five types of technologies: Gene Expression Service, DNA Sequencing and Genotyping Core, Bioinformatics Service, Protein Expression-Research Flow Cytometry Core, and Protein Multiplexing-Luminex Assay." .
SCR:015196 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cincinnati Digestive Health Center " ;
definition: "Center that is located within Cincinnati Children's Hospital Medical Center, that serves as a University of Cincinnati Academic Health Center resource to foster pediatric digestive disease research and make discoveries to restore digestive health." .
SCR:015197 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cincinnati Digestive Health Center Integrative Morphology " ;
definition: "Core that provides pathology research service, live microscopy service, and confocal imaging to facilitate morphologic studies in digestive diseases." .
SCR:015198 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Center for Diabetes Translation Research Health Communication and Health Literacy Core " ;
definition: "Core facility whose services include assisting with outreach and recruitment to various populations, developing strategic community partnerships, and developing materials and methods for effective health education within the community." .
SCR:015199 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cincinnati Digestive Health Center Pluripotent Stem Cell and Organoid Core " ;
definition: "Core whose services include generation of human induced pluripotent stem cells (iPSCs) from DHC-relevant patient cells and directed differentiation of human pluripotent stem cells (hPSCs) to human intestinal organoids (HIOs)." .
SCR:015200 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cincinnati Digestive Health Center Clinical Component-Data Analysis and Management " ;
definition: "Core that is meant to provide members with biostatistical support and the infrastructure to execute disease-based clinical research. Its services include advising on research designs, including project implementation and data collection methods, guidance on appropriate statistical methods based on study design, training and access to REDCap (Research Electronic Data Capture) for research studies, and reviewing REDCap Data Base Structure." .
SCR:015201 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for the Study of Inflammatory Bowel Disease Genetics Genomics and Molecular Biology Core " ;
definition: "Core that provides services in the utilization of advanced genetics and molecular biological techniques and facilitates the implementation of advances in genomics and molecular biology to IBD research. It provides access to capital or resource-intensive methodologies, such as laboratory automation cDNA and siRNA libraries, and BAC-centered recombinant DNA techniques." .
SCR:015202 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for the Study of Inflammatory Bowel Disease " ;
definition: "Multidisciplinary program which aims to define fundamental mechanisms underlying Crohn?s disease and ulcerative colitis. It actively promotes clinical and translational research efforts to apply insights gained in studying various disease mechanisms through its five biomedical cores: the Human Genetics and Microbiome Core, the Morphology Core, the Immunology Core, the Genetic Animal Models Core and the Clinical Core." .
SCR:015203 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Center for Diabetes Translation Research Policy and Systems Science Analysis in Diabetes Research Core " ;
definition: "Core facility whose services include policy consultation and research design advice, workshops on systems science analysis, and management of a resource library of policy and system science tools and datasets." .
SCR:015204 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Center for Diabetes Translation Research " ;
definition: "Research center for diabetes that offers regional and national resources to investigators for translation interventions into healthcare settings, communities, and populations at-risk. The CDTR supports studies investigating the root causes of diabetes and disparities as well as the prevention of obesity as a major contributing cause of Type 2 diabetes." .
SCR:015205 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Center for Diabetes Translation Research Administrative Core " ;
definition: "Management core which oversees the Vanderbilt University Medical Center Pilot and Feasability Program and promotes education, training, and outreach to the research community." .
SCR:015206 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Center for Diabetes Translation Research Health Informatics in Diabetes Research Core " ;
definition: "Core facility whose services include consultation for management of complex datasets and literature resources, as well as promoting education of data analysis tools for researchers." .
SCR:015207 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " CURE - Digestive Diseases Research Center Human Studies Core " ;
definition: "Core facility whose services include secretory tests, motility and pH tests, videoendoscopy, biopsy and histology, serum bank of patients with ulcer hemorrhage, and visceral sensitivity and autonomic function tests." .
SCR:015208 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Chicago Center for Diabetes Translation Research Quantitative Analysis Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 30,2023. Core facility that provides analytic support for a wide range of projects in diabetes translation research ranging from program evaluation to cost-effectiveness analysis." .
SCR:015209 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " CURE - Digestive Diseases Research Center Morphology and Imaging Core " ;
definition: "Core facility which provides services through centralized resources and facilities, as well as training and assistance for the application of morphological, imaging and stem cell biology technologies and promoting collaborations among CURE:DDRCC investigators with independently-funded research projects." .
SCR:015210 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cleveland Digestive Diseases Research Core Center " ;
definition: "Center that is focused on what produces the digestive diseases that affect millions of people in the U.S., such as inflammatory bowel disease, hepatitis, metabolic syndromes and obesity." .
SCR:015211 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mayo Clinic Center for Cell Signaling in Gastroenterology Optical Microscopy Core " ;
definition: "Core provides essential optical technologies and applications expertise to support faculty research by providing microscopic technology to all faculty members that facilitates their study of GI cellular signaling cascades, educating and training faculty members in the use of both basic and sophisticated cellular imaging methods, and developing and applying optical imaging technologies to GI tissues and cells based on faculty needs." .
SCR:015212 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Digestive Disease Centers " ;
definition: "Center of collaborating research centers working on the research of digestive and liver-related diseases. Each center focuses on etiology, treatment, and prevention of digestive and/or liver diseases." .
SCR:015213 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " CURE - Digestive Diseases Research Center Molecular Biology and Peptidomics Core " ;
definition: "Core whose aim is to promote and facilitate basic and translational GI research. Its services include consultation and troubleshooting in techniques for efficient gene delivery, as well as cloning and functional protein expression in mammalian cells in vitro and in vivo and consultation and to perform customized gene expression profiling, cytological phenotype profiling, and high-throughput molecular screening studies by utilizing high-throughput and highly automated robotic systems." .
SCR:015214 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Texas Medical Center Digestive Diseases Center Functional Genomics and Microbiome " ;
definition: "Core whose services include consultation in the choice of genomics methodologies to be applied to research problems being addressed by Digestive Diseases Center members, training in the conduct of functional genomics and metagenomics relevant to GI research, providing mammalian gene expression, cytokine/transcription factor/signaling pathway arrays, and gut microbial profiling/metagenomics to DDC members at discounted prices, and conducting periodic workshops and disseminating information about new technologies available in the Core and to obtain feedback on needed technologies / services." .
SCR:015215 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Center for Diabetes Translation Research Solutions to Diabetes in Black Americans Core " ;
definition: "Core facility whose services include consultation about the challenges that Black Americans face regarding diet and food advertising, study design and implementation assistance, and positing relevant questions to the larger core for relevant research questions." .
SCR:015216 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cleveland Digestive Diseases Research Core Facilities " ;
definition: "Collection of four cores: the biorepository core, for clinical specimen storage; the Histology/Imaging Core, for tissue preparation and sectioning; the Mouse Models Core, for education and training on various mouse modeling techniques; and the Clinical Component of the Administrative Core, for clinical study design consultation." .
SCR:015217 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " CURE - Digestive Diseases Research Center Animal Models Core " ;
definition: "Core that provides in vivo characterization of normal and pathophysiological mechanisms of hormonal and neural regulation of gastrointestinal (GI) function and brain-gut interactions in rodents to members and associate members of the CURE: DDRCC." .
SCR:015218 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Texas Medical Center Digestive Diseases Center Study Design and Clinical Research Core Services " ;
definition: "Core that provides epidemiological and biostatistical support for design and analysis, and also provides investigators with access to the clinical specimens required for their basic and translational research activities. It offers assistance as well as didactic training in issues involving local and foreign IRB?s, HIPPA regulations, and importing or exporting clinical specimens." .
SCR:015219 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Texas Medical Center Digestive Diseases Center Cellular and Molecular Morphology Core " ;
definition: "Core facility whose services include histology, immunohistochemistry, RNA in situ hybridization, mRNA probe generation, frozen sections for enzyme histochemistry, immunofluorescent antibody studies, live and fixed cell confocal, deconvolution microscopy and super resolution microscopy (SIM and STORM), and transmission electron microscopy, quantitative morphometric analysis, high throughput microscopy and high content analysis, laser capture microdissection for molecular genetic analyses, and digital images for internet communication and publication." .
SCR:015220 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Texas Medical Center Digestive Diseases Center Integrative Biology Core " ;
definition: "Core that aims to provide turnkey access to organoids/enteroid technologies to TMC-DDC researchers. These include samples (enteroids, organoids), reagents (specialized growth media, etc.), training, and consultative expertise. The core also provides access to gnotobiotic facilities and animals, training and consultative expertise." .
SCR:015221 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Chicago Center for Diabetes Translation Research Outcomes Improvement Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 30,2023. Core facility that provides support to investigators in designing and carrying out translational studies assessing outcomes for patients with diabetes, or populations at risk." .
SCR:015222 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Texas Medical Center Digestive Diseases Center Administrative Core " ;
definition: "Core that provides governance, financial and operational management, and strategic planning functions for the DDC. This core is also responsible for coordinating the annual Pilot Feasibility Awards program, as well as the weekly GI Research Forum and the annual Frontiers in Digestive Medicine Symposium." .
SCR:015223 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Digestive Disease Research Center Bioanalytical Mass Spectrometry and Proteomics Core " ;
definition: "Core that aims to further digestive disease research by providing services including identification of oxidized lipids by GC/MS and HR-LC/MS, proteomics for identification and characterization of proteins by MudPIT and LC-MS/MS techniques, quantification of protein expression by LC-MS/MS, interpretation and analysis of mass spectrometry data, and quantification of trace elements in physiologic fluids by ICP-MS." .
SCR:015224 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mayo Clinic Center for Cell Signaling in Gastroenterology " ;
definition: "Center whose mission is to improve understanding of the signaling pathways that control the function of gastrointestinal cells in health and disease. It serves as a hub that provides access to research resources and expertise to multidisciplinary groups of basic scientists and clinical researchers." .
SCR:015225 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Digestive Disease Research Center " ;
definition: "Center whose objectives include promoting digestive diseases-related research in an integrative, collaborative and multidisciplinary manner, developing and implementing programs for attracting, training, and retaining young investigators in digestive disease-related research, and facilitating the transfer of basic research discoveries to improvements in prevention and/or clinical care." .
SCR:015226 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mayo Clinic Center for Cell Signaling in Gastroenterology Gene Editing and Cell Engineering Core " ;
definition: "Core whose services include designing, constructing and validating custom plasmids and other DNA vectors, making custom genome engineering reagents, including TALENs, transposons, bacterial artificial chromosomes and CRISPRs, and providing consults and training on a variety of topics, including rodent and zebrafish transgenic and knockout model development support." .
SCR:015227 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for the Study of Inflammatory Bowel Disease Clinical Core " ;
definition: "Core whose objective is to provide an infrastructure that facilitates the translation of basic research findings into the clinic. Its services include consultation, training, and education, biospecimen services, and facilitating data collection and analysis." .
SCR:015228 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for the Study of Inflammatory Bowel Disease Morphology Core " ;
definition: "Core that provides CSIBD investigators with the technical support, expertise and access to instrumentation necessary for their morphological and cell biological studies related to IBD. These services include routine tissue fixation and processing for light microscopy, imaging flow cytometry, perfusion-fixation of organs, conventional electron microscopy, low temperature embedding in Lowicryl HM20, and immunocytochemistry." .
SCR:015229 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mayo Clinic Center for Cell Signaling in Gastroenterology Clinical Core " ;
definition: "Core facility which supports faculty research by facilitating access to human biospecimens. Its services include centralized access to participating Mayo Clinic GI biobanks and other institutional biospecimen resources, de-identified, phenotypic and demographic data, and coordination of fresh tissue acquisition from surgical pathology." .
SCR:015230 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Center for Diabetes Translation Research Dissemination and Implementation in Diabetes Research Core " ;
definition: "Core facility whose services include consultion for further dissemination of diabetes research and assistance with design methods for early dissemination of results." .
SCR:015231 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " CURE - Digestive Diseases Research Center Administrative Core " ;
definition: "Management core that develops mission, goals, and strategies relating to the functioning of the CURE:DDRCC." .
SCR:015232 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " USC Liver Transplant Program and Center for Liver Disease Analytical Metabolic Instrumentation Core " ;
definition: "Core that maintains and provides access and training in the use of a large base of major and expensive equipment, including thermocyclers, plate readers, centrifuges, a wide range of customized HPLC services, and Seahorse metabolic applications." .
SCR:015233 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " USC Liver Transplant Program and Center for Liver Disease Cell Separation and Culture Core " ;
definition: "Core facility which provides primary hepatocytes cultures of normal and diseased mice and rats and various cell lines to investigators. The cell separation subcore plays a role in translational research in DILI and alcoholic hepatitis, supporting funded studies of the role of innate and adaptive immune systems in elucidating pathophysiology, identifying biomarkers, and predicting response to treatments." .
SCR:015234 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " USC Liver Transplant Program and Center for Liver Disease Cell and Tissue Imaging Core " ;
definition: "Core that provides instrumentation (confocal and fluorescence microscopy) and technical support for cell biology and pathophysiology studies." .
SCR:015235 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Center for Diabetes Translation Research Administrative Core in Diabetes Research Core " ;
definition: "Management core whose main functions include organizing and managing membership committees, coordinating communication with the NIH and other research bases, and overseeing the use of funds." .
SCR:015236 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " USC Liver Transplant Program and Center for Liver Disease Liver Histology Core " ;
definition: "Core that provides standard and customized slide preparation, liver histochemistry and immunohistochemistry as well as laser-capture microscopy." .
SCR:015237 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " USC Liver Transplant Program and Center for Liver Disease " ;
definition: "Center whose goal is the facilitation and fostering of interdisciplinary collaborative research in the field of pathobiology of diseases of the liver and digestive tract and the development of new treatments for these diseases." .
SCR:015238 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for the Study of Inflammatory Bowel Disease Genetic Animal Models Core " ;
definition: "Core whose services include breeding and maintenance of mutant mouse stocks, characterization of murine models, bone marrow transfers and adoptive T cell transfers, in vivo tracking of fluorescently labeled bacteria and cells, and whole body imaging of bioluminescent and fluorescent signals." .
SCR:015239 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for the Study of Inflammatory Bowel Disease Immunology Core " ;
definition: "Core whose focus is on modern approaches to the study of the human immune system and their application to the study of IBD and related disorders. Its services include routine immunology tools, specialized immunology services, and education and training services." .
SCR:015240 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atomify LAMMPS" ;
NIFRID:synonym "Atomify" ;
definition: "Mobile simulation app for visualizing molecular interactions in liquids, solids and gases. The simulations are performed with the molecular dynamics code LAMMPS." .
SCR:015241 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuromembrane Simulator" ;
definition: "Simulator to help students understand basic properties of excitable membranes, particularly ion flow across an excitable membrane. The simulator is based on the equations developed by Alan Hodgkin and Andrew Huxley following their research on the excitability properties of the squid giant axon." .
SCR:015242 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Neurodata Without Borders - Neurophysiology",
"NWB:N",
"NWB:N 2.0" ;
NIFRID:abbrev "NWB" .
SCR:015243 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phandango" ;
definition: "Interactive web visualization tool for populations of bacterial genomes linked by a phylogeny." .
SCR:015244 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11546" ;
rdfs:label "jModelTest" ;
definition: "Software tool used to carry out statistical selection of best-fit models of nucleotide substitution without the aid of PAUP*. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests, Akaike and Bayesian information criteria, and a decision theory method. It also provides estimates of model selection uncertainty, parameter importances, and model-averaged parameter estimates." .
SCR:015245 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WholeBrain" ;
NIFRID:synonym "Whole Brain" ;
definition: "Software suite that provides an efficient way for scientist with minimal knowledge of computers to create anatomical maps and integrate this information with behavioral and physiological data for sharing on the web. It uses R for data analysis and graphical plotting and uses OpenCV for image analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015246 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ilastik" ;
NIFRID:synonym "ilastik",
"Interactive Learning And Segmentation Toolkit",
"Interactive Learning And Segmentation Toolkit (Ilastik)" ;
definition: "Tool for interactive image classification, segmentation and analysis, built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection." .
SCR:015247 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ltr_finder",
"SCR_020944" ;
rdfs:label "LTR_Finder" ;
NIFRID:synonym "LTR Finder" ;
definition: "Web software capable of scanning large-scale sequences for full-length LTR retrotranspsons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015248 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Statgraphics Centurion" ;
NIFRID:synonym "Statgraphics Centurion XVII" ;
definition: "Data analysis and visualization software with features that include a R interface, demographic maps, bivariate density estimation, multiple time series visualization, repeated ANOVA measures, and a multivariate visualizers." .
SCR:015249 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Imspector Software" ;
definition: "Software toolkit for data aquisition and analysis. Its features include remote control of Abberior Instruments microscopes via a Python/MATLAB script, third-party compatibility with other data-analysis softwares/methods, and the easyCommander graphical user interface for experimental set up." .
SCR:015250 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Digestive Disease Research Center Cellular Imaging Core " ;
definition: "Core facility whose goals include furnishing professional guidance in experimental design and data interpretation and providing access to optical and electron microscopy. Its services include confocal microscopy, wide-field microscopy, transmission electron microscopy, and processing and embedment of tissue or cells for EM." .
SCR:015251 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Vanderbilt Digestive Disease Research Center Flow Cytometry Core " ;
definition: "Core facility whose services include training, acquisition and analysis on cytometers for experiments that include different fluorochromes, imaging cytometry, and mass cytometry." .
SCR:015252 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Digestive Diseases Research Core Center " ;
definition: "Research center whose purpose is to advance research in digestive disease with a focus on interactions between host and environment. It provides research resources to basic and translational investigators through various core facilities." .
SCR:015253 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Digestive Diseases Research Core Center Administrative and Resource Access Core " ;
definition: "Core facility which provides DDRCC members facilitated access to technology and assistance for genetic profiling of clinical and experimental samples." .
SCR:015254 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Digestive Diseases Research Core Center Advanced Imaging and Tissue Analysis Core " ;
definition: "Core facility which provides comprehensive histologic and immunohistochemical support, advanced microscopic imaging and image analysis services to digestive disease researchers. The Tissue Analysis Component performs animal and human tissue embedding, sectioning, routine and special staining, and immunohistochemical analyses, and provides training in all services while the Advanced Image Analysis Component provides access to and training in routine light, fluorescent and inverted fluorescent microscopy and quantitative image analysis." .
SCR:015255 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Yale Liver Center " ;
definition: "Research center which supports investigation of liver structure, function and disease through access to its four core facilities (Administrative, Physiology, Clinical and Translational, and Morphology cores) and Pilot Feasability Projects." .
SCR:015256 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Digestive Diseases Research Core Center Biobank Core " ;
definition: "Core facility that collects and provides specimens and longitudinal clinical data from patients with digestive diseases. Specimens collected and processed by the core currently include blood, surgical resections, endoscopic biopsies, and stool. Clinical information is stored in a database and linked to specimens and data obtained from these specimens." .
SCR:015257 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Yale Liver Center Administrative Core " ;
definition: "Core facility which acts as the administrative structure of the Liver Research Center. The activities it oversees include all scientific and administrative supervisory functions of the Center and its administrative leadership, including the organization and supervision of Core facilities, the planning and scheduling of the enrichment program and the review and oversight of individual pilot feasibility projects." .
SCR:015258 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Yale Liver Center Cellular and Molecular Physiology Core " ;
definition: "Core facility that provides technical expertise, equipment and personnel to Liver Center Investigators who wish to work with animal models of liver disease, isolated liver cells, or gene expression in liver tissue. The Cell Isolation sub-core isolates hepatocytes and non-parenchymal liver cells primarily from rat and mouse, while the Molecular Biology sub-core provides equipment and expertise to Liver Center members in a centralized facility." .
SCR:015259 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Yale Liver Center Clinical and Translational Core " ;
definition: "Core facility which aims to develop an infrastructure for patient-oriented research by streamlining regulatory and compliance processes, obtaining and storing high-quality samples linked to clinical information, offering consultation in the design and implementation of clinical trials, and supplying statistical expertise for interpreting clinical and translational data." .
SCR:015260 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University Digestive Diseases Research Core Center Murine Models and Gnotobiotics Core " ;
definition: "Core facility that provides advice and technical services to DDRCC investigators that include production of transgenic and chimeric mice, derivation of speed congenics and assisted reproduction services for maintaining pedigrees via the Mouse Genetics Core, as well as gnotobiotic mouse provision, colonization and rederivation." .
SCR:015261 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mucosal HIV and Immunobiology Center " ;
definition: "Research center which investigates the interaction between microbes and mucosal tissues in humans. It provides three core facilities for research: the Genetically-Defined Microbe Core, the Molecular Pathology and Human Cell/Tissue Core, and the Gnotobiotic and Genetically-Engineered Mouse Core." .
SCR:015262 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mucosal HIV and Immunobiology Center Genetically-Defined Microbe Core " ;
definition: "Core composed of the Viral Unit, which provides labeled andn unlabeled viral components, and Bacterial Unit, which provides bacteria and bacterial proteins for research. The retroviral unit focues on the viral components of the retrovirus HIV-1." .
SCR:015263 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mucosal HIV and Immunobiology Center Gnotobiotic and Genetically-Engineered Mouse Core " ;
definition: "Core facility which generates and provides gnotobiotic and genetically engineered mice to research projects. It also provides specialized breeding, marker-assisted genotyping, and histopathologic evaluation services for studies using these mice." .
SCR:015264 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Yale Liver Center Morphology Core " ;
definition: "Core facility that provides instrumentation and technical expertise for the preparation, acquisition and analysis of images of cells and tissues at the light microscopic level. Its services include confocal and super-resolution microscopy, epifluorescent microscopy with quantitative and ratio imaging, timelapse microscopy with image processing and analysis, multiphoton microscopy, and cryosectioning." .
SCR:015265 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mucosal HIV and Immunobiology Center Molecular Pathology and Human Cell and Tissue Core " ;
definition: "Core that provides both morphological analysis of mucosal tissues and instructs investigators in the techniques used to prepare tissue sections and analyze the morphology and cellular components of the mucosa and primary human gut (intestinal and rectal) cells, gastric mononuclear cells and genital (cervical and vaginal) cells and instruction on how to construct mucosal tissue explants in a transwell chamber system." .
SCR:015266 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " George M. O'Brien Kidney Research Core Center - UT Southwestern Medical Center Physiology Core " ;
definition: "Core that provides measurement of serum and or urine Creatinine by Capillary Electrophoresis, measurement of serum and urine citrate by capillary electrophoresis, Microanalysis of serum and urine electrolytes by: Flame photometry, Atomic absorption or Ion-Selective Electrode, and Klotho IP-IB Assay." .
SCR:015267 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Duke O'Brien Center for Kidney Research Animal Models Core " ;
definition: "Core facility that provides access to a range of experimental models of kidney, heart and vascular diseases. It also provides comprehensive phenotyping services for kidney functions, blood pressure and other cardiovascular functions." .
SCR:015268 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Duke O'Brien Center for Kidney Research " ;
definition: "Research center which investigates the mechanisms underlying the impact kidney disease has on cardiovascular morbidity and mortality using genetic and basic science approaches." .
SCR:015269 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Duke O'Brien Center for Kidney Research Renal Genomics Core " ;
definition: "Core facility that provides resources for investigators researching the genetic mechanisms of chronic kidney disease, cardiovascular disease, and hypertension. Its services include pre-study consultation, standardized services for DNA isolation and storage, and assisstance in carrying out molecular genetic studies." .
SCR:015270 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " O'Brien Kidney Centers " ;
definition: "Research program whose aim is to make state-of-the art technologies and resources accessible to a broad spectrum of investigators pursuing studies in kidney research areas." .
SCR:015271 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana O'Brien Center for Advanced Microscopic Analysis " ;
definition: "Imaging center which provides renal and urological researchers access to intravital optical microscopy and 3-dimensional quantitative digital image analysis." .
SCR:015272 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Duke O'Brien Center for Kidney Research Clinical and Translational Core " ;
definition: "Core facility which investigates the connections between chronic kidney disease, cardiovascular disease, and hypertension. It focuses specifically on investigating the pathophysiology, epidemiology, and therapeutic response in on-going studies or existing datasets of one of the three diseases with the aim of relating data from individual diseases to each other." .
SCR:015273 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana O'Brien Center for Advanced Microscopic Analysis Intravital Microscopy Core " ;
definition: "Core facility which primarily provides service, animal models, consultation training and intravital optical microscopy customized to kidney and urologic research. It also develops and characterizes novel biosensor probes and in vivo delivery methods for these probes, as well as intravital multiphoton microscopy technologies." .
SCR:015274 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana O'Brien Center for Advanced Microscopic Analysis Probe Delivery Core " ;
definition: "Core facility which develops and characterizes methods for expressing fluorescent biosensors in the rodent kidney to be paried with intravital microscopy." .
SCR:015275 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana O'Brien Center for Advanced Microscopic Analysis Education Core " ;
definition: "Core faciltiy which provides instructional workshops, a visiting speakers program, and a web resource for the dissemination of methods, educational materials and software relating to imaging technologies." .
SCR:015276 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana O'Brien Center for Advanced Microscopic Analysis Digital Image Analysis Core " ;
definition: "Core facility which develops and implements software and methods of image segmentation for fluorescence microscopy data." .
SCR:015277 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana O'Brien Center for Advanced Microscopic Analysis Administration Core " ;
definition: "Core facility which manages and directs the activities of the O'Brien Center, facilitates interactions and collaborations among the research base, ensures quality control of the core services and promotes scientific development and enrichment on the IU SOM campus." .
SCR:015278 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " UAB-UCSD Core Center for Acute Kidney Injury Research Pre-Clinical Studies of AKI " ;
definition: "Core that provides services such as expertise in development and training in the use of rodent models of AKI, specifically in the setting of ischemia/reperfusion (I/R) injury, sepsis and renal transplantation, gamma-ray imaging (gamma camera, microSPECT/CT, microPET/CT), metabolic assessments of kidney O2 consumption, and technical expertise in isolation of primary renal and vascular cell in culture." .
SCR:015279 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " UAB-UCSD Core Center for Acute Kidney Injury Research Administrative Core " ;
definition: "Core facility which coordinates the various activities of the center. Its various duties include facilitating interactions and collaboration among the researchers of the center, promoting scientific development through education and Pilot funding, organizing and supporting seminars, journal clubs and symposia, and maintaining communication with members." .
SCR:015280 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " UAB-UCSD Core Center for Acute Kidney Injury Research Bioanalytical Core " ;
definition: "Core that provides bioenergetics, oxidative stress analysis and metabolite analysis support for AKI research. It includes protocols and technology for bioanalytical analysis of oxidative stress and cellular bioenergetics as well as post-translational modifications." .
SCR:015281 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana O'Brien Center for Advanced Microscopic Analysis Biosensor Development Core " ;
definition: "Core facility which develops, characterizes and validates fluorescence protein biosensors for intravital multiphoton microscopy." .
SCR:015282 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " UAB-UCSD Core Center for Acute Kidney Injury Research " ;
definition: "Research center for kidney research, specifically acute kidney injury. It supports shared core facilities, encourages collaboration between investigators from different backgrounds and disciplines whose shared interest is in kidney research, and provides intellectual resources and infrastructure." .
SCR:015283 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Alabama at Birmingham-University of California San Diego O'Brien Center for Acute Kidney Injury Research Biostatistical Core" ;
NIFRID:synonym "Biostatistical Core",
"Biostatistics resource",
"Core Center for Acute Kidney Injury Research",
"O'Brien Center",
"UAB-UCSD" ;
NIFRID:abbrev "UAB-UCSD O'Brien Center" ;
definition: "Core provides statistical expertise in the conceptualization and design of projects, expertise in data management for the resulting clinical and bioinformatics data, and assistance with the preparation of project reports, presentations and manuscripts." .
SCR:015284 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pittsburgh Center for Kidney Research Cellular Physiology " ;
definition: "Core that provides investigators with in vitro systems for the study of transport processes at the molecular, cell, and epithelial levels." .
SCR:015285 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pittsburgh Center for Kidney Research Single Nephron and Metabolomics " ;
definition: "Core that offers functional (in vitro microperfusion of isolated segments, measurements of transepithelial ion/solute fluxes, fluorescence functional imaging of single tubular cells), biochemical (microassays of enzyme/transporter activity), molecular (quantitation and analysis of RNA and protein), and analytical (targeted renal metabolomics of interrelated networks of small molecules) strategies applied to microdissected tubules, single cells, and urinary exosomes to address relevant questions proposed by users. It also provides analytical services for determining concentrations of exogenous pharmacological agents and molecular probes achieved within the tissue of interest." .
SCR:015286 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pittsburgh Center for Kidney Research " ;
definition: "Center whose focus is to advance knowledge of normal kidney function, cellular mechanisms that contribute to kidney disease, and the myriad altered cellular functions that occur in the setting of renal insufficiency." .
SCR:015287 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " UAB-UCSD Core Center for Acute Kidney Injury Research Clinical Studies of AKI " ;
definition: "Core facility which provides investigators access to patients with AKI through an established international network of collaborating investigators. It also provides core resources to support the design and conduct of clinical research in AKI and genomics resources to perform systematic genomic analyses and allow correlation with clinical phenotypic information." .
SCR:015288 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pittsburgh Center for Kidney Research Model Organisms " ;
definition: "Core that uses the yeast S. cerevisiae and the zebrafish D. rerio to dissect fundamental aspects of kidney development and protein structure and function." .
SCR:015289 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pittsburgh Center for Kidney Research Kidney Imaging " ;
definition: "Core that provides qualitative and quantitative image analysis of the kidney and lower urinary tract through performing light and electron microscopic analysis of epithelial cells and tissues, quantifying and reconstructing kidney and lower urinary tract-associated tissues and organs in 3D, and visualizing and quantifying molecular and cellular dynamics in living animals." .
SCR:015290 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pittsburgh Center for Kidney Research Biostatistical Analysis Services " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on Feb 16, 2022. Core that offers biostatistical analysis to users of the Pittsburgh Center for Kidney Research. Available to the Pittsburgh Center for Kidney Research community." .
SCR:015291 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center Clinical and Translational Core Resource " ;
definition: "Core facility that provides clinical applications and methods to make kidney research translational and applicable to care settings." .
SCR:015292 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " George M. O'Brien Kidney Research Core Center - UT Southwestern Medical Center Animal Models Core " ;
definition: "Core that generates and distributes several kidney-specific Cre recombinase and tetracycline-inducible activator and repressor lines to be crossed to floxed or tet responder lines provided by co-investigators." .
SCR:015293 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " George M. O'Brien Kidney Research Core Center - UT Southwestern Medical Center " ;
definition: "Center whose goal is to generate new animal models to study the pathogenesis and treatment of human kidney diseases and their cardiovascular complications, accelerate the clinical application of discoveries made in renal basic science laboratories, and provide investigators with specialized tools and expertise to study kidney development, physiology, and pathophysiology." .
SCR:015294 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " George M. O'Brien Kidney Center at Yale " ;
definition: "Center that facilitates translational and clinical research that will advance the prevention and treatment of kidney diseases." .
SCR:015295 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " George M. O'Brien Kidney Research Core Center - UT Southwestern Medical Center Clinical and Translational Core " ;
definition: "Core whose aim is to translate basic science research into effective diagnostic and therapeutic strategies that will improve the lives of patients by interrupting the pathogenesis of chronic kidney disease and its attendant high risk of cardiovascular disability and death. It combines comprehensive human genetics with phenotyping of subjects." .
SCR:015296 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " George M. O'Brien Kidney Center at Yale Renal Physiology Core " ;
definition: "Core provides specialized services and training for assessing renal function in small animals at the level of single tubules in vitro and in vivo (e.g. micropuncture, microperfusion, and tubule-specific microdissection), the whole kidney (e.g. clearance studies in anesthetized animals, perfusion fixation for histology studies), and the intact organism (e.g. balance studies in metabolic cages, acute and chronic BP measurements)." .
SCR:015297 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " George M. O'Brien Kidney Research Core Center - UT Southwestern Medical Center Cell Biology and Imaging Core " ;
definition: "Core that provides services such as imaging of rodent kidney and heart including functional MRI, processing of tissues for routine paraffin embedding, and single tubule isolation and immunocytochemistry." .
SCR:015298 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " George M. O'Brien Kidney Center at Yale Human Genetics and Clinical Research Core " ;
definition: "Core that provides infrastructure support for several key steps in translational research, including development of HIC protocols, patient recruitment, patient DNA extraction and archiving, tools for high throughput SNP genotyping and DNA sequencing, and analysis of genetic linkage and linkage disequilibrium." .
SCR:015299 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " George M. O'Brien Kidney Center at Yale Mouse Genetics and Cell Line Core " ;
definition: "Core provides services to generate unique in vivo mouse models and kidney specific cell lines." .
SCR:015300 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pediatric Centers of Excellence in Nephrology at Cincinnati Children's Hospital Medical Center Biomarker Core " ;
definition: "Core whose goals are to provide high throughput Clinical Biofluid Profiling Services (including initial web-based and in-person consultation, study design, sample preparation and processing, data acquisition, data analysis, protein purification, target identification, and specific assay development and validation) and services pertaining to Biomarker measurement and validation (including design of ELISA and Western Blots, measurement of known and emerging markers of acute and chronic kidney diseases, as well as consultation for biomarker statistics and clinical trials design)." .
SCR:015301 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pediatric Centers of Excellence in Nephrology at Cincinnati Children's Hospital Medical Center Gene Expression Core " ;
definition: "Core aims include to empower the Nephrology Center of Excellence investigators by providing access to integrated state of the art gene expression technologies with which to apply genomics methods to accelerate molecular nephrology research, educate, assist, and improve the use of global genomics approaches, infrastructure and specialized tools for the enhancement of research productivity and discovery by the Nephrology Center of Excellence investigators, and develop and disseminate specialized data sets and the use of advanced analytic techniques and/or protocols to facilitate translation of research data to accelerate basic and applied research and its translation to improved clinical care." .
SCR:015302 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pediatric Centers of Excellence in Nephrology at Cincinnati Children's Hospital Medical Center " ;
definition: "Center whose goal is to support basic, translational, and clinical research on critical pediatric kidney diseases by focusing on Acute Kidney Injury, Nephrotic Syndrome, and Lupus Nephritis." .
SCR:015303 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pediatric Centers of Excellence in Nephrology at Duke Division of Pediatric Nephrology " ;
definition: "Center that emphasizes diagnosis, treatment and management of all types of nephrologic and hypertensive disorders in infants, children, and adolescents. Therapies range from medical management to renal replacement therapy." .
SCR:015304 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester Human Imaging Core " ;
definition: "Core provides semiautomated MRI and computed tomography (CT) image and volumetric analyses of polycystic kidneys and liver as well as functional assessment of the kidney and heart, including measurements of renal blood flow. It also facilitates the transmission, collection and storage of anonymized imaging data used in translational PKD research and provides a system that enables PKD researchers to exchange images." .
SCR:015305 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Polycystic Kidney Disease Research and Translation Centers " ;
definition: "A portal with detailed information about various research centers that focus on kidney disease and translational research funded by NIDDK." .
SCR:015306 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cincinnati Children's Hospital Pediatric Center of Excellence" ;
NIFRID:synonym "Cincinnati Children's Hospital",
"PCEN",
"Pediatric Center of Excellence" ;
NIFRID:abbrev "Cincinnati Children's Hospital PCEN" ;
definition: "Core that provides quantitation and identification of protein changes by 2D gel-based methods and isotope tagging and nanoLC-MS/MS, identification of protein biomarkers detected from biofluids in the Biomarker Core, and provision of dedicated and expert Biostatistical and Bioinformatic support for data analysis." .
SCR:015307 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pediatric Centers of Excellence in Nephrology at University of Virginia " ;
definition: "Center for the study of the development of the kidney during embryonic, fetal and postnatal life. As a collaboration between the University of Virginia and Tulane University, they use an interdisciplinary and inter-institutional approach for their research." .
SCR:015308 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester Molecular Genetics and Biomarker Core " ;
definition: "Core services include mutation screening of cell lines derived from ADPKD patients, mutation screening of large, typical ADPKD populations, genetic screening of atypical PKD families, cystic Kidney and Liver Disease Biobank (CKLBB) from ADPKD patients, and urine collection and fractionation." .
SCR:015309 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " UAB Hepatorenal Fibrocystic Diseases Core Center Hepato-Renal Fibrocystic Diseases Translational Resource " ;
definition: "Core whose goals are to establish a national resource for clinical data, DNA, and tissue biopsies from human patients with HRFDs, develop algorithms to identify causative genetic mutations in HRFD patients and utilize a suite of new tools to assess the pathogenicity of sequence variants, and expand the portfolio of educational information and tools to encompass the HRFD spectrum of disorders." .
SCR:015310 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " UAB Hepatorenal Fibrocystic Diseases Core Center Engineered Models Resource " ;
definition: "Core whose goals include Generation of New Animal and Cell Models of HRFDs, to establish In Vivo Biosensors to Study Signaling Pathways Involved in HRFD Ciliopathies, and to generate and distribute HRFD Related Biologicals to the Center?s Investigator Base." .
SCR:015311 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " UAB Hepatorenal Fibrocystic Diseases Core Center " ;
definition: "Center that focuses on understanding the causes of Cystic Kidney Disease and other related disorder and the development of new therapeutic strategies." .
SCR:015312 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester Model Systems Core " ;
definition: "Core that makes available PKD model systems and technologies to PKD researchers at Mayo and at other institutions. Its services include C. elegans PKD-targeted services, Zebrafish PKD-targeted services, and Rodent PKD-targeted services." .
SCR:015313 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester " ;
definition: "Center that concentrates on the common, adult form of the disease, autosomal dominant PKD (ADPKD). The services provided focus on understanding the genetic basis of disease, more accurately monitoring disease progression and improving prognostics, and employing model systems to explore pathogenesis and conduct preclinical testing." .
SCR:015314 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " UAB Hepatorenal Fibrocystic Diseases Core Center Therapeutic Screening and Drug Development Resource " ;
definition: "Core goals include to develop in vitro predictive assays to identify and characterize HRFD lead compounds, develop in vivo predictive translational HRFD models to enhance efficacy assessment in preclinical testing, and develop advanced HRFD-specific toxicology and safety screens." .
SCR:015315 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center " ;
definition: "Center for research in polycystic kidney disease (PKD) with collaboration by international investigators. The center has several cores, including biomedical cores for antibody validation and cell cultures, educationa programs, and pilot programs for new projects." .
SCR:015316 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " UAB Hepatorenal Fibrocystic Diseases Core Center Cellular Physiology Resource " ;
definition: "Core whose goals include to characterize mouse models of HRFD in vivo, establish mTERT and hTERT immortalized cell lines, and the physiological and molecular characterization of HFRD cell lines." .
SCR:015317 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Yale Cooperative Center of Excellence in Hematology Cell Preparation and Analysis Core " ;
definition: "Core facility which provides emerging technologies in hematology and relevant training for junior investigators. Its services include in vitro hematopoiesis assays services, automated complete blood counts, morpholoigcal analyses, CRISPR based genomic editing, and FACsorting and analysis." .
SCR:015318 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center Antibody Validation and Vector Core " ;
definition: "Core which supports the work of the Baltimore Polycystic Kidney Disease research center by providing antibody validation services and vectors to researchers." .
SCR:015319 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center Mouse Models and Biobank " ;
definition: "Core facility which provides mouse models and a biobank of tissues and other materials for research." .
SCR:015320 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_015922" ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July,27,2022. Core facility that provides scientific and budgetary oversight for all CCEH activities. This includes training programs, high school summer internships, and and pilot and feasibility program for new projects." .
SCR:015321 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Hematology Centers " ;
definition: "Online portal with thorough information about hematology research centers and cores. Each entry details the center's research aims, its activities and core services, and links to pilot programs." .
SCR:015322 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Antibody Technology " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility that provides custom designed monoclonal antibodies made in mice, rats and rabbits. Services include design of antigens, immunization and screening strategies; hybridoma cell line production and optimization; and custom designed antibodies for biomarker discovery." .
SCR:015323 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center Cell Culture and Engineering" ;
definition: "Core faiclity that provides researchers with cell culturing and engineering services." .
SCR:015324 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_015907" ;
rdfs:label "Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource" ;
NIFRID:synonym "Bioinformatic Resource",
"Cancer Center",
"Co-operative Center for Excellence in Hematology",
"Fred",
"Hutch" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core provides bioinformatics specialists available to assist researchers with processing, exploring, and understanding genomics data." .
SCR:015325 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Yale Cooperative Center of Excellence in Hematology Imaging Core " ;
definition: "Core facility which provides access to and training and consultation for imaging technology and platforms for hematology research." .
SCR:015326 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Comparative Medicine " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility that provides a variety of animal housing, veterinary and research support services." .
SCR:015327 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Genomics Shared Resource " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility that provides expertise and support for generating genomics-based data. Services for DNA arrays, genetic analysis, and high-throughput screening are provided through three specialized laboratories." .
SCR:015328 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Arnold Library " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27, 2022. Library that provides physical and digital research resources for Fred Hutchinson's Center in Cancer Research. Physical resources include a library with high-speed internet and computer lab resources as well as access to digital research journals, databases and web services." .
SCR:015329 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Experimental Histopathology Shared Resource " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2022. Core facility which provides various histology, histochemistry, immunochemistry, and pathology services. They also provide technical training for histopathological methods and tools." .
SCR:015330 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Electron Microscopy " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2022. Core facility that provides transmission electron microscopy and scanning electron microscopy for Fred Hutch, Cancer Consortium and Seattle area researchers. Services include immunogold labeling, negative staining, and a variety of sample preparations including cryo techniques, high pressure freezing (HPF) and automatic freeze substitution (AFS)." .
SCR:015331 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Glassware Services " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility that provides cleaning and sterilization of reusable laboratory glassware. Services include washing, drying and sterilization of glassware, pipette plugging and autoclaving of laboratory liquids. The core also provides support for operation of media services and biohazardous waste processing." .
SCR:015332 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Specimen Processing/Research Cell Bank " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. A specimen processing/research cell bank that provides a broad range of services including processing of blood, urine, buccal, peripheral blood mononuclear cells (PBMC); DNA extractions; mycoplasma testing; and DNA fingerprinting for cell line verification. The facility also offers specimen storage options and tissue culture of B cells." .
SCR:015333 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Flow Cytometry " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility which offers various options for instrumentation, from single-laser benchtop analyzers to complex multi-laser cell sorts for cell analysis and sorting. Technical assistance is available for the evaluation and interpretation of data as well as assistance in experimental design." .
SCR:015334 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Research Freezers and Sample Storage Resource " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2022. Core facility that provides space for freezers used to store research samples, offers assistance with evaluating the space and power needs for new freezers, provides information on best practices, and provides access and allocates space in the shared freezer facility." .
SCR:015335 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Proteomics Resource " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core facility that provides support for characterizing proteins and peptides by mass spectrometry and high-performance liquid chromatography." .
SCR:015336 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for Iron and Heme Disorders at the University of Utah Iron and Heme Core " ;
definition: "Core facility that provides analysis of metals, precursor porphyrins and heme for cell pellets, tissue, whole blood, urine, feces and other complex biological materials. It also provides measurements of activity of the enzymes responsible for heme biosynthesis for cell pellets, tissue and blood." .
SCR:015337 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for Iron and Heme Disorders at the University of Utah Metabolomics Core " ;
definition: "Core facility which provides metabolite profiling analysis through three chemical analysis platforms, GC-MS, LC-MS and NMR." .
SCR:015338 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for Iron and Heme Disorders at the University of Utah Administrative Core " ;
definition: "Core facility which oversees the operational and financial functioning of the CIHD. It aims include periodically reviewing current membership and selecting new members, monitoring administrative and scientific activities of the CIHD, and selecting projects to be funded through the Pilot and Feasibility Program." .
SCR:015339 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for Iron and Heme Disorders at the University of Utah Mutation Generation and Detection Core " ;
definition: "Core facility which provides custom TALEN and Crispr-Cas9 DNA nucleases to induce targeted mutations in a genomic region of interest. It also provides hardware, reagents, and expertise for optimizing and performing HRMA for genes of interest." .
SCR:015340 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Scientific Imaging " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Scientific imaging service that serves as a centralized facility for imaging and visualization. The core facility provides access to time lapse and 3-D microscopy and quantitative autoradiography." .
SCR:015341 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Center for Iron and Heme Disorders at the University of Utah " ;
definition: "Research center for iron and hematology research. It hosts cores that provide services for mutation generation and detection, metabolomics, and iron and heme experiments and research. In addition to these cores, it has an Enrichment Program, and Internal and External Advisory Committees, and a Pilot and Feasibility program." .
SCR:015342 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana University Cooperative Center of Excellence in Hematology Experimental Mouse Resources Core " ;
definition: "Core facility which maintains on-site breeding colonies of mouse strains essential for study of murine and human hematopoietic cells in vivo. It also provides specialized core services and consultation to CHSCC investigators and serves as an educational resource for CHSCC laboratories." .
SCR:015343 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana University Cooperative Center of Excellence in Hematology " ;
definition: "Research center for hematology research. It provides services through four scientific core facilities: the Experimental Mouse Resources Core, the Optical Microscopy Services Core, the Angiogenesis Core, and the Flow Cytometry Core in addition to the Enrichment Program of the Center." .
SCR:015344 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Michigan Medical School Animal Care and Germ-Free Mouse Core " ;
definition: "Core that provides services to the University of Michigan community and can also ship germ-free mice to locations worldwide. Its projects include studies investigating inflammatory bowel disease and cancer, host microbiome interactions, infectious disease pathogenesis, and mammalian and bacterial metabolism." .
SCR:015345 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana University Cooperative Center of Excellence in Hematology Angiogenesis Core " ;
definition: "Core facility which conducts validated and reproducible in vitro and in vivo angiogenesis, endothelial, hematopoietic and multi-parametric flow cytometry assays and their role in normal and patient-related hematologic and cardiovascular disorders." .
SCR:015346 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2831" ;
rdfs:label "Indiana University School of Medicine Flow Cytometry Core Facility" ;
NIFRID:synonym "Flow Cytometry Resource Facility",
"Flow Cytometry Resource Facility (FCRF)",
"Indiana University Cooperative Center of Excellence in Hematology Flow Cytometry Core",
"Indiana University School of Medicine Flow Cytometry Core" ;
definition: "Core facility which provides flow cytometry consultation, technical advice, flow cytometric analysis and cell sorting services as well as flow cytometric image analysis." .
SCR:015347 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Indiana University Cooperative Center of Excellence in Hematology Optical Microscopy Core " ;
definition: "Core facility which provides access to and training on optical microscopy instruments to Indiana University researchers." .
SCR:015348 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Children's Hospital Center of Excellence in Molecular Hematology " ;
definition: "Research center investigating molecular hematology through mouse and zebrafish models." .
SCR:015349 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Yale Cooperative Center of Excellence in Hematology Animal Modeling Core " ;
definition: "Core facility which provides expertise, technical assistance, and mice for human-into-mouse xenotransplantation studies. Mouse models include MITRG-SKI (KnockIn) mice that express human cytokines and huSIRPa from the endogenous murine loci in the Rag-/- IL-2Ry -/- background. It also offers training and technical assistance in the study of hematopoiesis and benign hematologic questions in mice." .
SCR:015350 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Children's Hospital Center of Excellence in Molecular Hematology Mouse Embryonic Stem(ES) Cell and Gene Targeting Core " ;
definition: "Core facility which generates genetically modified mice with gene knockout/knockin lines for analysis gene function in hematopoiesis." .
SCR:015351 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Yale Cooperative Center of Excellence in Hematology " ;
definition: "Research center that provides access to and training in hematology technologies via three technology cores, Pilot and Feasibility funding, and an Enrichment Program." .
SCR:015352 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Children's Hospital Center of Excellence in Molecular Hematology Stem Cell Engineering and Analysis Core " ;
definition: "Core facility for basic and translational stem cell research. The core's areas of expertise include human pluripotent stem cell biology, cGMP cell manufacturing, reprogramming, genome editing, genotyping, laboratory automation, chemical screening, and imaging/image analysis." .
SCR:015353 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-Vanderbilt University School of Medicine Cardiovascular Pathophysiology Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 6th,2023. Core whose objective is to provide investigators at Vanderbilt and outside institutions a means to accurately assess cardiovascular phenotypes in mouse models of diabetes and metabolic disease. The CPC uses validated approaches and state-of-the-art instrumentation that allow for sensitive screening of phenotypic variations." .
SCR:015354 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Michigan Medical School Metabolism Bariatric Surgery and Behavior Core " ;
definition: "Core whose services include in vivo physiological assessments encompassing glucose homeostasis (glucose tolerance, insulin tolerance, hyperinsulinemic/euglycemic clamps), energy homeostasis (indirect calorimetry by CLAMS, dietary challenge), ultradian hormone secretion (Culex platform for serial biological fluid sampling from unrestrained mice), behavioral measurements (locomotor activity, meal pattern analysis, operant conditioning) and generation of bariatric surgery models." .
SCR:015355 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Children's Hospital Center of Excellence in Molecular Hematology Zebrafish Core " ;
definition: "Zebrafish core facility which generates and maintains transgenic and mutant fish lines for hematology research. It also provides expertise and training in model production, study design, and fish production for research." .
SCR:015356 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of California Davis Animal Care Surgery and Pathology Core " ;
definition: "Core that provides importation/exportation, colony management, customized mouse models, rederivation and creation of genetically-modified mutant mice (e.g. CRISPR), and re-animation of a variety of models cryopreserved within the KOMP or MMRRC repositories. It also provides ancillary services and procedures, including blood sampling for in vivo testing for glucose tolerance tests and insulin tolerance tests." .
SCR:015357 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of California Davis " ;
definition: "Center that provides the scientific community with metabolic and physiologic phenotyping tests, services, and procedures for mouse models of diabetes, diabetic complications, obesity and related disorders in order to advance medical and biological research." .
SCR:015359 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of California Davis Endocrinology and Metabolism Core " ;
definition: "Core that provides phenotyping services for the assessment of endocrine function and metabolic pathways in mouse models of obesity, diabetes, and related metabolic diseases including dyslipidemia and fatty liver disease." .
SCR:015360 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Cincinnati Medical Center Cardiovascular and Renal Function Core " ;
definition: "Core that offers services in testing animal physiological variables such as blood pressure, heart rate, pulse pressure and activity after inserting a PA-C10 telemetry device in them." .
SCR:015361 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of California Davis Microbiome and Host Response Core " ;
definition: "Core that offers measurement of gut permeability, plasma lipopolysaccharide binding protein (LBP) assay, and inflammatory profiling." .
SCR:015362 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of California Davis Administrative Core " ;
definition: "Core responsible for oversight and coordination of all aspects of the scientific and administrative operations of the MMPC-UCD. This includes providing full customer support services, overseeing management and operation of the Center, and foster interactions and synergism among cores and research projects. The ultimate goal of the Core is to ensure that the Center effectively and efficiently delivers services to its users." .
SCR:015363 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Cincinnati Medical Center Lipid Lipoprotein and Glucose Metabolism Core " ;
definition: "Core that provides services based on the testing and analysis of fat lipids, intestinal lipid absorption, and cholesterol in tissues." .
SCR:015364 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of California Davis Energy Balance Exercise and Behavior Core " ;
definition: "Core that provides investigators with services to accurately measure the major components of energy balance in their mouse models and tests that allow investigators to examine physiological factors that may influence food intake or energy expenditure." .
SCR:015365 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Massachusetts Medical School Analytical Core " ;
definition: "Core that provides analysis of hormones, cytokines, chemokines, metabolites, and electrolytes across multiple platforms (serum, tissues, homogenates, and cells) as well as liver function analysis through instrumentation." .
SCR:015367 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Cincinnati Medical Center " ;
definition: "Research center that provides metabolic and physiologic phenotyping services for mouse models of diabetes, diabetic complications, obesity and related disorders. It specializes in the immunological aspects of Type I diabetes, measurement of various glucose and lipid metabolism parameters relevant to Type II diabetes as well as diabetic complications such as heart disease and obesity." .
SCR:015368 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Massachusetts Medical School Animal Care Core " ;
definition: "Core which provides services and facilities for stable, biocontainment housing, husbandry, and health care of mice. The Core manages transfer of mice from the user's institution and testing of mice for the quarantine process." .
SCR:015369 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Massachusetts Medical School Metabolism Core " ;
definition: "Core that conducts specialized and non-invasive metabolic experiments to measure insulin sensitivity, glucose/lipid/protein metabolism, pancreatic beta-cell function, body composition and energy balance. Its services include access to hyperglycemic clamps to assess insulin secretion and pancreatic beta cell function in awake mice and exercise studiesl with acute, chronic endurance, and exhaustive exercise protocols and using in-house cage wheels." .
SCR:015370 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Massachusetts Medical School Islet Core " ;
definition: "Core which provides comprehensive in vivo, ex vivo, and in vitro analysis of pancreatic function and islet structure. Its services include mouse pancreas preparation for histological experiments, surgical isolation of mouse islets, and islet structural analysis." .
SCR:015371 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Cincinnati Medical Center Energy Metabolism Food Intake and Body Weight Regulation Core " ;
definition: "Core that specializes in total body/carcass analysis, measurement of oxygen consumption and carbon dioxide production, meal pattern analysis, and feeding mass/bouts, drinking volume, VO2 and VCO2." .
SCR:015372 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Massachusetts Medical School Humanized Mouse Cell Transplantation and Assessment Core " ;
definition: "Core which provides humanized mice that enable clinically relevant in vivo studies of human cells, tissues, and immune system without putting patients at risk and expert in vivo functional analysis of transplanted human islets and stem cell-derived b-cells in immunodeficient mice that are highly valuable to the mouse research community." .
SCR:015373 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Michigan Medical School " ;
definition: "Research center which aims to contribute to a national database of metabolic phenotyping data in wild-type mouse strains and a broad range of mouse models relevant to the pathogenesis and treatment of diabetes, obesity and associated metabolic disorders. It also aims to foster continued technical development, refinement of assay sensitivity and specificity, data reproducibility, and transmission of best research practices within the areas of fundamental and applied diabetes and obesity research." .
SCR:015374 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-Vanderbilt University School of Medicine " ;
definition: "Research center whose mission is to advance research in the area of diabetes by providing experimental tools to the scientific community for phenotyping mouse transgenic models of diabetes and related disorders." .
SCR:015375 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Massachusetts Medical School Cardiovascular Core " ;
definition: "Core that provides phenotyping of cardiovascular system in mouse models of metabolic disease and an easily accessible cardiovascular disease model pipeline. It services include 2D and M-mode echocardiography in lightly-anesthetized mice to non-invasively assess cardiac structure and function using state-of-the-art high-frequency, high-resolution in vivo digital imaging platform as well as Transverse Aortic Constriction (TAC) model to investigate pressure-overload hypertrophy, congestive heart failure, and aortic stenosis." .
SCR:015376 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Michigan Medical School Microvascular Complications Core " ;
definition: "Core which provides a complete range of microvascular phenotyping of murine models of diabetes, obesity and metabolic disease, including validated, reproducible and standardized phenotyping of the three major microvascular complications: diabetic polyneuropathy, nephropathy and retinopathy." .
SCR:015377 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-Vanderbilt University School of Medicine Metabolic Regulation Core " ;
definition: "Core whose services include determining the components of energy balance with high precision and time resolution, providing robust imaging technology to monitor the dynamics of cellular process, and providing innovative mouse bariatric surgery models with application to basic and translational research." .
SCR:015378 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-University of Michigan Medical School Microbiome Core " ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 16,2025. Core whose mission is to provide analytical tools to investigators to permit determination of the structure of the microbiome in mouse models of disease and assistance in the cultivation of microbes that will permit hypothesis testing in murine models including the germfree animals that are available in the Animal Care Core." .
SCR:015379 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-Vanderbilt University School of Medicine Analytical Resources Core " ;
definition: "Core that consists of three subcores: Hormone Assay and Analytical Services, Lipids, Lipoproteins, and Atherosclerosis, and Mouse Pathology. The Hormone Assay and Analytical Services provides analyses that facilitate research in diabetic, cardiovascular, and obese animal models. Lipids and Lipoproteins Subcore provides quantitative and qualitative measurements of plasma and tissue lipids and lipoproteins to researchers who use mice to study atherosclerosis, dyslipidemia, diabetes, obesity, hypertension, and other metabolic diseases. Mouse Pathology services include standard pathology testing in hematology, clinical chemistry, parasitology, microbiology, serology, molecular diagnostics, necropsy, and research histology and pathology expertise and counseling." .
SCR:015380 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " MMPC-Vanderbilt University School of Medicine Animal Health and Welfare Core " ;
definition: "Core that ensures the health and welfare of mouse models by assuring that mice admitted to the MMPC meet defined health criteria and that post-quarantine protocol assignment. It diagnoses disease and identifies unique metabolic or cardiovascular phenotypes of mice through interaction with the Comparative Pathology Subcore." .
SCR:015381 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PsychoFit" ;
definition: "Software that fits s-shaped psychometric functions to psychophysical data using a maximum-likelihood technique. The psychometric functions available are logistic, Weibull, Gaussian integral, cumulative Poisson and step. PsychoFit produces, among other things, files with graphic information suitable for importing in a graphic program for plotting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015382 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nuance Multispectral Imaging Systems" ;
definition: "Microscope that can visualize multiple nuclear, cytoplasmic and membrane markers in the same tissue section and with intact morphology. Its features include detection and measurement of weakly expressed and overlapping biomarkers in fixed tissue sections, autofluorescence removal technology, and the ability to work with both fluorescence and brightfield samples." .
SCR:015383 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis Research and Translation Centers " ;
definition: "Research centers that provide support for basic, preclinical, and clinical research efforts to advance scientific knowledge and new therapies for cystic fibrosis." .
SCR:015384 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Molecular Biology Core " ;
definition: "Core facility that provides expertise, equipment, training, and reagents to serve the molecular biology needs for cystic fibrosis research." .
SCR:015385 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Histology Core " ;
definition: "Core that provides light microscopy services like prosection, tissue fixation, processing, embedding, sectioning, staining and cover slipping of paraffin, frozen and soft plastic tissue sections, as well as specialized and routine fixation, tissues processing, ultramicrotomy, staining, photomicrograph production, and analysis." .
SCR:015386 a owl:NamedIndividual ;
rdfs:label "Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Functional Analysis Core" ;
definition: "Core that analyzes ion channel properties and correction efficiency of human bronchial epithelial (HBE) cells from harvested CF lungs to provide a full characterization report to investigators, measures ion transport function of CFTR and ENaC in HBE and human nasal epithelial (HNE) cultures by bioelectric and organoid assays to asses efficacy of candidate therapies, evaluates CFTR expression and processing by biochemical analyses to assess efficacy of CFTR modulation strategies, and validates the suitability of reagents, supplies, and techniques for optimizing HBE and HNE cell integrity." .
SCR:015387 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Pre-Clinical Core " ;
definition: "Core whose objectives include evaluation of pre-clinical drug candidates in vitro, pre-clinical drug candidates ex vivo, and pre-clinical drug candidates in vivo." .
SCR:015388 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center " ;
definition: "Research team dedicated to finding a cure for cystic fibrosis lung disease. This team utilizes ion transport physiology, transgenic and gene-targeted mouse models, Phase I clinical trials, and more to research this cause." .
SCR:015389 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Mouse Models Core " ;
definition: "Core that provides support and expertise for mouse colony maintenance, breeding strategies, mouse lung phenotyping protocols, and submission of live-animal applications to maintain compliance with IACUC guidelines." .
SCR:015390 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Michael Hooker Microscopy Core Facility" ;
NIFRID:synonym "Michael Hooker Microscopy Core Facility",
"The Michael Hooker Microscopy Core Facility" ;
NIFRID:abbrev "MHMF" ;
definition: "Core that provides advanced digital light microscopy, image processing and analysis resources for users from the UNC Chapel Hill campus. It also offers instrumentation and instruction to enable users to acquire, process and analyze images from a wide variety of sample types." .
SCR:015391 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Clinical Translational Core " ;
definition: "Core whose services include biospecimen collection and storage, development of lung imaging outcomes, imaging training, and biostatical analysis." .
SCR:015392 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Gregory Fleming James Cystic Fibrosis Research Center " ;
definition: "Research center that maintains core facilities available for studies of cell biology, ion transport, and translational aspects of cystic fibrosis research." .
SCR:015393 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Mucus and Mucin Biochemistry and Biophysics Core " ;
definition: "Core that provides a service to quantify the concentration of given mucus samples for both total mucus concentration and the absolute relative contributions of each secreted mucin. It also provides quantitation of extracellular DNA. The mucus biphysics subcore component, provides core users with information on the biophysical properties of the mucus layer and its interaction with the cell surface." .
SCR:015394 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center Tissue Procurement and Cell Culture Core " ;
definition: "Core that provides standardized cell cultures for cystic fibrosis research, notably normal, cystic fibrosis and disease control cells, tissues and fluids. Its functions include tissue procurement, airway epithelial cell isolation and culture, collecting airway surface liquid from in vivo and in vitro samples, genetic manipulation of cell cultures, creating and characterizing novel cell lines, and translation of technology and reagents to the greater cystic fibrosis research community." .
SCR:015395 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Gregory Fleming James Cystic Fibrosis Research Center Cell Model and Evaluation Core " ;
definition: "Core that assists with patch clamp and single channel analysis relevant to ion channel gating. The core also provides primary murine airway epithelial cells." .
SCR:015396 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Gregory Fleming James Cystic Fibrosis Research Center Cystic Fibrosis Animal Models Core " ;
definition: "Core that assists in mouse line generation by both oocyte micro-injection and by embryonic stem cell gene targeting technologies. It also establishes breeding colonies of cystic fibrosis mice, and genotypes and provides these to UAB investigators and furnishes electrophysiology tests of CFTR activation, including murine nasal potential difference assays and intestinal short circuit current measurements." .
SCR:015397 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Gregory Fleming James Cystic Fibrosis Research Center Cystic Fibrosis Transmembrane Conductance Regulator Expression Core " ;
definition: "Core that maintains a repository of reagents for studying CFTR and assists with expression technologies using vaccinia, adenovirus and other methodologies and antibody based detection of cystic fibrosis related gene products." .
SCR:015398 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis Center - University of California San Francisco " ;
definition: "Research center that focuses on developing novel therapies for cystic fibrosis, enhancing research projects examining the mechanisms of the disease, and developing new small-molecule therapies that can be translated into the clinic." .
SCR:015399 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Gregory Fleming James Cystic Fibrosis Research Center Cystic Fibrosis Clinical and Translational Core " ;
definition: "Core that provides human primary nasal airway epithelial cells and bronchial airway epithelial cells, expertise in the nasal potential difference measurement, and a means to understand pathogenesis of cystic fibrosis and other metabolic diseases." .
SCR:015400 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis Center University of Pittsburgh " ;
definition: "Research center whose goal is to understand and translate the basic mechanisms of cystic fibrosis. It uses the molecular and cell biology of CFTR, CFTR mutants, infection, and inflammation with the overall theme of translating preclinical science into clinical investigations." .
SCR:015401 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis Center - University of Washington " ;
definition: "Research center that aims to provide resources and expertise to expedite development of potential new therapeutic approaches to correct dysfunctional CFTR and its secondary consequences, enhance understanding of evolving bacterial ecosystems and resultant host response in CF gastrointestinal and respiratory tracts, and how these interactions impact health. It also aims to develop improved assays, new drug screening assays, biomarkers and improved clinical outcome measures, as well as to better understand the metabolic and inflammatory consequences of CFTR dysfunction." .
SCR:015402 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis Center - University of Washington Clinical Core " ;
definition: "Core that aims to provide preclinical support for novel therapeutics, work with other biomedical cores to enhance and support bacterial and human specimen repositories, and support developmental research and training." .
SCR:015403 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis Center - University of Washington Microbiology Core " ;
definition: "Core facility which provides tools, reagents, and training for microbiological researchers investigating cystic fibrosis. They specifically provide resources for research in anti-bacterial therapies," .
SCR:015404 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Washington Genomics Core Cystic Fibrosis Research Translation Center and Research Development Program" ;
NIFRID:synonym "CFRTC",
"Cystic Fibrosis Research Translation Center",
"Genomics Core",
"Research Development Program",
"University of Washington" ;
NIFRID:abbrev "CF Research Translation Center and Research Development Program" ;
definition: "Core provides genomics-based tools, data management and analysis tools, and creates platforms that integrate data from the Clinical and Immunology Cores for human samples and bacterial isolates. Services include consultation and experimental design assistance for using new-generation sequencing technology, data analysis, bioinformatic support, data access and storage, high throughput and new-generation whole-genome sequencing, and RNA-seq analysis of transcriptomes." .
SCR:015405 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis Center - University of Washington Host Response Core " ;
definition: "Core whose objective is to obtain information on relevant parameters of the host response that is unique to cystic fibrosis using a variety of techniques, including in vivo and in vitro imaging, immunohistochemistry, imaging and image analysis, cells and bacteria in tissues, and quantification of chemokines, cytokines, and other factors with ELISA." .
SCR:015406 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis " ;
definition: "Research center whose focus is on developing effective gene vectors derived from recombinant viruses. Much of their research is in the development of new adeno-associated virus (AAV) vectors, although some of their research involves both adenoviruses and lentiviruses." .
SCR:015407 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Gregory Fleming James Cystic Fibrosis Research Center Assay Core " ;
definition: "Core that provides Ussing chamber capabilities and expertise for testing vectoral anion transport in polarized airway epithelial monolayers, and florescent dye-based methods for evaluating CFTR activity in cells grown on coverslips. The core also performs immunolocalization for proteins relevant to cystic fibrosis pathogenesis." .
SCR:015408 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Cystic Fibrosis Center - University of Washington Administrative and Enrichment Core " ;
definition: "Core that manages and oversees the UW CFRTC and its cores and pilot and feasibility programs." .
SCR:015409 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Immunology Core " ;
definition: "Core facility which provides a variety of assay services to evaluate cell-mediated and humoral responses to in animal models of gene therapies." .
SCR:015410 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Iowa Center for Gene Therapy Cell Tissue Core " ;
definition: "Core that provides centralized access to non-cystic fibrosis and cystic fibrosis tissue specimens and airway cells used for model systems to assess gene transfer to the airway and pathophysiology in cystic fibrosis." .
SCR:015411 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Iowa Center for Gene Therapy Comparative Pathology Core " ;
definition: "Core facility which provides comprehensive necropsy, histology, and pathology services for animal models in order to facilitate translational research in animal models of cystic fibrosis. It also houses instrumentation which allows for high-throughput optimization of immunostaining protocols and has access to morphologic equipment that allow for the scanning of large tissue areas and morphometric quantification of histologic endpoints." .
SCR:015412 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Iowa Center for Gene Therapy " ;
definition: "Research center which provides access to core facilities and services to aid gene therapy researchers." .
SCR:015413 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Iowa Center for Gene Therapy Animal Model Core " ;
definition: "Core that provides support to investigators who use animal models to study the pathogenesis of cystic fibrosis and who develop gene and other molecular therapies for cystic fibrosis. Specifically, it provides centralized production, care, breeding, genotyping, and quality control of cystic fibrosis mouse and ferret models used by investigators in the Center." .
SCR:015414 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " New York Obesity Nutrition Research Center Animal Phenotyping Core " ;
definition: "Core that allows investigators to efficiently and cost effectively define the phenotypes of small rodents in ways that are relevant to the study of obesity, nutrition, and metabolism. Its services range from whole animal measurements of body composition and energy utilization, to ex vivo measurements of substrate fluxes, to histological analyses of adipose tissue." .
SCR:015415 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Iowa Center for Gene Therapy Clinical Core " ;
definition: "Core facility which aims to provide cystic fibrosis researchers with a biobank of archived biosamples collected during routine clinical visits and research-related visits. Biospecimens include normal and CF specimens including DNA, bronchoalveolar lavage fluid, whole blood, plasma, feces, urine, and bacterial isolates. It also aims to facilitate patient recruitment and enrollment in clinical trials." .
SCR:015416 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Cell Morphology Core " ;
definition: "Core facility which provides a range of technologies for morphologically based studies and technically more complex support in the detection of transgenes and transgene products using techniques of in situ hybridization and immunohistochemistry." .
SCR:015417 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Iowa Center for Gene Therapy Vectore Core " ;
definition: "Core facility which provides support to cystic fibrosis investigators in gene transfer technologies through consultation, development of novel vectors, collaborative testing of vectors for function and purity, and routine vector preparations." .
SCR:015418 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Alabama at Birmingham Nutrition and Obesity Research Center " ;
definition: "Research center that aims to understand the causal factors underlying nutrition and obesity-related health problems and the generation and evaluation of evidence on their consequences, prevention, and alleviation." .
SCR:015419 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Nutrition and Obesity Research Centers Adipose Biology and Nutrient Metabolism Core " ;
definition: "Core that facilitates and fosters research on mechanisms regulating white, brite or beige and brown adipose tissue mass, distribution, nutrient signaling and depot-specific metabolic and endocrine functions in health and disease." .
SCR:015420 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Nutrition and Obesity Research Centers " ;
definition: "Center that is organized to address cross-cutting themes that represent gaps in understanding the relationship between nutrition and health, and the pathogenesis of obesity and its associated metabolic diseases." .
SCR:015421 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Nutrition and Obesity Research Centers Epidemiology and Genetics Core " ;
definition: "Core that provides a central focus to translate the findings from clinical and cellular studies to applications in ongoing epidemiologic studies." .
SCR:015422 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Nutrition and Obesity Research Centers at Harvard " ;
definition: "Research center at Harvard University that seeks to establish a research environment which encourages the approach to defining common clinical nutrition research problems. It aims to promote, facilitate and enhance research relating to nutrition and health within the Boston area." .
SCR:015423 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Nutrition and Obesity Research Centers Functional Genomics and Bioinformatics Core " ;
NIFRID:synonym "Bioinformatics",
"BNORC",
"Boston Nutrition and Obesity Research Center",
"Core",
"Functional Genomics" ;
definition: "Core provides services to investigators within BNORC and the Boston area looking to expand their research using state-of-the-art genomic applications. This core utilizes technologies and sequencing platforms to help identify the complex molecular mechanisms underlying human disease." .
SCR:015424 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Nutrition and Obesity Research Centers at Harvard Administrative Core " ;
definition: "Core that supports and coordinates the NORCH and all the components of the center. It provides insight into the processes that govern the center, to recruit and vet new members, and to communicate with all our members about center happenings." .
SCR:015425 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Nutrition and Obesity Research Centers Administrative Core " ;
definition: "Core that provides administrative support and direction to all of the participating institutions and BNORC members. These services include financial management, payment requests, policy development and data management." .
SCR:015426 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Nutrition and Obesity Research Centers at Harvard Metabolic Imaging Core " ;
definition: "Core that links a variety of imaging facilities providing services to NORCH investigators who currently require or plan to conduct human studies using imaging research instrumentation and expertise. Its goal is to provide users with access to imaging technology for in-vivo phenotyping of human tissues for nutrition, obesity and metabolism studies." .
SCR:015427 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Nutrition and Obesity Research Centers at Harvard Genomics and Cell Biology Core " ;
NIFRID:synonym "Genomics and Cell Biology Core",
"Harvard",
"NORCH",
"Nutrition and Obesity Research Center" ;
NIFRID:abbrev "NORCH at Harvard" ;
definition: "Core that facilitates the application of genomics, bioinformatics, cell biology, and immunology techniques to nutrition and metabolic research." .
SCR:015428 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Nutrition and Obesity Research Centers at Harvard Statistical Consultation " ;
definition: "Core that provides consultations for study design and analysis, preparation of grant applications, preparation of statistical methods and results for manuscripts on completed studies, responses to reviewer comments for manuscript resubmissions, identification of possible long term statistical collaborators for grants." .
SCR:015429 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Nutrition and Obesity Research Centers at Harvard Metabolic Phenotyping Core " ;
definition: "Core that provides NORCH investigators with access to model creation and detailed metabolic phenotyping. Its services include: model generation, including genomic targeting and production of metabolically relevant cell types; metabolic characterization of patient-derived, user-provided, or model generated samples; consultation on model development and metabolic characterization projects; and training for Core techniques in model generation and detailed metabolic characterization." .
SCR:015430 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mid-Atlantic Nutrition Obesity Research Center " ;
definition: "Center that fosters multidisciplinary research approaches to understanding the impact of nutrition on risk for chronic disease and aims to translate this knowledge into effective clinical treatments and prevention efforts." .
SCR:015431 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mid-Atlantic Nutrition Obesity Research Center Clinical and Translational Research Core " ;
definition: "Core that facilitates the conduct of clinical nutrition and obesity research. Its team of experts in nutrition, exercise physiology, body composition, metabolism and behavioral therapy aim to assist and train NORCH investigators in the skills necessary to conduct clinical nutrition and obesity research." .
SCR:015432 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mid-Atlantic Nutrition Obesity Research Center Biological Mechanisms and Functional Genomics Core " ;
definition: "Core that provides investigators with access to adipose tissue samples from well-characterized subjects. It also assists investigators with analysis of adipose tissue morphology and metabolism, specialized cell and organ culture methods, and analysis of gene and protein expression." .
SCR:015433 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Boston Nutrition and Obesity Research Centers Transgenic Core " ;
definition: "Core that utilizes investigator-derived DNA constructs or investigator derived (or obtained) genetically modified embryonic stem cells to create founder transgenic organisms that can be used to address questions relevant to obesity, diabetes and nutrition, including questions related to brain control of feeding, metabolism and reward." .
SCR:015434 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mid-Atlantic Nutrition Obesity Research Center Biostatistics and Medical Informatics Subcore " ;
definition: "Core that provides biostatistical consultation to other investigators who are doing research in the fields of obesity and nutrition at University of Maryland and the Baltimore VA Medical Center. It aims to develop new methods for data collection data from older subjects." .
SCR:015435 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018691" ;
rdfs:label "Louisiana State University Pennington Biomedical Nutrition Obesity Research Center Core Facility" ;
NIFRID:synonym "Pennington Biomedical Research Center Nutrition and Obesity Research Center Administrative Core",
"Pennington NORC" ;
definition: "Provides scientific cores including Molecular Mechanisms Core (genomics and cellular), Human Phenotyping Core (characterization of phenotypes predisposing to obesity and metabolic syndrome and behavioral interventions to counteract those) and Animal Models and Phenotyping Core. Includes organizing administrative process to announce, collect, review and award Pilot and Feasibility grants, setting criteria for use of core facilities, and maintaining access to data management services." .
SCR:015436 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " New York Obesity Nutrition Research Center Molecular Biology and Molecular Genetics Core " ;
definition: "Core whose goal is to assist investigators in applying the tools and technologies of molecular genetics and genomics to elucidate the molecular-genetic bases of obesity and its comorbidities. Its services include consultation on study design, analysis, and applicable molecular biological techniques and developing and making research tools and reagents." .
SCR:015437 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " New York Obesity Nutrition Research Center Human Phenotyping Core " ;
definition: "Core which provides obesity and other medical eating disorder researchers with specialized measurements in body composition, energy expenditure, imaging analysis, and adipose tissue analysis in human subjects." .
SCR:015438 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pennington Biomedical Research Center Nutrition and Obesity Research Center " ;
definition: "Research center that supports clinical investigation addressing the etiology of nutritionally induced chronic diseases across the entire age span, from gestational and perinatal development through childhood and adolescence. It provides core services to promote the investigations around the theme of molecular mechanisms of nutritional programming induced by environmental factors." .
SCR:015439 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Administrative Core " ;
NIFRID:synonym "Administrative Core",
"Chapel Hill",
"Nutrition and Obesity Research Center",
"University of North Carolina" ;
NIFRID:abbrev "NORC",
"UNC",
"UNC NORC" ;
definition: "Core facility that is responsible for managing and organizing the activities of the internal governance committee and the external advisory board, promoting the techniques, methodologies, instrumentation, and resources offered by the core facilities, and supporting the integration of bioinformatics, biostatistics, clinical research, and metabolomics into clinical and translational research." .
SCR:015440 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pennington Biomedical Research Center Nutrition and Obesity Research Center Human Phenotyping Core " ;
definition: "Core that provides users with expertise and phenotyping services for different stages in life. It specifically provides services for obesity research, unique populations (pregnant women, children, infants, etc.), and clinical and translational studies through their Energy Balance subcore and Behavioral subcore." .
SCR:015441 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pennington Biomedical Research Center Nutrition and Obesity Research Center Molecular Mechanisms Core " ;
definition: "Core that includes a genomics subcore that provides services in genomics such as Sanger DNA sequencing and fragment analysis service, microarray analysis service, quantitative PCR, robotic pipetting for quantitative PCR and custom pipetting projects, and software analysis solutions. The Cell Biology &and Bioimaging subcore provides histology and specipmen preparation, imaging, and flow cytometry/cell sorting." .
SCR:015442 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " New York Obesity Nutrition Research Center " ;
definition: "Obesity research center which provides access to core facilities, seminars, and collaborations for researchers." .
SCR:015443 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pennington Biomedical Research Center Nutrition and Obesity Research Center Animal Models and Phenotyping Core " ;
definition: "Core that is comprised of the Animal Models Subcore and Animal Phenotyping Subcore. The former provides expertise and services for design and construction of transgenes, ES cell transfection and screening, pronuclear injection, and cryopreservation. The latter provides expertise and services for metabolism, physical activity, body composition, and behavioral research." .
SCR:015444 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Clinical Nutrition Research Facilitation Program " ;
definition: "Core for nutrition researchers that consists of two subcores: the Human Research Core and the Nutrition Research Kitchen and Metabolism Core. The Human Research Core provides human metabolism and body composition assessments, clinical laboratory and support services, and preparation and delivery of precisely designed meals for study participants. The Nutrition Research Kitchen and Metabolism Core offers nutrition research assistance to complement clinical studies." .
SCR:015445 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Alabama at Birmingham Nutrition and Obesity Research Center Metabolism Core " ;
definition: "Core whose services include energy expenditure, substrate metabolism and body composition analysis to provide assessments of human energy expenditure, substrate metabolism, body composition, body fat distribution, and bone quality." .
SCR:015446 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of California San Francisco Nutrition and Obesity Research Center " ;
definition: "Research center whose goal is to define the underlying mechanisms of disease and to contribute to the prevention and treatment of obesity and its complications. It provides collective research facilities, a lecture program that fosters interactions amongst laboratories conducting cellular, animal, translational, clinical and epidemiologic research, pilot funding for new and interdisciplinary research directions plus administrative infrastructure that promotes these integrative goals." .
SCR:015447 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of California San Francisco Nutrition and Obesity Research Center Genetics and Genomics Core " ;
definition: "Core that provides services for genetic and genomic research, including DNA extraction, SNP genotyping, and gene expression, ES cell services with a high probability of germline transmission, microinjection of DNA for producing transgenic mice, microinjection of ES cells for producing gene knock-out mice, and 8 cell microinjection, and collection in vitro maturation and embryo transplant." .
SCR:015448 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of California San Francisco Nutrition and Obesity Research Center Human Metabolism Core " ;
definition: "Core that renders services that provide consulting with study design, subject recruitment, and statistical analyses, conducting clinical research, and an array of specialized NORC-focused methods, instruments, and facilities for human body composition/metabolism, radiologic imaging and biobehavioral measurements for human nutrition, obesity and metabolism research." .
SCR:015449 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Alabama at Birmingham Nutrition and Obesity Research Center Biostatistics Core " ;
definition: "Core which provides services and expertise in the design, management and analysis of nutrition-related research projects. Its services include coordination and management of statistical activities within the Core, statistical consultation on study design, research proposal development and manuscript submission, and statistical analysis." .
SCR:015450 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of California San Francisco Nutrition and Obesity Research Center Mouse Metabolism and Imaging Core " ;
definition: "Core that provides access to instrumentation used in metabolic studies. Instruments include a 12-chambered Comprehensive Lab Animal Monitoring System (CLAMS), an EchoMRI, and dual energy X-ray absorptiometry." .
SCR:015451 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center " ;
definition: "Research center that aims to provide an infrastructure to support ongoing nutrition and obesity research by providing measurements and expertise. It also aims to promote interdisciplinary collaborative, vertically integrated research among members of the Colorado research community, as well as translate basic and clinical research into programs to improve health and wellness and reduce obesity in the community." .
SCR:015452 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mayo Clinic O'Brien Urology Center Biostatistics and Epidemiology Core " ;
definition: "Core that is responsible for all statistical, data management and epidemiological aspects of studies in the Mayo Clinic O'Brien Urology Research Center. Its services include consultation to project investigators regarding study design, data analysis and interpretation of results, maintanence of the Olmsted County kidney stone database, and development of additional linkable databases and quality control procedures." .
SCR:015453 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mayo Clinic O'Brien Urology Center " ;
definition: "Core that aims to define the pathogenesis of nephrolithiasis in order to improve patient care and treatment and prevention strategies" .
SCR:015454 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mayo Clinic O'Brien Urology Center Imaging Core " ;
definition: "Core that provides renal stone imaging and analysis techniques, including dual energy CT data acquisition and analyses, dual energy material decomposition analysis, high-resolution image reconstruction and analysis, and coordination of micro-CT scanning and data analysis." .
SCR:015455 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mayo Clinic O'Brien Urology Center Urine Phenotyping Core " ;
definition: "Core that aims to increase understanding of the factors that modulate the interface of urinary proteins and crystals, and hence their subsequent interaction with other crystals or cells. Its services include quantification of urinary components of the supersaturation profile, quantification of urinary inhibitor activity, quantification of known urinary macromolecular inhibitors, and application of differential proteomics to urine samples of stone forming and control populations." .
SCR:015456 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Michigan Nutrition and Obesity Research Center Molecular Phenotyping Core " ;
definition: "Core that provides analytical tools to MMOC investigators to permit structural identification and quantification of metabolites as well as perform metabolic studies in in vitro systems. It also provides consultation and collaboration to apply metabolomics platforms in nutrition and obesity research." .
SCR:015457 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Michigan Nutrition and Obesity Research Center " ;
definition: "Research center for obesity investigators which aims to provide researchers with infrastructure, expertise, and training to facilitate improved data integration, analysis and modeling from properly designed basic, clinical, and population-based studies in obesity and metabolism-related diseases." .
SCR:015458 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Michigan Nutrition and Obesity Research Center Animal Phenotyping Core " ;
definition: "Core whose services include infrastructure to perform advanced, standardized, metabolic phenotyping of animal models of obesity or metabolic diseases that arise from dietary, genetic, pharmacologic or other perturbations. It also provides centralized equipment and services and aims to develop new techniques and acquire new technologies for rodent phenotyping." .
SCR:015459 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Mid-Atlantic Nutrition Obesity Research Center Molecular Genetics and Nutrigenomics Core " ;
definition: "Core that aims to discover genes and gene-nutrient interactions associated with risk of obesity, diabetes, hypertension, atherogenesis and longevity. Its goal is to understand the molecular, cellular and physiological roles of genes in the etiology of obesity, diabetes, and associated metabolic abnormalities." .
SCR:015460 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Michigan Nutrition and Obesity Research Center Human Phenotyping Core " ;
definition: "Core that aims to enhance and expand the research capabilities of investigators performing clinical and translational studies related to nutritional interventions, obesity, or obesity-related disorders in humans. Its services include standardized nutritional assessments and physiological testing of human subjects, researcher assistance in conducting dietary, behavioral, and/or exercise intervention in human subjects, and training in techniques or the assistance in development of new techniques and technologies for the metabolic and neurobehavioral assessment of humans." .
SCR:015461 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Communication for Health Applications and Interventions Core " ;
definition: "Core that uses technologies to facilitate the translation of traditional evidence-based behavioral interventions into effective web- and mobile-based interventions in fields such as obesity and cancer prevention." .
SCR:015462 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of North Carolina at Chapel Hill Nutrition and Obesity Research Center " ;
definition: "Center whose goals include providing resources and support to investigators conducting multidisciplinary and interdisciplinary research in nutritional sciences and obesity, strengthening clinical nutrition training programs for medical students, practicing physicians, and allied health personnel, and translating findings from obesity and nutrition research to the general public." .
SCR:015463 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Metabolic Molecular Phenotyping Core " ;
definition: "Core whose goals are to encourage and facilitate the use of biomarkers for nutritional epidemiological and intervention studies. It provides access to techniques and equipment to bench scientists, as well as assays for investigators without lab facilities." .
SCR:015464 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Nutrigenetics Core " ;
definition: "Core facility whose services include grant writing assistance and consultation, laboratory analyses, brokerage services, and analytical services." .
SCR:015465 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Animal Metabolism Phenotyping Core " ;
definition: "Core that offers technical support and expertise for measuring traits related to metabolism in mouse models of obesity and nutritionally relevant disease. It provides access to methods, equipment, and populations to support high quality and high throughput phenotyping of energy balance components in mice." .
SCR:015466 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Alabama at Birmingham Nutrition and Obesity Research Center Animal Models Core " ;
definition: "Core that provides specialized expertise in the use of animal models and instrumentation to facilitate animal research related to nutrition and obesity." .
SCR:015467 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Biostatistics Program " ;
definition: "Core whose services include data management, manuscript development, sample size and power calculations, statistical consultation, and statistical programming for nutrition and/or obesity researchers." .
SCR:015468 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Michigan Nutrition and Obesity Research Center Administrative Core " ;
definition: "Core that provides leadership, infrastructure and resources to promote the integration of basic research technologies into preclinical, clinical and translational research studies, oversee the Investigational Weight Management Clinic, and recruit, train and retain basic, clinical and population-based researchers in the area of nutrition interventions and obesity and related metabolic disorders." .
SCR:015469 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Washington Nutrition and Obesity Research Center Energy Balance Core " ;
definition: "Core that provides affiliated investigators with a resource for measuring energy balance and body composition in rodent models, and for applying neuroscience techniques to nutrition and obesity-related research." .
SCR:015470 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Washington Nutrition and Obesity Research Center Analytic Core " ;
definition: "Core that provides affiliated investigators with access to nutritional assays, new methods development, and consultation services. Services also include quantitative measures of nitrogen-containing compounds, carbohydrates and related compounds, lipids and related compounds, and more." .
SCR:015471 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Washington Nutrition and Obesity Research Center Administrative and Enrichment Core " ;
definition: "Core that is responsible for the overall administrative coordination of the NORC. It also administers the Biostatistics Subcore, Pilot and Feasibility Program, and Enrichment Seminar Series." .
SCR:015472 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Washington University St. Louis Nutrition Obesity Research Center " ;
definition: "Research center whose activities aim to enhance understanding of the basic and clinical aspects of nutrition in the prevention, etiology, pathophysiology and therapy of nutrition-related diseases." .
SCR:015473 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " O'Brien Urology Centers " ;
definition: "Program that aims to enhance the effectiveness of research related to noncancerous urologic dysfunction by encouraging collaboration amongst investigators." .
SCR:015474 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Alabama at Birmingham Nutrition and Obesity Research Center Physical Activity Core " ;
definition: "Core that provides physical activity services and consultation for UAB investigators. Services include aerobic fitness tests, supervised resistance training, submaximal ease/economy locomotion tests, and strength and functional tests, with respective measurements taken." .
SCR:015475 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Washington Nutrition and Obesity Research Center " ;
definition: "Research center that facilitates the integration and coordination of the ongoing activities of the University of Washington system. Its overarching goals are to foster interdisciplinary research collaborations, stimulate new research activities, improve nutrition and obesity education, and facilitate optimal nutritional management of patients." .
SCR:015476 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " O'Brien Center for Benign Urologic Research at University of Wisconsin-Madision and University of Massachusetts-Boston " ;
definition: "Research center that is dedicated to improving urologic health in aging men by promoting development of urologic research, disseminating urologic research knowledge, and performing other research-related tasks." .
SCR:015477 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " O'Brien Center for Benign Urologic Research at University of Wisconsin-Madision and University of Massachusetts-Boston Rodent Urinary Function Testing Core " ;
definition: "Core that designs, validates, and disseminates protocols for rodent urinary function testing. It also provides urinary function testing services, expertise, laboratory space, vivarium, and equipment for complete mouse urinary function testing." .
SCR:015478 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Michigan Nutrition and Obesity Research Center Integrative Biostatistics and Informatics Core " ;
definition: "Core facility whose services include expertise in experimental design and modeling for preclinical, clinical and translational research studies that integrate clinical, molecular, neurobehavioral and other phenotype data. It also offers support for data acquisition and analysis by the MMOC phenotyping Cores and Investigational Weight Management Clinic, expertise in database construction, maintenance and security relevant to investigators studies, and development and use of database and software tools for information organization and visualization of tightly-linked multiscale data for T1 translation of research knowledge relevant to obesity." .
SCR:015479 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Columbia University George M. O'Brien Urology Center " ;
definition: "Research center that brings together research programs in human genetics and mouse models to address the causes of congenital urinary tract malformations." .
SCR:015480 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Research Facilitation Program " ;
NIFRID:synonym "NORC",
"Nutrition and Obesity Research Center",
"UNC" ;
NIFRID:abbrev "UNC NORC",
"UNC Nutrition and Obesity Research Center" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 23,2019. Center that provides bioinformatics and metabolomics support to UNC members for nutrition and obesity-related clinical and translational research." .
SCR:015481 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " University of Washington Nutrition and Obesity Research Center Adipose Tissue and Obesity Core " ;
definition: "Core that provides affiliated investigators with assistance for in vivo and in vitro studies in both subcutaneous and visceral human adipose tissue. Body and liver fat measurement by DXA and MRI are also provided, as is support for translational studies that assist investigators in the design conduct of clinical obesity research." .
SCR:015482 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Encode" ;
NIFRID:synonym "ENCODE Project" ;
definition: "Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present." .
SCR:015483 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Transcriptome architecture of adult mouse brain" ;
definition: "Image collection of transcriptome architecture of adult mouse brain revealed by sparse coding of genome-wide in situ hybridization images." .
SCR:015484 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spine Detection and Extraction" ;
definition: "Code that segments, detects and extracts the spines from three dimensional in vivo images of dendrites with spines." .
SCR:015485 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "FluoroFinder" ;
definition: "Platform provides tools and web services for multicolor fluorescence experiment design, flow cytometry, and microscopy. Provides online spectra viewer and flow cytometry panel design tools and spectral analysis. By integrating experiment design tools featuring preloaded instrument configurations with comprehensive antibody database, panel builder speeds up flow cytometry experiment design." .
SCR:015486 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BZ 9000 Fluorescence Microscope" ;
NIFRID:synonym "BZ-9000 Fluorescence Microscope" ;
definition: "Microscope system performs fluorescence, bright-field and phase-contrast imaging on various specimen holders. The system allows users to switch between four fluorescent channels, automatically adjusting the filter and exposure time while preserving the longevity of the specimen." .
SCR:015487 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StatCheck" ;
definition: "Statistical checking software for psychology manuscripts. Users can upload APA-formatted PDF or HTML files to find errors in statistical reporting." .
SCR:015488 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Spectrum Labs" ;
NIFRID:synonym "Spectrum Labs Inc" ;
definition: "Commercial organization which supplies products for bioseparation and cell line management." .
SCR:015489 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Marshall BioResources" ;
definition: "Commercial provider of purpose-bred animals for biomedical research. They provide dogs, pigs, ferrets, mice, and guinea pigs in physically and psychologically healthy condition." .
SCR:015490 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "wMICA" ;
definition: "Weighted implementation of Maximal Information Component Analysis, a co-expression network analysis algorithm for analysis of large interconnected networks and the identification of modules of similarly-acting nodes within the larger network." .
SCR:015491 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:lncrnadb" ;
rdfs:label "lncRNAdb" ;
NIFRID:synonym "lncRNAdb v2.0",
"Long Noncoding RNA Database",
"Long Noncoding RNA Database v2.0" ;
definition: "Searchable database of comprehensive annotations of eukaryotic long non-coding RNAs. Entries are manually curated from referenced literature." .
SCR:015492 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HomeoDB" ;
definition: "Database of homeobox genes in humans, mice, chickens, frogs, zebrafishes, amphioxuses, fruitflies, beetles, honeybees, and nematodes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015493 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mamit tRNA" ;
NIFRID:synonym "Mamit-tRNA" ;
definition: "Compilation of mammalian mitochondrial tRNA genes. Sequences are classified into families according to the amino acid specificity of the different tRNAs as defined by the anticodon triplets. Each sequence is displayed linearly with color codes indicating secondary structural domains." .
SCR:015494 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioParadigms" ;
NIFRID:synonym "Bioparadigms" ;
definition: "Web-based transporter resource that provides access to the TransCure interdisciplinary research network, the Genomic Transporter Database, and the Biomedical Transporter Conferences page." .
SCR:015495 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KZNF Catalog" ;
definition: "Searchable, manually curated collection of Kruppel-type zinc finger genes (KZNFs) in primates with finished or high quality draft genomes." .
SCR:015496 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Assessment and Accreditation of Laboratory Animal Care International" ;
NIFRID:synonym "AAALAC International",
"Assessment and Accreditation of Laboratory Animal Care",
"Assessment and Accreditation of Laboratory Animal Care (AAALAC)" ;
NIFRID:abbrev "AAALAC" ;
definition: "Private, nonprofit organization that promotes the humane treatment of animals in science through voluntary accreditation and assessment programs." .
SCR:015497 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Montreal Pain and Affective Face Clips" ;
definition: "Collection of standardized stimuli of dynamic, prototypical facial expressions of pain, the six basic emotions, and a neutral display. The set can be used in cognitive, social, clinical, and neuroscience studies on facial expressions and their social communicative functions." .
SCR:015498 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QuantPrime" ;
definition: "Fully automated tool for primer pair design in small- to large-scale real-time reverse transcription qPCR analyses. It offers design and specificity checking with highly customizable parameters and is available for use with publicly available eukaryotic transcriptomes." .
SCR:015499 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21699" ;
rdfs:label "SEER" ;
definition: "Sequence element enrichment analysis tool to perform pan-genome-wide association studies in bacteria." .
SCR:015500 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MSM" ;
NIFRID:synonym "Multi-State Markov and Hidden Markov Models in Continuous Time",
"Multi-State Markov and Hidden Markov Models in Continuous Time (MSM)" ;
definition: "Source code for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. It was originally designed for processes observed at arbitrary times in continuous time but some other observation schemes are supported. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time." .
SCR:015501 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:fasttree",
"OMICS_14703" ;
rdfs:label "FastTree" ;
definition: "Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution." .
SCR:015502 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_12499" ;
rdfs:label "phytools" ;
definition: "Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species." .
SCR:015503 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "warpedLMM" ;
definition: "Source code in Python for implementation of the warped linear mixed model. It automatically learns an optimal \"warping function\" (or transformation) for the phenotype as it models the data." .
SCR:015504 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LDAK" ;
definition: "Software that analyzes and estimates heritability. LDAK adjusts for linkage disequilibrium (LD) by calculating SNP weightings which downweight the contribution of SNPs in highly tagged regions." .
SCR:015505 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "glmnet" ;
NIFRID:synonym "Lasso and Elastic-Net Regularized Generalized Linear Models" ;
definition: "Procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. The algorithm uses cyclical coordinate descent in a path-wise fashion." .
SCR:015506 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FaST LMM" ;
NIFRID:synonym "Factored Spectrally Transformed Linear Mixed Models",
"fastlmm" ;
definition: "FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a set of tools for efficiently performing genome-wide association studies (GWAS), prediction, and heritability estimation on large data sets." .
SCR:015507 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_07360" ;
rdfs:label "GIIRA" ;
definition: "Gene prediction method that identifies potential coding regions based on the mapping of reads from an RNA-Seq experiment." .
SCR:015511 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChIP-Atlas" ;
definition: "Database for visualizing and making use of public ChIP-seq data. ChIP-Atlas covers almost all public ChIP-seq experiments and data submitted to the SRA (Sequence Read Archives) in NCBI, DDBJ, or ENA." .
SCR:015512 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ClinicalStudyDataRequest.com (CSDR)" ;
NIFRID:synonym "Clinical Study Data Request",
"ClinicalStudyDataRequest",
"ClinicalStudyDataRequest.com" ;
NIFRID:abbrev "CSDR" ;
definition: "Consortium of clinical study data providers. Its aim is to help the data sharing community drive scientific progress and improve medical care by facilitating access to patient-level data from clinical studies." .
SCR:015513 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MagicBlast" ;
NIFRID:synonym "Magic - Blast",
"Magic Blast",
"Magic-Blast" ;
definition: "Software tool for making a BLAST database from various data structures. It maps large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome." .
SCR:015514 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mixed Effect Model of Genetic-Set and Environment Interaction" ;
NIFRID:synonym "Mixed Effect Model of Genetic Set and Environment Interaction",
"Mixed Effect Model of Genetic Set and Environment Interaction Toolbox",
"MixGE Toolbox" ;
definition: "MATLAB Toolbox which provides a mixed effect model for gene-environment interaction (MixGE) on neuroimaging phenotypes, such as structural volumes and tensor-based morphometry (TBM). This model incorporates both fixed and random effects of genetic-set and environment interaction in order to investigate homogeneous and heterogeneous contributions of sets of genetic variants and their interactions with environmental risks to phenotypes." .
SCR:015515 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhenVar" ;
definition: "Software tool used to generate a list of PubMed IDs to query and generate associations between publications. It utilizes a local SQLite cache in a configurable location to keep a local copy of relevant SRIDs, PMIDs, and the Abstract sections for the PMIDs." .
SCR:015516 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Template Project" ;
NIFRID:synonym "NeuroImaging and Analysis Group" ;
NIFRID:abbrev "NIAG" ;
definition: "Project to house templates used to build other projects. It is also known as the NeuroImaging and Analysis Group, which employs various physiological, functional and structural neuroimaging methodologies in both research and clinical domains." .
SCR:015517 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PREDiCT" ;
NIFRID:synonym "Patient Repository for EEG Data and Computational Tools",
"Patient Repository for EEG Data and Computational Tools (PREDiCT)" ;
definition: "Patient database that contains EEG data sets, executable tasks, and computational tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015518 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TurboFIRE" ;
definition: "Real-time task-based and resting-state fMRI analysis software. This software is developed and distributed to researchers by NeurInsight LLC." .
SCR:015519 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bcbtoolkit" ;
rdfs:label "BCBtoolkit" ;
NIFRID:synonym "BCBtoolkit 4.0" ;
definition: "Software toolkit that provides several multi-modal tools to assess brain disconnections and remote effects of lesions. All modules are designed to process brain lesion data with a normalization algorithm, a module to estimate the probability and the severity of white matter disconnections, and a tool to build a map of the disconnected areas." .
SCR:015520 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurocare | Neuroconn DC-Stimulator Plus" ;
NIFRID:abbrev "tDCS" ;
definition: "Device for administering transcranial electrical stimulation. It has applications in cranial electrotherapy that provides a weak direct current for non-invasive Interventional Neurophysiology." .
SCR:015521 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DTI FiberTrak MR Clinical application" ;
NIFRID:synonym "DTI FiberTrak",
"Philips DTI FiberTrak" ;
definition: "Instrument and software tool used to visualize, trace, analyze, and process white matter fiber tracts of Diffusion Tensor Imaging (DTI) data in real-time. It supports pre-operative surgical planning, post-surgery evaluation, and general evaluation of fiber tracts around tumors and lesions in connection with functional areas." .
SCR:015523 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIAG Addiction Data" ;
NIFRID:synonym "NeuroImaging and Analysis Group Addiction Data" ;
definition: "Data set of addiction studies compiled by the NeuroImaging and Analysis Group (NIAG)." .
SCR:015524 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MOCA" ;
NIFRID:synonym "Metric Optimization for Computational Anatomy",
"Metric Optimization for Computational Anatomy (MOCA)" ;
definition: "Collection of software tools for the computational analysis of brain anatomy with MRI data. It includes automated software tools from surface reconstruction to their mapping via metric optimization in the Laplace-Beltrami embedding space. It is general and can be applied to a wide range of anatomical structures including cortical, sub-cortical, and fiber bundle surfaces." .
SCR:015525 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UManitoba - JHU Functionally Defined Human White Matter Atlas" ;
NIFRID:synonym "UManitoba JHU Functionally Defined Human White Matter Atlas",
"UManitoba-JHU Functionally-Defined Human White Matter Atlas" ;
definition: "Probabilistic atlas of human white matter tracts/regions underlying several well-known resting state brain networks. The atlas includes group probability maps for each network, as well as each individual tract that are aligned to both the SPM and MRIStudio ICBM templates." .
SCR:015526 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenCV" ;
NIFRID:synonym "Open Source Computer Vision Library" ;
definition: "Computer vision and machine learning software library which provides a common infrastructure for computer vision applications. The algorithms within the library can be used to detect and recognize faces, identify objects, classify human actions in videos, track camera movements and moving objects, extract 3D models of objects, produce 3D point clouds from stereo cameras, stitch images together to produce a high resolution image of an entire scene, find similar images from an image database, and follow eye movements, recognize scenery and establish markers to overlay it with augmented reality. It has C++, C, Python, Java and MATLAB interfaces." .
SCR:015527 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:danpos" ;
rdfs:label "DANPOS2" ;
NIFRID:synonym "DANPOS" ;
definition: "Software toolkit with various functions for the analysis of nucleosome and protein occupancy by sequencing." .
SCR:015528 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_28977" ;
rdfs:label "cwltool" ;
NIFRID:synonym "Common Workflow Language Tool",
"CWLtool" ;
definition: "Reference implementation of the Common Workflow Language standards. It provides complete features and tools and comprehensive validation of CWL. The reference implementation consists of two packages. The cwltool package is the primary Python module containing the reference implementation in the cwltool module and console executable by the same name. The cwlref-runner package is optional and provides an additional entry point under the alias cwl-runner, which is the implementation-agnostic name for the default CWL interpreter installed on a host." .
SCR:015529 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Hologic" ;
NIFRID:synonym "Hologic Inc" ;
definition: "Commercial organization that provides services and products in global healthcare and diagnostics." .
SCR:015530 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:hisat2",
"OMICS_07225" ;
rdfs:label "HISAT2" ;
NIFRID:synonym "HISAT" ;
definition: "Graph-based alignment of next generation sequencing reads to a population of genomes." .
SCR:015531 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Platanus" ;
NIFRID:synonym "Platanus - PLATform for Assembling NUcleotide Sequences",
"Platanus Genome Assembler",
"PLATform for Assembling NUcleotide Sequences" ;
definition: "De novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015532 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R38F5N",
"DOI:10.24433",
"DOI:10.25504/FAIRsharing.thskvr" ;
rdfs:label "Code Ocean" ;
NIFRID:synonym "Code Ocean Inc" ;
definition: "Cloud-based executable research platform for discovering and running scientific code. Code Ocean is designed to give researchers and developers a way to share, discover and run code published in academic journals and conferences. Users can upload code and data in various programming languages and link working code in a computational environment with the associated article, with Code Ocean assigning a Digital Object Identifier (DOI) to the algorithm." .
SCR:015533 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FMAToolbox" ;
NIFRID:synonym "FMA Toolbox",
"Freely Moving Animal Toolbox" ;
definition: "Matlab toolbox used to help analyze electrophysiological and behavioral data recorded from freely moving animals." .
SCR:015534 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hybrid Coordinate Ocean Model" ;
NIFRID:synonym "HYbrid Coordinate Ocean Model",
"HYbrid Coordinate Ocean Model (HYCOM)" ;
NIFRID:abbrev "HYCOM" ;
definition: "Ocean general circulation model; more specifically, a data-assimilative hybrid isopycnal-sigma-pressure (generalized) coordinate ocean model." .
SCR:015535 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MassBank" ;
definition: "Public repository of mass spectral data which allows users to search similar spectra on a peak-to-peak basis, on a neutral loss-to-neutral loss basis, or by the m/z value and molecular formula, search chemical compounds by substructures, and keyword search chemical compounds" .
SCR:015536 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012318" ;
rdfs:label "MassBank of North America" ;
NIFRID:synonym "MassBank of North America (MoNA)" ;
NIFRID:abbrev "MoNA" ;
definition: "Metadata-centric, auto-curating repository designed for storage and querying of mass spectral records. It contains metabolite mass spectra, metadata and associated compounds." .
SCR:015537 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "In vivo - In silico Metabolite Database" ;
NIFRID:synonym "In vivo In silico Metabolite Database",
"In vivo/ In silico Metabolite Database (IIMDB)",
"In vivo/In silico Metabolite Database" ;
NIFRID:abbrev "IIMDB" ;
definition: "Database of known biochemical compounds collected from existing biochemical databases, as well as computationally generated human phase I and phase II metabolites of known compounds." .
SCR:015538 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XCMS" ;
NIFRID:synonym "XCMS Online" ;
definition: "Cloud-based mass spectrometry data processing platform for metabolomics and lipidomics." .
SCR:015539 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016717" ;
rdfs:label "MetaboAnalyst" ;
NIFRID:synonym "MetaboAnalyst 3.0",
"MetaboAnalyst 4.0" ;
definition: "Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification." .
SCR:015540 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Intronless Genes Database" ;
definition: "Non-redundant collection of publicly annotated DNA, CDS, and protein sequences of protein coding intronless genes from human genome." .
SCR:015542 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VALiDATe29 Squirrel Monkey Brain Atlas" ;
NIFRID:synonym "VALiDATe29 Atlas" ;
definition: "Atlas was created from MRI scans of squirrel monkey brains. The atlas is currently comprised of multiple anatomical templates, diffusion MRI templates, and ex vivo templates. In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels." .
SCR:015546 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Helmsley Cellular Research Hub" ;
definition: "Cell repository that aims to share cell samples for the scientific advancement of Type 1 Diabetes research. Cell lines can be requested from their cell bank inventory." .
SCR:015547 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HKL-2000" ;
definition: "Software package for structural determination and other functions in the field of structural biology. Its programs can perform strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, and other functions." .
SCR:015548 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iRNAi" ;
NIFRID:synonym "iRNAi Software" ;
definition: "Software tool for designing short interfering error-free RNA oligos." .
SCR:015549 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phi Toolbox" ;
NIFRID:synonym "integrated information matlab toolbox",
"phi toolkit",
"Φ toolbox" ;
definition: "Toolkit of MATLAB functions for computing integrated information ('phi' or 'Φ') from neural data. The toolbox consists of downloadable codes that perform practical computation." .
SCR:015559 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroManager" ;
definition: "Simulation submission manager for computational neuroscience. It manages simulation processing, file transfers, and job submission for a heterogeneous mixture of standalone server, cluster, and cloud servers." .
SCR:015560 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Proteome Map" ;
definition: "Web-based resource that reorganizes mass spectrometry-based proteomics data to explore expressed proteins in fetal tissues/adult tissues/hematopoietic cells obtained from human. All samples used to generate these data were obtained from histologically normal samples." .
SCR:015561 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COMPARTMENTS Subcellular localization database" ;
NIFRID:synonym "COMPARTMENTS",
"Compartments Database" ;
definition: "Web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. All evidence is mapped to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell." .
SCR:015562 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:proteomicsdb",
"r3d100013408" ;
rdfs:label "ProteomicsDB" ;
definition: "Database for the identification of the human proteome and its use across the scientific community. Users can browse proteins and chromosomes and contribute to the data repository." .
SCR:015563 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BloodSpot" ;
definition: "Database that provides gene expression profiles of genes and gene signatures in healthy and malignant hematopoiesis and includes data from both humans and mice. In addition to the default plot, which displays an integrated expression plot, two additional levels of visualization are available: an interactive tree showing the hierarchical relationship between the samples, and a Kaplan-Meier survival plot. The database is sub-divided into several datasets that are accessible for browsing." .
SCR:015570 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:opentrials" ;
rdfs:label "Open Trials" ;
definition: "Database that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally." .
SCR:015571 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Diabetes Biobank Brussels" ;
NIFRID:synonym "Diabetes Biobank Brussels (DBB)" ;
NIFRID:abbrev "DBB" ;
definition: "Non-profit initiative of the Belgian Diabetes Registry (BDR), the Beta Cell Therapy consortium (BCT), the Flemish Center for Medical Innovation (CMI) and the Brussels Institute for Research and Innovation (Innoviris). It aims to support medical research into the epidemiology, prevention, diagnosis and treatment of diabetes." .
SCR:015572 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nikon Eclipse 80i Advanced Research Microscope" ;
NIFRID:synonym "Eclipse 80i",
"Nikon Eclipse Microscope" ;
definition: "Digital-imaging microscope that uses Nikon's CFI60 optics and high signal-to-noise ratios to produce fluorescence images. It utilizes Nikon’s “fly-eye” technology, VC Plan Apo objectives and both intelligent and motorized digital imaging heads." .
SCR:015573 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nikon DS-Ri1 High Resolution Color Camera" ;
NIFRID:synonym "DS-Ri1",
"DS-Ri1 Color Camera",
"DS-Ri1 Microscope Camera",
"Nikon DS-Ri1" ;
definition: "High-resolution microscope camera designed for low magnifications and enlargements in brightfield imaging. Its features include fast focusing, a large native pixel size, and a supported cooling combine for clear fluorescent imaging and documentation." .
SCR:015574 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Duolink ImageTool" ;
NIFRID:synonym "DUO90806",
"ImageTool" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 7, 2017. Software designed for objective quantification/counting of PLA signals in cells and tissue images generated from fluorescence microscopy. The nuclei are automatically detected and cytoplasm size estimated, enabling single cell statistical analysis of expression levels in tissue or cell populations." .
SCR:015575 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Glo-Max Multi Detection System" ;
NIFRID:synonym "Glo Max Multi Detection System",
"GloMax Multi Detection System" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented August 6, 2017. Detection instrument that gathers absorbance, fluorescence, and luminescence data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015578 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MPlus" ;
NIFRID:synonym "Mplus Version 8" ;
definition: "Statistical modeling program that provides a wide choice of models, estimators, and algorithms in a program that has graphical displays of data and analysis results. Mplus allows the analysis of both cross-sectional and longitudinal data, single-level and multilevel data, data that come from different populations with either observed or unobserved heterogeneity, and data that contain missing values. Analyses can be carried out for observed variables that are continuous, censored, binary, ordered categorical (ordinal), unordered categorical (nominal), counts, or combinations of these variable types. In addition, Mplus has extensive capabilities for Monte Carlo simulation studies, where data can be generated and analyzed according to any of the models included in the program. The Mplus modeling framework draws on the unifying theme of latent variables. The generality of the Mplus modeling framework comes from the unique use of both continuous and categorical latent variables. Continuous latent variables are used to represent factors corresponding to unobserved constructs, random effects corresponding to individual differences in development, random effects corresponding to variation in coefficients across groups in hierarchical data, frailties corresponding to unobserved heterogeneity in survival time, liabilities corresponding to genetic susceptibility to disease, and latent response variable values corresponding to missing data. Categorical latent variables are used to represent latent classes corresponding to homogeneous groups of individuals, latent trajectory classes corresponding to types of development in unobserved populations, mixture components corresponding to finite mixtures of unobserved populations, and latent response variable categories corresponding to missing data." .
SCR:015579 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Geneticist Biorepository of Human Tissue Samples" ;
definition: "Biorepository that stores human tissue, blood, and biofluid samples in frozen, ffpe, and tissue microarray form for research." .
SCR:015580 a "Resoure",
owl:NamedIndividual ;
rdfs:label "GRatio for ImageJ" ;
NIFRID:synonym "GRatio" ;
definition: "ImageJ plugin that performs semiautomated analysis of randomly selected sets of nervous system fibers." .
SCR:015581 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Drug Target Ontology" ;
NIFRID:synonym "Drug Target Ontology (DTO)" ;
NIFRID:abbrev "DTO" ;
definition: "Ontology of drug targets to be used as a reference for drug targets, with the longer-term goal of creating a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The project itself aims to develop a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families." .
SCR:015582 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Center TBI" ;
NIFRID:synonym "Center Traumatic Brain Injury",
"Center-TBI",
"Center-Traumatic Brain Injury" ;
definition: "European project that aims to improve the care for patients with Traumatic Brain Injury. It provides general information and aims to be a communication platform for patients, scientific participants and investigators." .
SCR:015583 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_07548" ;
rdfs:label "Gwyddion" ;
definition: "Modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry." .
SCR:015584 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RootNav" ;
NIFRID:synonym "RootNav 2.0",
"RootNav v1",
"RootNav-2.0" ;
definition: "Software tool for quantification of root system architectures in range of plant species, grown and imaged in variety of ways. Root phenotyping software driven by deep learning. Measurements can be exported directly in RSML format, where additional traits can be calculated later using simple plug-in system." .
SCR:015585 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RootTrace" ;
definition: "Software tool which allows the automatic and high throughput measure of root length, as well as extra associated measures such as curvature. The user must supply start points for each root, and exemplar patches of nearby background. The software will then trace the main root to the tip, in every image in a timeseries, and record the results." .
SCR:015586 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Integrative Human Microbiome Project" ;
NIFRID:synonym "Integrative Human Microbiome Project (iHMP)" ;
NIFRID:abbrev "iHMP" ;
definition: "Provides human microbiome datasets and minimum reporting standards established by DCC, from both initial HMP-1 phase and iHMP. Offers to query and retrieve metagenomic, metatranscriptomic, human genetic, microbial culture, and many other data types from each project. Provides integrated longitudinal datasets from both microbiome and host from different cohort studies of microbiome associated conditions." .
SCR:015587 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harvard Digestive Disease Center" ;
NIFRID:abbrev "HDDC" ;
definition: "Community of scientists focused on the study of epithelial cell function and mucosal biology including inflammation and host defense of the gastrointestinal tract. It focuses on the intestinal and inflammatory bowel diseases; gut microbiology; and stem cell and developmental biology of the intestine and liver in organ physiology, regenerative medicine, and metabolism." .
SCR:015588 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harvard Digestive Diseases Center Biomedical CORE C: Epithelial Cell and Mucosal Immunology" ;
definition: "Core facility that provides the infrastructure, biologic resources, expertise, and training for cross-disciplinary research on epithelial biology and immune function in mucosal surfaces and solid organs of the GI tract." .
SCR:015589 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hopkins Conte Digestive Diseases Basic and Translational Research Core Center" ;
NIFRID:abbrev "HDDBTRCC",
"JHUGICC" ;
definition: "Center that aims to advance basic science and translational digestive diseases research at the Johns Hopkins University School of Medicine. Its goal is to improve the health of patients with the broad spectrum of gastrointestinal and hepatic disorders." .
SCR:015590 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harvard Digestive Diseases Center Bio-Repository and Data Registry for Human Material" ;
definition: "Core facility that supports basic, translational, and clinical research in the digestive diseases by providing access to human materials and resources in statistics and study design. It also aims to to forge connections and support collaboration between HDDC Clinical Associates and Members, support a well-organized infrastructure for acquisition and storage of clinical samples, and provide professional support in biostatistics and study design to HDDC members and Clinical Associates." .
SCR:015591 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Integrated Physiology Core" ;
definition: "Core facility that provides Center investigators and their laboratories the tools and advice needed to establish and study mouse (including transgenic and knockout) and human (i.e. GI organoids) physiology of GI disease." .
SCR:015592 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harvard Digestive Diseases Center Clinical Translational Research Program" ;
definition: "Core facility that supports basic, translational, and clinical research in the digestive diseases by providing access to human materials and resources in statistics and study design. Its services promote translation of basic research advances into improved clinical care by offering fresh and archived human specimens, associated clinical metadata, biostatistics and aid in study design." .
SCR:015593 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Image Core" ;
definition: "Core facility that provides state-of-art light microscopy technology to the members of the Hopkins Basic Research Digestive Disease Development Center and to the whole Hopkins scientific community." .
SCR:015594 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Translational Research Enhancement Core" ;
NIFRID:abbrev "HDDBTRCCTREC",
"TREC" ;
definition: "Core facility whose services include establishing Best Practices (BP) and uniform Standard Operating Procedures (SOPs) for the collection, annotation, processing, storage, management, distribution, and ethical use of human specimens, and to provide access to specimens by investigators as well as patient identification, patient recruitment, facilitation of patient trials, translational research and basic research through creation of a patient registry and database." .
SCR:015595 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCSF Liver Center" ;
definition: "Center whose goal is to integrate bench science with clinical investigation, in support of its vision to understand and cure human liver diseases." .
SCR:015596 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCSF Liver Center Immunology Core" ;
definition: "Core that takes advantage of local expertise and resources to enable Center members to analyze cell populations in mouse or human livers. It performs complex analyses on small numbers of human cells, such as those obtained from liver biopsies." .
SCR:015597 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hopkins Conte Digestive Diseases Basic and Translational Research Core Center Proteomics Core" ;
definition: "Core facility that uses mass spectrometry coupled to one (1D) and two (2D) dimensional separations by column chromatography or gel electrophoresis to identify, quantify or characterize proteins and their post-translational modifications, that are expressed in well characterized protein fractions from the small intestine, colon, kidney, liver and pancreas. Techniques such as difference gel electrophoresis (DIGE), isobaric tag for relative and absolute quantitation (iTRAQ), tandem mass tags (TMT) and stable isotope labeling of amino acids in cell culture (SILAC) as well as non-labeling methods (MudPIT, multi-dimensional protein identification technology) are available for quantifying relative differences in protein expression and post-translational modifications, such as acetylation, glycosylation, phosphorylation, nitrosation, ubiquitination and novel cleavage sites." .
SCR:015598 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCSF Liver Center Clinical & Translational Core" ;
definition: "Core that supports study design to sample procurement and storage, to data analysis and presentation, and also focuses on research involving human subjects." .
SCR:015599 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCSF Liver Center Pathology & Imaging Core" ;
definition: "Core that provides services from routine liver histology to complex microscopy and image analysis." .
SCR:015600 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCSF Liver Center Cell Biology Core" ;
definition: "Core whose purpose is providing primary and immortalized liver cells for experimental use as well as other material such as human liver cells, primary hepatocytes, and immortalized cell lines." .
SCR:015601 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Chicago Digestive Diseases Research Core Center" ;
NIFRID:abbrev "DDRCC" ;
definition: "Center whose goals include fostering collaboration among basic and clinical investigators, facilitating the use of new technologies in the study of treatment of digestive diseases, and providing education and training for improved treatment and diagnosis." .
SCR:015602 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Chicago Digestive Diseases Research Core Center Administrative Core" ;
definition: "Core that has oversight of the other four cores of University of Chicago's Digestive Disease Research Core Center and determines the center's overall direction." .
SCR:015603 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Chicago Digestive Diseases Research Core Center Host-Microbe Core" ;
definition: "Core that consists of two components: The Enteric Microbiology and The Gnotobiotic Mouse components. The Enteric Microbiology component offers novel screening and advanced technologies for compositional and functional profiling of the resident microbial communities in the gastrointestinal tract. The Gnotobiotic Mouse component enables investigators to study the effects and causal role of specific microorganisms or profiles in vivo." .
SCR:015604 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Chicago Digestive Diseases Research Core Center Tissue Engineering and Cell Models Core" ;
NIFRID:abbrev "TECM" ;
definition: "Core that provides services such as a repository for intestinal cell lines, Tissue Engineering Models, experimental materials, and supplies for digestive disease research." .
SCR:015605 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Michigan Center for Gastrointestinal Research" ;
NIFRID:abbrev "UMCGR" ;
definition: "Center whose goal is to investigate signal transduction mechanisms regulating homeostasis and GI disorders. Their approach includes studies on genetics and gene regulation, cellular signaling pathways, receptors and ion channels." .
SCR:015606 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core" ;
definition: "Core that serves as both a central repository for all the samples and data shared by the other cores and a catalyst for interdisciplinary research." .
SCR:015607 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Chicago Digestive Diseases Research Core Center Tissue and Cell Imaging Core" ;
definition: "Core whose services include anatomic pathology review of human and experimental animal tissues as well as consultation in the best approaches for such analyses, cost-effective and high quality processing and staining of formalin-fixed paraffin-embedded tissues, and making collections of human tissue and imaging technologies available to researchers." .
SCR:015608 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Michigan Center for Gastrointestinal Research In Vivo Animal and Human Studies Core" ;
definition: "Core facility that consists of the following 4 distinct programs: In Vivo Small Animal Studies Program, Organoid/Enteroid Modeling Program, Biospecimens Banking Service, and Clinical Design and Statistics." .
SCR:015609 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Michigan Center for Gastrointestinal Research Protein Localization, Identification and Folding Core" ;
definition: "Core facility whose services include the following programs: Imaging Core Program, Proteomics Core Program, Protein Folding Core Program, and Consultation." .
SCR:015610 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Michigan Center for Gastrointestinal Research Molecular Biology Core" ;
definition: "Core whose services include the following programs: Transgenic Rodent Program, Genome Editing Program, Viral Vector Program, and Integrated Genomics Program." .
SCR:015611 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Michigan Center for Gastrointestinal Research Microbiome and Metabolomics Core" ;
NIFRID:synonym "Center for Gastrointestinal Research",
"Metabolomics Core",
"Microbiome",
"University of Michigan" ;
NIFRID:abbrev "MMC",
"UMCGR" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8,2025. Core whose services include consultation, Nucleic Acid Isolation, Microbiome (16S) Data Analysis, MiSeq-base 16S rRNA Gene Sequencing, Genomic/Metagenomic shotgun sequencing, Bacterial transcriptomics and metatranscriptomics, Multiplatform Metabolomic Profiling, Metabolomic sample preparation, and Germ-free & Gnotobiotic Mouse Facilities." .
SCR:015612 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of North Carolina Center for Gastrointestinal Biology and Disease" ;
NIFRID:abbrev "CGIBD",
"UNCCGBD" ;
definition: "Center at UNC Chapel Hill and North Carolina State University for collaborative GI research. Its mission is to promote and enhance multidisciplinary digestive disease research." .
SCR:015613 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of North Carolina Center for Gastrointestinal Biology and Disease Advanced Analytics Core" ;
definition: "Core facility provides solutions for studying proteins, peptides, and other molecules, including mRNA and cDNA. The Core's immunotechnologies (IT) component provides consultation, ordering, and immunoassay services, and supports a variety of analytes in both traditional ELISA/EIA and xMAP-based multiplex bead assay formats." .
SCR:015614 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of North Carolina Center for Gastrointestinal Biology and Disease Histology Core" ;
definition: "Core facility that provides a full range of histology services, encompassing routine and specialized grossing, tissue processing, paraffin embedding, microtomy, H&E and special staining, and immunohistochemistry. It also offers image analysis and consultations to CGIBD members and non-members." .
SCR:015615 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of North Carolina Center for Gastrointestinal Biology and Disease Gnotobiotic Core" ;
definition: "Core facility that supports animal model and basic research projects of CGIBD investigators. Investigators use this resource to examine physiologic and pathophysiologic differences in germ-free, gnotobiotic, and specific pathogen free colonized mice of various genetic backgrounds." .
SCR:015616 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of North Carolina Center for Gastrointestinal Biology and Disease Biostatistics and Data Management Core" ;
definition: """Core facility that provides comprehensive statistical and data management services. Its statistical analysis services include study design, power and sample size analysis, randomization, statistical programming, consultation and the development of analysis plans, graphs, figures and reports.
""" .
SCR:015617 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases" ;
NIFRID:abbrev "UPCMSDLD" ;
definition: "Center that aims to unite investigators with interests in digestive, liver and pancreatic physiology and disease in the exploration of creative experimental approaches. The scientific focus of the Center revolves around the molecular controls of cellular growth and differentiation in the digestive tract, liver and pancreas with the goal of achieving a new level of integration in biology, pathobiology, and therapy." .
SCR:015618 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Molecular Pathology and Imaging Core" ;
definition: "Core facility that provides histological services, equipment usage, and technical expertise to digestive and liver research projects." .
SCR:015619 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of North Carolina Center for Gastrointestinal Biology and Disease Large Animal Models Core" ;
definition: "Core facility that provides consultation and procedural expertise on development on novel models of relevant digestive diseases in large animals." .
SCR:015620 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Host-Microbial Analytic and Repository Core" ;
definition: "Core facility that provides services that will enhance the analysis of both host and microbial biological processes as well as facilitate translation into the clinical arena via human subject research." .
SCR:015621 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Cell Culture Core" ;
definition: "Core facility that maintains a centralized repository of cells and reagents pertinent to digestive, liver and pancreatic disease research. It also provides training for labs in new cell culture (2D and 3D) techniques." .
SCR:015622 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Genetically-Modified Mouse Core" ;
definition: "Core facility that provides a centralized service to efficiently produce genetically altered mice for basic research, resulting in reduction in effort and cost to participating investigators." .
SCR:015624 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:snpsift" ;
rdfs:label "SnpSift" ;
NIFRID:synonym "SnpEff" ;
definition: "Software toolkit for filtering and manipulating annotated files. After annotation, the software's filter function can find relevant genomic variants in large data files." .
SCR:015625 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LINKDATAGEN" ;
definition: "Perl tool that generates linkage mapping input files using data from HAPMAP Phase III populations. It provides rudimentary error checks and is easily amended for personal linkage mapping preferences." .
SCR:015626 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChAS (Chromosome Analysis Suite)" ;
NIFRID:synonym "Chromosome Analysis Suite" ;
NIFRID:abbrev "ChAS" ;
definition: "Software customized for copy number and cytogenetics research analysis and reporting. ChAS enables the user to view and summarize chromosomal aberrations, which may include copy number gain or loss, mosaicism, or loss/absence of heterozygosity (LOH/AOH)." .
SCR:015627 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "STATISTICA_dup" ;
NIFRID:synonym "Statistica",
"Statistica 10",
"Statistica 10 Software",
"STATISTICS Product Index" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Analytics platform with various sub platforms, each with specific performance capabilities for tasks such as data analysis, data management, data visualization, and data mining procedures." .
SCR:015628 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cerebrovascular Disease Knowledge Portal" ;
NIFRID:synonym "Cerebrovascular Disease Knowledge Portal (CDKP)" ;
NIFRID:abbrev "CDKP" ;
definition: "Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data." .
SCR:015629 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018327" ;
rdfs:label "BoxPlotR" ;
definition: "Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox." .
SCR:015630 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CUDAICA" ;
definition: "Software that implements Infomax ICA, which is an algorithm to perform Independent Component Analysis, in CUDA (a parallel computing platform and programming model)." .
SCR:015631 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuroglancer" ;
definition: "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)." .
SCR:015632 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BABAM" ;
NIFRID:synonym "Browsable Atlas of Behavior-Anatomy Maps",
"Browsable Atlas of Behavior-Anatomy Maps (BABAM)" ;
definition: "Graphical user interface for exploring hypotheses of correlations between neural activity in regions of the brain and behavior for Drosophila melanogaster. These correlation hypotheses are the result of our thermogenetic neural activation screen from the Janelia GAL4 collection." .
SCR:015634 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuronUnit" ;
definition: "Software toolkit for data-driven validation of neuron and ion channel models using SciUnit. NeuronUnit implements an interface to several simulators and model description languages, handles test calculations according to domain standards, and enables automated construction of tests based on data from several major public data repositories." .
SCR:015635 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ndmg" ;
NIFRID:synonym "ndmg (Nutmeg)",
"NeuroData’s MR Graphs package",
"Nutmeg" ;
NIFRID:abbrev "NDMG" ;
definition: "Software that creates graphs from brain scan data. ndmg is a 1-click structural connectome estimation pipeline and is the successor of the MRCAP, MIGRAINE, and m2g pipelines." .
SCR:015637 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpineCreator" ;
NIFRID:synonym "SpineCreator: Graphical Editor for SpineML" ;
definition: "Graphical editor software which can be used to create and edit neural network models. Models can be read from, and saved in the SpineML format." .
SCR:015638 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Visibiome" ;
definition: "Search engine for querying novel microbiome samples against a comprehensive database of curated samples. Visibiome accepts rRNA data in the form of BIOM files." .
SCR:015640 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpineML_2_BRAHMS" ;
definition: "Simulation software which can execute neural network models specified in the SpineML format (an extension of the INCF's NineML). It is used as the canonical simulator backend by SpineCreator and translates the SpineML specification of the model into object code and a SystemML specification of the network." .
SCR:015641 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpineML" ;
NIFRID:synonym "The Spiking Neural Mark-up Language",
"The Spiking Neural Mark-up Language (SpineML)" ;
definition: "Declarative XML based model description language for large scale neural network models. Its syntax is designed primarily for the specification of large scale networks of point neurons but also has the flexibility to describe biologically constrained models consisting of non standard components (such as gap junctions)." .
SCR:015642 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BRAHMS" ;
definition: "Simulation software that runs network simulations where the network is specified in its own format called SystemML. The components of the network can be implemented in C, C++, Python or Matlab and are used in SpineML_2_BRAHMS to provide a simulation back-end for SpineML models." .
SCR:015643 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018767" ;
rdfs:label "Phobius" ;
NIFRID:synonym "PHOBIUS" ;
definition: "Web application for combined transmembrane topology and signal peptide prediction. Used for whole genome annotation of signal peptides and transmembrane regions. Predictor is based on hidden Markov model (HMM) that models different sequence regions of signal peptide and different regions of transmembrane protein in series of interconnected states." .
SCR:015644 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SignalP" ;
definition: "Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks." .
SCR:015645 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018388" ;
rdfs:label "X!Tandem" ;
definition: "Software tool that can match tandem mass spectra with peptide sequences, in process known as protein identification. Database search engine for matching tandem mass spectra with protein sequences. Command line tool for matching tandem mass spectra with peptide sequences." .
SCR:015646 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ms-gf" ;
rdfs:label "MS-GF+" ;
NIFRID:synonym "MSGF+",
"MSGFPlus" ;
definition: "Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database." .
SCR:015647 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Transeq" ;
NIFRID:synonym "EMBOSS Transeq" ;
definition: "Software that translates nucleic acid sequences to their corresponding peptide sequences. It can translate to the three forward and three reverse frames, and output multiple frame translations at once." .
SCR:015648 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ATSAS" ;
NIFRID:synonym "Data Analysis Software ATSAS" ;
definition: "Software toolkit for small-angle scattering data analysis from biological macromolecules." .
SCR:015649 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Soma-Segmentation" ;
definition: "Source code for a soma segmentation method suitable for datasets with touching soma distributions. The method contains three main parts: soma detection based on DT and local maximum searching and refining; an improved Rayburst sampling algorithm for isolated and touching soma surface detection; and ellipsoid fitting to generate the segmentation results." .
SCR:015650 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Challenge Competitions Collection" ;
definition: "Portal for platforms available to conduct and compete in challenges aiming to improve scientific progress. Challenges allow researchers to share their research and problems with other subject matter experts for collaborative progress." .
SCR:015651 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BIOVIA Discovery Studio" ;
definition: "Simulation software tool that performs comprehensive predictive science application for for small molecules." .
SCR:015652 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XDS Program Package" ;
NIFRID:synonym "XDS",
"XDS Package" ;
definition: "Software for x-ray detection and processing single-crystal monochromatic diffraction data recorded by the rotation method. XDS can process data images from CCD-, imaging-plate-, multiwire-, and pixel-detectors in a variety of formats." .
SCR:015653 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BUSTER" ;
definition: "Software for structure refinement." .
SCR:015654 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:lme4" ;
rdfs:label "lme4" ;
NIFRID:synonym "lme4.0",
"lme4: Linear Mixed-Effects Models",
"lme4: Linear Mixed-Effects Models using 'Eigen' and S4",
"R package: lme4" ;
definition: "Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' \"glue.\"" .
SCR:015655 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "R package: nlme" ;
definition: "Software to fit and compare Gaussian linear and nonlinear mixed-effects models." .
SCR:015656 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "R package: lmerTest" ;
NIFRID:synonym "lmerTest: Tests in Linear Mixed Effects Models" ;
definition: "Source code of statistical tests for linear mixed effects models as implemented in lme4. The package also provides the calculation of population means for fixed factors with confidence intervals and corresponding plots." .
SCR:015657 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "R package: RVAideMemoire" ;
NIFRID:synonym "Package 'RVAideMemoire'",
"RVAideMemoire",
"RVAideMemoire: Testing and Plotting Procedures for Biostatistics" ;
definition: "Software package that contains miscellaneous functions useful in biostatistics, such as univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions shorten existing procedures and implement plotting functions that can be used with a variety of methods and packages." .
SCR:015658 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "R package: LMERConvenienceFunctions" ;
NIFRID:synonym "LMERConvenienceFunctions",
"LMERConvenienceFunctions: Model Selection and Post-hoc Analysis for (G)LMER Models",
"Package ‘LMERConvenienceFunctions’" ;
definition: "Software package that performs backward selection of fixed effects, forward fitting of the random effects, and post-hoc analysis using parallel capabilities. Other functionality includes the computation of ANOVAs with upper- or lower-bound p-values and R-squared values for each model term, model criticism plots, data trimming on model residuals, and data visualization." .
SCR:015659 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "R package: Deducer" ;
NIFRID:synonym "Deducer",
"Deducer: A Data Analysis GUI for R" ;
definition: "Data Analysis GUI for R. The program is based on Java's Swing GUI library and includes an Excel-like spreadsheet for easy data viewing and editing." .
SCR:015660 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "R package: psy" ;
NIFRID:synonym "Package ‘psy’",
"psy",
"psy: Various procedures used in psychometry" ;
definition: "Software package implementing various statistical procedures used in psychometry." .
SCR:015661 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneMarker" ;
NIFRID:synonym "GeneMarker: The Biologist Friendly Software" ;
definition: "Genotype analysis software which enhances the speed, accuracy, and ease of analysis. The software is an alternative to Applied BioSystems Genotyper®, GeneScan®, and other genotype analysis software." .
SCR:015662 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "R package: lattice" ;
NIFRID:synonym "lattice",
"lattice: Trellis Graphics for R",
"Package ‘lattice’" ;
definition: "Data visualization software inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs as well as most nonstandard requirements." .
SCR:015663 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DrugCentral" ;
NIFRID:synonym "Drug Central",
"DrugCentral: Online Drug Compendium" ;
definition: "Database of drug information created and maintained by the Division of Translational Informatics at University of New Mexico. It provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic action." .
SCR:015664 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:diseases" ;
rdfs:label "DISEASES" ;
definition: "Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence." .
SCR:015665 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:tissues" ;
rdfs:label "TISSUES" ;
NIFRID:synonym "Tissue Expression Database",
"TISSUES: Tissue Expression Database" ;
definition: "Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence." .
SCR:015666 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DOAF" ;
NIFRID:synonym "Disease Ontology Annotation Framework",
"Disease Ontology Annotation Framework (DOAF)" ;
definition: "Project portal for a collaborative database aiming to provide a comprehensive annotation to human genome.It uses the computable, controlled vocabulary of Disease Ontology (DO) and NCBI Gene Reference Into Function (GeneRIF)." .
SCR:015667 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LabeledIn" ;
definition: "Database of annotations of drug indications in FDA drug labels. LabeledIn contains an expert curated set of indications and a crowdsourced set of indications." .
SCR:015668 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MEDI" ;
NIFRID:synonym "MEDI (MEDication Indication)",
"MEDI--an Ensemble MEDication Indication Resource",
"MEDication Indication" ;
definition: "Medication indication software for primary and secondary uses of electronic medical record (EMR) data. MEDI was created based on multiple commonly used medication resources (RxNorm, MedlinePlus, SIDER 2, and Wikipedia ) and by leveraging both ontology and natural language processing (NLP) techniques." .
SCR:015669 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Evolutionary Rate Covariation" ;
NIFRID:synonym "ERC: Evolutionary Rate Covariation",
"Evolutionary Rate Covariation (ERC)",
"Evolutionary Rate Covariation (ERC) Analysis" ;
NIFRID:abbrev "ERC" ;
definition: "Web-based statistical application that measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. It can identify new functional connections between genes." .
SCR:015670 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Reference Protein Interactome Project" ;
NIFRID:synonym "HuRI: The Human Reference Protein Interactome Mapping Project" ;
NIFRID:abbrev "HuRI" ;
definition: "Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies." .
SCR:015671 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R3DD11",
"DOI:10.17632",
"DOI:10.25504/FAIRsharing.3epmpp",
"r3d100011868" ;
rdfs:label "Mendeley Data" ;
definition: "Cloud-based data repository for storing, publishing and accessing scientific data. Mendeley Data creates a permanent location and issues Force 11 compliant citations for uploaded data." .
SCR:015672 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cogent 2000" ;
NIFRID:synonym "Cogent" ;
definition: "MATLAB Toolbox for presenting stimuli and recording responses with precise timing. It also provides additional utilities for the manipulation of sound, keyboard, mouse, joystick, serial port, parallel port, subject responses and physiological monitoring hardware." .
SCR:015673 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpiSOP" ;
NIFRID:synonym "Spindles Slow Oscillation and Power-spectral-density" ;
definition: "Software for detection and reporting of spindle or slow oscillation events, simple automatic EMG artifacts, and their co-occurance or respective matching non-events. SpiSOP was designed to process large data quanta at once and multiple datasets in parallel." .
SCR:015674 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Connectivity Map 02" ;
NIFRID:synonym "Broad Institute Connectivity Map 02 Build",
"cmap" ;
definition: "Collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. camp aims to enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015675 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DIAGRAM" ;
NIFRID:synonym "DIAGRAM (DIAbetes Genetics Replication And Meta-analysis) consortium",
"DIAGRAM consortium" ;
definition: "Consortium of researchers aiming to characterize the genetic basis of type 2 diabetes with a principal focus on samples of European descent. DIAGRAM also features a database of DIAGRAM publications and diabetes-related research data." .
SCR:015677 a owl:NamedIndividual ;
rdfs:label "Trans-Omics for Precision Medicine (TOPMed) Program" ;
NIFRID:abbrev "TOPMED" ;
definition: "Funding program for Precision Medicine genome sequencing from the National Institutes of Health, NHBLI." .
SCR:015678 a owl:NamedIndividual ;
rdfs:label "BioBankEngine" ;
definition: "This engine presents case-control association results from the UK Biobank hospital in-patient health-related outcomes summary information data (Data-Field 41202); computational grouping of phenotypes with cancer (Category 100092) registry, death registry data (Category 100093), algorithmically-defined outcomes (Category 42), and verbal questionnaire data (Category 100071); and manually curated grouping of phenotypes." .
SCR:015679 a owl:NamedIndividual ;
rdfs:label "AllofUs Research Program Biobank" ;
definition: "A biobank is a repository that stores and manages biological samples known as biospecimens for use in research. The Precision Medicine Initiative (PMI) Cohort Program biobank has been awarded to Mayo Clinic in Rochester, Minnesota. The biobank will support the collection, analyses, storage and distribution of biospecimens for research use. Data from laboratory analyses of biospecimens will be combined with an array of other lifestyle and health information provided by volunteers to help researchers continue to unravel individual differences that contribute to disease and response to treatments." .
SCR:015680 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CRowd Extracted Expression of Differential Signatures" ;
NIFRID:synonym "CREEDS: CRowd Extracted Expression of Differential Signatures" ;
NIFRID:abbrev "CREEDS" ;
definition: "Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures." .
SCR:015681 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:clustergrammer" ;
rdfs:label "clustergrammer" ;
definition: "Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer enables intuitive exploration of high-dimensional data and has several optional biology-specific features." .
SCR:015682 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:gen3va" ;
rdfs:label "GEN3VA" ;
NIFRID:synonym "GENE Expression and Enrichment Vector Analyzer" ;
definition: "Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme." .
SCR:015683 a owl:NamedIndividual ;
rdfs:label "ARCHS4" ;
definition: "ARCHS4 provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO and SRA. The website enables downloading of the data in H5 format for programmatic access as well as a 3-dimensional view of the sample and gene spaces. Search features allow browsing of the data by meta data annotation, ability to submit your own up and down gene sets, and explore matching samples enriched for annotated gene sets. Selected sample sets can be downloaded into a tab separated text file through auto-generated R scripts for further analysis. Reads are aligned with Kallisto using a custom cloud computing platform. Human samples are aligned against the GRCh38 human reference genome, and mouse samples against the GRCm38 mouse reference genome." .
SCR:015684 a owl:NamedIndividual ;
rdfs:label "FAIRShake" ;
definition: """A web interface for the scoring of biomedical digital objects by user evaluation according to the FAIR data principles: Findability, Accessibility, Interoperability, and Reusability.
Prototype currently available at: http://amp.pharm.mssm.edu/fairshake""" .
SCR:015685 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fluidigm Singular Analysis Toolset" ;
definition: "Software toolkit for analyzing and visualizing data of single cell qPCR/RNA-seq. It offers methods for identifying gene expression and mutation patterns at the single-cell level and is designed for use with Biomark and C1 systems." .
SCR:015686 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fluidigm Real-time PCR Analysis software" ;
NIFRID:synonym "Real-time PCR Analysis",
"Real-time PCR Analysis Software" ;
definition: "Sequence analysis software for rt-qPCR analysis. It establishes standard curves, calculates delta delta Ct and automatically determines the ideal threshold setting for each run." .
SCR:015687 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:deseq2" ;
rdfs:label "DESeq2" ;
definition: "Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates." .
SCR:015688 a owl:NamedIndividual ;
rdfs:label "Cuffmerge" ;
definition: """The main purpose of Cufflinks.cuffmerge is to merge together several Cufflinks assemblies, making it easier to produce an assembly GTF file suitable for use with Cufflinks.cuffdiff. Cufflinks.cuffmerge also runs Cuffcompare in the background and automatically filters out transcribed fragments (transfrags) that are likely to be artifacts.
Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 2013;31:46-53.""" .
SCR:015689 a owl:NamedIndividual ;
rdfs:label "SetRank " ;
definition: """Implements an algorithm to conduct advanced gene set enrichment analysis on the results of genomics experiments.
Simillion C, Liechti R, Lischer HE, Ioannidis V, Bruggmann R. Avoiding the pitfalls of gene set enrichment analysis with SetRank. BMC bioinformatics. 2017;18(1):151. doi: 10.1186/s12859-017-1571-6.""" .
SCR:015690 a "Commercial organization",
owl:NamedIndividual ;
rdfs:label "Oncotopix Discovery" ;
definition: "Oncotopix Discovery is a comprehensive solution powered for whole slide image analysis of tissue sections, TMA slides across any image analysis application. Simple to program also for scientists without an IT background." .
SCR:015692 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Verywell Hepatitis Portal" ;
definition: "Disease portal for Hepatitis that provides information about causes, symptoms, treatments, and other characteristics of Hepatitis. This webpage is curated by Verywell, a health and wellness organization." .
SCR:015693 a owl:NamedIndividual ;
rdfs:label "Australian Bipolar Families" ;
definition: "The Black Dog Institute is dedicated to understanding, preventing and treating mental illness. We are about creating a world where mental illness is treated with the same level of concern, immediacy and seriousness as physical illness; where scientists work to discover the causes of illness and new treatments, and where discoveries are immediately put into practice through health services, technology and community education." .
SCR:015694 a owl:NamedIndividual ;
rdfs:label "Torrent Variant Caller Standalone" ;
definition: "A variant vcf file analysis tool." .
SCR:015695 a owl:NamedIndividual ;
rdfs:label "Zeiss AIM 4.2 SP1 software " ;
definition: "A commercial software package that works with Carl Zeiss microscopy; AIM 4.2 software." .
SCR:015696 a owl:NamedIndividual ;
rdfs:label "BioToolBox" ;
definition: """Tools for querying and analysis of genomic data. These libraries provide a useful interface for working with bioinformatic data. Many bioinformatic data analysis revolves around working with tables of information, including lists of genomic annotation (genes, promoters, etc.) or defined regions of interest (epigenetic enrichment, transcription factor binding sites, etc.). This library works with these tables and provides a set of common tools for working with them.
Opening and saving common tab-delimited text formats
Support for BED, GFF, VCF, narrowPeak files
Scoring intervals with datasets from microarray and sequencing
ChIPSeq, RNASeq, microarray expression
Support for Bam, BigWig, BigBed, wig, and USeq data formats
Intersection with other known annotation
Works with any genomic annotation in GTF, GFF3, and UCSC formats
The libraries provide a unified and integrated approach to analyses. In many cases, they provide an abstraction layer over a variety of different specialized BioPerl and related modules. Instead of writing numerous scripts specialized for each data format (wig, bigWig, Bam), one script can now work with any data format.""" .
SCR:015697 a owl:NamedIndividual ;
rdfs:label "bam2wig" ;
definition: "A script to convert Bam alignments into a wig representation file." .
SCR:015698 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IITC Life Sciences | Rotarod Test" ;
NIFRID:synonym "IITC Life Sciences Rotarod Treadmill",
"IITC Rotarod Test",
"IITC Rotarod Treadmill",
"IITC's Rotarod Test",
"Rotarod Test Rats and Mice",
"Rotarod Treadmill for mice and rats" ;
definition: "Kit for assessing motor function and endurance in mice and rats. IITC’s Rotarod Test is capable of having up to five mice or rats tested at a time standard." .
SCR:015699 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:GenePattern_notebook" ;
rdfs:label "GenePattern Notebook " ;
NIFRID:synonym "GenePattern Notebook environment" ;
definition: "Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code." .
SCR:015700 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MacVector" ;
definition: "Software application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, agarose gel simulation and a variety of other functions." .
SCR:015701 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rosetta" ;
NIFRID:synonym "Rosetta modeling software" ;
definition: "Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes." .
SCR:015702 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mouse Thalamic Projectome Dataset" ;
definition: "Data set of thalamo-centric mesoscopic projection maps to the cortex and striatum. The maps are established through two-color, viral (rAAV)-based tracing images and high throughout imaging." .
SCR:015703 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GelQuantNET" ;
definition: "Software for image analysis, processing and quantitation. This software analyzes standard JPEG, BMP, PNG, TIFF images; 16-bit TIFF images; and .GEL files produced by Phosphorimager, Typhoon and Storm instruments." .
SCR:015704 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MIDAS" ;
NIFRID:synonym "Metabolite Imaging and Data Analysis System",
"MIDAS Software",
"MIDAS: Metabolite Imaging and Data Analysis System" ;
definition: "Software for processing, display, and analysis of magnetic resonance spectroscopic imaging data. MIDAS supports a \"whole-brain\" MRSI acquisition method that has been implemented on MRI systems from three major manufacturers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015705 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GET_HOMOLOGUES" ;
definition: "Software package for pan-genome analysis. This software is suitable for bacterial genomes and the study of intra-specific eukaryotic pan-genomes." .
SCR:015706 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "chloroplast_assembly_protocol" ;
definition: "Software scripts for the assembly of chloroplast genomes out of whole-genome sequencing reads." .
SCR:015707 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "split_pairs.pl" ;
NIFRID:synonym "split_pairs" ;
definition: "Software for processing NGS sequence reads in FASTQ and FASTA formats. split_pairs.pl is suited particularly for the task of sorting pair end reads and for modifying their headers with Perl-style regular expressions." .
SCR:015708 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mebs" ;
rdfs:label "MEBS: Multigenomic Entropy-Based Score " ;
NIFRID:synonym "metagenome_Pfam_score",
"Multigenomic Entropy-Based Score",
"Multigenomic Entropy-Based Score (MEBS)" ;
NIFRID:abbrev "MEBS" ;
definition: "Open source software to evaluate, quantify, compare, and predict the metabolic machinery of interest in large ‘omic’ datasets. This protocol finds informative protein families and uses them to score metagenomic sets." .
SCR:015709 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "barleyGO" ;
definition: "Perl software script that can annotate barley sequences with Gene Ontology terms inferred by homology. It uses the IBSC2012 barley GO annotation and supports both nucleotide and peptide sequences." .
SCR:015710 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BARLEYMAP" ;
definition: "Barleymap was designed to search the position of barley genetic markers on the Barley Physical Map and the POPSEQ map. Its three main functions are finding markers, aligning sequences, and locating by position." .
SCR:015711 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "footprintDB" ;
definition: "Web application for predicting transcription factors which bind a specific DNA site or motif, as well as DNA motifs or sites likely to be recognized by a specific DNA-binding protein. footprintDB also lists several databases and repositories relevant to DNA transcription." .
SCR:015712 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TFcompare" ;
definition: "Web application for structural alignment of DNA motifs and protein domains from DNA binding protein complexes in Protein Data Bank." .
SCR:015713 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:3d-footprint" ;
rdfs:label "3D-footprint" ;
definition: "Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats." .
SCR:015714 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:primers4clades" ;
rdfs:label "primers4clades" ;
definition: "Web application for the design of PCR primers for cross-species amplification of novel sequences from metagenomic DNA or from uncharacterized organisms belonging to user-specified phylogenetic lineages. It implements an extended CODEHOP strategy and evaluates thermodynamic properties of the oligonucleotide pairs." .
SCR:015715 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TFmodeller" ;
definition: "Web application that scans a library of protein-DNA complexes and builds comparative models of proteins bound to DNA. Its results include complex coordinates, schematic interface diagrams, interface alignments and DNA motifs." .
SCR:015717 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SomaDetection" ;
NIFRID:synonym "Soma Detection" ;
definition: "Source code for a machine learning method to detect somas on confocal microscopic images of the Drosophila brain. The method can be applied to the original raw images where the noises are not removed and the number of somas is unknown." .
SCR:015718 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RandomForest Package in R" ;
NIFRID:synonym "randomForest: Breiman and Cutler's Random Forests for Classification and Regression" ;
definition: "Software package for classification and regression based on a forest of trees using random inputs." .
SCR:015720 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Object-Image" ;
definition: "Image analysis software package that allows non-destructive image marking, input for further image processing, and marking the results of automatic measurements. Object-Image integrates measurements, macros, graphical objects and image names in a closed unit called 'object file' so that it reduces file clutter." .
SCR:015721 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Pediatric Centers of Excellence in Nephrology" ;
definition: "Portal with detailed information about various research centers that focus on pediatric medicine and nephrology. These centers are funded by NIDDK." .
SCR:015722 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NLREG" ;
NIFRID:synonym "NLREG: Nonlinear Regression and Curve Fitting",
"Nonlinear Regression and Curve Fitting" ;
definition: "Statistical analysis program that performs linear and nonlinear regression analysis as well as surface and curve fitting. NLREG can handle linear, polynomial, exponential, logistic, periodic, and general nonlinear functions." .
SCR:015723 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CHOPCHOP" ;
NIFRID:synonym "CHOPCHOP v2" ;
definition: "Web application for designing gRNAs for CRISPR/Cas9 experiments. It selects target sites for CRISPR/Cas9, CRISPR/Cpf1 or TALEN-directed mutagenesis." .
SCR:015724 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroExpresso" ;
definition: "Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression." .
SCR:015725 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dynamic Spatial Illuminator Software" ;
definition: "Software used in tandem with the Polygon 400 from Mightex systems to define areas of illumination, control light intensity and duration, and calibrate the device." .
SCR:015726 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Effective_connectivity" ;
NIFRID:synonym "Effective connectivity in vitro",
"Effective_connectivity in vitro" ;
definition: "Repository of matlab code for reconstruction and analysis of effective connectivity in vitro." .
SCR:015727 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bs-virus-finder" ;
rdfs:label "BSVF" ;
NIFRID:synonym "Bisulfite Sequencing Virus integration Finder",
"BSVF: Bisulfite Sequencing Virus integration Finder" ;
definition: "Software code for bisulfite sequencing virus integration. This finder is for directional libraries only and does not support PBAT and indirectional libraries." .
SCR:015729 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:oligo" ;
rdfs:label "oligo" ;
NIFRID:synonym "oligo package" ;
definition: "Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files)." .
SCR:015730 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hipposeq" ;
NIFRID:synonym "Hippocampus RNA-seq atlas" ;
definition: "Database of RNA-seq gene expression in hippocampal principal neurons. Hipposeq can analyze and visualize RNA-seq data for all excitatory cell populations in the hippocampus at multiple levels of granularity." .
SCR:015731 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Functional Network Connectivity (FNC)" ;
NIFRID:synonym "FNC Toolbox",
"Functional Network Connectivity Toolbox",
"GIFT toolbox" ;
NIFRID:abbrev "FNC" ;
definition: "Software toolbox which finds and displays temporal relations amongst components. This can help determine causal relations in the brain." .
SCR:015732 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Pennsylvania Diabetes Research Center" ;
NIFRID:abbrev "DRC" ;
definition: "NIDDK center that serves diabetes-oriented investigators from University of Pennsylvania as well as additional institutions from the mid-Atlantic region. The Penn DRC represents many basic science and clinical departments at Penn and the other institutions, and supports research in diabetes and obesity via Scientific Cores, a Pilot and Feasibility Grant Program, and a series of seminars, retreats, and other academic enrichment activities." .
SCR:015733 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Joslin Diabetes Center Molecular Phenotyping and Genotyping Core" ;
NIFRID:synonym "Molecular Phenotyping and Genotyping Core" ;
definition: "Core facility that supports the study of molecular mechanisms of disease by providing equipment, expertise, and services in molecular phenotyping, including nucleic acid sequence analyses, gene expression, and other \"omics\" analyses, which would be too specialized or costly for individual laboratories to perform independently. Formerly known as the Advanced Genomics and Genetics Core, the Molecular Phenotyping Core is newly-named in recognition of the expansion of its analytical capacities to reflect not only genetic and genomic analyses but also metabolic phenotyping." .
SCR:015734 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atlas of Human Cardiac Anatomy" ;
definition: "Database of cardiology information and ex-vivo human hearts. The atlas features information about specific regions of the heart as well as patient information from ex-vivo subjects." .
SCR:015735 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReMESH" ;
NIFRID:synonym "ReMESH - Edit and Repair Polygon Meshes" ;
definition: "3D editing software for manifold triangle meshes with advanced repairing features. It can post-process polygon meshes coming from digitization sessions and automatically filter out most of the typical flaws that models may have when coming from a 3D digitization session (degenerate triangles, isolated vertices, noise, topological artefacts, holes, ...)." .
SCR:015736 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Autodesk Meshmixer" ;
NIFRID:synonym "MeshMixer" ;
definition: "3D visualization software for working with triangle meshes. This software also can clean up 3D scans, design objects for 3D printing, and perform other 3D design-related functions." .
SCR:015737 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MareNostrum" ;
definition: "Operating software for a supercomputer in Spain. The software is maintained and updated by the Centro Nacional de Supercomputación (Barcelona Supercomputing Center) and is used for research projects on climate change, gravitational waves, a vaccination against AIDS, new radiation treatments to fight cancer, and other subjects." .
SCR:015739 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:off-spotter" ;
rdfs:label "Off-Spotter" ;
NIFRID:synonym "Off-spotter sgRNA algorithm",
"Off-Spotter: tool for CRISPR/Cas design" ;
definition: "Web application that identifies genomic instances for a given combination of gRNA(s), PAM, number of mismatches, and seed. This tool is limited to a single 1,000 nucleotides sequence or fewer than twenty CR-separated 20-mers." .
SCR:015740 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rotor-Gene Q Series Software" ;
NIFRID:synonym "Q-Rex Software",
"Rotor-Gene Q Software" ;
definition: "Operating software for QIAGEN's PCR cycler the Rotor-Gene Q. This software works with the instrument to streamline qPCR workflows and perform complex data analysis functions." .
SCR:015741 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CHIPS" ;
NIFRID:synonym "Cellular and Hemodynamic Image Processing Suite",
"CHIPS: an open-source Cellular and Hemodynamic Image Processing Suite" ;
definition: "Image processing software designed to analyse functional images of cells and blood vessels, primarily from two-photon microscopy. CHIPS is a set of classes and functions for MATLAB that integrates a number of algorithms, both novel and existing, into a complete image processing pipeline." .
SCR:015742 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent ChemStation Software" ;
NIFRID:synonym "ChemStation",
"ChemStation Software" ;
definition: """THIS RESOURCE HAS BEEN DISCONTINUED. Documented October 3, 2017.
Operational software created by Agilent Technologies to operate with its ChemStation hardware. The software can manage all parameters for instrument control, data acquisition
and evaluation, including integration, quantification and reporting.""" .
SCR:015743 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Range-based people tracker classifiers Benchmark Dataset" ;
NIFRID:synonym "Benchmark dataset for evaluation of range-based people tracker classifiers in mobile robots",
"Tracking Benchmark Data Set" ;
definition: "Dataset for performance evaluation of different approaches for detecting and tracking people by using lidar sensors. Information contained at the dataset is specially suitable to be used as training data for neural network-based classifiers." .
SCR:015744 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpiCoDyn" ;
definition: "Software for the analysis of multi-site neuronal spike signals. SPICODYN processes electrophysiological signals, focusing on spiking and bursting dynamics and functional-effective connectivity analysis." .
SCR:015745 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scrubber2" ;
NIFRID:synonym "Scrubber" ;
definition: "Software designed to clean-up biosensor data. It can zero and crop data, align injection times, correct for DMSO effects and fit binding curves and offrates." .
SCR:015746 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:xia2" ;
rdfs:label "xia2 pipeline" ;
definition: "Data processing software that performs X-ray diffraction data processing. It handles multi-pass, multi-wavelength data sets and supports remote access to synchrotron facilities." .
SCR:015747 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AIMLESS" ;
definition: "Data processing software for x-ray diffraction data. AIMLESS scales together multiple observations of reflections, and merges multiple observations into an average intensity." .
SCR:015748 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "autoPROC" ;
definition: "Data processing software for X-ray diffraction data. autoPROC is a set of tools and programs to automate steps involved in data processing, such as image analysis, integration, indexing, and determination." .
SCR:015749 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PISA" ;
NIFRID:synonym "PDBePISA",
"Proteins Interfaces Structures and Assemblies" ;
definition: "Web application for exploration of macromolecular interfaces. It calculates structural and chemical properties of macromolecular surfaces and interfaces, as well as quaternary structures (assemblies), their structural and chemical properties and dissociation patterns." .
SCR:015750 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iNPS" ;
NIFRID:synonym "iNPS: An improved algorithm for accurate nucleosome positioning from sequencing data" ;
definition: "Software for nucleosome detection that builds on the NPS software. Its application to T-cell activation data demonstrates a greater ability to facilitate detection of nucleosome repositioning, uncovering additional biological features underlying the activation process., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015751 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LSQMAN" ;
definition: "Software for alignment, comparison of macromolecules, and performing least-squares superpositioning of biomacromolecules. The program offers a superset of the LSQ- functionality inside O and removes some of the limitations and irritations of the LSQ-commands." .
SCR:015752 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CNVcaller" ;
definition: "Software for detecting the integrated copy number variation regions (CNVRs) using population sequencing data. The high-confidence CNVRs are discovered and refined by both individual and population criteria, and the result is a VCF format genotype file which can be used in GWAS/QLT research." .
SCR:015753 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Perseus" ;
definition: "Software that supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiplehypothesis testing." .
SCR:015754 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GrowthToolbox" ;
NIFRID:synonym "GFtbox" ;
definition: "Analysis software for analysis of finite elements and simulations of 3D shape changes in a tissue that result from patterns of growth. It works with Matlab to model biological growth of leaves, petals, and similar organs." .
SCR:015755 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MVGC Multivariate Granger Causality Matlab Toolbox" ;
NIFRID:synonym "MVGC Matlab Toolbox",
"MVGC Matlab® Toolbox" ;
NIFRID:abbrev "MVGC" ;
definition: "Matlab software toolkit designed to facilitate Granger-causal analysis with multivariate and possibly multi-trial time series data. Annotated demonstration scripts are available which may be used as templates to assist in this the toolbox's functions." .
SCR:015756 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Real time localization system for autonomous robots Benchmark Dataset" ;
NIFRID:synonym "Benchmark dataset for analysis of cyber-attacks to an indoor real time localization system for autonomous robots" ;
definition: "Dataset that can be used to analyze cyber-attacks to an indoor real time localization system for autonomous robots. Data have been gathered in an indoor mock-up apartment using an autonomous robot with an on-board Real Time Location System (RTLS)." .
SCR:015757 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Machine learning models cyber-attack detection Benchmark Dataset" ;
NIFRID:synonym "Benchmark dataset for training/testing of Machine Learning Models to detect cyber-attacks to an indoor real time localization system for autonomous robots" ;
definition: "Dataset that can be used to train and test Machine Learning Models to detect cyber-attacks to an indoor real time localization system for autonomous robots. The data was gathered in an indoor mock-up apartment using an autonomous robot with an on-board Real Time Location System (RTLS)." .
SCR:015758 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "doGlycans" ;
NIFRID:synonym "doGlycans - Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins Glycolipids and Carbohydrate Polymers for GROMACS" ;
definition: """Software toolkit for atomistic simulations to explore how carbohydrates function.
Applications include the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins.""" .
SCR:015759 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NAPR: Neuroanatomical Age Prediction using R" ;
NIFRID:synonym "Neuroanatomical Age Prediction using R" ;
NIFRID:abbrev "NAPR" ;
definition: "Cloud-based framework that allows users to estimate the age of individual subjects using cortical thickness maps derived from their own locally processed T1-weighted whole brain MRI scans. The provided age prediction models were trained using (i) relevance vector machines and (ii) Gaussian processes machine learning methods applied to cortical thickness surfaces obtained using Freesurfer v5.3." .
SCR:015760 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AQUARIUM" ;
NIFRID:synonym "The Aquarium Project" ;
definition: "Workflow software and methods language to improve the reproducibility of research results in the scientific community. The Aquarium Project aims to provide the means to specify, as precisely as possible, how to obtain a result using a combination of formal statements, informal descriptions, and photographs." .
SCR:015761 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Antha" ;
NIFRID:synonym "Synthace Antha" ;
definition: "Software language for methods to simplify protocols into reusable components that can be exchanged or removed to produce simple, reproducible, and scalable workflows. It allows users to develop, execute, and analyse biological experiments faster, while also introducing standardization and modularity to bioengineering." .
SCR:015762 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Opentrons | Opentrons Robot" ;
NIFRID:synonym "OT-One",
"OT-One S" ;
NIFRID:abbrev "OT" ;
definition: "Robot with open source software that allows for configurable robotic science. The robot's primary function is automating pipette functions in biological research in order to save time for research labs." .
SCR:015763 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "METAFLUIDICS" ;
NIFRID:synonym "METAFLUIDICS: Open Repository for Fluidic Systems" ;
definition: "Protocol repository for microfluidics experiments and chips. METAFLUIDICS provides a home for digital design files and other information necessary to reproduce or remix a microfluidic device." .
SCR:015764 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Autoprotocol" ;
NIFRID:synonym "BioIO" ;
definition: "Language standard for automating English language protocols. Autoprotocol specifies experimental protocols for biological research as a way to define experiments that could be run over the internet on remote robotic automation." .
SCR:015765 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HOMINID" ;
NIFRID:synonym "Hominid: host-microbiome interaction identification" ;
definition: "Software for identifying associations between host genetic variation and microbiome composition. HOMINID is a computational approach based on Lasso linear regression, that given host genetic variation and microbiome taxonomic composition data, identifies host SNPs that are correlated with microbial taxa abundances." .
SCR:015766 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SchizConnect" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 6,2026. Platform for mediation and integration of schizophrenia neuroimaging-related databases. It provides access to federated databases, novel mediation software, and large-scale data-sharing features." .
SCR:015769 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ABCD Study" ;
NIFRID:synonym "The Adolescent Brain Cognitive Development Study" ;
NIFRID:abbrev "ABCD" ;
definition: "Long-term study of brain development and child health in the United States. The study tracks subjects' biological and behavioral development through adolescence into young adulthood to determine how childhood experiences (such as sports, videogames, social media, unhealthy sleep patterns, and smoking) interact with each other and with a child’s changing biology to affect brain development and social, behavioral, academic, health, and other outcomes." .
SCR:015770 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneSys" ;
definition: "Imaging software that works with G:BOX Chemi and PXi imaging systems to automatically or manually capture images. GeneSys also includes a database containing information about applications such as fluorescence, chemiluminescence and chemifluorescence." .
SCR:015772 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sim3C" ;
definition: "Software for read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC). Sim3C's potential applications include addressing questions directed at the spatial organization of DNA in samples of eukaryotic tissue, single cells, and microbial communities." .
SCR:015773 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StreamPix" ;
definition: "Software for digital video camera recording that allows users to control and acquire dadta from multiple cameras simultaneously in a singleuser interface. StreamPix provides a complete management console for cameras, simplifying the setup, control and acquisition from any number and type of camera." .
SCR:015774 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:tfbs",
"OMICS_20526" ;
rdfs:label "TFBS" ;
definition: "Perl software for transcription factor binding site detection and analysis. It implements classes for the representation of objects encountered in analysis of these protein-binding sites." .
SCR:015775 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:genesis_microarray" ;
rdfs:label "Genesis" ;
NIFRID:synonym "Genesis: Cluster analysis of microarray data" ;
definition: "Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments." .
SCR:015776 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SOAPBarcode" ;
NIFRID:synonym "metabarcoding" ;
definition: "Software for metabarcoding of DNA. SOAPBarcode takes advantage of high throughput capacity of next-generation-sequencing (NGS) platforms and can characterize the biodiversity of large volumes of eukaryote samples." .
SCR:015777 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "kCSD-python" ;
NIFRID:synonym "kCSD inverse method",
"Kernel Current Source Density Method",
"kernel current source density method - python" ;
definition: "Source code for the Python implementation of the kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes." .
SCR:015778 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "funRiceGenes" ;
NIFRID:synonym "RICENCODE" ;
definition: "Dataset of functionally characterized rice genes and members of different gene families. The dataset was created by integrating data from available databases and reviewing publications of rice functional genomic studies." .
SCR:015779 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dat Project" ;
NIFRID:synonym "Dat",
"Dat Protocol",
"datproject.org",
"The Dat Project" ;
definition: "Community portal for a distributed data sharing platform and open protocol for building apps. The Dat Project imagines a web of commons created by global communities on open and secure protocols." .
SCR:015780 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BeatBox" ;
NIFRID:synonym "BeatBox—HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology." ;
definition: "Simulation environment that combines flexible script language user interface with computational tools in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level. It aims to include cell excitation, tissue/anatomy models, and stimulation protocols in BeatBox scripts so that simulation run either sequentially or in parallel (MPI) without re-compilation." .
SCR:015781 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Flowing Software 2.5.1 " ;
NIFRID:synonym "Flowing Software" ;
definition: "Software for flow cytometry data analysis. Flowing Software has many common analysis tools, such as dot plots, histograms, quadrants, statistics, overlay histograms etc." .
SCR:015784 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CluePedia Cytoscape plugin" ;
NIFRID:synonym "CluePedia: A ClueGO plugin",
"CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data" ;
definition: "Data analysis software and search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data and investigates interrelations within each pathway to reveal associations through gene/protein/miRNA enrichments." .
SCR:015785 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Analyst®TF Software" ;
NIFRID:synonym "Analyst",
"Analyst Software",
"Analyst TF",
"Analyst TF Software" ;
definition: "Acquisition software for mass spectrometry data from TripleTOF instrument(s). Analyst provides functionality for instrument control, data analysis, reporting, and audit trail." .
SCR:015786 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PeakView® Software" ;
NIFRID:synonym "PeakView",
"PeakView Software" ;
definition: "Software for spectral analysis and data interrogation to identify, superimpose, compare samples, and label peaks. PeakView Software supports mass spectrometer systems for qualitative review of LC-MS and MS/MS data as well as optional detectors such as UV and DAD." .
SCR:015787 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Proteobotics" ;
definition: "Private company offering a wide range of mass spectrometry-based proteomics data analysis services, including large-scale peptide and protein identification and quantitative proteomics. Notably, the company offers robust analysis of isobaric tagging and label-free quantification experiments, along with guidance in design of experiments and quality control issues." .
SCR:015788 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BlobFinder" ;
definition: "Software that can perform calculations on cells from fluorescence microscopy images. BlobFinder can perform two types of analysis: an average count analysis to count the number of fluorescent signals and nuclei in an image, and a single cell analysis to simulate a cytoplasm and assign each signal to a particular cell." .
SCR:015789 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bertec | Fully Instrumented Treadmill (FIT)" ;
NIFRID:abbrev "FIT" ;
definition: "Research standard treadmill that reduces gait lab space requirements and eliminates the limitations inherent in a traditional gait walkway. Researchers and clinicians can perform numerous testing conditions in a compact 2 meter space with variable incline and speed settings." .
SCR:015790 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "INCell Developer Toolbox" ;
NIFRID:synonym "IN Cell Developer Toolbox",
"IN Cell Developer Toolbox v1.6" ;
definition: "Image analysis software for developing new cellular assay analysis routines. This software provides a selection of advanced segmentation, pre-processing and post-postprocessing tools." .
SCR:015792 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ACCESSPOINT" ;
NIFRID:synonym "ACCESSPOINT Suite" ;
definition: "Software for viewing and analyzing medical DICOM images. The software suite includes a viewer, a report generating feature, and a DICOM network connection." .
SCR:015793 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NOTOCORD-hem" ;
definition: "Software that acquires, displays and analyzes physiological signals. It covers cardiovascular, respiratory and nervous system research areas and technologies from in vitro action potentials to live in vivo physiological signals monitoring with video and implantable telemetry." .
SCR:015794 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:circlncrnanet" ;
rdfs:label "circlncRNAnet" ;
definition: "Web application for mapping functional networks of long or circular forms of non-coding RNAs. It supports the uploading and processing of user-defined NGS-based gene expression matrix data." .
SCR:015795 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LI-COR Image Studio Software" ;
NIFRID:synonym "Image Studio™ Software",
"LI-COR Image Studio" ;
definition: "Image analysis software that acquires, analyzes, and archives research data without altering raw findings. It integrates data and changes how pixels are mapped to the screen for clearer display, rather than altering the pixels of the image data itself." .
SCR:015796 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adobe Audition" ;
NIFRID:synonym "Adobe Audition CC" ;
definition: "Software for sound analysis, audio editing, and audio recording. It features multitrack, waveform, and spectral display for creating, mixing, editing, and restoring audio content for research or non-research purposes." .
SCR:015797 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:vadir" ;
rdfs:label "VaDiR" ;
NIFRID:synonym "VaDiR: an integrated approach to Variant Detection in RNA" ;
definition: "Method for uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets." .
SCR:015798 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "McIlwain | Tissue Chopper" ;
NIFRID:synonym "Campden Instruments Inc. McIlwain Tissue Chopper" ;
definition: "Equipment for preparing samples of tissue for metabolic experiments that can also prepare small and irregular samples for biopsy or from small organs. It can perform rapid chopping of tissue without causing excessive stress damage." .
SCR:015799 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sigma | Millicell Cell Culture Inserts" ;
NIFRID:synonym "Millicell® Cell Culture Inserts" ;
definition: "Equipment that provides physical support for cell cultures. These cell culture inserts feature attachment and suspension cells that can access media from both their apical and basolateral sides." .
SCR:015800 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hypoxia Incubator Chamber" ;
definition: "Equipment that is a chamber for generation of a hypoxic environment for tissue culture. It is a self-contained and sealed chamber that fits inside existing laboratory incubators and utilizes a surface-type seal in which all portions of the O-ring are uniformly compressed." .
SCR:015801 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus IX-53 " ;
NIFRID:synonym "IX53",
"IX53 Inverted Microscope",
"Olympus IX53 Inverted Microscope" ;
NIFRID:abbrev "IX-53" ;
definition: "Equipment that is a microscope for routine inverted microscopic analysis. Its features include pre-centered phase contrast, relief contrast, and UIS2 DIC optics for visualization across all magnifications for both thin and thick specimens." .
SCR:015802 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Intracellular InCyt Software" ;
NIFRID:synonym "InCyt",
"InCyt Software",
"Intracellular Imaging Software" ;
definition: "Software toolkit that analyzes changes in fluorescence by using videocameras, photomultipliers, and photometry. It also combines the advantages of both imaging and photometry." .
SCR:015804 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoDrop 3300 Fluorospectrometer" ;
NIFRID:synonym "NanoDrop 3300",
"NanoDrop™ 3300",
"NanoDrop™ 3300 Fluorospectrometer" ;
definition: "Fluorospectrometer for broad spectrum fluorescence analysis. It uses as little as 1 μL of sample volume and lowers the mass detection limit more than an order of magnitude." .
SCR:015805 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | StepOnePlus Real-Time PCR System" ;
NIFRID:synonym "StepOnePlus",
"StepOnePlus™ Real-Time PCR System" ;
definition: "Equipment and software system that is a real-time thermal cycler for intuitive data analysis of polymerase chain reactions. It comes with analysis software, instrument control software, and a LED-based 4-color optical recording feature." .
SCR:015806 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sequence Detector System" ;
NIFRID:synonym "Sequence Detection System (SDS)",
"Sequence Detection System (SDS) Software" ;
NIFRID:abbrev "SDS" ;
definition: "Software for high-throughput gene expression and genotyping analysis for use with the Applied Biosystems® 7900HT Fast Real Time PCR System. It features automation software tools to fully automate high-throughput applications for gene expression and SNP genotyping." .
SCR:015808 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FP-3W" ;
NIFRID:synonym "FP-3W Fluidic Platform" ;
definition: "Equipment that is a re-sealable 3 well fluidic platform optimized for effective perfusion. It supports the dynamic testing of pancreatic islets for glucose-stimulated insulin secretion (GSIS) and concomitant live-cell imaging." .
SCR:015810 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CaTCh FISH Chip" ;
definition: "Equipment that is a magnetic micropore chip for rapid unbiased circulating tumor cell isolation and in situ RNA analysis. The chip detects tumor cells and can help doctors treat patients with these tumors." .
SCR:015811 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica HCS A" ;
NIFRID:synonym "High Content Screening Automation Leica HCS A",
"Leica High Content Screening Automation" ;
definition: "Software supporting Leica Microsystem microscopes by performing high content screening automation. The software combines the flexibility of a point-scanning confocal with the high speed of a camera-based widefield system to compensate for specimen drift, single object tracking and immersion fluid." .
SCR:015812 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "End Sequence Analysis ToolKit (ESAT)" ;
NIFRID:synonym "End Sequence Analysis ToolKit" ;
NIFRID:abbrev "ESAT" ;
definition: "Software for the analysis of short reads obtained from end-sequence RNA-seq. ESAT is designed for expression analysis of Digital expression (DGE) libraries that target transcript \"ends.\"" .
SCR:015813 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProphTools" ;
NIFRID:synonym "ProphTools: Heterogeneous network prioritization tools" ;
definition: "Source code for tools that perform general prioritization for heterogeneous biological networks. It prioritizes from a query network to the target network by means of a hybrid approach." .
SCR:015814 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:lordec" ;
rdfs:label "LoRDEC" ;
definition: "Software that performs hybrid error correction for long, PacBio reads. LoRDEC can correct insertions, deletions, and substitutions in PacBio reads." .
SCR:015815 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:larvalign" ;
rdfs:label "larvalign" ;
definition: "Software package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping." .
SCR:015816 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vevo 2100" ;
NIFRID:synonym "Vevo",
"Vevo 2100 System",
"Vevo® 2100 system" ;
definition: """Imaging software for high-frequency processing and analysis. Some of its features include
modes for blood flow quantification, single line acquisition, 3D-Mode imaging & volume analysis, nonlinear contrast imaging, and other image processing functions.""" .
SCR:015817 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuroscan Quik-Cap EEG Cap" ;
NIFRID:synonym "Quik-Cap",
"Quik-Cap EEG Cap" ;
definition: "Equipment that is a 10-20 configuration Lycra EEG cap. Quik-Caps are available in electrode configurations from 12 to 256 channels as well as in 5 different sizes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015818 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuroscan SynAmps RT 64-channel Amplifier" ;
definition: "Equipment that is an EEG signal amplifier for 64-channel montages. It is suitable for recording data from high sampling rate (20,000 Hz) Auditory Brain Stem recordings and Spike Spindles to true DC recordings of CNV and P300." .
SCR:015819 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Time in Motor Games (Tiempo en Juegos Motores)" ;
NIFRID:synonym "Tiempo en Juegos Motores",
"Time in Motor Games" ;
definition: "Web application that records the time devoted to each of the actions that are performed while playing motor games or active games. This recording system has applications in physical activity research and physical education." .
SCR:015820 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_017266" ;
rdfs:label "BICCN" ;
NIFRID:synonym "BICCN 2.0",
"BRAIN Initiative Cell Census Network",
"BRAIN Initiative Cell Census Network (BICCN)" ;
definition: "Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains." .
SCR:015821 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "G6GFINDR" ;
NIFRID:synonym "G6GFINDR System" ;
definition: "Query-based web application that helps users find bioinformatics and artificial intelligence (AI) software. G6GFINDR is powered by \"semantic annotation\" vs. keyword search, which take advantage of semantic web graph technology." .
SCR:015822 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DiPDE" ;
NIFRID:synonym "dipde",
"DiPDE (Integro-partial differential equation with displacement)" ;
definition: "Simulation platform for numerically solving the time evolution of coupled networks of neuronal populations. DiPDE can facilitate the fast exploration of mesoscale (population-level) network topologies, where large populations of neurons are treated as homogeneous with random fine-scale connectivity." .
SCR:015823 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JASP" ;
definition: "Statistics software that performs common frequentist analyses and Bayesian analyses. It conducts ANOVA, linear regression, and correlation, among other statistical tests." .
SCR:015824 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WormSizer" ;
definition: "Software plug-in for ImageJ that allows users to determine the size of worms. It can calculate volume, surface area, and other parameters of worm specimens." .
SCR:015825 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioVoxxel Toolbox" ;
NIFRID:synonym "BioVoxxel",
"BioVoxxel Toolbox (ImageJ/Fiji)" ;
definition: "Software toolkit for analyzing tool for microscopic images. It contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis." .
SCR:015826 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FiberApp" ;
NIFRID:synonym "and Fibrous Objects",
"Biomacromolecules",
"FiberApp: An Open-Source Software for Tracking and Analyzing Polymers",
"Filaments" ;
definition: "Software for tracking and analysis based on algorithms describing structural and topological features of fiber-like objects. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects." .
SCR:015827 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:UALCAN" ;
rdfs:label "UALCAN" ;
definition: "Web application and database for analyzing cancer transcriptome data. It also has applications is facilitating tumor subgroup gene expression and survival analyses." .
SCR:015828 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCODE" ;
definition: "Software that clusters a given network based on topology to find densely connected regions. It can be used to find protein complexes and parts of pathways in protein-protein interaction networks or protein families in protein similarity networks." .
SCR:015846 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BECA" ;
NIFRID:synonym "BECA - Brain Explorer for Connectome Analysis",
"Brain Explorer for Connectome Analysis (BECA)" ;
definition: "Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version." .
SCR:015847 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chemoproteomic identification and therapeutic validation of proteins of metabolic significance" ;
definition: "Database portal for a project that aims to discover and characterize new molecular pathways that can be targeted pharmacologically to revert obesity-linked adipocyte defects that drive systemic insulin resistance and type 2 diabetes. It works to identify in tandem physiologically-relevant proteins and chemical tools in order to expedite their functional annotation and therapeutic validation." .
SCR:015848 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "p-[(123)I]iodo-L-phenylalanine (IPA)-SPECT template in MNI-coordinates" ;
NIFRID:synonym "p-[(123)I]iodo-L-phenylalanine( IPA)-SPECT template" ;
definition: "Template for p-[(123)I]iodo-L-phenylalanine( IPA)-SPECT in MNI-coordinates. This template was obtained from 12 human subjects in an NITRC study." .
SCR:015849 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CalR" ;
NIFRID:synonym "A Web Application for Indirect Calorimetry Analysis" ;
definition: "A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates." .
SCR:015850 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Alliance of Genome Resources " ;
NIFRID:synonym "The Alliance" ;
definition: "Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN)." .
SCR:015851 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nPOD TCR/BCR Search" ;
NIFRID:synonym "nPOD TCRBCR Search",
"TCR/BCR Search",
"TCRBCR Search" ;
definition: "Database of sequence data generated from high-throughput immunosequencing of the TCR beta chain (TRB) and B cell receptor (BCR) immunoglobulin heavy chain (IGH). This data comes from cells from NPOD donors." .
SCR:015852 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_06933" ;
rdfs:label "ABACAS" ;
NIFRID:synonym "ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences",
"Algorithm Based Automatic Contiguation of Assembled Sequences",
"Algorithm Based Automatic Contiguation of Assembled Sequences (ABACAS)" ;
definition: "Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account." .
SCR:015854 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ARCHER" ;
definition: "Supercomputing service located in the UK for researchers who study problems with a global impact. It is part of the PRACE initiative giving leading scientific users access to a European pool of supercomputers." .
SCR:015855 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Quantum Biology Institute" ;
definition: "Institute that provides resources and researches the concepts and mechanisms which underlie the complexities of biology. In particular, it incorporates concepts in physics and mathematics to resolve, unravel, and explain complex biological mechanisms and conditions." .
SCR:015856 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford Diabetes Research Center " ;
definition: "University-affiliated center that promotes research in diabetes and related metabolic and endocrine disorders at Stanford University." .
SCR:015857 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UltraMegaSort 2000" ;
NIFRID:synonym "UltraMegaSort" ;
definition: "Matlab-based routines for the detection and clustering of putative single units from a multi-unit time series, along with quality metrics. This sofwtare was developed by the David Kleinfeld Laboratory at UC San Diego." .
SCR:015858 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Elastica2D" ;
definition: "Software for a 2D elastic beam model that can be used to model quasistatic bending of the vibrissa to compute forces and bending moments at the base. Elastica2D is part of the Digital Rat software project that that aims to enable morphologically and mechanically accurate modelling of the rat head and vibrissal (whisker) array." .
SCR:015859 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clinical Trials in Organ Transplantation (CTOT) " ;
NIFRID:synonym "Clinical Trials in Organ Transplantation" ;
NIFRID:abbrev "CTOT" ;
definition: "Project portal for a cooperative research program to improve short and long-term graft and patient survival. CTOT is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for transplant recipients." .
SCR:015860 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clinical Trials in Organ Transplantation in Children (CTOT-C)" ;
NIFRID:synonym "Clinical Trials in Organ Transplantation in Children",
"NIAID Clinical Trials in Organ Transplantation in Children",
"NIAID CTOT-C" ;
NIFRID:abbrev "CTOT-C" ;
definition: "Project portal for a cooperative research program sponsored by the National Institute of Allergy and Infectious Diseases (NIAID). CTOT-C is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for pediatric heart, lung, or kidney transplant recipients." .
SCR:015861 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Growing Gene and Cell Therapy Cooperative" ;
NIFRID:synonym "GGACT Cooperative" ;
NIFRID:abbrev "GGACT" ;
definition: "Project portal for a collaboration between Boston Children’s Hospital, Cincinnati Children’s Hospital Medical Center, and the University of California Los Angeles with funding from NIH NCATS. It aims to support investigators to rapidly translate complex gene and cell therapies to early phase, investigator-initiated clinical trials." .
SCR:015862 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Preventing Early Renal Loss in Diabetes (PERL)" ;
NIFRID:synonym "Preventing Early Renal Loss in Diabetes" ;
NIFRID:abbrev "PERL" ;
definition: "PERL is a clinical trial for people with type 1 diabetes who have early signs of kidney problems. Its goal is to test a new way to reduce loss of kidney function using a safe and inexpensive medicine." .
SCR:015864 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012439" ;
rdfs:label "G-Node Data Infrastructure Services" ;
NIFRID:synonym "GIN: Modern Research Data Management for Neuroscience" ;
NIFRID:abbrev "GIN" ;
definition: "Data services that provides a platform for comprehensive and reproducible management and sharing of neuroscience data. Building on well established versioning technology, GIN offers the power of a web based repository management service combined with a distributed file storage." .
SCR:015865 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "M-Track" ;
definition: "Source code that allows users to simultaneously track the movement of individual paws during spontaneous grooming episodes and walking in multiple freely-behaving mice/rats. This toolbox provides a simple platform to perform trajectory analysis of paw movement." .
SCR:015866 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:hybrid-denovo" ;
rdfs:label "Hybrid-denovo" ;
definition: "Software for a de novo OTU-picking pipeline integrating single- and paired-end 16S sequence tags. It is designed to take Illumina paired-end sequencing reads as input and output the OTU BIOM table, together with their representative sequences and a phylogenetic tree of OTUs." .
SCR:015867 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ximbio" ;
NIFRID:synonym "Ximbio Biobank" ;
definition: "Biobank for reagents such as antibodies, mice, and cell lines. Ximbio aims to maximise scientists' commercial opportunities and encourage the sharing of tools and information among the research community." .
SCR:015868 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IMACEL" ;
definition: "Artificial intelligence image analysis platform that facilitates life science research. It offers data analysis, processing functions, and security features to accelerate research productivity." .
SCR:015869 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OSort" ;
NIFRID:synonym "OSort: spike sorting package" ;
definition: "Framework for spike sorting that includes tools for pre-processing, spike detection, spike sorting, and sorting quality evaluation. It is principally designed for sorting of single-wire microwire recordings in humans, but is being used for other types of recordings as well." .
SCR:015870 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_12777" ;
rdfs:label "Short Read Sequence Typing for Bacterial Pathogens" ;
NIFRID:synonym "Short Read Sequence Typing v2",
"SRST2: Short Read Sequence Typing for Bacterial Pathogens" ;
NIFRID:abbrev "SRST2" ;
definition: "Software that is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes." .
SCR:015871 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "braincog" ;
definition: "Software package to elucidate complex interactions between subsets of neuroanatomical features and subsets of cognitive features. briancog specializes in differential correlation analysis." .
SCR:015872 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCSF ChimeraX" ;
NIFRID:synonym "ChimeraX" ;
definition: "Software for 3D/4D image reconstruction. UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera." .
SCR:015873 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:niftypet" ;
rdfs:label "NiftyPET" ;
definition: "Python software package that offers quantitative PET image reconstruction and analysis with high accuracy and precision. It is written in CUDA C and embedded in Python C extensions." .
SCR:015874 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COMPASS" ;
NIFRID:synonym "ICACOMPASS" ;
definition: "Algorithm for MATLAB and the EEGLAB toolbox that enables the automatic detection of independent components from an ICA that represent event-related brain potentials. It performs automatic Independent Component (IC) selection with respect to the contributions of the ICs to a certain ERP." .
SCR:015875 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CMake" ;
definition: "Software toolkit designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files, and generate native makefiles and workspaces that can be used in the compiler environment of your choice." .
SCR:015876 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RIPPLELAB" ;
NIFRID:synonym "RIPPLELAB Multi Analysis EEG Project" ;
definition: "Source code for processing continuous local field potentials (LFP). The interface implements different documented algorithms for HFO detection, and provides several tools for signal visualization and manipulation." .
SCR:015877 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012181" ;
rdfs:label "Brain-CODE" ;
definition: "Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders." .
SCR:015878 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ASaiM" ;
NIFRID:synonym "ASaiM (Auvergne Sequence analysis of intestinal Microbiota)",
"ASaiM: Auvergne Sequence analysis of intestinal Microbiota",
"Auvergne Sequence analysis of intestinal Microbiota" ;
definition: "Software that analyzes intestinal microbiota data. This environment is composed of a framework to process and analyze microbiota data from raw sequences to taxonomic and functional assignations." .
SCR:015879 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:poretools" ;
rdfs:label "Poretools" ;
definition: "Software toolkit for analyzing nanopore sequence data." .
SCR:015880 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:canu",
"OMICS_14592" ;
rdfs:label "Canu" ;
definition: "Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION)." .
SCR:015881 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:swisstree" ;
rdfs:label "SwissTree" ;
definition: "Project that aims to provide a collection of Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure." .
SCR:015882 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaNetX" ;
NIFRID:synonym "MetaNetX: Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks",
"MNXref" ;
definition: "Web application to perform automated model construction and genome annotation for large-scale metabolic networks. Platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways." .
SCR:015883 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Monogenic Diabetes Registry" ;
NIFRID:synonym "MODY Registry",
"Neonatal Diabetes Registry" ;
NIFRID:abbrev "MDR",
"MODYR",
"NDR" ;
definition: "Research project that aims to learn more about the number of people who have monogenic diabetes, why and how it happens, and how best to treat it. Any adult or child with a known genetic cause of diabetes may join the MODY Registry." .
SCR:015884 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NBLAST" ;
definition: "Algorithm for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry and works by decomposing a query and target neuron into short segments; matched segment pairs are scored using a log-likelihood ratio scoring matrix empirically defined by the statistics of real matches and non-matches." .
SCR:015885 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Glycohemoglobin Standardization Program" ;
NIFRID:synonym "NGSP: National Glycohemoglobin Standardization Program" ;
NIFRID:abbrev "NGSP" ;
definition: "Project that aims to standardize Hemoglobin A1c test results to those of the Diabetes Control and Complications Trial (DCCT) and United Kingdom Prospective Diabetes Study (UKPDS) which established the direct relationships between HbA1c levels and outcome risks in patients with diabetes." .
SCR:015886 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chronic Prostatitis Collaborative Research Network Clinical Trial- Alfuzosin " ;
NIFRID:synonym "Efficacy & Safety Study of Pregabalin to Treat Chronic Prostatitis/Chronic Pelvic Pain Syndrome (CP/CPPS) (CPCRN RCT#2)" ;
definition: "Clinical trial by the Chronic Prostatitis Collaborative Research Network (CPCRN chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS)) that was established to conduct randomized clinical trials of promising therapies for this syndrome. In response to the findings of previous trials, the CPCRN conducted a multicenter, randomized, placebo-controlled trial of alfuzosin to determine whether the symptoms CP/CPPS could be reduced in men who had recently received a diagnosis of CP/CPPS and who had not previously been treated with this class of drug." .
SCR:015887 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eHistology" ;
definition: "Image repository that allows researchers to interactively explore a collection of cellular-resolution colour histology images detailing mouse development. The original histological sections have been re-digitised at high resolution, in colour and in collaboration with Elsevier, the eHistology Atlas provides the annotations as presented in the original printed version." .
SCR:015888 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Braineac" ;
definition: "Database for the UK Brain Expression Consortium (UKBEC) dataset that comprises of brains from individuals free of neurodegenerative disorders. The aim of Braineac is to release to the scientific community a valid instrument to investigate the genes and SNPs associated with neurological disorders." .
SCR:015889 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "UK Brain Expression Consortium" ;
NIFRID:abbrev "UKBEC" ;
definition: "Consortium studying the regulation and alternative splicing of gene expression in multiple tissues from human brains. The UKBEC dataset comprises of brains from individuals free of neurodegenerative disorders." .
SCR:015890 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ICN_Atlas" ;
definition: "Software toolbox for SPM that is aimed at facilitating the interpretation of fMRI data in the context of intrinsic connectivity networks (ICNs) by describing fMRI maps in function-oriented, objective and quantitative way using a set of 15 metrics conceived to quantify the degree of ‘engagement’ of ICNs for any given statistical map of interest. Besides the functionally-derived atlasing capabilities (based on the BrainMap ICN data) the toolbox provides anatomy-based atlasing (based on the JHU and Brainnetome Atlas data), as well." .
SCR:015891 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pattern Component Modelling Toolbox" ;
NIFRID:synonym "Pattern component modeling (PCM)",
"Pattern Component Modeling toolbox for multivariate analysis",
"PCM Toolbox" ;
NIFRID:abbrev "PCM" ;
definition: "Software for a Bayesian approach for evaluating representational models that specify how complex patterns of neural activity relate to visual stimuli, motor actions, or abstract thoughts. PCM evaluates the ability of models to predict novel brain activity patterns and integrates over all possible activity profiles and computes the marginal likelihood of the data under the activity profile distribution specified by the representational model." .
SCR:015892 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:phyd3" ;
rdfs:label "PhyD3" ;
definition: "Web application that is a phylogenetic tree viewer based on d3.js. It was developed as an alternative to Archaeopteryx inspired by d3.phylogram.js." .
SCR:015896 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BOINC - Berkeley Open Infrastructure for Network Computing" ;
NIFRID:synonym "Berkeley Open Infrastructure for Network Computing",
"Berkeley Open Infrastructure for Network Computing (BOINC)" ;
NIFRID:abbrev "BOINC" ;
definition: "Software to orchestrate the distribution of computational work units (data and applications) to volunteers and have results collected back. It supports diverse applications, including those with large storage or communication requirements, and addresses unsolved issues in biology, medicine, physics, astronomy and computer science." .
SCR:015897 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Albacore" ;
definition: "Data processing basecaller for the Oxford Nanopore sequencer that identifies DNA sequences directly from raw data. It enhances accuracy of the single-read sequence data, contributing to high consensus accuracy for nanopore sequence data." .
SCR:015898 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Natural Stress Relief" ;
NIFRID:abbrev "NSR" ;
definition: "Organization that provides instructions for and research on the Natural Stress Relief (NSR) meditation method." .
SCR:015900 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_18668" ;
rdfs:label "RNAcompete" ;
NIFRID:synonym "RNAcompete Tool" ;
definition: "Method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. RNAcompete identifies expected and previously unknown RNA binding preferences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015901 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vanderbilt Digestive Disease Research Center Biostatistics Administrative Core" ;
definition: "Core facility for the Vanderbilt Digestive Disease Research Center." .
SCR:015902 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Emory Epithelial Pathobiology Research Development Center" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th, 2023. Center for pathobiology research development." .
SCR:015903 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Michigan Kidney Translational Core Center" ;
NIFRID:synonym "George M. O'Brien Michigan Kidney Translational Core Center" ;
definition: "Center for kidney research at the University of Michigan to assist investigators and clinicians worldwide in kidney disease research. Core services are available to Center researchers to promote their basic, translational and clinical kidney disease research." .
SCR:015904 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Emory Epithelial Pathobiology Research Development Center Cell Culture Core" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th, 2023. Core facility for the Emory Epithelial Pathobiology Research Development Center." .
SCR:015905 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_015923" ;
rdfs:label "MMPC Vanderbilt University School of Medicine Body Weight Regulation Core" ;
NIFRID:synonym "Body Weight Regulation Core" ;
definition: "Core facility for MMPC Vanderbilt University School of Medicine for studying impact of genetic, surgical, dietary and pharmacologic manipulations on body weight regulation. Core provides measurement of food intake, energy expenditure, and behavioral factors. Energy balance studies are performed in mouse home cage to minimize stress. Mitochondrial function is assessed on permeabilized tissues, isolated cells, or isolated mitochondria. Mouse models of bariatric surgery have been developed and studied extensively." .
SCR:015906 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Emory Epithelial Pathobiology Research Development Center Gene Expression Analysis Core" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Core facility for the Emory Epithelial Pathobiology Research Development Center." .
SCR:015908 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_015925" ;
rdfs:label "Cystic Fibrosis Center - University of Pennsylvania Animal Models Core" ;
definition: "Core facility for the Cystic Fibrosis Center - University of Pennsylvania." .
SCR:015909 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Emory Epithelial Pathobiology Research Development Center Image Analysis Core" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Core facility for the Emory Epithelial Pathobiology Research Development Center." .
SCR:015910 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_015927" ;
rdfs:label "University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center Molecular and Cellular Analytical Core Facility" ;
definition: "Core facility for University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center. Supports investigation of human and non-human metabolism from cellular/molecular perspective. Investigation areas include Lipidomics and mass spectrometry, Bioinformatic analysis of RNAseq data, Mitochondrial respiration." .
SCR:015911 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MMPC-Vanderbilt University School of Medicine Microvascular Complications Core" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 6th,2023. Core facility for the MMPC-Vanderbilt University School of Medicine." .
SCR:015912 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_015926" ;
rdfs:label "University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center Clinical Intervention and Translation Core Facility" ;
definition: "Core facility for the University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center. Core provides NORC members assistance with clinical research studies involving modification of body weight." .
SCR:015913 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_015928" ;
rdfs:label "University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center Enrichment Program Core Facility" ;
definition: "Core facility for the University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center. Promotes research in obesity and nutrition on campus by coalescing team science ventures, fostering development of trainees that are well positioned for interdisciplinary collaboration, and leveraging resources from existing institutional programs to spawn interdisciplinary team science and translational outreach programs related to nutrition and obesity." .
SCR:015914 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_015924" ;
rdfs:label "University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center Energy Balance Assessment Core Facility" ;
NIFRID:synonym "Energy Balance Core" ;
NIFRID:abbrev "EBAC" ;
definition: "Core facility for University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center. Provides support for measurement of components of energy balance and for assessing consequences of alterations in energy balance. Provides expertise and support for obesity and nutrition related basic, clinical, translational, and transdisciplinary research for NORC investigators and its affiliates. Provides services to assess body composition, bone density, physical fitness, and energy expenditure values in research participants." .
SCR:015915 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vanderbilt Digestive Disease Research Center Biostatistics Component Core" ;
NIFRID:synonym "Vanderbilt Digestive Disease Research Center Biostatistics Administrative Core",
"Vanderbilt Digestive Disease Research Center Biostatistics Component of the Administrative Core" ;
definition: "Core facility for the Vanderbilt Digestive Disease Research Center. Provides professional expertise in biostatistics for all DDRC projects, investigators, and participants. Functions provided by this component include development of experimental designs, power analysis, and sample size computation; data acquisition and database development; statistical analysis and interpretation of findings; collaboration on presentation of results; education in biostatistical methods; and development of tools with application to clinical trials and laboratory research." .
SCR:015916 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Emory Epithelial Pathobiology Research Development Center" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Center for pathobiology research development." .
SCR:015917 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Emory Epithelial Pathobiology Research Development Center Image Analysis Core" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th, 2023. Core facility for the Emory Epithelial Pathobiology Research Development Center." .
SCR:015919 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Emory Epithelial Pathobiology Research Development Center Cell Culture Core" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th, 2023. Core facility for the Emory Epithelial Pathobiology Research Development Center." .
SCR:015920 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Emory Epithelial Pathobiology Research Development Center Gene Expression Analysis Core" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Core facility for the Emory Epithelial Pathobiology Research Development Center." .
SCR:015921 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MMPC - Vanderbilt University School of Medicine Microvascular Complications Core" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 6th,2023. Core facility for the MMPC-Vanderbilt University School of Medicine." .
SCR:015929 a owl:NamedIndividual ;
rdfs:label "Marion Bessin Liver Research Center Administrative and Supporting Services" ;
definition: "Core facility for the Marion Bessin Liver Research Center." .
SCR:015932 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cross-species scaffolding" ;
NIFRID:synonym "cross-species-scaffolding" ;
definition: "Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Super-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references." .
SCR:015934 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fast-SG" ;
NIFRID:synonym "Fast SG" ;
definition: "Algorithm for alignment-free scaffolding graph construction from short or long reads. It allows the reuse of efficient algorithms designed for short read data and permits the definition of novel modular hybrid assembly pipelines." .
SCR:015935 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CRISPOR" ;
definition: "Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track." .
SCR:015936 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BIAevaluation Software" ;
NIFRID:synonym "BIAevaluation",
"BIAevaluation Software Kit" ;
definition: """Analysis software for life science data. This software package is for presentation and
evaluation of sensorgram data from real-time BIA analyses.""" .
SCR:015937 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Airtrack" ;
NIFRID:synonym "Air-Track" ;
definition: "Software for a head-fixed behavioral environment that uses a lightweight physical maze floating on an air table that moves around the animal’s body under the direct control of the animal itself, solving many problems associated with using virtual reality for head-fixed animals. It works with recording equipment (e.g., 2-photon imaging, patch recordings, etc.) that frequently requires head fixation." .
SCR:015938 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenBehavior" ;
NIFRID:abbrev "OB" ;
definition: "Repository of open source tools for behavioral neuroscience research. OpenBehavior features hardware (tools, devices, apparatuses), as well as software for data acquisition and analysis and for the investigation of animal behavior and cognition. Dedicated to accelerating research through promotion of collaboration and open source projects." .
SCR:015939 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MicrobeTracker" ;
definition: "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. Software for bacterial microscopy image analysis. It is designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them." .
SCR:015940 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LiGeA" ;
NIFRID:synonym "cancer cell LInes GEne-fusions portAl",
"LiGeA - a comprehensive database of human gene fusion events",
"LiGeA Portal",
"LiGeA: a comprehensive database of human gene fusion events" ;
definition: "Portal provides an easy access to a comprehensive database designed for storing, displaying and annotating gene fusion events detected from NGS data. It can query a database of somatic fusion genes events predicted and annotated starting from paired-end RNA-seq data." .
SCR:015941 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Piggy" ;
definition: "Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary)." .
SCR:015942 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Feeding Experimentation Device project" ;
NIFRID:synonym "FED1",
"FED2",
"Feeding Experimentation Device",
"Feeding Experimentation Device system" ;
NIFRID:abbrev "FED" ;
definition: "Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging." .
SCR:015943 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bpod" ;
definition: "Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller." .
SCR:015944 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "National Gene Vector Laboratories" ;
NIFRID:abbrev "NGVL" ;
definition: "The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies." .
SCR:015945 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gblocks" ;
definition: "Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015946 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:treedyn" ;
rdfs:label "TreeDyn" ;
definition: "Visualization software that links unique leaf labels to lists of variables/values pairs of annotations (meta-information), independently of the tree topologies, remaining fully compatible with the basic newick format. These relationships are used by dynamic graphics operators, information visualization methods like Projection, Localization, Labelization, Reflection allowing an interaction from annotations to trees, from trees to annotations and from trees to trees through annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015947 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhotoCaptMw" ;
definition: "Software tool for image processing and analysis." .
SCR:015950 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chiron" ;
definition: "Software basecaller for Oxford Nanopore Technologies' sequencers." .
SCR:015951 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "loadBAM2ge_db" ;
NIFRID:synonym "loadBAM2ge_db (PE)" ;
definition: "Software pipeline that visualizes mapping results (in BAM format) on Genome Explorer." .
SCR:015952 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCDE" ;
definition: "Software package that implements a set of statistical methods for analyzing single-cell RNA-seq data, including differential expression analysis (Kharchenko et al.) and pathway and geneset overdispersion analysis (Fan et al.)" .
SCR:015953 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:sc3" ;
rdfs:label "SC3" ;
NIFRID:synonym "SC3 package",
"Single-Cell Consensus Clustering" ;
definition: "Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients." .
SCR:015954 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:scater" ;
rdfs:label "scater" ;
NIFRID:synonym "scater (single-cell analysis toolkit for gene expression data in R)" ;
definition: "Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data." .
SCR:015955 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LASERduo" ;
definition: "Laser equipment that contains two wavelengths on the same handset, Red Laser and Infrared Laser. Currently Lasertherapy has acted in the different dental specialties as an indispensable technological tool. The use of this Photonic Therapy, associated to the most different dental procedures, provides greater comfort to the patients and greater reliability in the work of the dental surgeon." .
SCR:015956 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRTool" ;
definition: "Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12." .
SCR:015957 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroImage Field-of-View Normalization Tool" ;
NIFRID:synonym "Normalize FOV",
"normalizefov" ;
definition: "FSoftware for field-of-view normalization to minimize mismatch in different subjects' images. It aids that streamline analysis of large-scale brain MRI datasets." .
SCR:015959 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microm HM450 " ;
definition: "Freezing microtome. Microm Laborgerate GmbH. Equipment for obtaining thick slices from small organs." .
SCR:015961 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProLong. Fluoromount G Mounting Medium" ;
definition: "Thermo Fisher Scientific. Catalog number. P36934. ProLong™ Gold Antifade Mountant. Cellular Imaging" .
SCR:015962 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Periflux system 5000" ;
definition: "Perimed. Monitor blood circulation in real-time. Range of probes for different flaps. Sensitive laser Doppler technique" .
SCR:015963 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LSM 800" ;
rdfs:label "Zeiss | LSM 800 with Airyscan Microscope" ;
definition: "Compact confocal microscope with highly sensitive GaAsP detection and fast linear scanning. The airyscan system allows capture images with high sensitivity and superresolution compared with conventional confocal microscope., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015964 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Marmoset Brain Connectivity Atlas" ;
NIFRID:synonym "Marmoset Monkey Cerebral Cortex Connectivity Atlas" ;
definition: "Brain connectivity atlas to create systematic, digital repository for data on connections between different cortical areas, in primate species. Data repository for connections between different cortical areas in marmoset monkeys. Allows access to data set and enables other interpretations of data, in light of future evolution of knowledge about marmoset cortex." .
SCR:015965 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19721" ;
rdfs:label "Aegean" ;
NIFRID:synonym "Aegean Toolkit",
"AEGeAn: analysis and evaluation of genome annotations" ;
definition: "Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more." .
SCR:015966 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aevol" ;
definition: "Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences)." .
SCR:015967 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_08280" ;
rdfs:label "Alien-hunter" ;
definition: "Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer." .
SCR:015968 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:alter",
"OMICS_19786" ;
rdfs:label "ALTER" ;
NIFRID:synonym "ALignment Transformation EnviRonment",
"ALTER: ALignment Transformation EnviRonment" ;
definition: "Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats." .
SCR:015969 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19787" ;
rdfs:label "AMAP" ;
NIFRID:synonym "amap-align" ;
definition: "Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method." .
SCR:015970 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UMMPerfusion" ;
NIFRID:synonym "OsiriX plugin" ;
definition: "Analysis software for dynamic contrast enhanced magnetic resonance images with implementation of a pixel-by-pixel deconvolution approach. It quantifies T1-weighted contrast-enhanced dynamic MR imaging (DCE-MRI) perfusion data as an OsiriX plug-in." .
SCR:015971 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:andi",
"OMICS_09287" ;
rdfs:label "andi" ;
definition: "Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes." .
SCR:015972 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Anfo" ;
NIFRID:synonym "Anfo Short Read Aligner/Mapper" ;
definition: "Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle." .
SCR:015974 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_04227" ;
rdfs:label "Aragorn" ;
definition: "Software that detects tRNA genes and tmRNA genes in nucleotide sequences. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base‐paired cloverleaf., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015975 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_09783" ;
rdfs:label "Arden" ;
NIFRID:synonym "ARDEN: Artificial Reference Driven Estimation of false positives in NGS data",
"Artificial Reference Driven Estimation of false positives in NGS data" ;
definition: "Software for specificity control of read alignments using an artificial reference. It estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation." .
SCR:015976 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_17327" ;
rdfs:label "Ariba" ;
definition: "Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling." .
SCR:015977 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "P300-Dataset" ;
NIFRID:synonym "BCI P300 Speller Kaggle Dataset for Healthy subjects",
"P300 Dataset",
"P300 Dataset for Healthy subjects",
"P300 dataset of 8 healthy subjects" ;
definition: """Dataset replicating the experiment done on BNCI-HORIZON 008-2014 dataset.
BCI P300 Speller Kaggle Dataset for Healthy subjects""" .
SCR:015978 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Decision Decoding Toolbox" ;
NIFRID:synonym "DDTBOX: Decision Decoding Toolbox",
"The Decision Decoding Toolbox (DDTBOX)" ;
NIFRID:abbrev "DDTBOX" ;
definition: "Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB." .
SCR:015980 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:atac",
"OMICS_29044" ;
rdfs:label "Atac" ;
definition: "Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences." .
SCR:015982 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Autogrid" ;
NIFRID:synonym "Autogrid toolkit",
"Autogrid: automated grid" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock." .
SCR:015983 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:avogadro",
"OMICS_04967" ;
rdfs:label "Avogadro" ;
definition: "Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas." .
SCR:015984 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19788" ;
rdfs:label "Axe" ;
NIFRID:synonym "Axe-demultiplexer" ;
definition: "Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples." .
SCR:015985 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11740" ;
rdfs:label "Baitfisher" ;
definition: "Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments." .
SCR:015986 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_05049" ;
rdfs:label "BALLView" ;
NIFRID:synonym "BALL:Biochemical Algorithms Library",
"Biochemical Algorithms Library" ;
definition: "Software for molecular visualization and modeling. It provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features." .
SCR:015987 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bamtools",
"OMICS_11315" ;
rdfs:label "Bamtools" ;
NIFRID:synonym "API:Application Programming Interface",
"BAM:Binary Alignment Map",
"SAM:Sequence Alignment Map" ;
definition: "Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies." .
SCR:015989 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Belvu" ;
definition: "Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments." .
SCR:015991 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14099" ;
rdfs:label "Eagle" ;
NIFRID:synonym "Bio-eagle",
"Eagle1",
"Eagle2" ;
definition: "Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods." .
SCR:015993 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bio-tradis",
"OMICS_11083" ;
rdfs:label "Bio-tradis" ;
NIFRID:abbrev "TraDIS:Transposon Directed Insertion Sequencing" ;
definition: "Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools." .
SCR:015994 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Blixem" ;
NIFRID:synonym "SEQtools Blixem" ;
definition: "Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites." .
SCR:015995 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:barrnap",
"OMICS_13988" ;
rdfs:label "Barrnap" ;
NIFRID:synonym "Barrnap: Basic rapid ribosomal RNA predictor" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:015996 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "loadBED2ge_db" ;
NIFRID:synonym "Management and Analysis System for Enormous Reads:loadBED2ge_db" ;
definition: "One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadBED2ge_db software is for visualizing mapping data by Genome Explorer on the web." .
SCR:015997 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "loadGffToGe_db for custom genome" ;
NIFRID:synonym "Management and Analysis System for Enormous Reads: loadGffToGe_db for custom genome" ;
definition: "One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGffToGe_db for custom genome software loads GFF files of custom genomes to a database for Genome Explorer. It allows the user to browse the results through the GE." .
SCR:015998 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "loadGtfToGe_db" ;
NIFRID:synonym "Management and Analysis System for Enormous Reads: loadGtfToGe_db" ;
definition: """One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide.
loadGtfToGe_db software loads GTF files to a database for Genome Explorer. It allows the user to browse the results through the GE.""" .
SCR:015999 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "regist custom genome" ;
NIFRID:synonym "Management and Analysis System for Enormous Reads: regist custom genome" ;
definition: "One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide.. Regist custom genome software registers custom genomes to Genome Explorer (IN: FASTA)." .
SCR:016001 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016005" ;
rdfs:label "ReproNim: A Center for Reproducible Neuroimaging Computation" ;
NIFRID:abbrev "ReproNim" ;
definition: "Center to help neuroimaging researchers to find and share data in FAIR fashion, to describe their data and analysis workflows in replicable fashion, to manage their computational resource options so that outcomes of neuroimaging research are more reproducible." .
SCR:016002 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "NPI electronic " ;
NIFRID:abbrev "NPI" ;
definition: "Commercial organization that builds and supplies research-related equipment such as amplifiers." .
SCR:016003 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sound Analysis Pro" ;
NIFRID:abbrev "SAP" ;
definition: "Software for birdsong analysis that performs automated recording and analysis of animal vocalization. It can record, analyze and manage sound data over prolonged periods." .
SCR:016004 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vocal Inventory Clustering Engine (VoICE)" ;
NIFRID:synonym "VoICE (Vocal Inventory Clustering Engine)",
"VoICE: A semi-automated pipeline for standardizing vocal analysis across models",
"VoICE: Vocal Inventory Clustering Engine" ;
NIFRID:abbrev "VoICE" ;
definition: "Software that groups vocal elements of birdsong by creating a high dimensionality dataset through scoring spectral similarity between vocalizations." .
SCR:016006 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HermiT OWL Reasoner" ;
definition: "Algorithm for a reasoner for ontologies written using the Web Ontology Language (OWL). Given an OWL file, HermiT can determine whether or not the ontology is consistent, identify subsumption relationships between classes, and much more." .
SCR:016007 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "geocoding" ;
NIFRID:synonym "ABCD geocoding",
"ABCD geocoding project",
"geocoding project" ;
definition: "Software that uses a geo-location database to determine individuals' residential environment in Adolescent Brain Cognitive Development (ABCD) study. It performs queries given individuals' residential history in longitude and latitude." .
SCR:016008 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016009",
"SCR_016010" ;
rdfs:label "redcap-to-nda" ;
NIFRID:synonym "Redcap: Research electronic data capture" ;
definition: "Software for metadata-driven electronic data capture to export REDCap data dictionaries and data to the NIMH National Data Archive (NDA). Prepares data submissions as csv formatted spreadsheets for data dictionary spreadsheets and for data spreadsheets." .
SCR:016011 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "enroll" ;
definition: "Software which provides a framework for the secure storage of Personal Identifyable Information (PII) for a multi-site longitudinal project centrally. Used in Adolescent Brain Cognitive Development (ABCD) Study." .
SCR:016012 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016013",
"SCR_016014" ;
rdfs:label "FIONASITE" ;
definition: "Software for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive." .
SCR:016015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "auto-scoring" ;
definition: "Visualization software that calculates derived scores for the electronic record system REDCap (Research Electronic Data Capture) to build and manage online surveys and databases. Used in the ABCD-STUDY (Adolescent Brain Cognitive Development - STUDY) report framework." .
SCR:016016 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Minimally-Processed-Image-Sharing" ;
definition: "Software to share ABCD minimally processed data. It uploads minimally-processed MRI data to the NDA ( Non-Disclosure Agreement) ABCD (Adolescent Brain Cognitive Development) repository." .
SCR:016017 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "timeline-followback" ;
definition: "Software to capture subject information about substance use using local copies of external files provided by the abcd-report framework of ABCD. No connection to REDCap is attempted to get events and participant names but local files are read in to supply this information." .
SCR:016018 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "little-man-task" ;
definition: "Software tool to manage data and derived results. It is used for import of derived measures into REDCap (Research Electronic Data Capture)." .
SCR:016019 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "redcap-completion" ;
definition: "Software to measure item level completion in a large REDCap project. It provides a web-interface to review data and it is used in the ABCD project to assess data collection sites for the reached level of completion." .
SCR:016020 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eprime-data-clean" ;
definition: "Software to convert E-Prime (software tool for psychology computerized experiment design, data collection, and analysis) generated files to CSV files without errors during conversion. The ABCD project is using E-Prime to run behavioral tests." .
SCR:016021 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fast-Track-Image-Sharing" ;
definition: "Software for sharing the ABCD (Adolescent Brain Cognitive Development) study data on the National Data Archive (NDA)." .
SCR:016022 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "simple-t1-motion-detection" ;
definition: "Software to measure the amount of ghosting artifacts in T1-weighted DICOM images. This program reads DICOM images and calculates a measure of the noise structure in one part of the image." .
SCR:016023 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tick-tock" ;
definition: "Software for research study observation that visualizes study related events per day. Any event generating function sends a 'tick' event to this application which will be visible on this applications web-interface." .
SCR:016024 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FIONA-QC-PHANTOM" ;
definition: "Software for online quality control operations performed on Phantom MRI data. It checks the accuracy and reproducibility of data." .
SCR:016025 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "numerical-fitting" ;
definition: "Software for a numerical computation library that performs numerical calculations. Used in ABCD study." .
SCR:016026 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "aux-file-upload" ;
definition: "Software application to upload functional MR imaging runs produce auxilary data that can be collected centrally. Connects to a subject database research electronic data capture (REDCap)." .
SCR:016027 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FIONA-protocol-compliance" ;
definition: "Software that contains multiple sequential lines of MATLAB commands and function calls for numerical computing for ABCD study protocol compliance." .
SCR:016028 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "redcap-hook-framework" ;
definition: "Software tool to organize and deploy custom hooks in a single project or across the entire instance. It features multi-language support for data entry and survey pages, a bar-code for text fields, and highlighting of rows on data entry and survey pages that have been filled out." .
SCR:016029 a NLX:63400,
owl:NamedIndividual ;
definition: "Data collection software for centrally and securely storing data from the NIH iPad application. It allows users to capture results from multiple iPads at a central location." .
SCR:016030 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ABCDreport" ;
definition: "Software application as a simple system to review study progress. Used in ABCD study." .
SCR:016031 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "delay-discounting" ;
definition: "Software that performs a delay-discounting task measuring impulsivity. Used in ABCD study." .
SCR:016032 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "redcap-importer" ;
definition: "Software that automates the process of retrieving and converting data to the format of a RedCap table and allows selection of directories and files for import." .
SCR:016033 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "stroop-task" ;
definition: "Software that conducts the Stroop Color Task. Used in the ABCD Study." .
SCR:016034 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pearson-central-end-point" ;
definition: "Data collection software as an end-point for centrally storing data from the Pearsons Q-Interactive." .
SCR:016036 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FINDTHECAT" ;
definition: "Software that conducts a jspsych test for response time evaluation. Used in the ABCD Study." .
SCR:016037 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NPI DPA-2FS" ;
definition: "µV Amplifier filter with offset compensation and gain." .
SCR:016038 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ELC-03XS" ;
NIFRID:synonym "ELC-03XS Amplifier" ;
definition: "Amplifier that records with patch, sharp, metal or carbon fiber electrodes. It includes a variety of other neuroimaging functions." .
SCR:016039 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EXT-HS-M" ;
definition: "Hardware resource. Connector Module for EPMS for up to 4 standard headstages." .
SCR:016040 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CED | Power1401" ;
NIFRID:synonym "CED Power1401 3A",
"POWER1401-3 Data Acquisition Interface",
"Power1401-3A" ;
definition: "Data acquisition interface from Cambridge Electronic Design Limited. Works with Spike2 to provide continuous acquisition tasks. Records waveform data, digital and marker information, and can generate waveform and digital outputs simultaneously for real-time, multi-tasking experiment control." .
SCR:016041 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Solomon Coder" ;
definition: "Software for coding video data for research purposes such as animal behavior. Solomon Coder can handle several video formats, represent behaviors and events with buttons, analyze various types of data, and perform other necessary video coding functions." .
SCR:016042 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:rtips" ;
rdfs:label "Research-tested Intervention Programs (RTIPs)" ;
NIFRID:synonym "Research-tested Intervention Programs" ;
NIFRID:abbrev "RTIPs" ;
definition: "Database of cancer control interventions and program materials. It is designed to provide program planners and public health practitioners easy and immediate access to research-tested materials." .
SCR:016043 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Grid-Enabled Measures Database" ;
NIFRID:synonym "GEM Database" ;
NIFRID:abbrev "GEM" ;
definition: "Database that contains behavioral and social science measures organized by theoretical constructs. GEM is designed to enable researchers to use common measures with the goal of exchanging harmonized data." .
SCR:016044 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BMap" ;
definition: "Software that maps whole-genome and targeted bisulfite sequence reads to reference genomes. It is especially useful for reads obtained using post-bisulfite adaptor tagging (PBAT)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016045 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IMAGEN" ;
NIFRID:synonym "IMAGEN Consortium",
"IMAGEN Project",
"IMAGEN Study" ;
definition: "Research project examining how biological, psychological, and environmental factors during adolescence may influence brain development and mental health. Using brain imaging and genetics, the project will help develop prevention strategies and improved therapies for mental health disorders in the future., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016046 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "G-Anchor" ;
NIFRID:synonym "G-Anchor: A novel approach for cross-species comparison" ;
definition: "Software for comparing large genomes and exploiting highly conserved sequences as evolutionary-stable \"anchors\". The pipeline maps a newly sequenced genome (assembled in scaffolds) on a reference genome without the need of a supercomputer." .
SCR:016047 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IC Capture Software" ;
NIFRID:synonym "IC Imaging Control" ;
definition: "Software for acquiring images from a video source, such as vision cameras, frame grabbers and video converters. It can capture single images, sequences of single images, and live video streams from connected video sources." .
SCR:016048 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "m6ASNP: Annotation of genetic variants by m6A function" ;
NIFRID:synonym "m6ASNP" ;
definition: """Web server implemented in JAVA and PHP for annotating genetic variants by m6A function.
It predicts and annotates N6-methyladenosine (m6A) alterations from genetic variants data such as germline SNPs or cancer somatic mutations. It employs two accurate prediction models for human and mouse using Random Forest algorithm.
It conducts a statistical analysis for all the predicted m6A alterations. Provides statistical diagrams and a genome browser to visualize the topology characteristics of predicted m6A alterations.""" .
SCR:016049 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gannet" ;
NIFRID:synonym "Gannet - Batch Analysis of Edited Magnetic Resonance Spectroscopy (MRS) Data" ;
definition: "Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data." .
SCR:016050 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stimfit" ;
definition: "Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy." .
SCR:016051 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CloudMerge" ;
definition: "Software for merging massive VCF files into a single VCF file or TPED file. Source codes can be slightly modified to fit into other types of sorted merging of Omics data." .
SCR:016052 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:enrichmentmap" ;
rdfs:label "EnrichmentMap" ;
definition: "Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together." .
SCR:016053 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:gag" ;
rdfs:label "Genome Annotation Generator" ;
NIFRID:synonym "gag.py" ;
NIFRID:abbrev "GAG" ;
definition: "Command line program to read, modify, annotate and generate genomic data. Can write files to .gff3 or to the NCBI's .tbl format." .
SCR:016054 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:clinotator" ;
rdfs:label "Clinotator" ;
NIFRID:synonym "clinotator.py" ;
definition: "Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics." .
SCR:016055 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:biopp",
"OMICS_15696" ;
rdfs:label "Bio++" ;
NIFRID:synonym "Bio++ Phylogenetic Viewer",
"Bio++ program suite",
"Bppphyview",
"Bppsuite" ;
definition: "Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016056 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19794" ;
rdfs:label "Cassiopee" ;
NIFRID:synonym "cassiopee-c" ;
definition: "Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity." .
SCR:016057 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19793" ;
rdfs:label "Cdbfasta" ;
NIFRID:synonym "Constant DataBase" ;
NIFRID:abbrev "CDB" ;
definition: "Software tool for indexing and retrieval of nucleotide sequences from FASTA (DNA and protein sequence alignment software) record databases. It has the option to compress data records." .
SCR:016058 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_09488" ;
rdfs:label "Circlator" ;
definition: "Software that automates assembly circularization and produces accurate linear representations of circular sequences. It is used for assembling of DNA sequence data of complete bacterial and small eukaryotic genomes." .
SCR:016059 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_15083" ;
rdfs:label "Clearcut" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023.Software as a stand-alone reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm. Used in distance-based phylogenetic tree reconstruction method to process large sequence datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016060 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14623" ;
rdfs:label "Clonalframe" ;
NIFRID:synonym "ClonalFrameML" ;
definition: "Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance." .
SCR:016061 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_18881" ;
rdfs:label "ClonalOrigin" ;
definition: "Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry." .
SCR:016063 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_04161" ;
rdfs:label "Concavity" ;
definition: "Software for predicting protein ligand binding sites that integrate evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. Used in predicting catalytic sites and drug binding pockets." .
SCR:016064 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Conservation" ;
NIFRID:synonym "Conservation-code" ;
definition: "Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands." .
SCR:016065 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_09827" ;
rdfs:label "Computational Structural Biology Toolbox" ;
NIFRID:synonym "Computational Structural Biology Toolbox (CSB)",
"CSB Toolbox" ;
NIFRID:abbrev "CSB" ;
definition: "Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses." .
SCR:016066 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Daligner" ;
definition: "Software alignment tool to find all significant local alignments between long and noisy, up to 15% on average reads encoded in a Dazzler database. Used for DNA sequence assembly, specifically for next generation long-read sequencers such as the Pacbio RS II and Sequel sequencers." .
SCR:016067 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Datamash" ;
NIFRID:synonym "GNU Datamash" ;
definition: "Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts." .
SCR:016068 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dawg" ;
NIFRID:synonym "Dawg: DNA assembly with gaps" ;
definition: "Software application to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation. The application accepts phylogenies in Newick format and can return the sequence of any node, allowing for the exact evolutionary history to be recorded at the discretion of users." .
SCR:016069 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dazzler" ;
NIFRID:synonym "DAZZ_DB",
"Dazzdb",
"The Dazzler Database" ;
definition: "Software library and database to manage nucleotide sequencing read data. It stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files and avoid duplicating data." .
SCR:016070 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14561" ;
rdfs:label "DeepNano" ;
NIFRID:synonym "DeepNano: alternative basecaller for MinION reads",
"DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads" ;
definition: "Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate." .
SCR:016071 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:diamond",
"OMICS_08011" ;
rdfs:label "DIAMOND" ;
definition: "Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search." .
SCR:016072 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:disulfind",
"OMICS_04214" ;
rdfs:label "DISULFIND" ;
NIFRID:synonym "Cysteines Disulfide Bonding State and Connectivity Predictor" ;
NIFRID:abbrev "Disulfinder" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks." .
SCR:016073 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Boutiques" ;
NIFRID:synonym "Boutiques Python Tool",
"Boutiques Tool" ;
definition: "Software toolkit for a cross-platform JSON-framework for describing command-line tools and their parameters. It is accompanied by a Python tool which facilitates the creation, validation, simulation, execution, publishing, evaluation, and testing of tools described in this format." .
SCR:016074 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "statsmodel" ;
NIFRID:synonym "Statsmodels: Econometric and Statistical Modeling with Python" ;
definition: """Statistical software that provides classes and functions for the estimation of many different models, as well as for conducting statistical tests, and statistical data exploration. The results are tested against existing statistical packages to ensure that they are correct.
http://conference.scipy.org/proceedings/scipy2010/seabold.html""" .
SCR:016075 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FFmpeg" ;
definition: "Software for handling multimedia files. FFmpeg can record, convert and stream audio and video." .
SCR:016077 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Comenius University; Bratislava; Slovakia" ;
definition: "University in Bratislava, Slovakia." .
SCR:016079 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID:501100001314",
"grid.8250.f",
"ISNI:0000 0000 8700 0572",
"Wikidata:Q16848806" ;
rdfs:label "Durham University; Durham; England" ;
definition: "University in Durham, England." .
SCR:016080 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dotter" ;
NIFRID:synonym "Seqtools Dotter" ;
definition: "Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences." .
SCR:016081 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_08451" ;
rdfs:label "E-mem" ;
NIFRID:synonym "E-mem: Efficient-maximal exact match" ;
definition: "Software for an efficient maximal exact match (MEM) computation program that does not use full text indexes, uses less space and is amenable to parallelization. It can be used as a stand alone application or a drop-in replacement for MUMmer3 system for rapidly aligning entire genomes." .
SCR:016082 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19861" ;
rdfs:label "Ecopcr" ;
NIFRID:synonym "Ecopcr: Electronic polymerase chain reaction" ;
definition: "Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016083 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_16795" ;
rdfs:label "Edtsurf" ;
NIFRID:synonym "EDTSurf: Quick and accurate construction of macromolecular surfaces" ;
definition: "Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening." .
SCR:016084 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DOMAINATRIX" ;
NIFRID:synonym "Embassy-domainatrix" ;
definition: "Software for protein domain search. It is a part of Embassy software package." .
SCR:016085 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DOMALIGN" ;
NIFRID:synonym "Embassy-domalign" ;
definition: "Software commands for Extra EMBOSS and protein domain alignment. The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress." .
SCR:016086 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Embassy-domsearch" ;
definition: "Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt." .
SCR:016087 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ExaML",
"OMICS_08024" ;
rdfs:label "Examl" ;
NIFRID:synonym "Examl:Exascale Maximum Likelihood" ;
definition: "Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers." .
SCR:016088 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:exonerate" ;
rdfs:label "Exonerate" ;
definition: "Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016089 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_13514" ;
rdfs:label "Falcon" ;
definition: "Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes." .
SCR:016090 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_20516" ;
rdfs:label "Fastahack" ;
definition: "Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths." .
SCR:016091 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19987" ;
rdfs:label "Fastaq" ;
definition: "Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together." .
SCR:016092 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:fastml",
"OMICS_08650" ;
rdfs:label "Fastml" ;
NIFRID:synonym "The FastML Server" ;
definition: "Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences." .
SCR:016093 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_10934" ;
rdfs:label "Fastqtl" ;
NIFRID:synonym "Fastqtl: Fast quantitative trait loci" ;
definition: "Software for mapping of molecular phenotypes that implements a new permutation scheme to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels in large-scale datasets. It is used to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq." .
SCR:016094 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Department of Computer Science; University of Western Ontario; London; Ontario; Canada" ;
definition: "University of Western Ontario; Department of Computer Science; London; Ontario; Canada" .
SCR:016095 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Highcharts" ;
NIFRID:synonym "Highcharts Suite" ;
definition: "Software toolkit for a charting library written in pure JavaScript. It offers a way to add interactive charts to a web site or web application." .
SCR:016096 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bootstrap CSS" ;
NIFRID:synonym "Bootstraps" ;
definition: "Programming language framework for HTML, CSS, and JS. It is used for developing responsive, mobile projects on the web." .
SCR:016097 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Food Repo" ;
NIFRID:synonym "OpenFood",
"The Open Food Repo" ;
definition: "Database of barcoded food products. Food Repo provides data that is on the package of each product, and collects its data via food distributors and volunteer contributors." .
SCR:016098 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MultiStackReg" ;
definition: "Software plug-in for ImageJ that was developed for registering 3D volumes of images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016100 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoMotor" ;
definition: "Hardware for performing patch clamping for in vivo cell recordings of freely moving animals. The setup consists of a support column with an enlarged base for mounting the assembly, a clip which allows for flexibility in placement, and an actuated axis fitted with a capillary holder for the reference electrode." .
SCR:016101 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Wave_clus" ;
NIFRID:synonym "WaveClus",
"WaveClus spike-sorting algorithm" ;
definition: """Algorithm for spike detection and sorting that uses wavelets and super-paramagnetic clustering. It generates an unsupervised solution, but this can be modified according to the experimenters’ preference for semi-automatic sorting.
""" .
SCR:016102 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NPI Electronic Miniature Headstage" ;
definition: "Hardware that is a miniature headstage (without casing) for in-vivo experiments in freely moving animals'." .
SCR:016103 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:necklace" ;
rdfs:label "Necklace" ;
NIFRID:synonym "Lace software" ;
definition: "Software that combines reference and assembled transcriptomes for RNA-Seq analysis. It replaces many manual steps in the pipeline of RNA-Seq analyses involving species with incomplete genome or annotations." .
SCR:016104 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "METH" ;
definition: "Software toolkit of MATLAB functions that conduct data analysis of MEG and EEG data. It performs tasks such as EEG and MEG forward calculations, inverse calculations, power and coupling measures, decomposition, statistics, and visualization." .
SCR:016105 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scientific Filesystem" ;
NIFRID:synonym "Scientific Filesystem (SCIF)",
"The Scientific Filesystem" ;
NIFRID:abbrev "SCIF" ;
definition: "Organizational software that supports exposure of executables and metadata for discoverability. The software includes a known filesystem structure, a definition for a set of environment variables describing it, and functions for generation of the variables and interaction with the libraries, metadata, and executables located within." .
SCR:016106 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ModFit LT" ;
NIFRID:synonym "Verity Software House ModFit LT" ;
definition: "Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software." .
SCR:016107 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "The Experiment Factory" ;
NIFRID:synonym "EXPFACTORY" ;
definition: "Software that generates container-based behavioral experiments for reproducible science. It offers a library of experiments, games, and surveys, support for multiple kinds of databases, and robust documentation for the provided tools." .
SCR:016108 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mass Univariate ERP Toolbox" ;
definition: "Software toolkit of Matlab functions for analyzing and visualizing large numbers of t-tests performed on event-related potential data. The toolbox supports within-subject and between-subject t-tests with false discovery rate controls and control of the family-wise error rate via permutation tests." .
SCR:016109 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iELVis" ;
NIFRID:synonym "iELVis (intracranial electrode visualization)",
"Intracranial ELectrode VISualization" ;
definition: "Software toolkit consisting of MATLAB and Bash scripts for intracranial electrode localization/visualization. It maps electrodes to various anatomical and functional atlases, and overlays electrode data over functional neuroimaging data. Software for intracranial electrode localization and visualization." .
SCR:016110 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ffindex" ;
definition: "Database and index for huge amounts of small files. Files are stored concatenated in one big data file, with second file contains plain text index, giving name, offset and length of small files." .
SCR:016111 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Filo" ;
definition: "Software package that sorts data into groups, shuffles the order of data, and computes descriptive statistics based on the data. These FILe and stream Operations can be used independently or together." .
SCR:016112 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fermi-lite" ;
NIFRID:synonym "FermiKit",
"Fml-asm" ;
definition: "Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling." .
SCR:016113 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_03520" ;
rdfs:label "FreeContact" ;
definition: "Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud)." .
SCR:016114 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FSA" ;
NIFRID:synonym "Fast Statistical Alignment",
"FSA: Fast Statistical Alignment" ;
definition: "Software for a statistical multiple sequence alignment algorithm which uses a \"distance-based\" approach to align homologous protein, RNA or DNA sequences. The GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned." .
SCR:016115 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_28406" ;
rdfs:label "Fsm-lite" ;
NIFRID:synonym "Frequency-based String Mining",
"Frequency-based String Mining (lite)",
"fsm" ;
definition: "Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data." .
SCR:016116 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21302" ;
rdfs:label "Gamgi" ;
NIFRID:synonym "GAMGI: General Atomistic Modelling Graphic Interface",
"General Atomistic Modelling Graphic Interface" ;
NIFRID:abbrev "GAMGI" ;
definition: "Software application which provides a graphical interface to build, view and analyze atomic structures. It provides a graphical interface to study atomic structures, to prepare images for presentations, and teach the atomic structure of matter." .
SCR:016117 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_04234" ;
rdfs:label "GARLI" ;
NIFRID:synonym "Genetic Algorithm for Rapid Likelihood Inference" ;
definition: "Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution." .
SCR:016118 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21303" ;
rdfs:label "Garlic" ;
definition: "Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences." .
SCR:016119 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19946" ;
rdfs:label "gdpc" ;
definition: "Software application for visualizing output data from molecular dynamics simulations. It can be customized to read almost any input file format, animate it, and output images of each frame." .
SCR:016120 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_16119" ;
rdfs:label "GenomeTools" ;
NIFRID:synonym "Genome Tool",
"Genome Tools",
"GenomeTool" ;
definition: "Software toolkit for biological sequence analysis and -presentation combined into a single binary. It is used for genome analysis, efficient processing of structured genome annotations and contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization." .
SCR:016121 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MICtools" ;
NIFRID:synonym "Maximal Information Coefficient (MIC) Tools",
"Maximal Information Coefficient Tools",
"MIC Tools" ;
definition: "Software which combines the TICe and MICe measures into a two-step procedure that allows to identify relationships of various degrees of complexity in large datasets. TICe is used to perform an efficient high throughput screening of all the possible pairwise relationships and a permutation based approach is used to assess their significance." .
SCR:016124 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ,
;
rdfs:label "Brain Imaging Data Structure (BIDs)" ;
NIFRID:synonym "BIDS",
"Brain Imaging Data Structure",
"Brain Imaging Data Structure (BIDS)",
"Brain Imaging Data Structure v1.4.0" ;
definition: "Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data." .
SCR:016126 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Localite TMS Navigator" ;
definition: "An instrument. Navigation system for transcranial magnetic stimulation (TMS)." .
SCR:016127 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_18307" ;
rdfs:label "Gentle" ;
NIFRID:synonym "GENtle" ;
definition: "Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more." .
SCR:016128 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19949" ;
rdfs:label "Gff2aplot" ;
definition: "Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis." .
SCR:016129 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Glam2" ;
NIFRID:synonym "Glam2: Gapped local alignment of motifs 2" ;
definition: "Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets." .
SCR:016130 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11549" ;
rdfs:label "GraPhlAn" ;
NIFRID:synonym "Graphlan" ;
definition: "Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016131 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14386" ;
rdfs:label "Gubbins" ;
NIFRID:synonym "Gubbins: Genealogies Unbiased By recomBinations In Nucleotide Sequences" ;
definition: "Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016132 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_08468" ;
rdfs:label "Harvest-tools" ;
definition: "Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations." .
SCR:016133 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:hh-suite" ;
rdfs:label "HH-suite" ;
definition: "Software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). Used for sequence-based protein function and structure prediction what depends on sequence-search sensitivity and accuracy of the resulting sequence alignments." .
SCR:016134 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_13393" ;
rdfs:label "HiLive" ;
definition: """Software tool for performing read mapping that maps Illumina HiSeq sequencer
read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications.""" .
SCR:016135 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_12339" ;
rdfs:label "Hinge" ;
definition: "Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution." .
SCR:016137 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microsoft Excel" ;
NIFRID:synonym "MS Excel" ;
definition: "Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data." .
SCR:016139 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:zumis" ;
rdfs:label "zUMIs" ;
NIFRID:synonym "zumi" ;
definition: "Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information." .
SCR:016140 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clinker" ;
NIFRID:synonym "Clinker - Fusion Super Transcript generator and Plotter" ;
definition: "Software for a bioinformatics pipeline that generates a superTranscriptome from popular fusion finder outputs (JAFFA, tophatFusion, SOAP, deFUSE, Pizzly, etc). They can be then be either viewed in genome viewers such as IGV or through the included plotting feature developed with GViz." .
SCR:016141 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scikit-feature" ;
definition: "Software for a Python feature selection repository that contains a variety of feature selection algorithms, including traditional feature selection algorithms and some structural and streaming feature selection algorithms. It serves as a platform for facilitating feature selection application, research and comparative study." .
SCR:016142 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "jamovi" ;
NIFRID:synonym "the jamovi project" ;
definition: "Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience." .
SCR:016143 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IITC Incapacitance Meter" ;
NIFRID:synonym "Incapacitance Meter",
"The IITC Incapacitance Test Meter" ;
definition: "Hardware that is used to test and assess pain and inflammation of the hind limbs on mice and rats. Dynamic weight bearing enables the test to be implemented on both limbs, while inflicting less stress on the subject animal." .
SCR:016144 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bioplex_2.0" ;
rdfs:label "BioPlex" ;
NIFRID:synonym "Biophysical Interactions of Orfeome-based comPLEXes (BioPLEX)",
"BioPlex (biophysical interactions of ORFeome-based complexes)",
"Harvard BioPlex" ;
definition: "Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection." .
SCR:016145 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HumanBase" ;
NIFRID:synonym "GIANT",
"GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues)" ;
definition: "Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing \"biological knowledge\" represented in the literature to identify novel, data-driven associations." .
SCR:016146 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HumanNet" ;
definition: "Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes." .
SCR:016147 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "inBio Map" ;
NIFRID:synonym "inBio" ;
definition: "Database for investigating and visualizing protein-protein interactions. It aims to maintain coverage, quality, convenience, and transparency in the field of PPI research." .
SCR:016148 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mentha",
"r3d100011124" ;
rdfs:label "mentha" ;
definition: "Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium." .
SCR:016149 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MultiNet" ;
definition: "Software for an integrated network combining multiple biological network database sources into a single human protein interactome. The software package contains gene interaction pairs corresponding to the unified global network." .
SCR:016151 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AMBER" ;
NIFRID:synonym "AMBER: Assessment of Metagenome BinnERs" ;
definition: "Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects." .
SCR:016152 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeMOarchive" ;
NIFRID:synonym "NeMO Archive",
"Neuroscience Multi-Omic Archive",
"Neuroscience Multi-omic Data Archive",
"The Neuroscience Multi-Omic Archive" ;
NIFRID:abbrev "NeMO" ;
definition: "Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility." .
SCR:016153 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Linear Fascicle Evaluation" ;
definition: "Software that implements a framework to encode structural brain connectomes into multidimensional arrays (tensors). Encoding Connectomes provides an agile framework for computing over connectome edges and nodes." .
SCR:016154 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Data Biosphere" ;
definition: "Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations." .
SCR:016155 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Field of Genes" ;
NIFRID:synonym "Field of Genes Proof of Concept" ;
definition: "Software repository holding a cloud-ready demonstration of the use of Kafka as a genomic database." .
SCR:016156 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Parkinsons Disease Map" ;
NIFRID:synonym "Parkinsons Map",
"Parkinsons Map Viewer" ;
definition: "Knowledge repository established to describe molecular mechanisms of Parkinson's Disease. It compiles literature-based information on PD into an easy to explore and freely accessible molecular interaction map and offers research-facilitating functionalities such as the overlay of experimental data and the identification of drug targets on the map" .
SCR:016157 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:nanopolish",
"OMICS_16545" ;
rdfs:label "Nanopolish" ;
definition: "Software package for signal-level analysis of Oxford Nanopore sequencing data." .
SCR:016158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DEAP - Data Exploration and Analysis Portal" ;
NIFRID:synonym "DEAP: Data Exploration and Analysis Portal" ;
NIFRID:abbrev "DEAP" ;
definition: "Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States." .
SCR:016159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mikado" ;
definition: "Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus. " .
SCR:016160 a owl:NamedIndividual ;
rdfs:label "GAAIN toolset" ;
definition: "The Alzheimer's Association created The Global Alzheimer's Association Interactive Network (GAAIN) to connect Alzheimer’s and dementia researchers and speed discovery by connecting potential collaborators to those sharing data (GAAIN Data Partners). GAAIN's powerful interactive tools allow users to explore data and create cohorts across multiple data sources and run immediate preliminary analysis while upholding the data control, security, and privacy policies of the data owners. These tools are freely accessible to all at www.gaaindata.org. A wide and vastly varying range of metadata from nearly 500,000 subjects can be explored using these tools. Attributes include demographics, assessments, health factors, biologicals, imaging and genetics." .
SCR:016161 a owl:NamedIndividual ;
rdfs:label "MuseScore" ;
definition: "Music composition and manipulation software." .
SCR:016162 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:HyPhy",
"OMICS_04235" ;
rdfs:label "HyPhy" ;
NIFRID:synonym "Hyphy-pt",
"HyPhy:Hypothesis Testing using Phylogenies" ;
definition: "Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning." .
SCR:016163 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_15369" ;
rdfs:label "Indelible" ;
definition: "Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time." .
SCR:016164 a owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ipig",
"OMICS_06913" ;
rdfs:label "iPiG" ;
NIFRID:synonym "iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations" ;
definition: "Standalone software tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations." .
SCR:016165 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NGSimple" ;
NIFRID:synonym "NGSimple (Next-Generation illumina SIMulation PipeLinE)" ;
definition: "NGSimple (Next-Generation illumina SIMulation PipeLinE), mainly written in perl is designed to simulate NGS parameters (illumina sequencing type, read length, insert size and coverage) based on a given reference, and give a report to choose the best parameter combination that could contribute to a good assembly." .
SCR:016166 a owl:NamedIndividual ;
rdfs:label "ReadCleaner4Scaffolding" ;
definition: "This pipeline and the included scripts are used to filter useful reads for SSPACE." .
SCR:016167 a owl:NamedIndividual ;
rdfs:label "OlyVIA " ;
definition: """Virtual Slide Microscope Software by Olympus.
This software will be read the data captured by VS120/cellSens. Images saved with VSI or Multi-Tiff file format can be read.""" .
SCR:016168 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Berkeley Advanced Reconstruction Toolbox" ;
NIFRID:abbrev "BART" ;
definition: "Image reconstruction software for MRI. Its library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms." .
SCR:016169 a owl:NamedIndividual ;
rdfs:label "CytoBackBone" ;
definition: "CytoBackBone is an R package for merging of phenotype information from different cytometric profiles. Single-cell technologies are the most suitable techniques for the characterization of cells by the differential expression of the molecules that define their roles and functions in tissues. Among these techniques, mass cytometry represents a leap forward by increasing the number of available measurements to approximately 40 cell markers. Thanks to this technology, detailed immune responses were described in several diseases. However, the study of immune responses, such as that due to viral infections or auto-immune diseases, could be further improved by increasing the number of simultaneously measurable markers. To increase this number, we designed an algorithm, named CytoBackBone, which combines phenotypic information of different cytometric profiles obtained from different cytometry panels." .
SCR:016170 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CATNAP" ;
NIFRID:synonym "CATNAP - Compile Analyze and Tally Neutralizing Antibody Panels" ;
definition: """Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data.
PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.""" .
SCR:016171 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:idepi" ;
rdfs:label "IDEPI - IDentify EPItopes" ;
definition: "IDEPI is a domain-specific and extensible software library for supervised learning of models that relate genotype to phenotype for HIV-1 and other organisms. IDEPI makes use of open source libraries for machine learning (scikit- learn, scikit-learn.org/), sequence alignment (HMMER, hmmer.janelia.org/), sequence manipulation (BioPython, biopython.org), and parallelization (joblib, pythonhosted.org/joblib), and provides a programming interface to allow the users to engineer sequence features and select machine learning algorithms appropriate for their application." .
SCR:016172 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "International Institute for the Advancement of Medicine" ;
NIFRID:abbrev "IIAM" ;
definition: "Biomaterial supplier that links organ and tissue donors with the scientific community. After securing the appropriate consent, IIAM provides non-transplantable organs and tissues to researchers for use in medical discovery and education." .
SCR:016173 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ObservableHQ" ;
definition: "Web application for a code and text writing environment. It uses javascript and can be used to produce executable papers." .
SCR:016174 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:datasets2tools" ;
rdfs:label "Datasets2Tools" ;
definition: "Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools." .
SCR:016175 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "L1000 Fireworks Display" ;
NIFRID:synonym "L1000FWD: Large-scale Visualization of Drug-Induced Transcriptomic Signatures" ;
NIFRID:abbrev "L1000FWD" ;
definition: "Web application that provides interactive visualization of drug and small-molecule induced gene expression signatures. L1000FWD enables coloring of signatures by different attributes such as cell type, time point, concentration, as well as drug attributes such as MOA and clinical phase." .
SCR:016176 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harmonizome" ;
definition: "Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources." .
SCR:016177 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "L1000 Characteristic Direction Signature Search Engine" ;
NIFRID:abbrev "L1000CDS2" ;
definition: "LINCS L1000 characteristic direction signatures search engine. Software tool to find consensus signatures that match user’s input gene lists or input signatures. Underlying dataset is LINCS L1000 small molecule expression profiles generated at Broad Institute by Connectivity Map team. Differentially expressed genes of these profiles were calculated using multivariate method called Characteristic Direction." .
SCR:016178 a owl:NamedIndividual ;
rdfs:label "InterLex" ;
definition: """The InterLex project - a core component of SciCrunch and supported by projects such as the Neuroscience Information Framework project (NIF), the NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury - is a dynamic lexicon of biomedical terms. Unlike an encyclopedia, a lexicon provides the meaning of a term, and not all there is to know about it. InterLex is being constructed to help improve the way that biomedical scientists communicate about their data, so that information systems like NIF and dkNET can find data more easily and provide more powerful means of integrating that data across distributed resources. One of the big roadblocks to data integration in the biomedical sciences is the inconsistent use of terminology in databases and other resources such as the literature. When we use the same terms to mean different things, we cannot easily ask questions that span across multiple resources. For example, if three databases have information about what genes are expressed in cortex, but they all use different definitions of cerebral cortex, then it is hard to compare them. InterLex allows for the association of data values (i.e. the value of a field or text within a field) to terminologies enabling the crowdsourcing of data-terminology mappings.
InterLex was built on the foundation of NeuroLex (see Larson and Martone 2013 Neurolex: An online framework for neuroscience knowledge. Frontiers in Neuroinformatics, 7:18) and contains all of the existing NeuroLex terms. The initial entries in NeuroLex were built from the NIFSTD ontologies. NIFSTD currently has about 60,000 concepts (includes both classes and synonyms) that span gross anatomy, cells, subcellular structures, diseases, functions and techniques. InterLex models terms using primitives of the Web Ontology Language (OWL) and can export directly to a variety of standard ontology formats.
A primary goal of interlex is to provide a stable layer on top of the many other existing terminologies, lexicons, and ontologies (i.e. provide a way to federate ontologies for data applications) and to provide a set of inter-lexical and inter-data-lexical mappings. In the future, InterLex will support user specific namespaces so that users can customize the exact definitions or ontologies they source from, as well as the relationships on those terms. Importantly, however, InterLex enforces a simple rule which is that terms which represent the same concept under the same superclass will maintain the same identifier fragment (i.e. 'ilx_1234567'). However, each user will be able to 'fork' a term into their own namespace (e.g. http://uri.interlex.org/user/ilx_1234567). This enables the various perspectives on a term or concept to have equal space so that the full diversity of views on a term can be seen and expressed. Sign-up for updates to get notified about updates to InterLex and when new features are available. """ .
SCR:016179 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MPVS Ultra Pressure Volume Loop System " ;
definition: "System to record continuous measurements of left ventricular pressure with a conductance pressure-volume catheter." .
SCR:016180 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Prucka CardioLab System" ;
definition: "Prucka CardioLab system delivers the EP data and visualization we need for electrophysiological study and catheter ablation." .
SCR:016181 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LINCS Joint Project - Breast Cancer Network Browser" ;
NIFRID:synonym "Breast Cancer Network Browser",
"LINCS Joint Project" ;
NIFRID:abbrev "BCNB",
"LJP",
"LJP-BCNB" ;
definition: "Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations." .
SCR:016182 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kaluza" ;
definition: "Flow cytometry analysis software." .
SCR:016183 a owl:NamedIndividual ;
rdfs:label "Sirenia Acquisition" ;
definition: "EEG/EMG, biometric data, and synchronized video recording software." .
SCR:016184 a owl:NamedIndividual ;
rdfs:label "Sirenia Seizure" ;
definition: "Software for EEG and synchronized video playback and seizure detection based on RMS and line length." .
SCR:016185 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PDB-Dev" ;
definition: "Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations." .
SCR:016186 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IHM-dictionary" ;
definition: "Software resource for a data representation for integrative/hybrid methods of modeling macromolecular structures." .
SCR:016187 a owl:NamedIndividual ;
rdfs:label "Johns Hopkins University Integrated Imaging Center Core Facility" ;
definition: "Imaging and flow cytometry core facility at Johns Hopkins University Homewood Campus." .
SCR:016188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Direct Infusion Metabolite Database" ;
NIFRID:synonym "Direct Infusion Metabolite Database (DIMEdb)" ;
NIFRID:abbrev "DIMEdb" ;
definition: "Database of metabolite structures and annotations. The sources are from multiple existing metabolic and chemical databases such as HMDB, PubChem, CHEBI, BioCyc, and KEGG." .
SCR:016189 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GoldWave" ;
definition: "Software that enables users to digitally edit audio files. GoldWave can record, edit, and analyze audio for research-related purposes." .
SCR:016190 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Raven" ;
definition: "Software for the acquisition, visualization, measurement, and analysis of sounds. Raven supports annotations for research-related analysis." .
SCR:016191 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DAMSystems308" ;
definition: "Data acquisition software for TriKinetics activity monitors. TriKinetics systems quantify animal movement over time, and can be used to measure behaviors such as circadian rhythm, sleep, longevity, social interaction, geotaxis, phototaxis, learning, and drug response in various species." .
SCR:016192 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Grass Stimulator Model S88" ;
NIFRID:synonym "Cyberonics VNS 103",
"Grass Technologies Stimulator Pulse",
"Pulse Stimulator",
"S88 DUAL OUTPUT SQUARE PULSE" ;
definition: "Hardware that is a electrical pulse generator." .
SCR:016193 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroPlex" ;
definition: "Software for acquisition and analysis for imaging applications. The acquisition section has a variety of triggering and averaging modes, while the analysis section has extensive provisions for displaying traces (intensity vs time) and movies of propagating activity." .
SCR:016194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LR Gapcloser" ;
NIFRID:synonym "LR_Gapcloser" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th, 2023. Software that uses long reads to close gaps in the assemblies." .
SCR:016196 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ;
rdfs:label "NIX" ;
NIFRID:synonym "NIX Project",
"Pandora" ;
definition: "Software that defines a data model for annotated scientific datasets. It includes data together with metadata, and a corresponding file format based on HDF5 for storing and sharing such datasets." .
SCR:016197 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pixelink Image Capture Software" ;
NIFRID:synonym "Image Capture Software",
"Pixelink Capture" ;
definition: "Software application for real-time, interactive, multi-camera recording. It is compatible with all Pixelink PL-B and PL-D line of cameras." .
SCR:016198 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "HIRN Consortium on Beta Cell Death and Survival" ;
NIFRID:synonym "Consortium on Beta Cell Death and Survival (HIRN-CBDS)" ;
NIFRID:abbrev "CBDS",
"HIRN-CBDS" ;
definition: "Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is using human tissues to discover highly specific biomarkers of beta cell injury in asymptomatic T1D and developing strategies to stop beta cell destruction early in the disease process." .
SCR:016199 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "HIRN Consortium on Human Islet Biomimetics" ;
NIFRID:synonym "Consortium on Human Islet Biomimetics (HIRN-CHIB)" ;
NIFRID:abbrev "CHIB",
"HIRN-CHIB" ;
definition: "Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is combining advances in beta cell biology and cell biology with tissue engineering technologies to develop microdevices that support functional human islets." .
SCR:016200 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "HIRN Consortium on Modeling Autoimmune Interactions" ;
NIFRID:synonym "Consortium on Modeling Autoimmune Interactions (HIRN-CMAI)" ;
NIFRID:abbrev "HIRN-CMAI" ;
definition: "Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is developing innovative approaches to model basic aspects of human T1D immunobiology using novel in vivo and in vitro platforms." .
SCR:016201 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "HIRN Consortium on Targeting and Regeneration" ;
NIFRID:synonym "Consortium on Targeting and Regeneration (HIRN-CTAR)" ;
NIFRID:abbrev "CTAR",
"CTR",
"HIRN-CTAR",
"HIRN-CTR" ;
definition: "Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is investigating methods to increase or maintain functional beta cell mass in T1D through targeted manipulation of islet plasticity or engineered protection of beta cells from immune-mediated destruction." .
SCR:016202 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HIRN Human Pancreas Analysis Program" ;
NIFRID:synonym "Human Pancreas Analysis Program (HIRN-HPAP)",
"PANC-DB" ;
NIFRID:abbrev "HIRN-HPAP",
"HPAP" ;
definition: "Program is performing deep phenotyping of human endocrine pancreas and its interaction with immune system to better understand cellular and molecular events that precede and lead to beta cell loss in Type-1 Diabetes (T1D) and islet dysfunction in Type-2 Diabetes (T2D)." .
SCR:016203 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "HIRN Bioinformatics Center" ;
NIFRID:abbrev "HIRN-BC" ;
definition: "The Bioinformatics Center is located within the Department of Diabetes and Cancer Discovery Science at City of Hope and was established in 2014 to support the Human Islet Research Network (HIRN). The overall objective of the Bioinformatics Center is to advance type 1 diabetes knowledge generated through HIRN by providing the bioinformatics capability and infrastructure needed to support the Network. To achieve this goal, the Bioinformatics Center provides investigators with tools, processes, and methods to facilitate long term sharing, maintenance, and management of HIRN developed resources, including datasets, technologies, documents, and bioreagents. Collaboration and communication are cultivated through consultation and outreach activities. In 2019, HIRN received funding to continue HIRN Coordinating Center (CC) and Bioinformatics Center (BC) as Human Islet Research Enhancement Center (HIREC)." .
SCR:016204 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:CMap" ;
rdfs:label "CMap" ;
NIFRID:synonym "Connectivity Map",
"ConnectivityMap",
"LINCS CMap",
"LINCS CMap L1000",
"LINCS L1000" ;
definition: "Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines." .
SCR:016205 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SL-quant" ;
NIFRID:abbrev "SLQ" ;
definition: "Source code for a bash pipeline that quantifies splice-leader (SL) trans-splicing events by genes in the nematode C. elegans. It is designed to work downstream of read mapping and takes the reads left unmapped as primary input." .
SCR:016206 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BrainPost" ;
NIFRID:synonym "Brain Post" ;
definition: "Blog for summaries of neuroscience journal papers and articles. BrainPost sends its subscribers digestible and accessible versions of scientific findings in the field of neuroscience." .
SCR:016207 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:biosyntax",
"OMICS_25594" ;
rdfs:label "bioSyntax" ;
definition: "Software for syntax highlighting for computational biology." .
SCR:016208 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UTHSCSA ImageTool" ;
NIFRID:synonym "UTHSCSA Image Tool",
"UTHSCSA ImageTool (IT)" ;
NIFRID:abbrev "IT" ;
definition: "Image processing and analysis program for Windows 95 NT and has many of the same capabilities as NIH Image. ImageTool can acquire, display, edit, analyze, process, compress, save and print gray scale and color images." .
SCR:016209 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nelpy" ;
NIFRID:synonym "Nelpy (Neuroelectrophysiology)" ;
definition: "Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data." .
SCR:016210 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Stanford Diabetes Research Center Diabetes Immune Monitoring Core" ;
NIFRID:synonym "Diabetes Immune Monitoring Core",
"SDRC Diabetes Immune Monitoring Core" ;
NIFRID:abbrev "DIMC",
"SDRC-DIMC" ;
definition: "Core facility that provides immune monitoring assays at the RNA, protein, and cellular level, as well as archiving, reporting, and data mining support for clinical and translational studies related to Diabetes. The DIMC is a specialized subcore of the Human Immune Monitoring Center (HIMC) at Stanford." .
SCR:016211 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Stanford Diabetes Research Center Stanford Islet Research Core" ;
NIFRID:synonym "SDRC Stanford Islet Research Core",
"Stanford Islet Research Core" ;
NIFRID:abbrev "SDRC-SIRC",
"SIRC" ;
definition: "Core facility whose services include: Islet Isolation, Islet transplantation, Islet Culture, Islet Perifusion & Islet Hormone Assays. The SIRC is supported by the Stanford Diabetes Research Center (SDRC)." .
SCR:016212 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Stanford Diabetes Research Center Diabetes Clinical and Translational Core" ;
NIFRID:synonym "Clinical and Translational Core",
"Diabetes Clinical and Translational Core",
"SDRC Diabetes Clinical and Translational Core" ;
NIFRID:abbrev "DCTC",
"SDRC-DCTC" ;
definition: "With the following services from the Diabetes Clinical and Translational Core (DCTC), members will receive training in biospecimen preservation, study design, data analysis, data management, use of statistical software and clinical trial conduct." .
SCR:016213 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford Diabetes Research Center Diabetes Genomics Analysis Core" ;
NIFRID:synonym "Diabetes Genomics Analysis Core",
"Genomics Analysis Core",
"SDRC" ;
NIFRID:abbrev "GDAC",
"SDRC-GDAC" ;
definition: "Core facility that offers library preparation and sequencing services on a variety of platforms - Illumina HiSeq 4000, MiSeq, HiSeq 2500 and PacBio Sequel - as well as bioinformatics analysis. It can sequence a variety of commercial sample preparation kits as well as custom workflows. DGAC provides access to high throughput sequencing and analysis to researchers at the Stanford Diabetes Research Center." .
SCR:016214 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "BraTS" ;
NIFRID:synonym "BraTS: Multimodal Brain Tumor Segmentation",
"Multimodal Brain Tumor Segmentation" ;
definition: "Organization that provides a conference about the methods for the segmentation of brain tumors in magnetic resonance imaging (MRI) scans. Its conferences utilize multi-institutional pre-operative MRI scans and focus on the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas." .
SCR:016215 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SegAN" ;
NIFRID:synonym "SegAN: Semantic Segmentation with Adversarial Learning",
"Semantic Segmentation with Adversarial Learning",
"Semantic Segmentation with Adversarial Learning (SegAN)" ;
definition: "Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps." .
SCR:016216 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fMRIPrep" ;
NIFRID:synonym "FMRI PREP" ;
definition: "Software tool as robust preprocessing pipeline for functional MRI.Used for preprocessing of diverse fMRI data." .
SCR:016228 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:odMLtables" ;
rdfs:label "odMLtables" ;
NIFRID:synonym "odML tables",
"odML-tables" ;
definition: "Software that facilitates the handling of metadata collections stored in the odML format. Some supported operations include reduction, merging of odml structures, and the conversion from the hierarchical odML format to tabular formats." .
SCR:016229 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bravissima" ;
NIFRID:synonym "Bravissima: Human Brain Artery NIfTI Atlas",
"Human Brain Major Artery Atlas" ;
definition: """Project that is a translation of the BraVa arterial vasculature database into the NIFTI MRI file format that can be applied to stroke studies, fMRI resting state imaging studies and other clinical neuroscience studies. Group artery region labels and arterial density maps are provided as well.
Human Brain Major Artery Atlas
10.7490/f1000research.1114378.1""" .
SCR:016230 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenEx" ;
NIFRID:synonym "OpenEx suite",
"The OpenEx Software Suite" ;
definition: "Software toolkit that is designed for configuration and control of TDT hardware. It can also display and analyze neurophysiology data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016231 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Elm Hill Labs" ;
NIFRID:synonym "Guinea pig resource at Elm Hill Labs" ;
NIFRID:abbrev "EHL" ;
definition: "Organism supplier that provides guinea pigs exclusively for the research community." .
SCR:016232 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mapping Population-based Structural Connectomes" ;
definition: "Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis." .
SCR:016233 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FITMASTER" ;
NIFRID:synonym "HEKA FITMASTER" ;
definition: "Software for analysis and fitting routines of electrophysiological data. Analysis can be performed on the levels of Sweeps/Traces and Series." .
SCR:016234 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Boruta" ;
NIFRID:synonym "Boruta algorithm",
"Boruta: Wrapper Algorithm for All Relevant Feature Selection" ;
definition: "Algorithm that performs feature selection. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows)." .
SCR:016235 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SVEngine" ;
NIFRID:synonym "SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator" ;
definition: "Software for analysis and simulation of gene sequences and structural variants. This software works with FASTA, FASTQ, BAM, VAR, META, and NEWICK file formats." .
SCR:016236 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "YAMP" ;
NIFRID:synonym "YAMP: Yet Another Metagenomic Pipeline",
"Yet Another Metagenomic Pipeline",
"Yet Another Metagenomic Pipeline (YAMP)" ;
definition: "Software for processing and analysis of sequencing data. It has a strong focus on quality control, timely processing, functional annotation, and portability." .
SCR:016237 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "International Initiative for Traumatic Brain Injury Research" ;
NIFRID:synonym "International Initiative for Traumatic Brain Injury Research (InTBIR)" ;
NIFRID:abbrev "InTBIR" ;
definition: "Project whose goal is to improve health care and lessen the global burden of TBI through the discovery of causal relationships between treatments and clinically meaningful outcomes. InTBIR seeks to encourage well-designed, hypothesis-driven studies that include the collection of high quality data followed by rigorous statistical analysis." .
SCR:016239 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "REmAb" ;
NIFRID:synonym "Antibody Sequencing Service" ;
definition: "Service for monoclonal antibody protein sequencing. It derives the sequences directly from the protein using mass spectrometry and without the need to access the cell line." .
SCR:016240 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WILD" ;
NIFRID:synonym "W-ion Isoleucine Leucine Determination",
"WILD (W-ion Isoleucine Leucine Determination)" ;
definition: "Service that distinguishes Isoleucine and Leucine using mass spectrometry experiments." .
SCR:016244 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:oufti" ;
rdfs:label "Oufti" ;
NIFRID:synonym "outfi" ;
definition: "Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions." .
SCR:016246 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Iterative Deconvolve 3D" ;
definition: "Software plugin for 2D and 3D non-negative, iterative, deconvolution." .
SCR:016248 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016247" ;
rdfs:label "Singularity Hub" ;
NIFRID:synonym "shub",
"Singularity Registry",
"singularity-registry",
"SingularityHub" ;
NIFRID:abbrev "SHUB" ;
definition: "Database for singularity containers. It hosts container collections as well as articles about scientific advancements." .
SCR:016249 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Singularity Registry" ;
NIFRID:synonym "Singularity Registry Server" ;
NIFRID:abbrev "sregistry" ;
definition: "Web application and registry for institutional deployment of Singularity containers." .
SCR:016250 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciBot" ;
NIFRID:synonym "Sci Bot",
"SciCrunch SciBot" ;
definition: "Software written in Python, and plugin to Hypothes.is, that creates automated annotations." .
SCR:016251 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciScore" ;
NIFRID:synonym "Sci Score",
"SciCrunch SciScore" ;
definition: "Text-mining software that reviews methods sections of scientific articles. It provides a numerical score to represent the \"reproducibility\" of the article's research." .
SCR:016252 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MediBeacon Studio Software" ;
NIFRID:synonym "MediBeacon Software",
"Preclinical Data Studio",
"Studio Software" ;
definition: "Software used to analyze glomerular filtration rate (GFR) measurement from MediBeacon GFR monitor. It is used with the Transdermal Continuous Renal Function Monitor." .
SCR:016253 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sednterp" ;
NIFRID:synonym "SEDNTERP" ;
definition: "Software for the interpretation of sedimentation equilibrium and sedimentation velocity experiments. Sednterp is useful both for computing molecular structural estimates from experimental data and for interpolating physical parameters of common buffers used in sedimentation experiments." .
SCR:016254 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SEDPHAT" ;
NIFRID:synonym "sedphat" ;
definition: "Software for the global analysis of sedimentation velocity, sedimentation equilibrium, and/or dynamic light scattering experiments. It is a stand-alone sedimentation equilibrium analysis software that also processes isotherms of weight-average sedimentation coefficients, weight-average molar mass values, and other components., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016255 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ASTRA" ;
NIFRID:synonym "ASTRA6",
"ASTRA Software",
"Wyatt Technologies ASTRA" ;
definition: "Software for the characterization of macromolecules and nanoparticles via multi-angle and dynamic light scattering. It simplifies MALS and DLS analysis for assessment of molar mass, size, conformation, conjugation, and other essential physical parameters." .
SCR:016256 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "qMRLab" ;
NIFRID:synonym "qMR Lab",
"qMTLab" ;
definition: "Software for quantitative MR image analysis, simulation, and protocol optimization. It aims to provide the community with a tool for data fitting, plotting, simulation and protocol optimization for a variety of different quantitative models." .
SCR:016257 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Reg-MaxS-N" ;
NIFRID:synonym "Reg-MaxS",
"RegMaxSN" ;
definition: "Algorithm for co-registration of pairs and groups of neuron morphologies based on maximization of spatial overlap. The algorithm is written in Python and work with SWC files." .
SCR:016258 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PHAROS" ;
NIFRID:synonym "Target Central Resource Database" ;
NIFRID:abbrev "TCRD" ;
definition: "Database of ligands and diseases. Its goal is to develop a knowledge-base for the Druggable Genome (DG) in order to illuminate the uncharacterized and/or poorly annotated portion of the genome. DG, focusing on four of the most commonly drug-targeted protein families: G-protein-coupled receptors (GPCRs); nuclear receptors (NRs); ion channels (ICs); and kinases." .
SCR:016259 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iHOMA2" ;
NIFRID:synonym "HOMA2",
"iHOMA" ;
definition: "Model of assessment with the baseline default characteristics of the HOMA2 computer model of fasting insulin glucose interaction. iHOMA2 enables the mathematical functions describing the organs and tissues involved in the glucose and hormonal compartments to be modified using simple visual analogue controls." .
SCR:016260 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "easyGV" ;
definition: "Software for calculating different measures of glycaemic variability (GV). It analyzes continuous glucose monitoring data using a simple interface." .
SCR:016261 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OVAL" ;
NIFRID:synonym "Observed Variability and Lability (OVAL)",
"OVAL (Observed Variability and Lability)",
"OVAL Calc",
"OVAL: Observed Variability and Lability" ;
definition: "Software that allows you to quantify glucose homeostasis in type 2 diabetes and control subjects. OVAL also has the capacity to quantify sequential deterioration and monitor effects of intervention." .
SCR:016262 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DALAN Atlas" ;
NIFRID:synonym "DALAN: Disconnectivity Atlas for Lesion Analysis of Networks" ;
NIFRID:abbrev "DALAN" ;
definition: "Atlas of human white matter diffusion streamlines for predicting medium/long range brain connectivity. The atlas uses the popular Harvard-Oxford (H-O) cortical and subcortical atlas as endpoint targets so that WM connectivity deficits can be analyzed in conjunction with corresponding GM deficits." .
SCR:016263 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SymPhoTime 64" ;
NIFRID:synonym "SymPhoTime" ;
definition: "Software for fluorescence lifetime imaging and correlation. SymPhoTime 64 is the data acquisition software for PicoQuant's time-resolved confocal microscope MicroTime 200 and LSM upgrade kits." .
SCR:016264 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus FV1200" ;
NIFRID:synonym "FV 1200 High resolution software module",
"FV 1200 Super resolution software module" ;
NIFRID:abbrev "FV1200" ;
definition: """THIS RESOURCE HAS BEEN DISCONTINUED. Documented May 7, 2018.
Software module for biological confocal laser scanning microscope FV 1200. Olympus's proprietary super resolution technology FV - OSR (Olympus Super Resolution) realizes XY resolution of about 120 nm exceeding the conventional 3D confocal microscope.""" .
SCR:016265 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Virtual Digital Brain" ;
NIFRID:abbrev "VDB" ;
definition: "Virtual resource for neuroscience." .
SCR:016266 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ASHLAR" ;
rdfs:label "ASHLAR" ;
NIFRID:synonym "ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration" ;
NIFRID:abbrev "Ashlar" ;
definition: "Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration." .
SCR:016267 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CycIF.org" ;
NIFRID:synonym "cycif.org" ;
definition: "Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence." .
SCR:016268 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Research Data Management Platform" ;
NIFRID:abbrev "RDMP" ;
definition: """Software toolkit which automates the loading, storage, linkage and provision of data sets.
It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”.""" .
SCR:016269 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018150" ;
rdfs:label "Center for Expanded Data Annotation and Retrieval" ;
NIFRID:abbrev "CEDAR" ;
definition: "Develops information technologies that make authoring complete metadata more manageable. Its products aim to facilitate using the metadata in further research.Center to improve metadata and its use throughout biomedical sciences. Develops information technologies that make authoring complete metadata more manageable through better interfaces, terminology, metadata practices, and analytics. Optimizes metadata pathway from provider to end user. Provides way for funders to specify what metadata they want to collect as part of research life cycle." .
SCR:016270 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CEDAR Workbench" ;
NIFRID:synonym "CEDAR suite",
"CEDAR tools",
"Center for Expanded Data Annotation and Retrieval Workbench" ;
definition: "Web application for creating, collecting, testing, and sharing metadata. It provides templates for metadata models or structures, and is capable of testing those models quickly using real data." .
SCR:016272 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AspireDB" ;
definition: "Web based software for analyzing genomic variants CNVs, SNVs, and Indels and phenotypes. It aims to represent the relationships between discovered variants and phenotypes." .
SCR:016273 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phenocarta" ;
definition: "Database that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. Part of Gemma, a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data." .
SCR:016274 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_15597" ;
rdfs:label "RELION" ;
NIFRID:synonym "REgularised LIkelihood OptimisatioN",
"RELION-3" ;
definition: "Software for determination of cryo-EM structures. It employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy." .
SCR:016275 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NetClamp" ;
definition: "Software for dynamic clamping. It uses National Instruments Boards." .
SCR:016276 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cOMet" ;
definition: "Software for error correction of optical mapping data." .
SCR:016277 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HLAsupE" ;
NIFRID:synonym "integrated database of HLA supertype specific epitopes" ;
definition: "Database of HLA supertype-specific epitopes. It describes major histocompatibility complex (MHC) molecules that bind short peptides derived from endogenous or exogenous antigens and present them onto the surface of antigen-presenting cells (APCs) for T-cell receptor (TCR) recognition." .
SCR:016278 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PeMtb" ;
NIFRID:synonym "Peptide Mycobacterium Tuberculosis" ;
definition: "Database for MHC antigenic peptide of Mycobacterium tuberculosis. It aims to make a comprehensive repository of synthetic antigenic peptides predicted from several MHC predication servers." .
SCR:016279 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EPIMHC" ;
NIFRID:synonym "EPIMHC Database" ;
definition: "Database of naturally processed MHC-restricted peptide ligands and epitopes for customized computational vaccinology." .
SCR:016280 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HUMAnN2 " ;
NIFRID:synonym "The HMP Unified Metabolic Analysis Network 2" ;
NIFRID:abbrev "HUMAnN2" ;
definition: "Software for profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data Used for millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members." .
SCR:016281 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Crossref EventData" ;
NIFRID:synonym "Event Data",
"EventData" ;
definition: "Database of events about articles that is run by CrossRef. It allows users to view social media mentions, news publication references, annotations, and more." .
SCR:016282 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Longitudinal neuroimaging hippocampal markers for diagnosing Alzheimer's disease" ;
definition: "Software based on robust registration and simultaneous hippocampal segmentation and longitudinal marker classification of brain MRI of an arbitrary number of time points. The framework comprises two parts: a longitudinal segmentation and a longitudinal classification step." .
SCR:016283 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ANSA Pre-Processor" ;
NIFRID:synonym "ANSA Preprocessor" ;
NIFRID:abbrev "ANSA" ;
definition: "Software that provides all the necessary functionality for full-model build up, from CAD data to ready-to-run solver input file. Its integrated Batch Meshing tool leads to results for both shell and volume meshing." .
SCR:016284 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SIGEN" ;
NIFRID:synonym "SIGEN: SImulation of Geometrical and Electrical properties of Neuron",
"SImulation of Geometrical and Electrical properties of Neuron" ;
definition: "Software to extract and trace neuronal structure from confocal laser scanning microscope images. It performs the automatic reconstruction of neurons for image stacks and can generate compartmental models of neurons as swc file format data." .
SCR:016285 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SV-plaudit" ;
definition: "Software for rapidly curating structural variant (SVs) predictions. SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis." .
SCR:016286 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "atacr" ;
definition: "Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes." .
SCR:016287 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nighres" ;
NIFRID:synonym "nighres" ;
definition: "Software package for processing of high-resolution neuroimaging data. Nighres is a community-developed project that aims to make neuroscience data tools easier to install, use and extend." .
SCR:016288 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:BLINK" ;
rdfs:label "BLINK" ;
NIFRID:synonym "BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway)" ;
definition: "Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power." .
SCR:016289 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EFMTool" ;
definition: "Software for computating and calculating elementary flux modes. EFMtool computes elementary flux modes (EFMs) of metabolic networks. EFM computation is a special case of extreme ray enumeration of polyhedral cones." .
SCR:016290 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:fluxmodecalculator",
"OMICS_10894" ;
rdfs:label "FluxModeCalculator " ;
NIFRID:synonym "Flux Mode Calculator" ;
definition: "Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016291 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NExT-EMA" ;
definition: "Software for combined elementary flux mode and network-embedded thermodynamic analysis." .
SCR:016293 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "clustree" ;
definition: "Software package which allows to produce clustering trees and visualize clusterings at different resolutions. Used in the analysis of large data sets to group together samples with similar properties." .
SCR:016294 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "star-for-criu" ;
definition: "Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability." .
SCR:016295 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lasergene PrimerSelect" ;
definition: "Software for advanced primer design. Can be used for some advanced primer functions, such as adjusting mispriming parameters and creating a primer catalog. Suitable for determining the best primer pairs or probes for PCR, sequencing, and hybridization experiments." .
SCR:016297 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GLIMMPSE" ;
NIFRID:synonym "GLIMMPSE Version 3" ;
definition: "Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016298 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FLIMfit" ;
definition: "Software package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016299 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XLSTAT" ;
NIFRID:synonym "XL STATistics" ;
definition: "Software for commercial data analysis and statistical software package for Microsoft Excel." .
SCR:016301 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:nels" ;
rdfs:label "NeLS" ;
NIFRID:synonym "Norwegian e-Infrastructure for Life Sciences" ;
definition: "Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project." .
SCR:016302 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SonoLab Software" ;
definition: "Software for Covaris Focused-ultrasonicators." .
SCR:016303 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Starbase V2.0" ;
definition: "Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes." .
SCR:016304 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Circular RNA Interactome" ;
NIFRID:synonym "Circular interactome" ;
NIFRID:abbrev "Circinteractome" ;
definition: "Web tool for exploring circular RNAs and their interacting proteins and microRNAs. Predicts the miRNAs which can potentially target the circRNA." .
SCR:016305 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CAPT" ;
definition: "Software for molecular weight, quantification of bands, colony counting and distance calculation in Vilber Lourmat gel documentation imaging systems. Used in molecular biology laboratories." .
SCR:016306 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Metafer" .
SCR:016307 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:x2k" ;
rdfs:label "eXpression2Kinases" ;
NIFRID:synonym "X2K" ;
definition: "Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures." .
SCR:016308 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018760" ;
rdfs:label "AxIS " ;
NIFRID:synonym "Axion Integrated Studio" ;
NIFRID:abbrev "AxIS" ;
definition: "Software for multi electrode array recording for Axion Biosystems. Used in enhancing cardiac and neural analysis through data processing and signal monitoring." .
SCR:016309 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhoxX Controller" ;
definition: "Software application for PhoxX® Diode Laser to support Omicron products. It is related to uManager open source microscopy software for control of microscopes." .
SCR:016310 a owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100010256" ;
rdfs:label "Data Sharing for Demographics Research (DSDR)" ;
NIFRID:synonym "Data Sharing For Demographic Research",
"DSDR" ;
definition: "DSDR disseminates, archives, and preserves data for population-based studies. By providing access to data on topics including mortality and health, fertility, family and household structure, and children and youth, DSDR aims to facilitate demographic research." .
SCR:016311 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Children's Study (NCS) Archive" ;
NIFRID:synonym "National Children's Study",
"National Children's Study Archive" ;
NIFRID:abbrev "NCS Archive" ;
definition: "Data and sample repository for National Children's Study. Provides access to data and samples collected from over 5,600 U.S. birth families to study environmental influences on child health and development. Data and biological and environmental samples are freely available, with approved request, for scientific research." .
SCR:016312 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhonBank" ;
definition: "Database for study of early phonological development using Phon program. Child phonology component of TalkBank system." .
SCR:016313 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FluencyBank" ;
NIFRID:synonym "Fluency Bank" ;
definition: "Database for study of development of fluency in both normal and disordered populations. Participants include normally-developing monolingual and bilingual children, children with disfluencies (CWD), adults with disfluencies (AWSD), and second language learners." .
SCR:016314 a owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012915" ;
rdfs:label "Data and Specimen Hub (NICHD DASH)" ;
NIFRID:synonym "Data and Specimen Hub",
"NICHD Data and Specimen Hub" ;
NIFRID:abbrev "DASH",
"NICHD DASH" ;
definition: "Repository to store and access de-identified data from NICHD funded research studies for purposes of secondary research use. It serves as mechanism for NICHD-funded extramural and intramural investigators to share research data from studies in accordance with NIH Data Sharing Policy and NIH Genomic Data Sharing Policy." .
SCR:016315 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Archive of Data on Disability to Enable Policy (ADDEP)" ;
NIFRID:synonym "Archive of Data on Disability to Enable Policy" ;
NIFRID:abbrev "ADDEP" ;
definition: "Provides access to data including wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of Americans with Disabilities Act and other disability policies." .
SCR:016316 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AMP-AD Knowledge Portal" ;
NIFRID:synonym "AMP-AD" ;
NIFRID:abbrev "AMP AD" ;
definition: "Repository for distribution of various types of molecular data from human, cell-based and animal model biosamples, analytical results and research tools generated through multiple NIA-supported programs. Currently Portal supports AMP-AD Target Discovery and Preclinical Validation and MOVE-AD Consortia and translational center, MODEL-AD." .
SCR:016317 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AphasiaBank" ;
NIFRID:synonym "Aphasia Bank" ;
definition: "Shared database of multimedia interactions for the study of communication in aphasia.Access to the data in AphasiaBank is password protected and restricted to members of the AphasiaBank consortium group." .
SCR:016319 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "The NINDS Human Cell and Data Repository (NHCDR)" ;
NIFRID:synonym "NINDS Human Cell and Data Repository (NHCDR)" ;
NIFRID:abbrev "NHCDR" ;
definition: "Cell sources currently include fibroblasts and/or induced pluripotent stem cells for Alzheimer's Disease, Amyotrophic Lateral Sclerosis (ALS), Ataxia-telangiectasia, Frontotemporal Lobar Degeneration (FTD), Huntington's Disease, Parkinson's Disease, and healthy controls. Cell sources, including isogenic cell lines for current and new diseases covered by the NINDS will be added over the next several years." .
SCR:016322 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OmicsBean" ;
definition: "Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users." .
SCR:016323 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:stringtie",
"OMICS_07226" ;
rdfs:label "StringTie " ;
definition: "Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ ." .
SCR:016326 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ANNOgesic" ;
definition: "Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data." .
SCR:016328 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "The Pancreatic Beta-Cell Consortium" ;
NIFRID:synonym "Pancreatic B Cell Consortium" ;
NIFRID:abbrev "PBC Consortium" ;
definition: "Portal to provide a repository for beta-cell data, to connect researchers from different backgrounds interested in contributing data, models and/or ideas for new insights into beta-cell biology. Used to understand beta-cell biology and diabetes through a cross-disciplinary approach for the assembly of spatiotemporal multi-scale whole cell models of human pancreatic beta-cells." .
SCR:016330 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FLIR tools" ;
definition: "Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data." .
SCR:016331 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016332" ;
rdfs:label "BrainVision Recorder" ;
definition: "Software for multifunctional recording designed to provide Brain Products GmbH- Solutions for Neurophysiological Research amplifier with a platform for recording setup and execution." .
SCR:016333 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BVA import/export EEGLAB plugin" ;
NIFRID:synonym "Brain Vision Analyser" ;
NIFRID:abbrev "bva-io" ;
definition: "Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software." .
SCR:016334 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Libeep EEGLAB plugin" ;
NIFRID:synonym "ANTeepimport" ;
definition: "Software as an EEGLAB tool used for LIBEEP recordings." .
SCR:016335 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "The Bergen fMRI Toolbox Plugin for EEGLab" ;
definition: "Software package as a set of Matlab tools which allow the correction of fMRI-related gradient artifacts from EEG data. Designed to work within the EEGLAB environment, providing a GUI to remove fMRI gradient artifacts from the EEG. Can also be used from the Matlab command line, providing expert users with the ability to use them in custom scripts." .
SCR:016336 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyPNS " ;
NIFRID:synonym "Python Peripheral Nerve Simulator" ;
NIFRID:abbrev "PyPNS" ;
definition: "Python based software module for the simulation of peripheral nerves. Used in the field of computational neuroscience." .
SCR:016337 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "migec" ;
NIFRID:synonym "Molecular Identifier Guided Error Correction" ;
NIFRID:abbrev "MIGEC" ;
definition: "Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires." .
SCR:016338 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TraCeR " ;
definition: """Software application for recovery of T cell receptor (TCR) data from single cell data.
Used to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. Links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles.""" .
SCR:016339 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Monocle2" ;
NIFRID:synonym "Monocle 2" ;
definition: "Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations." .
SCR:016340 a owl:NamedIndividual ;
rdfs:label "MAST" ;
NIFRID:synonym "Model based Analysis of Single Cell Transcriptomics" ;
definition: "Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data." .
SCR:016341 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Seurat" ;
definition: "Software as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data." .
SCR:016342 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rtsne" ;
NIFRID:synonym "R t-Distributed Stochastic Neighbor Embedding",
"R t-distributed stochastic neighbor embedding" ;
definition: "Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation." .
SCR:016343 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "jVenn" ;
definition: "JavaScript plug-in software application for web environments to analyze data. It is an interactive Venn diagram viewer.Used for comparing lists with Venn Diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized." .
SCR:016344 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Electrographic Seizure Analyzer" ;
definition: "Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting." .
SCR:016345 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:tensorflow" ;
rdfs:label "tensorflow" ;
definition: "Software as an open source machine learning framework for everyone. Library for high performance numerical computation. Allows deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices." .
SCR:016346 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioJupies" ;
definition: "Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text." .
SCR:016347 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LungMap" ;
NIFRID:synonym "The Molecular Atlas of Lung Development Program" ;
NIFRID:abbrev "LungMAP" ;
definition: "Portal for lung histochemistry data. For structural and molecular data regarding normal perinatal and postnatal lung development in the mouse and human. For public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology .Contains lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers. Used to serve as a research resource and public education tool." .
SCR:016348 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BZ-II Measurement Module" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 17, 2024. Software application as a high-accuracy quantification function that supports various biological specimens. Used in KEYENCE automated imaging system for images captured using BZ series fluorescence microscopes." .
SCR:016349 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "masked ICA (mICA) Toolbox" ;
NIFRID:synonym "masked Independent Component Analysis" ;
NIFRID:abbrev "mICA" ;
definition: "Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging." .
SCR:016350 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Altered States Database" ;
NIFRID:abbrev "ASDB" ;
definition: """Database as an open science framework with a scientific data extracted from scientific literature about various altered states of consciousness assessed with questionnaires.
Used to compare what experiences are elicited by different drugs and non-pharmacological methods that induce altered states to help to understand human consciousness functions.
Is listed by Neuroimaging Informatics Tools.""" .
SCR:016351 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "spykesim" ;
definition: "Software library of extended edit similarity measurement for high dimensional discrete-time series signal. Python module that offers functions for measuring the similarity between two segmented multi-neuronal spiking activities with implemented extended edit similarity measurement." .
SCR:016352 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ROIs selection with a non-graphical user interface" ;
definition: """It is non-graphical user interface in MATLAB which relies on keyboard callback functions.
Used for analyzing big data sets.""" .
SCR:016353 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Reglo ICC control with Matlab" ;
definition: "A Matlab adapter class and user interface to control the Reglo ICC peristaltic pump provided by Ismatec." .
SCR:016354 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Elephant: a convolutional network for spike detection from calcium traces" ;
definition: "Program based on convolutional neural networks for spike detection from calcium traces. It is written in Python and Keras." .
SCR:016358 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QModeling" ;
definition: "Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences." .
SCR:016359 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhenoSpD" ;
NIFRID:synonym "Pheno Spectral Decomposition" ;
NIFRID:abbrev "PSD" ;
definition: "Software toolkit for phenotypic correlation estimation and multiple testing correction (Spectral Decomposition, SpD) for human phenome using genome-wide association study (GWAS) summary statistics. It is a command line R based tool." .
SCR:016360 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:SMAGEXP" ;
rdfs:label "SMAGEXP" ;
NIFRID:synonym "Statistical Meta Analysis for Gene EXPression" ;
definition: "Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more." .
SCR:016361 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lilikoi" ;
definition: "Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction." .
SCR:016362 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fractalis" ;
definition: "Software as a scalable open-source service for platform-independent interactive visual analysis of biomedical data. It is a service and a library that work in tandem to equip existing platforms with visual analytical capabilities for explorative data analysis." .
SCR:016363 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:procon" ;
rdfs:label "ProCon - PROteomics CONversion" ;
NIFRID:synonym "PROteomics CONversion" ;
NIFRID:abbrev "ProCon" ;
definition: "Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories." .
SCR:016365 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroCurator" ;
definition: "Software application to perform systematic and collaborative curation of neuroscientific literature. Graphical User Interface (GUI) for the Python package NeuroAnnotation Toolbox (NAT). Used for the systematic annotation of relevant statements and model parameters to be traceable, reusable across projects, structured with controlled vocabularies." .
SCR:016366 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Deeptools" ;
definition: "Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches." .
SCR:016367 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ECIS Model" ;
NIFRID:synonym "Electric Cell-substrate Impedance Sensing",
"Electric Cell-substrate Impedance Sensing Model" ;
NIFRID:abbrev "ECIS" ;
definition: "Instrument that electronically monitors cells grown in tissue culture. It is a real-time, label-free, impedance-based method to study the activities of cells. Used for analysis in cell biological dynamics for cells that do not form tight monolayers such as cancer cell lines. The system supports communication to a PC, allowing data acquisition, analysis, and storage." .
SCR:016368 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bowtie2" ;
rdfs:label "Bowtie 2" ;
NIFRID:synonym "bowtie2 v 2.2.3",
"bowtie 2" ;
definition: "Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method." .
SCR:016369 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Death Index" ;
NIFRID:synonym "Death Index",
"National Mortality Index" ;
NIFRID:abbrev "NDI" ;
definition: "Database of death record information on file in state vital statistics offices. Working with these state offices, the National Center for Health Statistics (NCHS) established the NDI as a resource to aid epidemiologists and other health and medical investigators with their mortality ascertainment activities." .
SCR:016370 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "HMS LINCS Center" ;
NIFRID:synonym "Harvard Medical School (HMS) LINCS Center",
"Harvard Medical School LINCS",
"Harvard Medical School LINCS Center",
"LINCS Center" ;
NIFRID:abbrev "HMS LINCS" ;
definition: "Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation." .
SCR:016371 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BaSiC" ;
NIFRID:synonym "A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images" ;
definition: "Software plugin for Fiji/ImageJ that performs retrospective image correction for optical microscopy. It is based on low rank and sparse decomposition, which corrects both shading in space and background bleaching in time." .
SCR:016372 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroXM Brain Science Suite" ;
NIFRID:synonym "Brain Science Suite",
"NeuroXM",
"NeuroXM Suite" ;
definition: "Software toolkit for semantic integration of multi-modal brain data. It is used to collect, structure, connect, analyze and re-use brain data." .
SCR:016373 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Xenopus Express" ;
NIFRID:synonym "Xenopus Xpress" ;
NIFRID:abbrev "XEP" ;
definition: "Supplier of Frogs and Tadpoles for the scientific community." .
SCR:016374 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GPS" ;
NIFRID:synonym "GPS: Group-based Prediction System",
"Group-based Prediction System",
"Group-based Prediction System (GPS)" ;
definition: "Software that detects kinase-specific phosphorylation sites. GPS provides a platform able to perform its prediction based on a group-based phosphorylation scoring algorithm. It allows users to query multiple protein sequences through a batch prediction mode." .
SCR:016375 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MxPro QPCR" ;
NIFRID:synonym "MxPro QPCR Software" ;
definition: "Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016376 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenPipes" ;
definition: "Software for genomics and bioinformatics analysis. GenPipes includes several python pipelines that cover many genomics applications, such as RNASeq, ChIPSeq, DNASeq, WGBS, HiC, Metagenomics, PacBio assembly, etc." .
SCR:016377 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_iSeq 100",
"SCR_020125" ;
rdfs:label "Illumina | iSeq 100 Sequencing System" ;
NIFRID:synonym "iSeq100",
"iSeq 100" ;
definition: "Benchtop next-generation sequencer to sequence DNA and RNA." .
SCR:016378 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MiniSeq",
"SCR_020136" ;
rdfs:label "Illumina | MiniSeq System" ;
NIFRID:synonym "MiniSeq",
"MiniSeq System" ;
definition: "MiniSeq System to perform range of targeted DNA and RNA applications for low numbers of samples." .
SCR:016379 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MiSeq",
"SCR_020134" ;
rdfs:label "Illumina MiSeq System" ;
NIFRID:synonym "MiSeq" ;
definition: "MiSeq System offers wide range of sequencing applications. Capable of automated paired end reads and up to 15 Gb per run, delivering over 600 bases of sequence data per read. The library prep kits are optimized for variety of applications, including targeted gene, small genome, and amplicon sequencing, 16S metagenomics." .
SCR:016380 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MiSeqDx",
"SCR_020137" ;
rdfs:label "Illumina | MiSeqDx System" ;
NIFRID:synonym "MiSeqDx" ;
definition: "MiSeqDx System is FDA-regulated, CE-IVD-marked, NGS platform for in vitro diagnostic (IVD) testing. System offers both diagnostic and research modes." .
SCR:016381 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_020141" ;
rdfs:label "Illumina | NextSeq 550 System" ;
NIFRID:synonym "NextSeq 550" ;
definition: "The NextSeq 550 System brings the power of a high-throughput sequencing system to your benchtop. With tunable output and high data quality, it provides the flexible power you need for whole-genome, transcriptome, and targeted resequencing." .
SCR:016382 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MiSeq FGx",
"SCR_020133" ;
rdfs:label "Illumina | MiSeq FGx System" ;
NIFRID:synonym "MiSeq FGx",
"MiSeq FGx Forensic Genomics",
"MiSeq FGx Forensic Genomics System" ;
definition: "MiSeq FGx Forensic Genomics System is the first fully validated, next-generation sequencing (NGS) solution designed for forensic science. Dedicated library kits and analytical software take you from DNA-to-answer with streamlined efficiency." .
SCR:016383 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HiSeq 2500",
"SCR_020123" ;
rdfs:label "Illumina | HiSeq 2500 System" ;
NIFRID:synonym "HiSeq 2500" ;
definition: "High-throughput sequencing system. High-quality data using proven Illumina SBS chemistry has made it the instrument of choice for major genome centers and research institutions throughout the world.HiSeq 2500 System has been discontinued. Illumina will support the instrument and intends to supply the reagents through February 28, 2023." .
SCR:016384 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NextSeq 550Dx",
"SCR_020138" ;
rdfs:label "Illumina | NextSeq 550Dx System" ;
NIFRID:synonym "NextSeq 550Dx",
"NextSeq 550Dx System" ;
definition: "Sequencer that is CE-in vitro diagnostic (IVD) marked, enabling clinical laboratories to develop and perform a wide range of applications, from NGS IVD assays using targeted panels, to clinical research applications that include methods from targeted panels to whole genomes." .
SCR:016385 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HiSeq X",
"SCR_020131" ;
rdfs:label "Illumina | HiSeq X" ;
NIFRID:synonym "HiSeq X" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15,2023. Sequencer for whole-genome sequencing. System consists of HiSeq X ultra-high-throughput instruments that deliver over 18,000 human genomes per year." .
SCR:016386 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HiSeq 3000/4000",
"SCR_020127" ;
rdfs:label "Illumina HiSeq 3000/HiSeq 4000 Sequencing System" ;
NIFRID:synonym "HiSeq 3000",
"HiSeq 3000/4000",
"HiSeq 4000" ;
definition: "Sequencer that uses patterned flow cell technology to provide high-performance sequencing. Perform production-scale, high-throughput exome or transcriptome sequencing projects quickly and economically." .
SCR:016387 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NovaSeq_6000",
"SCR_020150" ;
rdfs:label "Illumina | NovaSeq 6000 Sequencing System" ;
NIFRID:synonym "Illumina NovaSeq 6000",
"Illumina NovaSeq 6000 Sequencing" ;
definition: "High-throughput platform used for next-generation sequencing (NGS) applications, including whole-genome, whole-exome, and whole-transcriptome sequencing. It is designed to provide a scalable, high-volume, and reliable way to sequence DNA and RNA for a wide range of genomic studies, from research to clinical applications." .
SCR:016388 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_iScan",
"SCR_020128" ;
rdfs:label "Illumina | iScan System" ;
NIFRID:synonym "iScan System" ;
definition: "Can scan thousands of array samples per day, without sacrificing data quality or reproducibility. Supports expansive portfolio of genetic analysis assays, from high-throughput genotyping to DNA methylation analysis." .
SCR:016390 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AfterQC" ;
NIFRID:synonym "After QC" ;
definition: "Software that performs automatic filtering, trimming, error removing, and quality control for fastq data." .
SCR:016391 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.423085.8",
"ISNI: 0000 0004 0595 5711",
"Wikidata: Q30284101" ;
rdfs:label "Avanti Polar Lipids" ;
NIFRID:synonym "Avanti",
"Avanti Lipids",
"Avanti Polar Lipids Inc" ;
NIFRID:abbrev "APL" ;
definition: "Supplier of polar lipids." .
SCR:016392 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Easy fMRI" ;
NIFRID:synonym "easyfMRI" ;
definition: "Software that employs machine learning techniques and high-performance computing for analyzing task-based fMRI datasets. It applies Feature Analysis, Hyperalignment, Multi-voxel Pattern Analysis (MVPA), Representational Similarity Analysis (RSA), and more." .
SCR:016393 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AngioTool" ;
definition: "Software that performs quantitative analysis of angiogenesis. It specializes in quantitative assessment of various vessel morphometric and spatial parameters, including vessel length and density, branching index, lacunarity, etc." .
SCR:016394 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vensim" ;
definition: "Simulation software for improving the performance of real systems. Used for developing, analyzing, and packaging dynamic feedback models." .
SCR:016395 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "HIRN Coordinating Center" ;
NIFRID:synonym "Human Islet Research Center Coordinating Center" ;
NIFRID:abbrev "HIRN CC",
"HIRNCC" ;
definition: "Consortium that provides infrastructure to promote communication and collaboration among current and future HIRN participants, facilitating scientific advances and the sharing of data, tools, and reagents among HIRN members and the research community at large. " .
SCR:016397 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AIIA-GMT" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 14, 2018. An XML-RPC client of a web-service server which provides the service to recognize named entities in the biomedical articles. It is Gene Mention Tagger (GMT) for Biological Text Mining." .
SCR:016398 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hierarchical Region Splitting" ;
NIFRID:synonym "Hierarchical Region Splitting (HRS)" ;
NIFRID:abbrev "HRS" ;
definition: "Algorithm for computational imaging of MRI data that detects and quantifies ischemic core–penumbra using only a single MRI modality (T2- or diffusion-weighted imaging, T2WI/DWI). It can be used with 3D data on lesions and normal-appearing brain matter (NABM) volumes." .
SCR:016399 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GOTrack" ;
definition: "Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis." .
SCR:016400 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Center for Animal Resources and Development" ;
NIFRID:synonym "CARD:Center for Animal Resources and Development" ;
NIFRID:abbrev "CARD" ;
definition: "Center for Animal Resources and Development is an international repository and distribution center for production, cryopreservation, and supply of genetically engineered mice.Provides a summary of institutions, organizations, and individuals contributing mouse resource information to the IMSR database." .
SCR:016401 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of North Carolina Systems Genetics Core Facility" ;
NIFRID:synonym "Chapel Hill - Systems Genetics Core",
"UNC Systems Genetics",
"University of North Carolina" ;
definition: "Core focused on systems genetics approach to understanding diseases, development, aging, and fertility in mouse. Projects range from development of new community resources, such as Collaborative Cross, to development of tools and assays for measuring genetic diversity and discerning genomic structure. Collaborative Cross is reference population for mapping multigenic traits that would be free of population structure and it is new panel of recombinant inbred lines generated by randomizing genetic diversity of existing inbred mouse resources." .
SCR:016402 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Animal Resources Centre" ;
NIFRID:synonym "ARC:Animal Resources Centre" ;
NIFRID:abbrev "ARC" ;
definition: "The Animal Resources Centre (ARC) is a self-funding Statutory Authority of the Government of Western Australia for biomedical research to produce and supply genetically-defined, specific pathogen free (SPF) research rats and mice. Provides contribution of mouse resource information to the IMSR database." .
SCR:016403 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "CMMT Mouse Animal Production Service" ;
NIFRID:synonym "Centre for Molecular Medicine and Therapeutics MAPS",
"Centre for Molecular Medicine and Therapeutics Mouse Animal Production Service",
"Dr. Elizabeth M. Simpson PhD",
"Elizabeth M. Simpson",
"Mouse Animal Production Service",
"Mouse Animal Production Service (MAPS)" ;
NIFRID:abbrev "CMMT EMS",
"CMMT MAPS",
"EMS",
"MAPS" ;
definition: "Supplier of mice for research purposes. The service is run by Dr. Elizabeth M. Simpson, Ph.D. and is affiliated with her lab." .
SCR:016404 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Oriental BioService Inc." ;
NIFRID:synonym "Oriental BioService",
"Oriental BioServices" ;
NIFRID:abbrev "OBS" ;
definition: "Supplier of mice for research purposes." .
SCR:016405 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "National Applied Research Laboratories" ;
NIFRID:synonym "National Applied Research Laboratory",
"National Laboratory Resource Center",
"National Laboratory Resource Center Rodent Model Resource Center",
"Rodent Model Resource Center" ;
NIFRID:abbrev "NARL",
"NLAC",
"NLAC RMRC",
"RMRC NARL",
"RMRC NLAC",
"RMRC-NLAC" ;
definition: "Supplier of mice for research purposes." .
SCR:016406 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "National Resource Center for Mutant Mice" ;
NIFRID:synonym "Model Animal Resource Imformation Platform",
"Model Animal Resource Information Platform",
"Nanjing University Model Animal Research Institute",
"National Resource Center for Mutant Mouse" ;
NIFRID:abbrev "MARIP",
"NRCMM" ;
definition: "Supplier of mice for research purposes." .
SCR:016407 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Shanghai Model Organisms Center" ;
NIFRID:synonym "Inc. SMOCShanghai Model Organisms Center",
"Shanghai Model",
"Shanghai Model Center",
"Shanghai Model Organism Center" ;
NIFRID:abbrev "SMOC" ;
definition: "Supplier of mice for research purposes. Provides technical services, model organisms, gene editing and decoding." .
SCR:016408 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JAX Mice and Services" ;
NIFRID:synonym "JAX Mice",
"JAX Mice Service",
"JAX Mouse and Services",
"JAX Mouse Service",
"Mice and Services" ;
NIFRID:abbrev "IMSR_JAX",
"JAX",
"JAX MS",
"JMS" ;
definition: "Supplier of mice for research purposes." .
SCR:016409 a NLX:152328,
owl:NamedIndividual ;
NIFRID:synonym "JAX Oak Ridge",
"Oak Ridge",
"Oak Ridge Collection",
"Oak Ridge Lab",
"Oak Ridge Laboratory",
"Oak Ridge National Laboratory",
"Oakridge",
"The Oak Ridge National Laboratory (ORNL)" ;
NIFRID:abbrev "ORC",
"ORNL" ;
definition: "Supplier of mice for research purposes." .
SCR:016410 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Taconic Biosciences" ;
NIFRID:synonym "eTaconic",
"Taconic",
"Taconic Bio Sciences",
"Taconic Bioscience",
"Taconic Mice",
"Taconic Mouse Supply" ;
NIFRID:abbrev "TAC",
"TB" ;
definition: "Supplier of mice for research purposes." .
SCR:016411 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MicroFilament Analyzer" ;
NIFRID:synonym "MFA" ;
NIFRID:abbrev "MFA:MicroFilament Analyzer" ;
definition: "Software package for image analysis to determine the orientation of filamentous structures on digital images. Used as an image‐processing tool for analyzing cytoskeleton and cellulose fiber orientation in pant imagesk." .
SCR:016414 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Letswave" ;
definition: "Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals." .
SCR:016415 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:metacyto" ;
rdfs:label "MetaCyto" ;
definition: "Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database." .
SCR:016416 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Monica monitor" ;
definition: "A peel and stick in-room ambulatory fetal monitoring solution by Monica Healthcare Ltd. Measures fetal heart rate (FHR), maternal heart rate (MHR) and uterine activity (UA)." .
SCR:016417 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "findMotif.pl" ;
definition: "Software tool to analyze the promoters of genes and look for motifs that are enriched in the target gene promoters relative to other promoters. Used for gene based analysis to provide a list of genes that should contain the same elements, such as genes that are co-regulated. It includes gene ontology analysis and can be used to look for RNA motifs in mRNAs." .
SCR:016418 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pheatmap",
"OMICS_26726" ;
rdfs:label "pheatmap" ;
NIFRID:synonym "pretty heatmap" ;
definition: "Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters." .
SCR:016420 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fetal Actocardiograph MT-516" ;
definition: "Fetal actocardiograph instrument provided by TOITU CO., LTD." .
SCR:016422 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KiloSort" ;
definition: "Software tool that implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings." .
SCR:016423 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BIOQUANT Life Science" ;
definition: "Software tool to collect and analyse data on images of tissue slides or welled plates.Supports high-throughput immunofluorescence and immunohistochemistry, stereology, densitometry, and 3D modeling. Used in bioscience research in animal models and human biopsy, developmental neuroscience, traumatic brain/spinal cord injury, glaucoma, eye-movement disorders, cardiovascular disease and muscle disorders." .
SCR:016424 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "kCSD-Matlab" ;
NIFRID:synonym "kernel Current Source Density" ;
NIFRID:abbrev "kCSD" ;
definition: "Software tool for analyzing recordings from multielectrodes. Source code for the Matlab implementation of the Kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes." .
SCR:016425 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OMA Orthology database" ;
NIFRID:synonym "Orthologous MAtrix" ;
NIFRID:abbrev "OMA" ;
definition: "Web based database interface for orthology prediction for the inference of orthologs among complete genomes. Used to relate genes across many species., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016427 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ximmer" ;
definition: "Software to help users of targeted high throughput genomic sequencing data to accurately detect copy number variants (CNVs). Framework for running and evaluating other copy number detection tools.Used for evaluating and improving performance of CNV detection in exome and targeted sequencing data." .
SCR:016428 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:nextflow" ;
rdfs:label "Lifebit Deploit" ;
definition: "Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines." .
SCR:016429 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:MGnify",
"r3d100011192" ;
rdfs:label "MGnify" ;
NIFRID:synonym "EBI Metagenomics" ;
definition: "Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020." .
SCR:016430 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ViewTool Cheng Lab" ;
NIFRID:synonym "ChengLab ViewTool",
"muCT Viewer",
"ViewTool ChengLab" ;
definition: "Web application viewer for large microscopy data." .
SCR:016431 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FCS Express" ;
definition: "Software tool for flow and image cytometry data analysis by De Novo Software company." .
SCR:016433 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013461" ;
rdfs:label "Canadian Open Neuroscience Platform" ;
NIFRID:synonym "CONP:Canadian Open Neuroscience Platform" ;
NIFRID:abbrev "CONP" ;
definition: "Web interface that facilitates open science for neuroscience community by simplifying global access to and sharing of datasets and tools. Portal internalizes typical data cycle of research project, beginning with data acquisition, followed by data processing with published tools, and ultimately publication of results with link to original dataset. Platform to form interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing. Provides unified interface to Canadian neuroscience research community. Open neuroscience research with sharing of both data and methods, to create large-scale databases, development of standards for sharing, facilitation of advanced analytic strategies, open dissemination to global community of neuroscience data and methods, and establishment of training programs for next generation of computational neuroscience researchers." .
SCR:016434 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Suite2P" ;
definition: "Software package for processing two-photon recordings. Available together with a graphical user interface that allows manual curation of the results. Used in two-photon microscopy for the analysis of data from two-photon imaging. Registers raw movies, detects active cells, extracts their calcium traces and infers their spike times." .
SCR:016435 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016621" ;
rdfs:label "Primate Data Exchange" ;
NIFRID:synonym "PRIME-DE:PRIMate Data Exchange" ;
NIFRID:abbrev "PRIME-DE" ;
definition: "Open resource for nonhuman primate imaging.Used for aggregation independently acquired non-human primate magnetic resonance imaging (MRI) datasets and openly sharing them via the International Neuroimaging Data-sharing Initiative (INDI).Consortium and data collection for the neuroimaging community to map the non-human primate connectome. Anatomical, functional, and diffusion MRI datasets openly shared via the International Neuroimaging Data sharing Initiative (INDI)." .
SCR:016436 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CReATE" ;
NIFRID:synonym "Clinical Research in ALS and Related Disorders for Therapeutic Development" ;
definition: "Biorepository of samples collected from patients with ALS, ALS-frontotemporal dementia (ALS-FTD), primary lateral sclerosis (PLS), progressive muscular atrophy (PMA), hereditary spastic paraplegia (HSP) and multisystem proteinopathy (MSP). Used by Consortium members and the scientific community to advance therapeutic development through study of the relationship between clinical phenotype and underlying genotype, and also through the discovery and development of biomarkers." .
SCR:016437 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Binder" ;
definition: "Open-source web application for managing digital repositories. Allows to create custom computing environments that can be shared and used by many remote users.Turns a GitHub repository containing a collection of Jupyter Notebooks into a collection of interactive notebooks. With Binder, open those notebooks in an executable environment, making your code immediately reproducible by anyone, anywhere." .
SCR:016438 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Toitu MT 325 fetal actocardiograph" ;
definition: "This equipment is used for the purpose of monitoring fetal status." .
SCR:016439 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Freiburg Vision Test ('FrACT')" ;
NIFRID:synonym "Freiburg Acuity and Contrast Test" ;
NIFRID:abbrev "FrACT" ;
definition: "Software tool for visual test battery in form of a free computer program.Can be run within your browser or download as a stand-alone program. Used by many vision labs, optometrists and ophthalmologists." .
SCR:016440 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Respironics Actiware" ;
definition: "Software package to analyze, manage, and export recorded activity data from all Actiwatch models. Used to view long-term sleep/wake patterns, activity, illuminance, and event markers in an easy-to-read actogram format." .
SCR:016441 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016537" ;
rdfs:label "Diabetes Epigenome Atlas" ;
definition: "Collects and provides data on the human genome and epigenome to facilitate genetic studies of type 2 diabetes and its complications. A component of the AMP T2D consortium, which includes the National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK) and an international collaboration of researchers." .
SCR:016442 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Portcullis" ;
definition: "Software for filtering invalid Splice junctions from pre-aligned RNA-seq data. It takes as input a BAM file generated by an RNAseq mapper, then analyses and quantifies all splice junctions in the file before filtering (culling) those which are unlikely to be genuine." .
SCR:016443 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MIES" ;
NIFRID:synonym "MIES - Multichannel Igor Electrophysiology Suite",
"MIES: Multichannel Igor Electrophysiology Suite",
"Multichannel Igor Electrophysiology Suite",
"Multichannel Igor Electrophysiology Suite (MIES)" ;
definition: "Software for Electrophysiology functions. It was developed by the Allen Institute." .
SCR:016444 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ACQ4" ;
NIFRID:synonym "ACQ4 Neurophysiology Acquisition and Analysis System",
"Acquisition4",
"Acquisition 4",
"Neurophysiology acquisition and analysis for Python" ;
definition: "Python-based software for experimental neurophysiology. It includes support for patch-clamp electrophysiology, multiphoton imaging, scanning laser photostimulation, and many other experimental techniques." .
SCR:016445 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Docker Desktop" ;
NIFRID:synonym "Docker",
"DockerDesktop" ;
NIFRID:abbrev "DD" ;
definition: "Software development environment that helps users build containerized software using Docker and Kubernetes softwares. It is executable on desktop and cloud, and allows access to a vast library of community containerized content in Docker Hub." .
SCR:016446 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Mutant Mouse Resource and Research Center - Jackson Laboratory" ;
NIFRID:synonym "Jackson Laboratory MMRRC",
"Jackson Laboratory Mutant Mouse Resource and Research Center",
"JAX Mutant Mouse Resource and Research Center",
"Mutant Mouse Resource and Research Center - JAX" ;
NIFRID:abbrev "JAX MMR",
"JAX MMRRC",
"MMRRC JAX" ;
definition: "Center for mutant mouse research and distribution. The objectives of the JAX MMRRC are to: identify and evaluate biomedically-significant mice, import/acquire and archive mouse strains, distribute mouse strains, and operate a control program to ensure genetic stability." .
SCR:016447 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Mutant Mouse Resource and Research Center - University of Missouri" ;
NIFRID:synonym "MMRRC University of Missouri",
"Mutant Mouse Resource and Research Center - UM",
"UM Mutant Mouse Resource and Research Center",
"University of Missouri MMRRC" ;
NIFRID:abbrev "MMRRC UM",
"UM MMRRC" ;
definition: "Center that supplies mice and conducts research projects focused on the role of mice as animal models. Some of these projects include refinement of models to ensure study reproducibility, as well as development and improvement of economical methods for cryopreservation of mouse strains." .
SCR:016448 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1650" ;
rdfs:label "University of California at Davis Mutant Mouse Resource and Research Center" ;
NIFRID:synonym "California MMRRC",
"Davis MMRRC",
"Mutant Mouse Resource and Research Center - UCD",
"Mutant Mouse Resource and Research Center - University of California at Davis",
"Mutant Mouse Resource and Research Center UC Davis",
"UC Davis MMRRC",
"UC Davis Mutant Mouse Resource and Research Center",
"UCD Mutant Mouse Resource and Research Center" ;
NIFRID:abbrev "MMRRC UCD",
"UCD MMRRC" ;
definition: "Center that imports, archives, maintains, and distributes mutant mouse alleles as live mice, frozen germplasm, stem cells, and molecular vectors for use in biomedical research. The MMRRC Davis receives transgenics, knockouts, and other kinds of mutant mouse lines at no cost to the donor, and after re-derivation and cryopreservation, distributes breeding stock, germplasm, cells, or tissues of genetically-defined and pathogen-free mice for a small fee to requesting investigators." .
SCR:016449 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Mutant Mouse Resource and Research Center - University of North Carolina" ;
NIFRID:synonym "Mutant Mouse Resource and Research Center UNC",
"Mutant Mouse Resource and Research Center University of North Carolina",
"UNC Chapel Hill MMRRC",
"UNC Chapel Hill Mutant Mouse Resource and Research Center",
"University of North Carolina Mutant Mouse Resource and Research Center" ;
NIFRID:abbrev "MMRRC UNC",
"MMRRC UNCCH",
"UNC MMRRC" ;
definition: "Center that is a mouse cryoarchive and distribution center, which incorporates research goals that synergize with and extend the value of the resource. The goals of the UNC Chapel Hill center are to streamline and improve operating procedures, establish a comprehensive cryoarchive, develop and disseminate computational tools for mouse genotyping, and examine the effect of paternal age and epigenetics on mutation rate." .
SCR:016450 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gaussian-Copula Mutual Information (GCMI)" ;
NIFRID:synonym "Gaussian-Copula Mutual Information",
"gcmi : Gaussian-Copula Mutual Information" ;
NIFRID:abbrev "GCMI" ;
definition: "Software package of functions for calculating mutual information and other information theoretic quantities using a parametric Gaussian copula." .
SCR:016451 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SwarmSight" ;
NIFRID:synonym "Swarm Sight",
"SwarmSight Software" ;
definition: "Software for video analysis with modules to track insect antenna and proboscis movements. Its purpose is to assess the aggregate movement or activity levels of groups or swarms of animals." .
SCR:016452 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Nebraska Medical Center Translational Mouse Model Core Facility" ;
NIFRID:synonym "Center for Humanized Mice",
"UNMC Translational Mouse Model Core Facility" ;
definition: "Center that conducts and supports research with mouse models. It also supplies mouse models to researchers." .
SCR:016453 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Referral Center for Animal Models of Human Genetic Diseases" ;
NIFRID:synonym "PennVet Referral Center for Animal Models of Human Genetic Diseases",
"University of Pennsylvania School of Veterinary Medicine Referral Center for Animal Models of Human Genetic Diseases",
"UPenn Referral Center for Animal Models of Human Genetic Diseases" ;
definition: "Center that aims to discover, characterize, maintain breeding colonies, and make available dog and cat models with hereditary diseases homologous to those found in human patients that can be used to translate preclinical trials from kennel to clinic. The animal models represent true orthologs of their respective human disease, involving defects in homologous genes resulting in similar molecular, biochemical, pathological, and clinical phenotype as in human patients." .
SCR:016455 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dormed Hellas | Monica AN24" ;
definition: "Monitors the electrical signals on the patient’s abdomen by using the abdominal fECG and mECG wave shape to uniquely identify and separate the maternal and fetal heart rates." .
SCR:016456 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PopMedNet" ;
NIFRID:synonym "Population Medicine Network" ;
definition: "Software as an open source informatics platform to facilitate the implementation and operation of distributed health data networks. Consists of a web-based portal for distributing requests and administering the network, and the DataMart Client. Designed by the Therapeutics Research and Infectious Disease Epidemiology (TIDE) group at the Department of Population Medicine (DPM) of the Harvard Pilgrim Health Care Institute (HPHCI) to enable creation, operation, and governance of distributed health data networks." .
SCR:016457 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eulerAPE" ;
NIFRID:synonym "Euler Ape" ;
definition: "Software that uses ellipses to automatically draw accurate area-proportional Venn diagrams for 3-set data. It generates an exact diagram for most of the cases, and when it fails, the best diagram obtained through the hill climbing search is displayed, together with the inaccuracy values for each region." .
SCR:016458 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nornir" ;
definition: "Software application to take large sets of overlapping images in 2D and 3D and produce registered 3D volumes of any size and scale. Registered slices may be exported as a single large images or viewed/annoted with Viking viewer. Used on transmission electron microscopy, scanning electron microscopy images, and light microscopy images." .
SCR:016459 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCBI Biocollections" ;
NIFRID:synonym "NCBI Biocollections:National Center for Biotechnology Information Biocollections" ;
definition: "Registry of bio-collections linked to genomes. Collection of curated dataset of metadata for culture collections, museums, herbaria and other natural history collections, including Darwin Core institution and collection codes, and URL formulae for mapping specimen ids to web pages at the collection site." .
SCR:016460 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100010696" ;
rdfs:label "Global Catalogue of Microorganisms" ;
NIFRID:synonym "GCM:Global Catalogue of Microorganisms" ;
NIFRID:abbrev "GCM" ;
definition: "Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information." .
SCR:016461 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MIRRI" ;
NIFRID:synonym "Microbal Resource Research Infrastructure" ;
definition: "Microbial stock center. Collaborative platform for the pan-European research infrastructure for microbial resources. Provides access to microorganisms, their derivatives, associated data and services for research, development and application." .
SCR:016463 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "1000 Fungal Genome Project" ;
definition: "Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment." .
SCR:016464 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "IALS Core Facilities" ;
NIFRID:synonym "Institute for Applied Life Sciences" ;
NIFRID:abbrev "IALS" ;
definition: "Center to help translate life science research into products that improve human health. Available to internal and external users, through the Institute for Applied Life Sciences (IALS)." .
SCR:016465 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "NRRL ARS Culture Collection" ;
NIFRID:synonym "ARS:Agricultural Research Service",
"NRRL:Northern Regional Research Laboratory" ;
NIFRID:abbrev "NRRL ARS" ;
definition: "Center that collects, deposits, maintains bacteria and fungi, and facilitates microbiological research to advance agricultural production, food safety, public health, and economic development. Housed within the Mycotoxin Prevention and Applied Microbiology Research Unit at the National Center for Agricultural Utilization Research in Peoria, Illinois." .
SCR:016466 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "UAMH Centre for Global Microfungal Biodiversity" ;
definition: "Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi." .
SCR:016467 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Centre for Agriculture and Biosciences International" ;
NIFRID:synonym "CABI:Centre for Agriculture and Biosciences International" ;
NIFRID:abbrev "CABI" ;
definition: "An international not-for-profit organization to solve problems in agriculture and the environment. Specialize in microbial identification and verification, and provide professional microbiology services in support of industry, academia and agriculture. Established by a United Nations." .
SCR:016469 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mentalist" ;
rdfs:label "MentaLiST" ;
definition: "Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes." .
SCR:016470 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Knowledge Maps" ;
definition: "Software tool as an open source knowledge mapping software that increases the visibility of research findings for science and society. Visual interface to the world's scientific knowledge." .
SCR:016471 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Unpaywall" ;
definition: "Database of free scholary articles. Content from over 50,000 publishers and repositories easy to find, track, and use. A website featuring web-based tools created and maintained by Impactstory, Inc." .
SCR:016472 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaPGN" ;
NIFRID:synonym "Meta PanGeNome" ;
definition: "Pipeline for construction and graphical visualization of annotated pangenome networks from microbial genomes. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data provides pangenome analysis to uncultured microbial taxa., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016473 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NAT/NCS2 Hound" ;
NIFRID:synonym "NCS2:Nucleobase Cation Symporter 2",
"Nucleobase Ascorbate Transporter" ;
NIFRID:abbrev "NAT",
"NCS2" ;
definition: "Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins." .
SCR:016474 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCOSS" ;
NIFRID:synonym "Sustainability Coalition for Open Science Services" ;
definition: "Network to facilitate funding to ensure the long-term sustainability of the world’s open science infrastructure. A community-led effort to provide a framework for libraries, policymakers and other stakeholders to collectively fund and stabilize an infrastructure of freely available open science services." .
SCR:016475 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lenntech activity coefficient calculator" ;
definition: "Software tool to calculate the activity coefficient of an ion in solution by Lenntech B.V. Determines the ionic strength of solution by using the concentration of ions present in drinking water." .
SCR:016476 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PiGx" ;
NIFRID:synonym "Pipelines in Genomics" ;
definition: "Software application as a collection of genomic pipelines used for raw fastq read data of bisulfite experiments, RNAseq samples, single cell dropseq analysis, reads from ChIPseq experiments, analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data." .
SCR:016477 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_681",
"SCR_019051" ;
rdfs:label "CERVO Canadian Optogenetics and Vectorology Foundry Core Facility" ;
NIFRID:synonym "Canadian Molecular Tools Platform Core Facility",
"Canadian Neurophotonics Centre Molecular Tools Platform Core Facility",
"Canadian Neurophotonics Platform - Viral Vector Facility",
"Canadian Neurophotonics Platform Viral Vector Core",
"Molecular Tools Platform",
"Neurophotonics Platform Viral Vector Core" ;
NIFRID:abbrev "CNP",
"COVF",
"MTP" ;
definition: "Core facility responsible for custom adeno-associated virus (AAV) and lentivirus production available through Canadian Neurophotonics Platform. Services include design, cloning and production of molecular constructions in order to produce plasmid expression vectors or to generate transgenic animals and design, including advice and assistance for choice of suitable vectors required by investigators." .
SCR:016478 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "K.Kucharczyk Electrophoretic Techniques (Techniki Elektroforetyczne Spzoo, Poland)" ;
definition: "Commercially available services for biomedical research. Includes the quantitative determination of the methylation level of selected epigenetic markers, designing and validation of primers and conditions for the multiplication of selected markers by PCR and determination of their methylation level by the pyrosequencing method. Service electro-optical laboratory equipment and offers specialized repair services: PCR thermal cyclers, Laboratory power supplies, ELISA plate readers." .
SCR:016479 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_019096",
"SCR_021965" ;
rdfs:label "IBM SPSS Statistics" ;
NIFRID:synonym "SPSS Statistics v24",
"SPSS Statistics v25",
"SPSS Statistics v26",
"SPSS Statistics v27" ;
definition: "Software package for statistics. Used to analyze and visualize data. Extensions can be used, Python and R programming language code, to integrate with open source software. Available for Windows and Mac operating systems.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. Versions that were released after the acquisition would be given origin or publisher of IBM Corp. in Armonk, NY." .
SCR:016481 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Viewbox4, Cephalometric software" ;
definition: "Software for cephalometric analysis. Customizable. Allows rendering, viewing and measuring of 3D data from CT scanners. Used in orthodontic departments for analysis of the dental and skeletal relationships of a human skull." .
SCR:016482 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "geomorph" ;
NIFRID:synonym "geometric morphometric" ;
definition: "Software package for performing all stages of geometric morphometric shape analysis of landmark points and curves in 2-and-3-dimensions as well as 3D surfaces in the R statistical computing environment." .
SCR:016483 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MorphoJ" ;
definition: "Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data." .
SCR:016484 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Covidence" ;
definition: "Software tool for systematic review. A not-for-profit service working in partnership with Cochrane library to improve the production and use of systematic reviews." .
SCR:016485 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PNNsMiceMachineVision" ;
NIFRID:synonym "Probabilistic Neural Networks MiceMachineVision" ;
definition: """Data and code (Python) related to research paper: V. Javier Traver, Filiberto Pla, Marta Miquel, Maria Carbo-Gas, Isis Gil-Miravet, Julian Guarque-Chabrera
"Cocaine-induced preference conditioning: a machine vision perspective".""" .
SCR:016486 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016487" ;
rdfs:label "LINCS Project" ;
NIFRID:synonym "Library of Integrated Network based Cellular Signatures",
"LINCS",
"LINCS Program" ;
definition: "Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center." .
SCR:016488 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Generalized Relevance Network" ;
NIFRID:synonym "GenRelNet:Generalized Relevance Network" ;
NIFRID:abbrev "GenRelNet" ;
definition: "Software tool with approaching infers network structure by measuring the pairwise associations between the data observed in the individual network nodes. It follows the more general statistical perspective of GRN inference, where no explicit model of the data is built or assumed." .
SCR:016489 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Drug Gene Budger" ;
NIFRID:abbrev "DGB" ;
definition: """Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only.
Application for ranking drugs to modulate specific gene based on transcriptomic signatures.""" .
SCR:016490 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Inxight" ;
definition: "Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use." .
SCR:016491 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VoxBlast" ;
definition: "Software application for science and medicine which offers 3-D Measurement, 3-D Volume Visualization, and 3-D Rendering for any 3-D data. It accepts stacks of registered 2-D images and creates 3-D projections from any viewpoint." .
SCR:016492 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:transit" ;
rdfs:label "TRANSIT" ;
definition: "Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions." .
SCR:016493 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016553" ;
rdfs:label "Kids First Data Resource Portal" ;
NIFRID:synonym "Data Resource Portal" ;
NIFRID:abbrev "DRP" ;
definition: "Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects." .
SCR:016494 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VGG-16" ;
NIFRID:synonym "Visual Geometry Group 16" ;
definition: "Software tool used in visual object recognition software research to analyze images for scenes, objects, faces, and other content. A convolutional neural network for large scale image recognition. Weights for the VGG-16 model architecture trained on an image database Imagenet." .
SCR:016495 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | Vibratome VT1000S Leica | Microsystems" ;
NIFRID:synonym "Leica Vibratome VT1000S Leica Biosystems" ;
definition: "Vibrating blade microtome for sectioning by Leica Biosystems. Used in neurophysiology, neuropathology, experimental pathology, botany (roots and plants) and industry (foams)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016496 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tests for deviation from Hardy-Weinberg equilibrium " ;
definition: "Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases." .
SCR:016497 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016758" ;
rdfs:label "Image Pro" ;
NIFRID:synonym "Image Pro Premier",
"Image-Pro",
"Image-Pro Premier" ;
definition: "Software platform to perform image processing, analysis, and data reporting for microscope-based research and quality inspection." .
SCR:016498 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:splicing_express" ;
rdfs:label "Splicing Express" ;
definition: "Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems." .
SCR:016499 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MotionCor2" ;
NIFRID:synonym "MotionCor" ;
definition: "Software tool for anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Used to describe the sample motion as a local deformation that varies smoothly throughout the exposure. A program running on Linux." .
SCR:016500 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GCTF" ;
NIFRID:synonym "GContrast Transfer Function" ;
definition: "Software tool as a Graphics Processing Units (GPU) accelerated computer program for real-time contrast transfer function (CTF) determination and correction. Used for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016501 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cryoSPARC" ;
definition: "Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery." .
SCR:016502 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:cistem" ;
rdfs:label "cisTEM" ;
NIFRID:synonym "computational imaging system for Transmission Electron Microscopy" ;
definition: "Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them." .
SCR:016503 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bsoft" ;
NIFRID:synonym "Bernard's Software" ;
definition: "Software package and a platform for the processing of electron micrographs in structural biology. Supports different image file formats used in electron microscopy (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016504 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Jpred" ;
NIFRID:synonym "Jprotein secondary structure PREDiction" ;
definition: "Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions." .
SCR:016505 a "Resources",
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:dinies" ;
rdfs:label "DINIES" ;
NIFRID:synonym "Drug target Interaction Network Inference Engine based on Supervised analysis" ;
definition: "Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference." .
SCR:016506 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CajaDB" ;
definition: "Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network." .
SCR:016507 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RNA22" ;
NIFRID:synonym "RiboNucleic Acid 22" ;
definition: "Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases." .
SCR:016508 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miRmap" ;
definition: "Software application as an open source Pyton library to search and predict miRNA targets." .
SCR:016509 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miRWalk" ;
definition: "Software tool to store the predicted and the experimentally validated microRNA (miRNA)-target interaction pairs. Predictions within the complete sequence of genes of human, mouse, and rat genomes. Integrates a comparative platform of miRNA-binding sites resulting from ten different prediction datasets." .
SCR:016510 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DIANA microT-CDS" ;
definition: "Software tool to search for the targets of annotated miRNAs based on microT-CDS algorithm." .
SCR:016511 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MIMMS microscope 1.0 (2016)" ;
NIFRID:synonym "Modular In vivo Multiphoton Microscopy System" ;
NIFRID:abbrev "MIMMS" ;
definition: "Modular platform for performing two‐photon laser scanning microscopy (TPLSM) optimized for in vivo applications." .
SCR:016512 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Dundee Behavioural Neuroscience Core Facility" ;
definition: "University service for testing behaviour of rodents. Provides facilities and training for researchers to conduct experiments themselves within the core facility." .
SCR:016513 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "brainlife.io" ;
definition: "Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain." .
SCR:016514 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EPSD Eukaryotic Phosphorylation Site Database" ;
NIFRID:synonym "EPSD",
"Eukaryotic Phosphorylation Site Database" ;
definition: "Software tool as an annotated database of protein phosphorylation sites in eukaryotes. Contains experimentally identified and conserved p-sites which were collected from phosphoproteomic studies." .
SCR:016517 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Nanodrop_1000",
"SCR_018035",
"SCR_020560" ;
rdfs:label "Thermo Fisher | Nanodrop 1000 Spectrophotometer" ;
NIFRID:synonym "NanoDrop 1000",
"NanoDrop 1000 Spectrophotometer",
"Nanodrop ND-1000",
"Thermo Scientific NanoDrop 1000" ;
definition: "Spectrophotometer for measurement and analysis of 1 ul samples with high accuracy and reproducibility. Full spectrum from 220nm to 750nm spectrophotometer utilizes patented sample retention technology that employs surface tension alone to hold sample in place. No need for cuvettes. Has capability to measure highly concentrated samples without dilution." .
SCR:016519 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Transcriptome Analysis Console" ;
NIFRID:synonym "TAC:Transcriptome Analysis Console" ;
NIFRID:abbrev "TAC" ;
definition: "Software tool for microarray analysis designed for biologists . Used for identification of differential expression by providing interactive visualizations." .
SCR:016522 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | GeneChip� Scanner 3000 7G" ;
definition: "Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis." .
SCR:016527 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AbundantOTU+" ;
NIFRID:synonym "Abundant OTU",
"AbundantOTU:Abundant Operational Taxonomic Unit" ;
NIFRID:abbrev "AbundantOTU" ;
definition: "Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset." .
SCR:016528 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Janelia 2016-027" ;
rdfs:label "Janelia | Tip-Tilt-Z Sample Positioner" ;
definition: "Positioner for automated rotation of a head-fixed rodent specimen about the anterior-posterior and medio-lateral axes for imaging or other purposes. Provides automated Z translation and can be customized to accommodate various head bar designs." .
SCR:016529 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mizutani Lab 3D Structure Portal" ;
definition: "Departamental portal of Applied Biochemistry, School of Engineering, Tokai University, Japan. Used for computed tomography (CT) and visualizing 3D structures of biological soft tissues represented with Cartesian coordinates." .
SCR:016530 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Cell Atlas" ;
definition: "Software tool as a catalog of comprehensive reference of human cells based on their stable properties, transient features, locations and abundances. Map to show the relationships among its elements. Open data international collaborative project involving diverse scientific communities to provide a framework for understanding cellular dysregulation in human disease." .
SCR:016531 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RecView" ;
definition: "Software tool as a program for tomographic reconstruction and image processing of micro/nano-CT data taken at SPring8 and APS Argonne." .
SCR:016532 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCTrace" ;
definition: "Software tool as a program for building skeletonized models of 3D structures with a graphical user interface. GUI based neuronal network model building." .
SCR:016533 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:sartools" ;
rdfs:label "SARTools" ;
definition: "Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data." .
SCR:016534 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "jPerfusionModule" ;
definition: "Software tool written in Java that reads DICOM-files from Dynamic Susceptibility Contrast (DSC) Magnetic Resonance Imaging (MRI) and calculates standardized Time-to-Peak (stdTTP) parameter. Maps from this calculation are provided as RGB- and Monochrom2-Dicom files and may be sent to a PACS automatically. Works on windows® platforms on PC’s (Intel® CPUs from Pentium I up to the I7-octo cores) together with the Philips 1.5T ACS-NT up to the Ingenia Systems (n> 20.000), with the Philips 3.0T Systems (n ~ 1.000), the Siemens 1.5T Avanto (SQ-machine) (n> 10.000) and the Siemens 3.0T TimTrio (n ~ 200) so far. Works with uncompressed DICOM-standard files." .
SCR:016536 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cardiovascular Disease Knowledge Portal" ;
definition: "Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data." .
SCR:016538 a owl:NamedIndividual ;
rdfs:label "Rodent tactile navigation" ;
definition: """Dataset. We have a DataNote paper in Gigascience, in press which introduces a large
videography dataset that is freely available for anyone to study the principles of tactile navigation.""" .
SCR:016539 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nonparametricGGC_toolbox" ;
NIFRID:synonym "nonparametric Granger Geweke Causality" ;
NIFRID:abbrev "nonparametricGGC" ;
definition: "Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions." .
SCR:016542 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID: 100005294",
"grid.32224.35",
"ISNI: 0000 0004 0386 9924",
"Wikidata: Q126412" ;
rdfs:label "Massachusetts General Hospital" ;
NIFRID:abbrev "Mass General",
"MGH" ;
definition: "Facility for biomedical research and a teaching hospital of Harvard Medical School located in the West End neighborhood of Boston, Massachusetts. The third oldest general hospital in the United States and conducts the largest hospital-based research program in the world." .
SCR:016543 a owl:NamedIndividual ;
rdfs:label "NetworkUnit" ;
definition: "Library of a test driven framework for formally validating scientific models against experimental data used for validation testing of spiking neuron network simulations on the network activity level." .
SCR:016544 a owl:NamedIndividual ;
rdfs:label "DCC" ;
NIFRID:synonym "Data Coordination Center" ;
definition: "Software tool as an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations and large-scale annotation efforts." .
SCR:016545 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VPV" ;
NIFRID:synonym "Volume Phenotype Viewer",
"volume phenotype viewer" ;
definition: "Software tool as a desktop 3D volume viewer. Used for analysing results of automatic phenotype detection from the LAMA pipeline. Developed in Python using QT, and the PyQtGraph." .
SCR:016546 a "Supercategory",
owl:NamedIndividual ;
definition: "Software as a cross platform application for automating the processing of μCT and OPT image data. Used for standarization of embryo images prior to export to the PhenoDCC. Capable of processing other image modalities and specimens. Can be download as a stand alone release." .
SCR:016547 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PMOD Software" ;
NIFRID:synonym "PET Modeling",
"PMOD",
"PMOD 4.0",
"PMOD 4.2" ;
definition: "Software environment for the quantification of biomedical images. Biomedical image processing, analysis, and modeling software. Consists of set of tools for kinetic modeling, parametric mapping, image registration, 3D rendering and pattern analysis. Used for quantification of PET data. Many quantification methods are generic and can be applied to other modalities such as SPECT, MR and CT." .
SCR:016548 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018202" ;
rdfs:label "Warsaw University of Technology; Warsaw; Poland" ;
NIFRID:synonym "Warsaw Institute of Technology" ;
definition: "The oldest technical university in Poland, located in Warsaw, with faculties including architecture, machine design, electrical engineering, automotive and construction machinery engineering, electronics , information technology, mechatronics , geoinformatics, automatic control and robots, and biomedical engineering." .
SCR:016549 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University Hospital Zurich; Department of Nuclear Medicine; PET Center; Zurich; Switzerland" ;
definition: "Center for functional imaging examinations on patients using radioactive substances by using scintigraphy, SPECT and PET to visualize biochemical processes in the body (such as active cancer, inflammation, tissue perfusion, etc.) and combine these technologies with cross-sectional methods such as CT and MRI for precise anatomical localization." .
SCR:016550 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "User Friendly Functional Connectivity - UF²C" ;
NIFRID:synonym "User Friendly Functional Connectivity" ;
NIFRID:abbrev "UF²C" ;
definition: "Software tool to standardize and facilitate connectivity studies through a graphical user interface and validated preset parameters." .
SCR:016551 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhenoDB" ;
definition: "Database for phenotype genotype associations for humans. Used by clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease." .
SCR:016552 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iMITS" ;
NIFRID:synonym "international Micro Injection Tracking System" ;
definition: "This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products." .
SCR:016554 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FFTW" ;
NIFRID:synonym "Fastest Fourier Transform in the West" ;
definition: "Software as a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST)." .
SCR:016555 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica Application Suite" ;
NIFRID:abbrev "LAS" ;
definition: "Microscope software platform which integrates Leica automated microscopes and digital cameras and provides one common user interface." .
SCR:016556 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thunder" ;
definition: "Software package for the analysis of image and time series data in Python. Provides data structures and algorithms for loading, processing, and analyzing these data. Runs locally or against a Spark cluster with an identical API." .
SCR:016557 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Apache Spark" ;
definition: "Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework." .
SCR:016558 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Frozen Noise" ;
definition: """Software analysis tools for electrophysiological somatosensory cortex databank.
Allows to estimate the information content of spiking in single neuron resolution. It accompanies the open source intracellular recording database by Lantyer and colleagues.""" .
SCR:016559 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sleep Heart Health Study" ;
NIFRID:abbrev "SHHS" ;
definition: "Portal for a multi-cohort study focused on sleep-disordered breathing and cardiovascular outcomes implemented by the National Heart Lung and Blood Institute. Recorded signals are: EEG, ECG, EOG, SaO2, HR, EOG, EMG, respiratory inductance plethysmography, respiration (thermistor), position, light." .
SCR:016560 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mib" ;
rdfs:label "Microscopy Image Browser" ;
NIFRID:synonym "MIB" ;
definition: "Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets." .
SCR:016561 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Venny 2.1" ;
definition: "Software tool for comparing lists with Venn's diagrams." .
SCR:016562 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MyAssays" ;
definition: "Software tool for assay data analysis." .
SCR:016563 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SINCERA Pipeline" ;
NIFRID:synonym "SINCERA",
"SINgle CEll RNA seq profiling Analysis" ;
definition: "Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis." .
SCR:016564 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Praat" ;
definition: "Software tool for phonetics research to analyse, synthesize, and manipulate speech." .
SCR:016565 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pymatgen" ;
NIFRID:synonym "PYthon MATerials GENomics" ;
definition: "Python library for materials analysis codes. Defines core object representations for structures and molecules." .
SCR:016566 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Simple Neurite Tracer" ;
definition: "Software tool for reconstruction, visualization and analysis of neuronal processes .Fiji's framework for semi-automated tracing of neurons and other tube-like structures (blood vessels) through 3D image stacks." .
SCR:016567 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MrDiffusion" ;
definition: "Software package for diffusion imaging analysis and visualization. Module of Vistasoft for processing diffusion weighted data and measuring and visualizing fractional anisotropy, mean diffusivity, axial and radial diffusivity, RGB fiber direction maps and analysis of MRI data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016568 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stitching" ;
definition: """Software package available through Fiji to image large biological specimen at high resolution.
Comes with 2 different plugins to reconstruct big images/stacks : Pairwise Stitching to stitch two 2d-5d images, and Grid/Collection Stitching to stitch an arbitrary amount of 2d-5d input images.""" .
SCR:016569 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:GEO2R" ;
rdfs:label "GEO2R" ;
definition: "Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance." .
SCR:016570 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "kbDNA Inc." ;
definition: "Commercial provider of antibodies, antigens and recombinant proteins from Braintree, Massachusetts . Biotechnology company which provides custom oligonucleotides synthesis service." .
SCR:016571 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Assemblosis" ;
definition: "Software tool as a Common Workflow Language (CWL) based automated bioinformatics workflow to assemble haploid/diploid eukaryote genomes of non-model organisms using PacBio long-reads and Illumina short-reads." .
SCR:016572 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SABRe CVD Initiative" ;
NIFRID:synonym "Systems Approach to Biomarker Research in CardioVascular Disease" ;
NIFRID:abbrev "SABRe CVD" ;
definition: "Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation." .
SCR:016573 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BeWith" ;
NIFRID:synonym "Between-Within",
"BEtweenWITHin" ;
definition: "Software tool for discovering relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions." .
SCR:016574 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MutaGene" ;
definition: "Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity." .
SCR:016575 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Apnea, Bariatric surgery, and CPAP study" ;
NIFRID:synonym "and Cpap study",
"Apnea",
"Bariatric surgery" ;
NIFRID:abbrev "ABC study" ;
definition: "Portal for randomized controlled trial to compare effectiveness of bariatric surgery versus continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea. Signals included in the polysomnography (PSG) montage are EEG, EMG, EOG, ECG, SpO2, airflow, CPAP pressure, CPAP flow, plethysmography, position, pulse, light, respiratory effort, snore." .
SCR:016576 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Sleep Research Resource (NSRR) " ;
NIFRID:synonym "National Sleep Research Resource" ;
NIFRID:abbrev "NSRR" ;
definition: "System for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community." .
SCR:016577 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VecScreen" ;
definition: "Software tool to screen a nucleic acid sequence for vector contamination. Detects foreign DNAs such as vector, linker, adapter, and primer regions involved in nucleotide sequences by using blast search against vector sequence database. The main unit of this tool is vecscreen program obtainable from NCBI." .
SCR:016580 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FUSION study" ;
NIFRID:synonym "Finland United States Investigation of NIDDM genetics" ;
NIFRID:abbrev "FUSION" ;
definition: "Portal to map and identify genetic variants that predispose to type 2 diabetes mellitus (T2D) or are responsible for variability in diabetes-related quantitative traits. Used for analysis of affected-sibling-pair (ASP) families in Finland, and association fine mapping based on these family members and additional T2D cases and controls." .
SCR:016581 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sequin" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 12,2024. Software tool for DNA sequence submission. Used for submitting and updating entries to the GenBank or EMBL sequence databases." .
SCR:016582 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:kallisto" ;
rdfs:label "kallisto" ;
NIFRID:synonym "kallisto v0.43.1" ;
definition: "Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads." .
SCR:016583 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Best Apnea Interventions for Research (BestAIR) sleep study" ;
NIFRID:synonym "Best Apnea Interventions for Research",
"Bestair",
"bestair" ;
NIFRID:abbrev "BestAIR" ;
definition: "Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume." .
SCR:016584 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cleveland Children's Sleep and Health Study" ;
NIFRID:abbrev "CCSHS" ;
definition: "Portal for population based pediatric cohorts studied with objective sleep studies. Includes children with in-home sleep studies, acoustic reflectometry, anthropometry, spirometry, blood pressure (BP), and neuropsychology (NP) and behavioral assessments. Signals recorded include EEG, ECG, EOG, EMG, SpO2, airflow (thermocouple) nasal pressure, respiratory effort, position, plethysmography, light, HR." .
SCR:016585 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cleveland Family Study" ;
NIFRID:abbrev "CFS" ;
definition: "Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore." .
SCR:016587 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Honolulu-Asia Aging Study of Sleep Apnea" ;
NIFRID:synonym "Honolulu Asia Aging Study of Sleep Apnea" ;
NIFRID:abbrev "HAASSA" ;
definition: "Portal for sleep-disordered breathing (SDB) in an elderly cohort of Japanese-American men under surveillance for Alzheimer disease (AD) and other dementias. Data to assess relationships between SDB and cognitive performance in late life." .
SCR:016588 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ngsrelate",
"biotools:ngsRelateV2" ;
rdfs:label "ngsRelate" ;
NIFRID:synonym "ngsRelateV2" ;
definition: "Software tool for estimating pairwise relatedness from next-generation sequencing data." .
SCR:016589 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Imaging WorkBench" ;
NIFRID:synonym "Imaging Workbench 6",
"Imaging Workbench 6.0",
"Imaging Workbench (IW) 6",
"IW 6",
"IW 6.0" ;
NIFRID:abbrev "IW" ;
definition: "Software for multichannel dynamic fluorescence image acquisition and analysis by INDEC BioSystems." .
SCR:016590 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "transfer_ learning_ ccnn" ;
NIFRID:synonym "CCNN",
"Connectome Convolutional Neural Network",
"connectome convolutional neural network" ;
NIFRID:abbrev "ccnn" ;
definition: "Software program to implement transfer learning for a connectome convolutional neural network trained to classify functional connectomes using Tensorflow." .
SCR:016591 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rsfMRI_fconn calculation" ;
NIFRID:synonym "resting state functional MRI and functional connectivity calculation",
"resting state functional MRI pre processing and Functional Connectivity calculation" ;
definition: "Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity." .
SCR:016592 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:nmrprocflow",
"SCR_022777" ;
rdfs:label "NMRProcFlow" ;
NIFRID:synonym "Nuclear Magnetic Resonance PROcessing FLOW",
"Nuclear Magnetic Resonance Processing Flow" ;
definition: "Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics." .
SCR:016593 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChemokineDB" ;
definition: "Resource of chemokines and receptors with detailed information including taxonomy, nomenclature, structure, physiological function, tissue information, and phenotype, collected from IUPHAR/BPS, UniGene, and UniProt public databases." .
SCR:016594 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:TB_Portals",
"r3d100013925" ;
rdfs:label "TB PORTALS" ;
definition: "Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data." .
SCR:016595 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:nephele" ;
rdfs:label "Nephele" ;
definition: "Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools." .
SCR:016596 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:biobakery" ;
rdfs:label "biobakery" ;
NIFRID:synonym "bioBakery" ;
definition: "Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016597 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "OCICB" ;
NIFRID:synonym "Office of Cyber Infrastructure and Computational Biology" ;
definition: "Office of Cyber Infrastructure and Computational Biology of NIAID." .
SCR:016598 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "NIAID" ;
NIFRID:synonym "National Institute of Allergy and Infectious Diseases" ;
definition: "National Institute of Allergy and Infectious Diseases is a leading research institution to understand, treat, and prevent infectious, immunologic, and allergic diseases." .
SCR:016599 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PaVE" ;
NIFRID:synonym "PapillomaVirus Episteme",
"Papillomavirus Episteme" ;
definition: "Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information." .
SCR:016600 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Database of Antimicrobial Activity and Structure of Peptides" ;
NIFRID:synonym "DataBase of Antimicrobial Activity and Structure of Peptides" ;
NIFRID:abbrev "DBAASP" ;
definition: "Collection of manually curated data regarding structure and antimicrobial activity of natural and synthetic peptides. Provides the information and analytical resources to develop antimicrobial compounds with the high therapeutic index." .
SCR:016601 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SciEx_8810",
"SCR_001055" ;
rdfs:label "University of FLorida College of Medicine Molecular Pathology Core Facility" ;
NIFRID:synonym "Molecular Pathology Core",
"University of Florida Molecular Pathology Core" ;
NIFRID:abbrev "MPC" ;
definition: """Histology and light microscopy facility for paraffin and frozen blocks and all aspects of sample preparation, fixation, embedding, sectioning, staining, and imaging. Consultations, technical assistance and training are also provided. Standard operating procedures compliant with good laboratory and clinical processes are followed for all procedures.
Services include cryosectioning, whole slide imaging, hematoxylin and eosin staining, immunfluorescence, and tissue microarrays..""" .
SCR:016602 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:CARD" ;
rdfs:label "CARD" ;
NIFRID:synonym "Comprehensive Analysis of RNAi-screen Data" ;
definition: "Web application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data." .
SCR:016603 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:spice" ;
rdfs:label "SPICE" ;
NIFRID:synonym "Simplified Presentation of Incredibly Complex Evaluations" ;
definition: "Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically." .
SCR:016604 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OMiCC" ;
NIFRID:synonym "OMics Compendia Commons" ;
definition: "Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016605 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:PhenoMeNal" ;
rdfs:label "PhenoMeNal" ;
NIFRID:synonym "Phenome and Metabolome aNalysis" ;
NIFRID:abbrev "phnmnl" ;
definition: "Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics." .
SCR:016606 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenMTA" ;
NIFRID:synonym "Open Material Transfer Agreement",
"open Material Transfer Agreement",
"Open MTA",
"openMTA",
"The Open Material Transfer Agreement" ;
definition: "MTA open version of the material transfer agreement for biological samples from the BioBricks Foundation. Supports the transfer of material between researchers at all types of institutions, including academic, industry, government and community laboratories." .
SCR:016607 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RandomPooling" ;
definition: "Software tool to identify the most reliable differences between any two groups . Used to identify differentially expressed genes between two groups." .
SCR:016608 a owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Libra_k-mer" ;
rdfs:label "Libra" ;
definition: "Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples." .
SCR:016609 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TRIAGE" ;
NIFRID:synonym "Throughput Ranking by Iterative Analysis of Genomic Enrichment" ;
definition: "Platform to facilitate prediction, analysis, and hypothesis generation from genome wide perturbation studies like those designed with RNAi and CRISPR technologies." .
SCR:016610 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NGlycPred" ;
NIFRID:synonym "N linked GLYCosylation PREDiction server",
"N linked Glycosylation Prediction server" ;
definition: "Web based server to discriminate between glycosylated and non-glycosylated N-X-(T/S) sequons by incorporating structural information and patterns." .
SCR:016611 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sleep Disorder Knowledge Portal" ;
definition: "Software platform for accelerating genetic discoveries for sleep disturbance and circadian traits." .
SCR:016612 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dCAS" ;
NIFRID:synonym "Desktop cDNA Annotation System" ;
definition: "Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016613 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPOT Advanced" ;
definition: "Suite of software applications for capturing, enhancing and analyzing microscope images for SPOT camera by SPOT Imaging, a division of Diagnostic Instruments, Inc." .
SCR:016614 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Database of Open Chromatin Regions" ;
definition: "Collection of open chromatin regions from sequencing data. Metadata as entire curated DNase-I hypersensitive sites (DHS) on the whole genome datasets and data specific to each chromosome." .
SCR:016615 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HASP" ;
NIFRID:synonym "HemAgglutinin Structure Prediction",
"Hemagglutinin Structure Prediction" ;
definition: "Web server to visualize phylogenetic, biochemical, and immunological hemagglutinin data in the three-dimensional context of homology models. Database and structural visualization platform for comparative models of influenza A hemagglutinin proteins." .
SCR:016616 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NetCirChro" ;
NIFRID:synonym "Networks on Circular Chromosome" ;
definition: """Software interactive tool for visualizing and analyzing network data in the spatial context of the chromosome. Used to discover the role of gene organization in functional regulatory networks.
Plugin enables users of Cytoscape to overlay networks onto a circular chromosomal map.""" .
SCR:016617 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ABC Bacterial Transporter Systems Database" ;
NIFRID:synonym "ABC Bacterial Transporter Systems",
"ABC-BAC" ;
definition: "Collection of classified bacterial ATP-binding cassette (ABC) transporter systems. The transporter systems identified fulfill the three roles characterized by the nucleotide-binding domain (NBD) , transmembrane domain (TMD), and solute-binding protein (SBP) domains." .
SCR:016618 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Simmune" ;
NIFRID:synonym "simulate immunological phenomena" ;
definition: "Software package to define the interactions between individual molecules in a large network or the behaviors of cells in response to external signals. It consists of three components: Modeler, Cell Designer and Simulator." .
SCR:016619 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JOINSOLVER" ;
definition: "Software tool to analyze human immunoglobulin V(D)J recombination and performing Ig nucleotide and amino acid alignment, as well as extensive mutation and Complementarity Determining Region 3 (CDR3H) analysis." .
SCR:016620 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Metascape" ;
rdfs:label "Metascape" ;
definition: "Web service to analyze gene or protein lists. Provides automated meta analysis tools to understand pathways within a group of orthogonal target-discovery studies." .
SCR:016623 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AFIDs" ;
NIFRID:synonym "Anatomical Fiducials" ;
definition: "Open framework for evaluating correspondence between brain images and teaching neuroanatomy." .
SCR:016624 a NLX:63400,
owl:NamedIndividual .
SCR:016625 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018509" ;
rdfs:label "Seek and Blastn" ;
NIFRID:synonym "Seek & Blastn",
"Seek and blastn" ;
definition: "Web server as semi automated tool that identifies nucleotide sequences in scientific publications, determines whether they are correctly identified. Seeks for nucleotide sequences in pdf files and then call local version of blastn. Text mining and text analysis tool to allow peers to identify errors in published or forthcoming scientific literature. Used to search and extract gene identifiers and nucleotide sequences against human genomic and transcript database." .
SCR:016633 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "maeparser" ;
definition: "Parser for Schrodinger Maestro files. This format is used for computational modeling, and stores molecules with 2D or 3D coordinates and detailed atom and bond information." .
SCR:016634 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Batch Entrez" ;
definition: "Software program for loading numbers of genome records. Allows the retrieval of a large number of nucleotide sequences or protein sequences, in a batch mode, by importing a file containing a list of the desired GI or accession numbers." .
SCR:016635 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cyflogic" ;
definition: "Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics." .
SCR:016636 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tbl2asn" ;
definition: "Software tool as a command-line program that automates the creation of sequence records for submission to GenBank. Records need no additional manual editing before submission." .
SCR:016637 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Whole Genome Shotgun (WGS) Project" ;
NIFRID:synonym "WGS Projects",
"Whole Genome Shotgun",
"Whole Genome Shotgun WGS",
"Whole Genome Shotgun WGS Project" ;
NIFRID:abbrev "WGS" ;
definition: "Project for assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required. The nucleotide and protein data from all WGS projects go into the BLAST database." .
SCR:016638 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Digital Differential Display (DDD)" ;
NIFRID:synonym "Digital Differential Display" ;
NIFRID:abbrev "DDD" ;
definition: "Software tool for comparing EST profiles in order to identify genes with significantly different expression levels." .
SCR:016639 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Attie Lab Diabetes Database" ;
definition: "Interactive database of gene expression and diabetes related clinical phenotypes. Allows to search gene expression in tissues as a function of obesity, strain, and age, in a mouse." .
SCR:016640 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Entrez" ;
definition: """Web application for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references.
Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.""" .
SCR:016641 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BLASTClust" ;
definition: "Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets." .
SCR:016642 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PASC " ;
NIFRID:synonym "PAirwise Sequence Comparison" ;
NIFRID:abbrev "PASC" ;
definition: "Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database." .
SCR:016643 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Reading Frame Finder" ;
NIFRID:synonym "Open Reading Frame finder" ;
NIFRID:abbrev "ORF finder" ;
definition: "Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long." .
SCR:016644 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MOLE-BLAST" ;
NIFRID:abbrev "MOLE BLAST",
"Mole Blast",
"moleblast" ;
definition: "Software tool that helps taxonomists find closest database neighbors of submitted query sequences by generating a phylogenetic tree from BLAST results." .
SCR:016645 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ncbi_genotyping" ;
rdfs:label "Genotyping" ;
definition: "Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus." .
SCR:016646 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:checkm" ;
rdfs:label "CheckM" ;
definition: "Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes." .
SCR:016647 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Particle Metrix | ZetaView Nanoparticle Tracking Analyzer" ;
NIFRID:synonym "ZetaView Nanoparticle Tracking Analyzer",
"ZetaView NTA" ;
definition: "Instrument for nanoparticle tracking analysis. A semi-automated method for the characterization of extracellular vesicles with associated analysis software by ParticleMetrix GmbH." .
SCR:016648 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SMI BeGaze" ;
NIFRID:synonym "SMI BeGaze™",
"SMI Behavioral and Gaze Analysis",
"SMI BehavioralGaze" ;
definition: "Software package for eye tracking studies by New Bio Technology Ltd. Used for designing eye movement studies and recording, analyzing, visualizing data of eye tracking results." .
SCR:016649 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RPPA Core Facility" ;
NIFRID:synonym "MD Anderson RPPA Core",
"Reverse Phase Protein Array (RPPA) Core",
"Reverse Phase Protein Array Core",
"RPPA" ;
definition: "Core provides technology for functional proteomics studies and centralized, standardized and quality controlled services locally and globally." .
SCR:016651 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "circular statistics" ;
NIFRID:synonym "CircStat for Matlab",
"circstat-matlab",
"Circular Statistics",
"Matlab Circular Statistics Toolbox" ;
NIFRID:abbrev "CircStat" ;
definition: "Software toolbox for MATLAB for the descriptive and inferential statistical analysis of directional data." .
SCR:016652 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fermi" ;
definition: "Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes." .
SCR:016653 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "metaPocket" ;
NIFRID:synonym "metaPocket 2.0" ;
definition: "Software tool to identify pockets on protein surface to predict ligand-binding sites." .
SCR:016654 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaXpress" ;
definition: "Software tool for multi level analysis of applications optimized for ImageXpress instruments. High-content image analysis software featuring time lapse analysis. Used for 2D and 3D imaging." .
SCR:016655 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DoG picker" ;
NIFRID:synonym "Difference of Gaussians Picker",
"Difference of Gaussians picker",
"Difference of Gaussians (DoG) picker" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software tool for general particle picking in the single-particle processing of unknown macromolecules. Reference free particle picker with ability to sort particles based on size or it can be used to bootstrap the creation of templates or training datasets for other particle pickers. Used to facilitate particle selection in single particle electron microscopy., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016656 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TSDiffAna" ;
definition: "Software tool developed for Statistical Parametric Mapping (SPM) that computes slicewise scan by scan difference and standard deviations. Used to examine quality of image timeseries." .
SCR:016657 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS" ;
definition: "Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise." .
SCR:016658 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:VisR" ;
rdfs:label "VisR" ;
NIFRID:synonym "VisRseq" ;
definition: "Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses." .
SCR:016659 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genotate" ;
definition: "Platform as a web-based interactive environment to automatically identify, explore and visualize homology and functional annotations for assembled transcripts." .
SCR:016661 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XYalign" ;
definition: "Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data." .
SCR:016662 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sequenza" ;
definition: "Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization." .
SCR:016663 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IndelGenotyper" ;
NIFRID:synonym "GATK Indel Genotyper",
"GATK IndelGenotyper",
"Genome Analysis Toolkit (GATK) Indel Genotyper",
"Indel Genotyper" ;
NIFRID:abbrev "GATK" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer." .
SCR:016664 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProteinLynx Global Server" ;
NIFRID:synonym "PLGS",
"Protein Lynx Global Server",
"Protein Lynx Global Server 2.4",
"ProteinLynx Global Server (PLGS)",
"ProteinLynx Global SERVER™ (PLGS)" ;
definition: "Platform for quantitative and qualitative proteomics research for Waters Corporation proteomics systems." .
SCR:016665 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:centrifuge",
"OMICS_12217" ;
rdfs:label "Centrifuge Classifier" ;
definition: "Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers." .
SCR:016666 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LoomPy" ;
NIFRID:synonym "Loom Python",
"Loompy v2.0",
"Loompy v2.0.14",
"LoomPython" ;
definition: "Python implementation of the Loom file format to store and organize very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations and sparse graph objects. Used to store single-cell gene expression data. Official Python library (API) used to create, read, and manipulate .loom files, supporting out-of-memory operations to handle datasets larger than RAM." .
SCR:016668 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MouseLight Project" ;
NIFRID:synonym "Janelia MouseLight project",
"Mouse Light",
"Mouse Light Project",
"MouseLight",
"The Mouse Light Project" ;
definition: "Software imaging platform to generate datasets of whole mouse brains imaged at submicron resolution that allow reconstructions of complete axonal arbors of individual neurons across the entire mouse brain." .
SCR:016669 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MouseLight Neuron Browser" ;
NIFRID:synonym "Neuron Browser",
"NeuronBrowser" ;
definition: "Interactive web platform for anyone to explore, search, filter and visualize the single neuron reconstructions." .
SCR:016672 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "microC" ;
definition: "Software tool to model genotypes in their microenvironment and to predict single- and multi-cellular behaviour. A 3D virtual microenvironment for perturbation biology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016673 a "Research",
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100014071" ;
rdfs:label "Open Data Commons for Spinal Cord Injury" ;
NIFRID:synonym "Open Data Commons at UCSD FDI Lab" ;
NIFRID:abbrev "ODC-SCI",
"odc-sci" ;
definition: "Portal for sharing spinal cord injury data from basic and clinical research to promote transparency, rigor and reproducibility. Community based repository for spinal cord injury research." .
SCR:016674 a NLX:63400,
owl:NamedIndividual .
SCR:016677 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "A-M SYSTEMS | Model 2100 Isolated Pulse Stimulator" ;
definition: """Instrument used for a variety of physiological stimulation protocols, including behavioral feedback, LTP/LTD, lesion making, electrode marking, ultrafast timing applications, orthodromic/antidromic
stimulation, and kindling. Used in a neurophysiological and physiological experiment protocols.""" .
SCR:016678 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuronexus | Neural Probe A1x16-3mm-100-703" ;
definition: "Instrument as a 16 channel linear electrode array from NeuroNexus Technologies, Ann Arbor, Michigan. Used to map brain function, detect neural activity, and stimulate or modulate neural circuits when brain function is impaired. Used for small and large animal models for neuroscience and clinical applications." .
SCR:016679 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pavian" ;
rdfs:label "Pavian" ;
definition: "Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome." .
SCR:016680 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Center for Computational Biology at JHU" ;
NIFRID:synonym "CCB at Johns Hopkins University",
"CCB at JHU",
"Center for Computational Biology at JHU",
"Center for Computational Biology at Johns Hopkins University" ;
definition: "Center for Computational Biology as a joint research center in the McKusick-Nathans Institute of Genetic Medicine, spanning the School of Medicine, the Whiting School of Engineering, the Bloomberg School of Public Health, and the Krieger School of Arts & Sciences. Multidisciplinary center dedicated to research on genomics, genetics, DNA sequencing technology, and computational methods for DNA and RNA sequence analysis." .
SCR:016681 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EnVision Manager" .
SCR:016682 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Studylog" ;
definition: "Commerciall organization to develop study protocols collaboratively to run and manage animal research studies for academic, government, biotech and pharmaceutical labs. Provides services, including product installation and configuration, user training, customization services and ongoing support." .
SCR:016683 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "loom-viewer" ;
definition: "Software tool for sharing, browsing and visualizing single-cell data stored in the Loom file format." .
SCR:016684 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Stanford Center for Reproducible Neuroscience" ;
definition: "Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects." .
SCR:016691 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpectraVis" ;
definition: "Web based neuroscience application for analyzing task-related functional networks over time and frequency. Interactive visualization tool for exploring functional brain connectivity." .
SCR:016692 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "factoextra" ;
definition: "R package from CRAN to extract and visualize the results of multivariate data analysis." .
SCR:016693 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dendsort" ;
NIFRID:synonym "dendrogram sorting" ;
definition: "Software R package from CRAN as a modular leaf ordering methods for dendrogram nodes. Used as sorting methods to improve readability and interpretability of tree structure. Used for comparison of different distance measures or linkage types, identification of tight clusters and outliers, and for coupled heatmap visualization." .
SCR:016694 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | EM UC7 ultramicrotome" ;
definition: "Instrument for cutting specimens at room and low temperature. Used to produce both semi- and ultra-thin sections as well as smooth surfaces of biological samples." .
SCR:016695 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FACSAria_III" ;
rdfs:label "BD Biosciences | FACSAria III Cell Sorter" ;
NIFRID:synonym "BD FACSARIA III",
"BD FACSARIA III cell sorter" ;
definition: "Instrument for cell sorting by BD Biosciences where positive air pressure forces sample cell through an optically gel-coupled cuvette . Hydrodynamic focusing guides particles in a single-file stream through the cuvette, where laser light intercepts the stream at the sample interrogation point.Fluorescence activated cell sorting instrument. Flow cytometer as high speed fixed alignment benchtop cell sorter. Enables multicolor analysis of up to 13 fluorescent markers and two scatter parameters at time." .
SCR:016696 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "viridis" ;
definition: "Software package which brings to R color scales. Created for the Python matplotlib library." .
SCR:016697 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RColorBrewer" ;
definition: "Software tool to provide color schemes for maps and other graphics. R package to create colorful graphs with pre-made color palettes that visualize data." .
SCR:016698 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "statmod" ;
NIFRID:synonym "Statistical Modeling",
"statistical modeling" ;
definition: "SoftwareR package from CRAN for statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families." .
SCR:016699 a NLX:63400,
owl:NamedIndividual ;
definition: "Software to study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment." .
SCR:016700 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GalliosTM Kaluza" .
SCR:016701 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioRevo microscope BZ II viewer software" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. BioRevo microscope BZ II viewer software, discontinued product, software for the BZ 9000 Fluorescence Microscope, no download available." .
SCR:016702 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gallios | Flow Cytometer" ;
definition: "Instrument provides acquisition of up to 12 parameters with optical design for enhanced sensitivity for multicolor assays. With customized forward scatter, to achieve accurate size measurement, and optimized electronics for high resolution and fast, accurate processing for researchers needs." .
SCR:016703 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss | libra 120 transmission electron microscope" ;
NIFRID:synonym "Carl Zeiss AG - LIBRA 120",
"libra 120",
"The LIBRA 120" ;
definition: "Electron microscope by Carl Zeiss AG which combines flexibility and ease of use of new control electronics, Windows® based user interface and a vacuum system." .
SCR:016705 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iMaps" ;
definition: "Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions." .
SCR:016706 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MAJIQ" ;
NIFRID:synonym "MAJIQ/Viola",
"Modeling Alternative Junction Inclusion Quantification" ;
definition: """Software package to detect and quantify local splicing variations (LSV) from RNA-Seq data.
Used to automatically detect and downweight outliers in RNA-Seq datasets with replicates for differential splicing (SD) analysis.""" .
SCR:016707 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MAxEntScan" ;
NIFRID:synonym "Maximum Entropy Scan",
"MAximumEntropyScan" ;
definition: "Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing." .
SCR:016708 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dplyr" ;
definition: "Software tool for working with data frame like objects, both in memory and out of memory. It is a grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges: mutate, select, filer, summerise, arrange." .
SCR:016710 a owl:NamedIndividual ;
rdfs:label "NanoAmpli-Seq" ;
definition: "Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing." .
SCR:016711 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "INC-Seq" ;
NIFRID:synonym "Intramolecular ligated Nanopore Consensus Sequencing" ;
definition: "Software for accurate single molecule reads using nanopore sequencing. Used for 16S rRNA-based profiling to investigate complex bacterial communities." .
SCR:016712 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iCount" ;
definition: "Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps." .
SCR:016713 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 501100000271",
"GRID grid.14467.30",
"ISNI 0000 0001 2237 5485",
"Wikidata Q1669366" ;
rdfs:label "Science and Technology Facilities Council " ;
NIFRID:synonym "Science and Technology Facilities Council",
"STFC" ;
NIFRID:abbrev "STFS" ;
definition: "One of nine Councils within United Kingdom Research and Innovation, an organisation that brings together the UK’s Research Councils, Innovate UK and Research England. Works in partnership with universities, research organisations, businesses, charities, and government to create the environment for research and innovation." .
SCR:016714 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Florida State University Physical Biochemistry Core Facility" ;
NIFRID:synonym "Physical Biochemistry Facility",
"The Physical Biochemistry Facility",
"The Physical Biochemistry Facility (PBF)" ;
NIFRID:abbrev "PBF" ;
definition: "Facility for biophysical studies of macromolecules with emphasis on providing resources, instrumentation, training, and guidance to graduate and undergraduate students." .
SCR:016715 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colour maps for brain imaging" ;
NIFRID:synonym "Brain colours",
"brain colours",
"brain_colours",
"Colour maps",
"colour maps",
"colour maps for brain imaging" ;
definition: "Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging." .
SCR:016716 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroAnatomy Toolbox" ;
NIFRID:synonym "Neuro Anatomy Toolbox",
"neuro anatomy toolbox",
"neuroanatomy toolbox" ;
NIFRID:abbrev "NAT",
"nat" ;
definition: "Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures." .
SCR:016718 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Columbus Instruments | Oxymax-CLAMS" ;
NIFRID:synonym "Comprehensive Lab Animal Monitoring System" ;
NIFRID:abbrev "CLAMS" ;
definition: """Instrumentation for monitoring behavior and physiology in lab animals by Columbus Instruments. Used for simultaneous multi parameter assessment of 1 to 32 test animals with automated operation for
experiments lasting up to three days.""" .
SCR:016719 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:anocva" ;
rdfs:label "ANOCVA" ;
NIFRID:synonym "ANalysis Of Cluster VAriability",
"Analysis of Cluster Variability" ;
definition: "Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders." .
SCR:016720 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iDTI-ESBoost" ;
NIFRID:synonym "identification of Drug Target Interaction using Evolutionary and Structural features with Boosting" ;
definition: "Software tool for identification of Drug Target Interaction using Evolutionary and Structural features with Boosting. Used to predict drug-protein interactions." .
SCR:016721 a NLX:63400,
owl:NamedIndividual .
SCR:016722 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BD FACS Sortware sorter software" ;
NIFRID:synonym "BD FACS Sortware",
"BD FACS Sortware software",
"Becton Dickinson FACS Sortware" ;
definition: "Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems." .
SCR:016723 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaboAnalystR" ;
definition: "Software R package for comprehensive analysis of metabolomics data. Contains the R functions and libraries underlying MetaboAnalyst web server, including functions for metabolomic data analysis, visualization, and functional interpretation." .
SCR:016724 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:omicsnet" ;
rdfs:label "OmicsNet" ;
definition: "Web based tool to create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space (genes/proteins, microRNAs, transcription factors or metabolites)." .
SCR:016726 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hfoGUI" ;
NIFRID:synonym "hfoGraphical User Interface" ;
definition: "Graphical user interface to visualize EEG data. The applications can vary from scoring High Frequency Oscillations, to observing Theta and Gamma Synchrony." .
SCR:016727 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaNeighbor" ;
definition: "Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting." .
SCR:016728 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Qualtrics Survey Platform" ;
definition: "Software tool for creation and distribution of surveys which can be taken on computers or smart phones to carry out complex research with advanced survey functionality and analytics. Qualtrics platform used to design, send and analyze surveys online." .
SCR:016729 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Walter Reed Biosystematics Unit" ;
NIFRID:synonym "The Walter Reed Biosystematics Unit",
"WRBU" ;
definition: "National resource for systematics research on medically important arthropods and maintainance of the U.S. mosquito collection based in the Smithsonian Institution. Provides an online repository for vector collection data and clearinghouse where individuals and organizations can contribute vector occurrence records, search for vector information, and use tools for the visualization of various vector collections." .
SCR:016730 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clonotator" ;
definition: "Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data." .
SCR:016731 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leginon" ;
definition: "System designed for automated collection of images from a transmission electron microscope." .
SCR:016732 a owl:NamedIndividual ;
rdfs:label "CTFFIND" ;
NIFRID:synonym "Contrast Transfer Function Finding",
"Contrast Transfer FunctionFinding",
"CTFFIND2",
"CTFFIND4",
"CTFFIND 3",
"CTFFinding" ;
definition: "Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4." .
SCR:016733 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Frealign" ;
NIFRID:synonym "FrealignX" ;
definition: "Software tool for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles. Used to process electron microscope images of single molecules and complexes to obtain reconstructions at the highest possible resolution." .
SCR:016734 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Appion Package" ;
NIFRID:abbrev "Appion" ;
definition: "Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools." .
SCR:016735 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PMI-Byonic" ;
NIFRID:synonym "Byonic",
"PMI Byonic",
"Protein Metrics Inc. Byonic" ;
definition: "Software package for advanced peptide and protein identification by tandem mass spectrometry. Allows to define unlimited number of variable modification type and allows the user to set a separate limit on the number of occurrences of each modification type." .
SCR:016736 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phenix.refine" ;
NIFRID:synonym "Phenix",
"Python-based Hierarchical ENvironment for Integrated Xtallography.refine" ;
definition: "Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB." .
SCR:016737 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GEROprotectors" ;
NIFRID:synonym "Geroprotectors" ;
definition: "Collection of structured and manually curated data of current therapeutic interventions in aging and age-related disease. Describes compounds and mechanisms using multiple chemical and biological databases." .
SCR:016738 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:monores" ;
rdfs:label "SCIPION" ;
definition: """Software framework for image processing to obtain 3D models of macromolecular complexes using Electron Microscopy. Open-source project for integration, reproducibility and validation in 3D electron microscopy. It integrates several software packages to execute workflows combining different software tools, while taking care of formats and conversions.
Electron Microscopy (3DEM).
waiting for pdf from Joe""" .
SCR:016739 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PrediXcan" ;
definition: "Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype." .
SCR:016740 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Columbia University Human Immune Monitoring Core Facility" ;
NIFRID:synonym "Columbia University Human Immune Monitoring Core",
"Human Immune Monitoring Core at Columbia University",
"The Human Immune Monitoring Core (HIMC)" ;
NIFRID:abbrev "HIMC" ;
definition: "Research core facility for advanced immunology studies including multiplex tissue and spatial analysis, high-parametric cytometry, single-cell sequencing, experimental design, sample processing, data acquisition and processing, data analysis and management." .
SCR:016741 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:kat" ;
rdfs:label "KAT" ;
NIFRID:synonym "K-mer Analysis Toolkit" ;
definition: "Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies." .
SCR:016742 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:rampart" ;
rdfs:label "Rampart" ;
definition: "Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems." .
SCR:016743 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPM U+" ;
NIFRID:synonym "Software Project Management U+",
"Software Project Management Univariate Plus",
"SPM Univariate Plus" ;
definition: "Software Project Management (SPM) tools which contain a collection of functions that can be used at different stage of a standard massive univariate fMRI data analysis. Used to improve mass univariate analysis." .
SCR:016744 a owl:NamedIndividual ;
rdfs:label "Canvas from Schrödinger" ;
definition: "Commercial comprehensive cheminformatics computing environment. Used in discovery of novel therapeutic agents." .
SCR:016745 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Epik" ;
definition: "Software program for pKa prediction and protonation state generation for drug like molecules." .
SCR:016746 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ligprep" ;
NIFRID:synonym "Ligand preparation",
"LigandPreparation",
"LigPrep" ;
definition: """Software tool to correct and optimize the ligands by generating different protonation states,
stereochemistry, tautomers, and ring conformations. Used to generate accurate, energy minimized 3D molecular structures.""" .
SCR:016747 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MacroModel" ;
definition: "Software package for molecular modeling. Computes free energy changes using free energy perturbation method. Used to examine molecular conformations, molecular motion, and intermolecular interactions, such as those in a ligand-receptor complex." .
SCR:016748 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Maestro" ;
definition: "Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data." .
SCR:016749 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Protein preparation Wizard" ;
NIFRID:synonym "Protein Preparation Wizard",
"protein preparation wizard" ;
definition: "Software tool for correcting common structural problems and creating reliable, all atom protein models." .
SCR:016750 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Shape screening" ;
definition: "Software tool for shape-based superposition and similarity searching. Identifies new compounds with shapes (and, if desired, other properties) that are similar to the known binder." .
SCR:016751 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stim2" ;
definition: "Software environment for custom stimulus and task design as well as presentation. Compumedics Neuroscan’s design system which can be integrated in fMRI, MEG, and other functional neuro-imaging applications. Provides interface to design and present visual and auditory stimulation paradigms." .
SCR:016752 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:tximport" ;
rdfs:label "tximport" ;
NIFRID:synonym "tximport v1.4.0" ;
definition: "Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis." .
SCR:016753 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Statcel3" ;
NIFRID:synonym "Statcel",
"Statcel4" ;
definition: "Software application for Excel statistics." .
SCR:016754 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioNano | Irys system" ;
definition: "System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies." .
SCR:016755 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Discovar",
"Discovar de novo" ;
definition: "Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes." .
SCR:016756 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Supernova assembler" ;
definition: "Software to generate phased, whole genome de novo assemblies from a Chromium prepared library. Used to create true diploid de novo assemblies and can separate homologous chromosomes over long distances." .
SCR:016757 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2915" ;
rdfs:label "Florida State University Protein Expression Core Facility" ;
NIFRID:synonym "PEF",
"Protein Expression Facility",
"The Protein Expression Facility" ;
definition: "Core to facilitate the large scale expression of recombinant proteins in bacterial, insects, and mammalian cells. Serves primarily faculty and students from the laboratories in the Kasha Laboratory Building and laboratories in Biology, Biochemistry, Chemistry and Nutrition at Florida State University, Tallahassee, FL." .
SCR:016759 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:PathwayMatcher",
"biotools:PathwayMatcher" ;
rdfs:label "PathwayMatcher" ;
definition: "Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome." .
SCR:016762 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Social Science Statistics" ;
NIFRID:synonym "socscistatistics" ;
definition: "Web site for resources (statistical calculators, p-value calculators, descriptive statistics) for students and researchers working with statistics in the social sciences. All the calculators and tools have been designed with ease of use." .
SCR:016768 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chemdraw" ;
definition: "Software used to draw chemical structure. ChemDraw, along with Chem3D and ChemFinder, is part of the ChemOffice suite of programs and is available for Macintosh and Microsoft Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016769 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "OptiQuant",
"OptiQuant 3.0",
"OptiQuant 5.0",
"OptiQuant software 5.0" ;
definition: """Software package for image acquisition, analysis, display, and archiving. Used to quantify the
autoradiography data from Cyclone apparatus from Perkin Elmer.""" .
SCR:016770 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mirDIP" ;
NIFRID:synonym "microRNA Data Integration Portal",
"mirDIP 4.1" ;
definition: "microRNA data integration portal to find microRNAs that target a gene, or genes targeted by a microRNA, in Homo sapiens. Software to integrate prediction databases to elucidate accurate microRNA:target relationships. Used for human microRNA prediction studies." .
SCR:016771 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.438178.1",
"Wikidata: Q30292046" ;
rdfs:label "Tecan Life Sciences" ;
NIFRID:abbrev "Tecan" ;
definition: "Commercial provider of automated laboratory instruments and solutions for clinical diagnostics, basic and translational research and drug discovery." .
SCR:016772 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.436825.e",
"Wikidata: Q30291029" ;
rdfs:label "NZYTech" ;
NIFRID:synonym "Lda. � Genes and Enzymes" ;
definition: "Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins." .
SCR:016773 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FibrilTool" ;
definition: "ImageJ plug-in to quantify fibrillar structures in raw microscopy images. Used to evaluate the orientation of fiber orientation pattern and plots the results in the image." .
SCR:016774 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:BISE" ;
rdfs:label "BISE" ;
definition: "Web platform for bio image analysis. Used to share knowledge between the different communities, to help biologists to find any tool or workflow available for a particular image analysis problem and to find the adequate image processing wording, to help software and algorithm developers to find missing tools (or components), and to help bioimage analyst to identify and edit workflows." .
SCR:016775 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NEUBIAS" ;
NIFRID:synonym "Network of European BioImage Analysts" ;
definition: "Network of European BioImage Analysts to advance life science imaging and to boost the productivity of bioimaging based research projects in Europe." .
SCR:016776 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.474679.f" ;
rdfs:label "NamesForLife" ;
definition: "Privately held Michigan based software company. They provide taxonomic and analytical services, data, software and technology licensing for the academic publishing industry, life sciences research, commercial partners and federal laboratories." .
SCR:016777 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "U.S. Culture Collection Network (USCCN)" ;
NIFRID:synonym "US Culture Collection Network" ;
NIFRID:abbrev "USCCN" ;
definition: "Research coordination network for ex situ Microbial Germplasm Collections to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of humankind by providing opportunities for US culture collection workers to engage with each other and with the broader culture collection community." .
SCR:016778 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Darwin Core" ;
definition: "Natural history collections. Offers a stable, straightforward and flexible framework for biodiversity data. Community-developed biodiversity data standard. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing identifiers, labels, and definitions. Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, samples, and related information." .
SCR:016781 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phaff Yeast Culture Collection" ;
definition: "Collection of wild yeast in the world. Academic and industrial resarchers utilize this collection for a variety of research and applications, including pigments, enzymes, food ingredients, and hosts for protein expression. Provides contract screening and strain selection services." .
SCR:016782 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Culture Collection of Algae at the University of Texas" ;
NIFRID:synonym "The UTEX Culture Collection of Algae",
"UTEX" ;
definition: "The UTEX Culture Collection of Algae includes different strains of living algae, representing most major taxa. Cultures in the Collection are used for research, teaching, biotechnology development, and various other projects throughout the world." .
SCR:016784 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Plant Cell Culture Library (PCCL)" ;
NIFRID:synonym "Plant Cell Culture Library",
"The Plant Cell Culture Library",
"the Plant Cell Culture Library (PCCL)" ;
NIFRID:abbrev "PCCL" ;
definition: "Collection of plant species for use by both academia and industry.The PCCL enables R&D exploitation of monocot, dicot and gymnosperm cultures." .
SCR:016785 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "National Plant Germplasm System (NPGS)" ;
NIFRID:synonym "National Plant Germplasm System",
"NPGS" ;
definition: "Cooperative effort by U.S. state and federal government and private organizations to preserve the genetic diversity of plants. The NPGS aids scientists and the need for genetic diversity by acquiring, preserving, evaluating, documenting and distributing crop germplasm. The NPGS is managed by the Agricultural Research Service (ARS), the in-house research agency of the United States Department of Agriculture (USDA). Funding for the NPGS comes primarily through appropriations from the U.S. Congress." .
SCR:016787 a "Research",
owl:NamedIndividual ;
rdfs:label "HCS Studio Cell Analysis software" ;
NIFRID:synonym "High Content Analysis Studio Cell Analysis software",
"High Content Screening Studio Cell Analysis software" ;
definition: "Software packages for quantitative cell analysis. Used in image cytometry, quantitative cell analysis or automated cell analysis in biological research and drug discovery." .
SCR:016788 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurolucida 360" ;
definition: "Software for automatic neuron 3D reconstruction and analysis. Used by neuroscientists to reconstruct intricate neuronal structures that range in scale from complex, multicellular networks of neurons to sub-cellular dendritic spines and putative synapses." .
SCR:016839 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Motion Sensing Superpixels (MOSES)" ;
NIFRID:synonym "MOSES",
"Motion Sensing Superpixels" ;
definition: "Computational Python library for the motion analysis of biological single-cell and collective motion for high content screens. Framework to quantify and discover cellular motion phenotypes." .
SCR:016840 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus | FV1000 Confocal Microscope" ;
definition: """FV1000 confocal laser scanning biological microscope features twin scan system which enables
spectroscopy of living intercellular contents and analysis of objects down to a 2nm wavelength resolution. Image size is increased to 4096x4096 pixels.""" .
SCR:016841 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HBio: Multichallel Systems | Electro Square Porator ECM 830, BTX" ;
NIFRID:synonym "ECM 830",
"ECM 830 generator",
"Electro Square Porator ECM 830" ;
definition: "ECM 830 is a square wave pulse generator designed for in vitro and in vivo applications for gene, drug and protein delivery for mammalian cells, zebra fish tissue and embryos, nuclear transfer, embryo manipulation, plant protoplast and basic bacteria and yeast transformations. Used in ECM 830 SQUARE WAVE ELECTROPORATION SYSTEM." .
SCR:016842 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sutter | Micropipette puller P-97" ;
definition: "P-97 Flaming / Brown Micropipette Puller is an instrument for fabricating micropipettes, patch pipettes and microinjection needles with improvements in mechanical, electronic and software design for better control of the pulling process and a higher degree of reproducibility." .
SCR:016843 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cd-CAP software" ;
definition: "Software designed for simultaneous detection of connected subnetworks of an interaction network where genes exhibit conserved alteration patterns across tumor samples." .
SCR:016844 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | CM3050 S Research Cryostat" ;
NIFRID:synonym "Leica CM3050 cryostat" ;
definition: "Instrument designed for cryosectioning in biomedical, neuro-anatomical and pharmaceutical research." .
SCR:016845 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "16p_resource Code" ;
definition: "Software tool as a code to support figure generation for the manuscript by Roth, Muench et al. Used to perform analysis." .
SCR:016846 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:XL-mHG",
"biotools:XL-mHG" ;
rdfs:label "XL-mHG" ;
NIFRID:synonym "XL-minimum HyperGeometric",
"XL-minimum HyperGeometric test",
"xlmhg",
"xlminimumhypergeometric" ;
definition: "Software Python package as a semiparametric test for enrichment in ranked lists. Used for determining gene set enrichment." .
SCR:016849 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TranscriptAchilles" ;
definition: "Software genome-wide tool to predict transcript biomarkers of gene essentiality in cancer. This tool can be used to predict new potential target genes with their corresponding biomarkers (either transcript or gene expression)." .
SCR:016850 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Polyman" ;
definition: "Software tool as an European Data Format EDF/EDF+ viewer and manual sleep scoring program. Used in EEG and Sleep investigations, but can be used for almost any (also non-medical) sequential time series and event lists." .
SCR:016851 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ragu " ;
NIFRID:synonym "Randomization Graphical User",
"Randomization Graphical User interface" ;
NIFRID:abbrev "Ragu" ;
definition: "Software tool for the analysis of EEG and MEG event-related scalp field data using global randomization statistics." .
SCR:016852 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:NanoPipe" ;
rdfs:label "NanoPipe" ;
NIFRID:synonym "nanopipe2" ;
definition: "Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms." .
SCR:016853 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Muenster; Muenster; Germany" ;
NIFRID:synonym "The University of Münster" ;
definition: "The University of Münster is a public university located in the city of Münster, North Rhine-Westphalia in Germany. It is Germany fifth largest university." .
SCR:016854 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:QuickNII" ;
rdfs:label "QuickNII" ;
definition: "Section series aligner to volumetric atlases. Software tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems." .
SCR:016855 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016856" ;
rdfs:label "PICRUSt" ;
NIFRID:synonym "Phylogenetic Investigation of Communities by Reconstruction of Unobserved States" ;
definition: "Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome." .
SCR:016859 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "glmmADMB" ;
NIFRID:synonym "generalized linear mixed models using AD Model Builder",
"generalized linear mixed models using ADMB",
"glmm AD Model Builder" ;
definition: "Software R package for fitting generalized linear mixed models (GLMMs) using AD Model Builder. Fits mixed-effects models to count data using Poisson or negative binomial response distributions." .
SCR:016860 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DREME" ;
NIFRID:synonym "Discriminative Regular Expression Motif Elicitation" ;
definition: "Software tool to discover short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in sequences compared with shuffled sequences or control sequences (sample output from sequences)." .
SCR:016861 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sashimiplot" ;
NIFRID:synonym "sashimi_plot" ;
NIFRID:abbrev "sashimiplot" ;
definition: "Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions." .
SCR:016862 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NineML" ;
NIFRID:synonym "Network Interchange for NEuroscience ML",
"Network Interchange for Neuroscience Modeling Language" ;
definition: "Simulator independent language for unambiguous description of spiking neuronal network models that aims to facilitate model sharing, portability, and re-usability. Used as a model description language for neuroscience." .
SCR:016863 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Molecular Signatures Database" ;
NIFRID:synonym "MSigDB",
"MSigDB database v6.2",
"The Molecular Signatures Database" ;
definition: "Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software." .
SCR:016864 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NetworkX" ;
definition: "Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks." .
SCR:016866 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PlantGSEA" ;
NIFRID:synonym "Gene Set Enrichment Analysis (GSEA)",
"Plant GeneSet Enrichment Analysis",
"The Plant GeneSet Enrichment Analysis Toolkit" ;
definition: "Websever for gene set enrichment analysis of plants. Used for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets." .
SCR:016867 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:eman" ;
rdfs:label "EMAN" ;
NIFRID:synonym "EMAN1",
"EMAN2" ;
definition: "Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography." .
SCR:016868 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:ascat",
"biotools:ascat" ;
rdfs:label "ascat" ;
NIFRID:synonym "Allele Specific Copy Number Analysis of Tumors",
"Allele-Specific Copy Number Analysis of Tumors",
"ASCAT 1.0",
"ASCAT 2.0",
"ASCAT 3.0",
"ASCAT 4.0" ;
NIFRID:abbrev "ASCAT" ;
definition: """Software R package to infer tumor purity, ploidy and allele-specific copy number profiles.
It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data.""" .
SCR:016869 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "International Affective Picture System" ;
NIFRID:synonym "The International Affective Picture System" ;
NIFRID:abbrev "IAPS" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 24,20225. Collection of pictures designed to provide a standardized set of pictures for studying emotion and attention. Provides normative ratings of emotion (pleasure, arousal, dominance) for a set of color photographs that provide a set of normative emotional stimuli for experimental investigations of emotion and attention. Used in psychological research." .
SCR:016870 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CropSight" ;
definition: "Software tool which is a PHP and SQL based server platform. Provides automated data collation, storage, and information management through distributed IoT sensors and phenotyping workstations. It provides a two-component solution to monitor biological experiments through networked sensing devices, with interfaces specifically designed for distributed plant phenotyping and centralized data management." .
SCR:016871 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:marrvel" ;
rdfs:label "MARRVEL" ;
NIFRID:synonym "Model organism Aggregated Resources for Rare Variant ExpLoration" ;
definition: "Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research." .
SCR:016872 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Geno2MP" ;
NIFRID:synonym "2 Mendelian Phenotype",
"The Genotype 2 Mendelian Phenotype database" ;
definition: "Collection of phenotypic profiles for affected individuals and, for unaffected individuals, the phenotypic profile of their affected. Collaborative, shared resource for the human genetics community." .
SCR:016873 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pyclone" ;
NIFRID:synonym "PyClone" ;
definition: "Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing." .
SCR:016874 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chromeleon Chromatography Data System (CDS) Software" ;
NIFRID:synonym "Chromeleon Chromatography Data System",
"Chromeleon Chromatography Data System (CDS)",
"Dionex Chromeleon7" ;
NIFRID:abbrev "CDS" ;
definition: "Software system to support chromatography operations, to ensure data quality and manage all the analytical processes from instrument control, to raw data storage and processing, through to generating the final results." .
SCR:016875 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KnowEnG" ;
NIFRID:synonym "Knowledge Engine for Genomics",
"The Knowledge Engine for Genomics" ;
definition: "Part of the NIH Big Data to Knowledge (BD2K) Initiative. One of 11 Centers of Excellence in Big Data Computing. Platform for genomics data analysis where user-supplied data sets will be analyzed in the context of existing knowledge. E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data." .
SCR:016876 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenBMI" ;
definition: "Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time." .
SCR:016877 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Metab" ;
NIFRID:synonym "Metab 1.0",
"Metabolome" ;
definition: "Software package as a metabolomic data processing pipeline in R codes." .
SCR:016878 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Growth Profiling Toolbox" ;
definition: "Software package as a growth curve automatic processing pipeline in Matlab." .
SCR:016881 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "ADMB",
"ADMB-12.0",
"Automatic Differentiation Model Builder" ;
definition: "Open source software suite environment for nonlinear statistical modeling enabling model development, numerical stability, computation, and accuracy parameter estimates. Language built around the AUTODIF Library, a C++ language extension which transparently implements reverse mode automatic differentiation." .
SCR:016883 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:sleuth",
"biotools:sleuth" ;
rdfs:label "sleuth" ;
definition: "Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance." .
SCR:016884 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:clusterprofiler" ;
rdfs:label "clusterProfiler" ;
NIFRID:synonym "Cluster Profiler" ;
definition: "Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters." .
SCR:016885 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SNP2TFBS" ;
NIFRID:synonym "Single Nucleotide Polymorphisms 2 Transcription Factor Binding Site" ;
definition: "Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs." .
SCR:016886 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aline" ;
definition: "Software interactive perl/tk application which can read common sequence alignment formats which the user can then alter, embellish, markup etc to produce the kind of sequence figure commonly found in biochemical articles. Extensible WYSIWYG protein sequence alignment editor for publication quality figures." .
SCR:016887 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CheckMyMetal" ;
NIFRID:abbrev "CMM" ;
definition: "Metal binding site validation server. Used for systematic inspection of the metal-binding architectures in macromolecular structures. The validation parameters that CMM examines cover the entire binding environment of the metal ion, including the position, charge and type of atoms and residues surrounding the metal." .
SCR:016888 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:ropls",
"biotools:ropls" ;
rdfs:label "ropls" ;
NIFRID:synonym "R Orthogonal Partial Least Squares" ;
NIFRID:abbrev "R OPLS" ;
definition: "Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables." .
SCR:016889 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mixOmics" ;
definition: "Software R package of multivariate methods for the exploration and integration of biological datasets with a focus on variable selection. Used to analyse data from high throughput sequencing technologies and spectral imaging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016890 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CCTop" ;
definition: "Web tool for CRISPR/Cas9 target prediction. Identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation." .
SCR:016891 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PESTO" ;
NIFRID:synonym "Parameter EStimation TOolbox" ;
definition: "Software customizable toolbox for parameter estimation in MathWorks MATLAB. Offers scalable algorithms for optimization, uncertainty and identifiability analysis which do not depend on any problem-specific assumptions." .
SCR:016892 a "Research",
owl:NamedIndividual ;
rdfs:label "smMIPfil" ;
NIFRID:synonym "single molecule Molecular Inversion Probesfil" ;
definition: "Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required." .
SCR:016893 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_016894" ;
rdfs:label "CIRCexplorer" ;
definition: "Software tool as a combined strategy to identify junction reads from back spliced exons and intron lariats. Computational pipeline to precisely identify junction reads from Circularized Exons. Used to identify circular RNAs (circRNAs and ciRNAs)." .
SCR:016895 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tools for NIfTI and ANALYZE image" ;
NIFRID:synonym "Neuroimaging Informatics Technology Initiative (NIfTI) and Analyze Image data" ;
definition: "Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform." .
SCR:016896 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CoSMoS_Analysis" ;
NIFRID:synonym "co-localization single molecule spectroscopy",
"co-localization single-molecule spectroscopy",
"Co-localization Single-Molecule Spectroscopy Analysis",
"CoSMoS" ;
NIFRID:abbrev "CoSMoS Analysis" ;
definition: "Software tools for analyzing co-localization single-molecule spectroscopy image data." .
SCR:016897 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:thunderstorm" ;
rdfs:label "Thunder STORM" ;
NIFRID:abbrev "ThunderSTORM" ;
definition: "Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging." .
SCR:016898 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:fretbursts" ;
rdfs:label "FRETBursts" ;
NIFRID:synonym "Förster Resonance Energy Transfer Bursts" ;
definition: "Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data." .
SCR:016899 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:flowsom" ;
rdfs:label "FlowSOM" ;
NIFRID:synonym "Flow Self Organizing Map" ;
definition: "Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise." .
SCR:016905 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Xenonucleic Acid Computing Group Wiki Template" ;
NIFRID:synonym "Xenonucleic Acid Computing Group" ;
NIFRID:abbrev "xacg" ;
definition: "Molecular computing based on XNA-built alphabets." .
SCR:016907 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "National Resource for Translational and Developmental Proteomics" ;
NIFRID:synonym "NRTDP",
"The National Resource for Translational and Developmental Proteomics" ;
definition: "Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists." .
SCR:016908 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:prosigh_lite" ;
rdfs:label "ProSight Lite" ;
definition: "Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data." .
SCR:016909 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:networkanalyst" ;
rdfs:label "NetworkAnalyst" ;
definition: "Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data." .
SCR:016911 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepNeuro" ;
definition: "Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners." .
SCR:016915 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PPR-Meta" ;
definition: "Software tool to identify metagenomic sequences of phages, chromosomes or plasmids. Used for identifying phages and plasmids from metagenomic fragments using deep learning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016916 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Java Treeview" ;
NIFRID:synonym "Java TreeView",
"Treeview",
"TreeView3" ;
NIFRID:abbrev "TreeView" ;
definition: "Software as a cross platform gene expression visualization tool. Extensible viewer for microarray data in the PCL or CDT format. Interactive display of clustered gene expression data. Java application for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it into a figure." .
SCR:016918 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ENteric Immunity SImulator (ENISI) Multi scale model" ;
NIFRID:synonym "ENteric Immunity SImulator Multi Scale Model" ;
NIFRID:abbrev "ENISI MSM" ;
definition: "Software tool for simulating the mucosal immune responses to Helicobacter pylori infection in stomach." .
SCR:016919 a "Research",
owl:NamedIndividual ;
rdfs:label "Phenograph" ;
NIFRID:abbrev "PhenoGraph" ;
definition: "Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity." .
SCR:016920 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kidney Precision Medicine Project" ;
NIFRID:synonym "The Kidney Precision Medicine Project" ;
NIFRID:abbrev "KPMP" ;
definition: "Project to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States." .
SCR:016921 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ValIdated Systematic IntegratiON of epigenomic data " ;
NIFRID:synonym "ValIdated Systematic IntegratiON",
"ValIdated Systematic IntegratiON of epigenomic data" ;
NIFRID:abbrev "VISION" ;
definition: "International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human." .
SCR:016922 a "Research",
owl:NamedIndividual ;
rdfs:label "The Human BioMolecular Atlas Program" ;
NIFRID:synonym "HuBMAP",
"Human BioMolecular Atlas Program",
"NIH HuBMAP" ;
definition: "Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows." .
SCR:016923 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Prevention of Lower Urinary Tract Symptoms" ;
NIFRID:synonym "PLUS",
"Prevention LUTS" ;
definition: "Research consortium from many different fields to plan, perform and analyze the studies that are needed to help researchers conduct future prevention and intervention for Lower Urinary Tract Symptoms (LUTS) in women." .
SCR:016924 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pharos" ;
rdfs:label "Illuminating the Druggable Genome" ;
NIFRID:synonym "IDG",
"Illuminating Druggable Genome",
"Pharos" ;
definition: "Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC)." .
SCR:016925 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "4D Nucleome " ;
NIFRID:synonym "4D Nucleome Network; 4DN Web Portal",
"4DN Portal",
"The 4D nucleome project" ;
definition: "Research project to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development and diseases. Portal provides free access to datasets, software packages, and protocols to advance biomedical research of nuclear architecture. Aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes." .
SCR:016926 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ALGGEN-PROMO" ;
NIFRID:synonym "ALGGEN",
"ALGorithmics and GENetics PROMO",
"PROMO" ;
definition: "Web tool to identify putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. Used for detection of known transcription regulatory elements using species-tailored searches." .
SCR:016928 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Med Associates | NIR Video Fear Conditioning Package for Mouse" ;
definition: "Equipment with product number MED VFC SCT M supplied by Med Associates. Fear conditioning package eliminates the need for bright visible light, visible light can be used within a session as a cue without impacting the video recording, real time video recordings allows software to distinguish between subtle movements such as whisker twitch or tail flick, as well as freezing behavior." .
SCR:016929 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Digital Expression Explorer 2 Project" ;
NIFRID:synonym "DEE2 Project" ;
NIFRID:abbrev "DEE2" ;
definition: """Software tool as a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Short Read Archive . DEE2 consists of three parts: Webserver where end-users can search for and obtain data-sets of interest,
Pipeline that can download and process SRA data as well as users own fastq files, Back-end that collects, filters and organises data provided by contributing worker nodes.""" .
SCR:016930 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Digital Expression Explorer 2 Source Code" ;
definition: "GitHub repository of the Digital Expression Explorer 2 resource. It contains information related to the pipeline, docker image, backend analysis, webserver, and R package getDEE2." .
SCR:016931 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Digital Expression Explorer 2 Docker Image" ;
definition: "Docker image that is used to process all of the data present in the Digital Expression Explorer 2 dataset. It can be freely used by anyone to process data on NCBI SRA or process their own RNA-seq fastq files. Used for bulk reprocessing of public RNA-seq data from SRA. The pipeline tallies the reads assigned to each gene or transcript." .
SCR:016933 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:dcmqi" ;
rdfs:label "dcmqi" ;
NIFRID:synonym "DCMQI",
"DICOM for Quantitative Imaging",
"Digital imaging and Communications in Medicine for Quantitative Imaging",
"The Digital imaging and Communications in Medicine for Quantitative Imaging" ;
definition: "Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer." .
SCR:016935 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open" ;
definition: "Data collected from subjects scanned 3 times (V1, V2, V3), with V1 and V2 on a scanner, V3 on another scanner in another site. Resting state blood oxygenation level dependent functional MRI (BOLD fMRI), pseudo continuous arterial spin labeling (pCASL), and high resolution 3D T1 imaging were performed under eyes open (EO) and eyes closed (EC) conditions." .
SCR:016936 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Hangzhou Normal University; Hangzhou; China" ;
NIFRID:synonym "Hangzhou Teachers College" ;
definition: "Public university in Hangzhou, the capital of Zhejiang Province, China. It is a comprehensive university with an excellence in teacher training and professional development." .
SCR:016937 a "Research",
owl:NamedIndividual ;
rdfs:label "International Human Epigenome Consortium" ;
NIFRID:synonym "IHEC" ;
definition: "Consortium to coordinate epigenome mapping and characterization worldwide to avoid redundant research effort, to implement high data quality standards, to coordinate data storage, management and analysis and to provide free access to the high resolution reference human epigenome maps for normal and disease cell types to the research community. Promotes data sharing. You may view, search and download the data already released by the different IHEC associated projects via the IHEC Data Portal." .
SCR:016938 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "duphold" ;
definition: "Software tool to annotate structural variant calls with sequence depth information that can add or remove confidence to SV predicted to affect copy number. Indicates the presence of a rapid change in depth relative to the regions surrounding the breakpoints. Allows the run time to be nearly independent of the number of variants important for large, jointly called projects with many samples. Annotates structural variant predictions made from both short read and long read data." .
SCR:016939 a "Research",
owl:NamedIndividual ;
rdfs:label "Wizard" ;
NIFRID:synonym "Wizard 1.9.27",
"Wizard 1.9.28",
"Wizardmac" ;
definition: "Software tool for data analysis and exploration. Statistics software for Mac." .
SCR:016941 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:CRISPR-P" ;
rdfs:label "CRISPR-P" ;
NIFRID:synonym "Clustered Regularly Interspaced Short Palindromic Repeats P",
"CRISPR P",
"CRISPR-P 2.0" ;
definition: "Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment." .
SCR:016942 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GENIST" ;
NIFRID:synonym "Gene Regulatory Network Inference" ;
definition: "Software tool as an algorithm to infer gene regulatory networks from spatial and temporal datasets. Spatial dataset or any data that can provide information about coexpression is used by the first step of the algorithm to perform clustering and separate the genes in the network in smaller coexpressed groups. Temporal dataset is used by the second step of the algorithm to infer regulations among the genes, based on Bayesian networks." .
SCR:016943 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XDSME" ;
NIFRID:synonym "X-ray Detector Software Made Easier",
"XDS Made Easier" ;
NIFRID:abbrev "xdsme" ;
definition: "Software package of python scripts made to simplify the processing of crystal diffraction images." .
SCR:016944 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:scran" ;
rdfs:label "scran" ;
NIFRID:synonym "SCRAN",
"Single-Cell Rna-seq data ANalysis" ;
definition: "Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection." .
SCR:016945 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:rsubread" ;
rdfs:label "Rsubread" ;
definition: "Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers." .
SCR:016947 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "riboSeqR" ;
definition: "Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments." .
SCR:016948 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "riboWaltz" ;
definition: "Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates." .
SCR:016949 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biostrings" ;
definition: "Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences." .
SCR:016950 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Numbers" ;
definition: "Software tool to create spreadsheets that include tables and images. You can use Apple Pencil on your iPad to add diagrams and colorful illustrations." .
SCR:016951 a owl:NamedIndividual ;
rdfs:label "Affinity Photo" ;
definition: "Software tool for professional photo editing." .
SCR:016952 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Affinity Designer" ;
definition: "Software tool for vector illustrations. Professional graphic design software." .
SCR:016953 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Whisker tracking macro" ;
definition: "ImageJ plugins and macros for whisker tracking. Set of Fiji plugins and macros for tracking a single whisker." .
SCR:016954 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:consensusclusterplus" ;
rdfs:label "ConsensusClusterPlus" ;
definition: "Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots." .
SCR:016955 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:CIbERSORt" ;
rdfs:label "CIBERSORT" ;
definition: "Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets." .
SCR:016956 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EpiFactors " ;
definition: "Manually curated collection of human epigenetic factors, their complexes, corresponding genes and products." .
SCR:016957 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tenx" ;
definition: "Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis." .
SCR:016958 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Science Dynamics" ;
definition: "Portal for Science Dynamics projects with open source framework to provide way to query datasets. Code framework, including tutorials for project, titled Over Optimization of Academic Publishing Metrics Observing Goodhart Law in Action, to interactively explore and understand how various properties of journals have changed over time. Datasets, software implementations, code tutorials and interactive web interface for investigating studied networks." .
SCR:016959 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DamMet" ;
definition: "Software tool as a full probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen." .
SCR:016960 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:genomicfeatures" ;
rdfs:label "GenomicFeatures" ;
definition: "Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database." .
SCR:016961 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "devtools" ;
definition: "Software tools to make developing R packages easier by providing R functions that simplify and expedite common tasks." .
SCR:016962 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fastp" ;
definition: "Software tool to provide fast all in one preprocessing for FastQ files. Developed in C++ with multithreading supported to afford high performance. Performs quality control, adapter trimming, quality filtering, per read quality pruning and many other operations with a single scan of the FASTQ data." .
SCR:016963 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:cctop" ;
rdfs:label "CCTOP" ;
NIFRID:synonym "Consensus Constrained TOPology" ;
definition: "Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them." .
SCR:016964 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TopDom" ;
NIFRID:synonym "TopDom_v0.0.1",
"TopDom_v0.0.2",
"TOPological DOMains",
"Topological Domains" ;
NIFRID:abbrev "TOPDOM" ;
definition: "Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016965 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BBmap" ;
definition: "Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform." .
SCR:016966 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoFilt" ;
definition: "Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data." .
SCR:016967 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_17306" ;
rdfs:label "Porechop" ;
definition: "Software tool for finding and removing adapters from Oxford Nanopore reads." .
SCR:016968 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bestus Bioinformaticus Tools" ;
NIFRID:synonym "BB Tools",
"BBTools" ;
definition: "Software suite of bioinformatics tools for analysis of DNA and RNA sequence data. Used for file formats such as fastq, fasta, sam, scarf, fasta plus qual, compressed or raw, with autodetection of quality encoding and interleaving. Written in Java and works on any platform supporting Java, including Linux, MacOS, and Microsoft Windows." .
SCR:016969 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bestus Bioinformaticus Duk" ;
NIFRID:synonym "BB Duk",
"BBDUK",
"BBDuk",
"BBDuk2",
"BBDuk 2",
"Bestus Bioinformaticus Decontamination Using kmers",
"Bestus Bioinformaticus Decontamination using kmers",
"Decontamination Using Kmers" ;
definition: "Software tool for trimming and filtering sequencing data. Used to combine data quality related trimming, filtering, and masking operations into a single tool adapter. BBDuk2 allows multiple kmer based operations in a single pass." .
SCR:016970 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bestus Bioinformaticus Merge" ;
NIFRID:synonym "BB Merge",
"BBMerge",
"BestusBioinformaticusMerge" ;
definition: "Software tool to merge two overlapping paired reads into a single read. Used in amplicon studies and in assembly, where longer reads allow the use of longer kmers or fewer comparisons." .
SCR:016971 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Reformat" ;
NIFRID:synonym "BB Reformat",
"BBReformat",
"Bestus Bioinformaticus Reformat" ;
definition: "Software tool for generic streaming read processing tasks that have low memory or computational demands, such as format conversion, sub sampling, and various filtering operations." .
SCR:016972 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "MindWare Technologies" ;
NIFRID:synonym "MindWare Technologies Ltd." ;
definition: "Commercial organization providing laboratory solutions in the fields of psychophysiology, neuroscience, social science, life science, child and behavioral development. Offers a wide array of products and services including signal acquisition hardware used to collect a variety of measures including Cardiac Impedance, HRV, GSR/GSC, ECG/EKG, HR, BP, and EMG supplemented with software suite of analysis applications." .
SCR:016973 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID: 100002418",
"grid.419318.6",
"ISNI: 0000 0004 1217 7655",
"Wikidata: Q248" ;
rdfs:label "Intel" ;
NIFRID:synonym "intel",
"Intel Corporation" ;
definition: "American multinational corporation and technology company headquartered in Santa Clara, California, in the Silicon Valley. Semiconductor chip maker being overtaken by Samsung. Inventor of the x86 series of microprocessors, the processors found in most personal computers (PCs). Intel supplies processors for computer system manufacturers such as Apple, Lenovo, HP, and Dell. Intel also manufactures motherboard chipsets, network interface controllers and integrated circuits, flash memory, graphics chips, embedded processors and other devices related to communications and computing." .
SCR:016974 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:heatmapper",
"OMICS_12077" ;
rdfs:label "Heatmapper" ;
NIFRID:synonym "heat mapper",
"HeatMapper" ;
definition: "Software tool to create and provide heat maps through a graphical interface. Allows to create an expression, pairwise comparison, image overlay, geomap, and geocoordinate heat maps for different data types and applications. Used to interactively visualize data." .
SCR:016975 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14042" ;
rdfs:label "Nuclear Hormone Receptor Scan" ;
NIFRID:synonym "NHR Scan",
"NHR-scan",
"NHRScan",
"Nuclear Hormoe Receptor Scan" ;
definition: "Web interface for computational prediction of nuclear hormone receptor binding sites in genomic sequences. Flexible Hidden Markov Model framework to allow for variable spacing and orientation of half sites. Allows for parameter modifications." .
SCR:016976 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "affydata" ;
NIFRID:synonym "Affymetrix Data",
"Affymetrix Data for Demonstration Purpose" ;
NIFRID:abbrev "AffyData" ;
definition: "Software R package for analysis of Affymetrix Data. Contains samples data files of a large size." .
SCR:016977 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Prism Clinical Imaging" ;
definition: "Provides Prism softwares and services that integrate advanced imaging into the clinical workflow for brain mapping from acquisition through processing, visualization, and export to PACS. Prism integrates functional MRI, diffusion MRI, perfusion, MR spectroscopy, and PET/CT into a unified workflow for diagnosis and treatment planning in brain disorders. Processing is also available as a cloud deployed service, Prism Serve. Research support includes import/export for imaging and derived quantitative data in both DICOM and research formats such as AFNI and Trackviz." .
SCR:016978 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GEOMAGIC Studio" ;
NIFRID:abbrev "GEOMAGIC Studio 12" ;
definition: "Software tool to convert 3D scans into parametric models. Transforms 3D scan data into highly accurate surface, polygon and native CAD models. Used for reverse engineering, product design, rapid prototyping and analysis." .
SCR:016979 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Keyence | BZ-X700 microscope" ;
definition: "Fluorescence microscope of BZ-X series by KEYENCE CORPORATION of America. Captures high resolution images without the blurring caused by out of focus fluorescent signals. Optical sectioning allows the user to obtain images comparable to those captured on a laser confocal microscope, but in a fraction of the time and without the damaging effects of a laser., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016980 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss | Axio Zoom.V16 for Materials���" ;
NIFRID:synonym "ZEISS Axio Zoom.V16 for Materials system" ;
definition: "ZEISS Axio Zoom.V16 microscope system includes high resolution zoom microscope for large fields. Focuses on reflected light microscopy of materials. Uses optical components to manage reflected light from specimen surface. Designed for observing surface properties and structures of materials using reflected light. System focuses on providing high resolution image quality and contrast for reflected light microscopy of solid materials., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:016982 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CCPN Data Model" ;
NIFRID:synonym "The CCPN Data Model" ;
definition: "Model to cover data for macromolecular NMR spectroscopy from the initial experimental data to the final validation. Used for the large scale data deposition, data mining and program interoperability. Enables movement from one software package to another without difficulties with data conversion or loss of information. Works with CcpNmr Analysis software for analysis and interactive display, CcpNmr FormatConverter for allowing transfer of data from programs used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment. Used within the CCPN software suite for NMR spectroscopy and at the BioMagResBank for converting existing deposited restraint lists to a standard IUPAC nomenclature." .
SCR:016983 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Collaborative Computing Project for NMR" ;
NIFRID:synonym "CCPN",
"The Collaborative Computing Project for NMR" ;
definition: "Project provides tools and knowledge to maximize the impact of the biological NMR studies. CCPN software facilitates data analysis and software integration. Project promotes the exchange of knowledge and provides training and best practices for the NMR community and has leading role in the development of NMR data sharing standard and coordination of NMR instrumentation proposals. Includes CCPN Data Model for macromolecular NMR and related areas, CcpNmr suite of programs like Analysis for spectrum visualization, resonance assignment and analysis, ChemBuild to create chemical structure templates in an NMR aware manner, FormatConverter for data exchange with common textual NMR formats and SpecView for swift, format independent peak and spectrum visualization." .
SCR:016984 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CCPN Analysis" ;
NIFRID:synonym "CCPN Analysis v2",
"CCPN Analysis v3",
"CcpNmr Analysis" ;
definition: "Software package for interactive NMR spectrum visualization, resonance assignment and data analysis. Graphical elements allow to enter information and to view status of data and library functions manipulate the CCPN data model objects to record the scientific information. Software is cross platform and works on Linux, Mac OSX, Windows and Unix." .
SCR:016985 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QDSpy" ;
NIFRID:synonym "Quality Data System python software" ;
definition: "Software Python tool for scripting and presenting stimuli for visual neuroscience." .
SCR:016986 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NONMEM" ;
NIFRID:synonym "NONlinear Mixed Effects Modeling software",
"Nonlinear mixed effects modelling software",
"NONMEM 7",
"NONMEM 7.2",
"NONMEM 7.4",
"population analysis" ;
NIFRID:abbrev "Nonmem" ;
definition: "Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions." .
SCR:016987 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Maize Database of Images and Genomes" ;
NIFRID:synonym "Maize Dig",
"MaizeDatabase of Images and Genomes",
"MaizeDIG",
"MaizeDig" ;
definition: "Genotype and phenotype database for maize images based on BioDIG. Supports multiple reference genomes and has been integrated with the MaizeGDB Genome Browser to make custom tracks showing mutant phenotypes within their genomic context. Allows for custom tagging of images to highlight regions related to the phenotypes. This is accomplished through an interface allowing users to create links from images to genomic coordinates and to curate and search images by gene model ID, gene symbol, and gene name." .
SCR:016990 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyMINEr" ;
definition: "Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq." .
SCR:016991 a NLX:63400,
owl:NamedIndividual .
SCR:016992 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:rnaSPAdes_autogenerated" ;
rdfs:label "rnaSPAdes" ;
definition: "Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9." .
SCR:016993 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:VAPPER" ;
rdfs:label "VAPPER" ;
NIFRID:synonym "VAP",
"VariantAntigenProfilingPER" ;
definition: "Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections." .
SCR:016994 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:rnaQUASt" ;
rdfs:label "rnaQUAST" ;
definition: "Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software." .
SCR:016995 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Region to Region " ;
NIFRID:synonym "3-D Connective Field Modeling Toolbox" ;
definition: "Software tool as a framework for fitting and describing connectivity patterns between regions that is a simple extension from the current population receptive field models in the visual neuroscience literature. The connectivity from each voxel in a designated seed region to a mapping region is modeled as a 3-dimensional Gaussian, providing location parameters and spread parameters. This allows the direct description of the relative mapping from one region to another." .
SCR:016996 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SRM atlas" ;
NIFRID:abbrev "SRMAtlas" ;
definition: "Collection of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. It results from high-quality measurements of natural and synthetic peptides conducted on a triple quadrupole mass spectrometer." .
SCR:016999 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018356" ;
rdfs:label "mousebrain.org" ;
NIFRID:synonym "Linnarsson lab Mouse Brain Atlas" ;
definition: "Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system." .
SCR:017000 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellTax vignette" ;
NIFRID:synonym "Cellular Taxonomy of the Mouse Visual Cortex",
"Cellular Taxonomy of the Mouse Visual Cortex Allen Institue for Brain Science" ;
definition: "Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing." .
SCR:017001 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_017530" ;
rdfs:label "Allen Brain Atlas" ;
NIFRID:synonym "Allen Human Brain Atlas",
"Allen Mouse Brain Atlas",
"Brain Atlases",
"The Allen Brain Atlas" ;
definition: "Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases." .
SCR:017002 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stemformatics" ;
definition: """Gene expression data portal developed for stem cell community, containing public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Portal to visualize and download curated stem cell data.
Provides easy to use and intuitive tools for biologists to visually explore data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others.""" .
SCR:017003 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LipidView Software" ;
definition: """Software tool for molecular characterization and quantification of lipid species from electrospray mass spectrometry data.
Enables lipid profiling by searching parent and fragment ion masses against lipid fragment database and reports numerical and graphical output for various lipid molecular species, lipid classes, fatty acids, and long chain bases.""" .
SCR:017004 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "INCF-Neurobot" ;
NIFRID:synonym "INCF Neurobot",
"International Neuroinformatics Coordinating Facility Neurobot" ;
definition: "Software tool for data management in clinical studies to improve care for patients with Traumatic Brain Injury (TBI). Used to search and find study variables with the associated information and export study data for further analysis." .
SCR:017005 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:rCASC" ;
rdfs:label "rCASC" ;
NIFRID:synonym "reproducible Cluster Analysis of Single Cells" ;
definition: "Software package for reproducible classification analysis of single cell sequencing data." .
SCR:017006 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:docker4seq" ;
rdfs:label "docker4seq" ;
definition: "Software R package to execute next generation sequencing computing applications, e.g. reads mapping and counting, wrapped in docker containers." .
SCR:017007 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Turin;Turin;Italy" ;
definition: "University in Turin in Piedmont region of north western Italy. One of the oldest universities in Europe, and continues to play an important role in research and training." .
SCR:017009 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bulked segregation analysis tools for outbreeding species" ;
NIFRID:synonym "BSATOS",
"Bulked Segregation Analysis Tools for Outbreeding Species" ;
definition: "Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data." .
SCR:017011 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_31363" ;
rdfs:label "OmicsSIMLA" ;
definition: "Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version." .
SCR:017012 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Slingshot" ;
definition: "Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics." .
SCR:017013 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_32475" ;
rdfs:label "Metacell" ;
NIFRID:abbrev "MetaCell" ;
definition: "Software package for single cell RNA-seq data analysis using k-NN graph partitions. Used to analyze group of scRNA profiles that are highly similar and provides features for deriving them. Can be used with large datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017014 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenomeScope" ;
NIFRID:abbrev "Genomescope" ;
definition: "Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach." .
SCR:017015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus | FluoView FV3000 Confocal Laser Scanning Microscope" ;
NIFRID:synonym "Olympus FV3000 microscope" ;
definition: "Microscope enables 2D-6D (x,y,z,t,λ,p) macro to micro imaging of cells, tissues, and small organisms. Supports complete workflows from image acquisition to processing and analysis. Used in cell biology, cancer research, stem cell research, neuroscience, electrophysiology, and developmental biology." .
SCR:017016 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Flye" ;
rdfs:label "Flye" ;
definition: "Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms." .
SCR:017017 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Anima" ;
definition: "Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows." .
SCR:017018 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LION/web" ;
NIFRID:synonym "LION",
"LIpid ONtology",
"Lipid Ontology",
"LIpid ONtology (LION)",
"The Lipid Ontology (LION)" ;
NIFRID:abbrev "Lipid Ontology (LION)" ;
definition: """Web based ontology enrichment tool for lipidomic data analysis. Used for lipidomics to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPIDMAPS, biophysical data, lipid functions and
organelle associations. Freely accessible in a platform independent way.""" .
SCR:017019 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:eda" ;
rdfs:label "Experimental Design Assistant" ;
NIFRID:synonym "EDA",
"Experimental Design Assistant (EDA)" ;
definition: "Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility." .
SCR:017020 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID: 501100000849",
"grid.453088.2",
"ISNI: 0000 0004 0626 8753",
"Wikidata: Q15637445" ;
rdfs:label "NC3Rs" ;
NIFRID:synonym "National Centre for the Replacement",
"Refinement and Reduction of Animals in Research" ;
definition: "UK’s national organization for the 3Rs (Replacement, Reduction and Refinement) to advance the 3Rs framework for performing more humane animal research by focusing on scientific impacts and benefits to better reflect contemporary scientific practice and developments." .
SCR:017021 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LR Gapcloser" ;
NIFRID:synonym "LR_Gapcloser" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th, 2023. Software that uses long reads to close gaps in the assemblies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017023 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker WinEPR program " ;
definition: """Software tool to operate the EMX series of spectrometers by Bruker. Provides rapid data analysis of 1D and 2D data sets,
provides environment for acquisition and processing of CW-EPR and CW-ENDOR spectra with the EMXplus and EMXmicro series of spectrometers.""" .
SCR:017024 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DMT Normalization" ;
NIFRID:synonym "DMT Normalization Add-On" ;
definition: "Software tool for calculating optimal pretension conditions for microvascular or any small tubular tissue research. DMT Normalization Add-On, provided by ADInstruments, is included as part of LabChart Pro or can be purchased separately." .
SCR:017025 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:scaffmatch",
"OMICS_08198" ;
rdfs:label "ScaffMatch" ;
definition: "Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes." .
SCR:017026 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Profinder" ;
NIFRID:synonym "Profinder 8" ;
definition: "Software tool as fast, batch processing feature extraction software for differential analysis that supports data from Agilent GC/MSD, GC/Q-TOF, LC/TOF and LC/Q-TOF instruments. Speeds up differential and flux analysis workflows using intuitive user interface. Used to analyze raw mass spectrometry data, choose peaks." .
SCR:017027 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "toxprofileR" ;
definition: "Software R package to derive toxicogenomic fingerprints from microarray data." .
SCR:017028 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Toxicogenomic Fingerprint Browser" ;
definition: "Software tool to visualize and explore toxicogenomic fingerprints of three model substances." .
SCR:017029 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PALM" ;
NIFRID:synonym "Permutation Analysis of Linear Models" ;
definition: "Software tool for inference using permutation methods. Requires Matlab or Octave. Can be executed from inside either environment, or directly from the shell and can be called from scripts. For users who are familiar with statistics and willing to use experimental analysis tools." .
SCR:017030 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_32242" ;
rdfs:label "MITE-Tracker" ;
NIFRID:synonym "Miniature Inverted repeats Transposable Elements Tracker",
"MITE Tracker" ;
definition: "Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences." .
SCR:017031 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LTRpred" ;
NIFRID:synonym "LTRpred(ict)" ;
definition: "Software package for automated functional annotation of LTR retrotransposons for comparative genomics studies. Used to perform de novo functional annotation of LTR retrotransposons from any genome assembly in fasta format." .
SCR:017032 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:PS-Plant" ;
rdfs:label "PS-Plant Framework" ;
NIFRID:abbrev "PS-Plant" ;
definition: "Software tool as end to end software for data acquisition, processing, and result extraction of Arabidopsis thaliana growth. Framework uses photometric stereo based 3D imaging system with computer vision and deep learning for tracking and quantifying both plant growth and movement parameters." .
SCR:017033 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_32232" ;
rdfs:label "PCAGO" ;
definition: "Interactive web service for analysis of RNA-Seq read count data with principal component analysis (PCA) and agglomerative clustering. Includes features like read count normalization, filtering read counts by gene annotation and visualization options." .
SCR:017034 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TransRate" ;
definition: "Open source software tool for de novo transcriptome assembly reference free quality analysis. Used to examine assembly in detail and compare it to sequencing reads, reporting quality scores for contigs and assemblies to allow to choose between assemblers and parameters, filter out bad contigs from an assembly, and help decide when to stop trying to improve assembly." .
SCR:017035 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:detonate" ;
rdfs:label "DETONATE" ;
NIFRID:synonym "DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation" ;
definition: "Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences." .
SCR:017036 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_09075" ;
rdfs:label "Salmon" ;
definition: "Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias." .
SCR:017037 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Shannon" ;
definition: "Software tool for de novo transcriptome assembly from RNA-Seq data." .
SCR:017038 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:binpacker",
"OMICS_11199" ;
rdfs:label "BinPacker" ;
definition: "Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux." .
SCR:017039 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bridger",
"OMICS_07535" ;
rdfs:label "Bridger" ;
definition: "Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux." .
SCR:017040 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "datastorr" ;
definition: "Software package for simple data retrieval and versioning." .
SCR:017041 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.26275",
"r3d100013719" ;
rdfs:label "SPARC Portal" ;
NIFRID:synonym "SPARC Project",
"SPARC Repository",
"Stimulating Peripheral Activity to Relieve Conditions" ;
NIFRID:abbrev "SPARC.science" ;
definition: "SPARC data repository as of 2023 is an open data repository developed as part of the NIH SPARC initiative and has been used by SPARC funded investigator groups to curate and publish high quality datasets related to the autonomic nervous system. We are thrilled that as of August 2022, SPARC is accepting datasets from investigators that are not funded through the NIH SPARC program. The NIH's Common Fund Stimulating Peripheral Activity to Relieve Conditions (SPARC) program aims to transform our understanding of these nerve-organ interactions and ultimately advance neuromodulation field toward precise treatment of diseases and conditions for which conventional therapies fall short." .
SCR:017045 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_12591",
"SCR_017243" ;
rdfs:label "RaceID" ;
NIFRID:synonym "RaceID2",
"RaceID3" ;
definition: "Algorithm for identification of rare and abundant cell types from single cell transcriptome data. Based on transcript counts obtained with unique molecular identifies. Used for discovering rare cell types and corresponding marker genes in healthy and diseased organs. Operating system Unix/Linux, Mac OS, Windows." .
SCR:017046 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GLEW" ;
NIFRID:synonym "OpenGL Extension Wrangler Library",
"openGL Extension Wrangler library",
"The OpenGL Extension Wrangler Library" ;
definition: "Cross platform open source extension loading library. Provides efficient run time mechanisms for determining which OpenGL extensions are supported on target platform. OpenGL core and extension functionality is exposed in single header file. Operating systems Windows, Linux, Mac OS X, FreeBSD, Irix, and Solaris." .
SCR:017047 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VORTEX" ;
NIFRID:synonym "VorteX Clustering Environment" ;
definition: "Software Java graphical tool for single cell analysis, clustering and visualization. Provides multithreaded implementations of clustering algorithms, including nonparametric density based X shift, Hierarchical clustering, Mean shift and K medoids." .
SCR:017048 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:umi-tools" ;
rdfs:label "UMI-tools" ;
NIFRID:synonym "Unique Molecular Identifiers tools" ;
definition: "Open source software package for handling Unique Molecular Identifiers in NGS data sets." .
SCR:017049 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:jamm" ;
rdfs:label "JAMM" ;
NIFRID:synonym "J oint A nalysis of NGS replicates via M ixture M odel clustering",
"Joint Analysis of NGS replicates via Mixture Model clustering" ;
definition: "Software tool as peak finder for joint analysis of NGS replicates. Used for peak finding in next generation sequencing broad and narrow datasets like ChIP-Seq, ATAC-Seq, DNase-Seq. Can integrate information from biological replicates and assign peak boundaries accurately." .
SCR:017050 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colony measure" ;
NIFRID:synonym "HT Colony Grid Analyzer" ;
definition: "Software tool as executable program that measures sizes and other properties of colonies arrayed in grid format from jpeg images. Intended for 768, 384, or 96 colonies on agar plates." .
SCR:017051 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:genomicranges" ;
rdfs:label "Genomic Ranges" ;
definition: "Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome." .
SCR:017052 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:goseq" ;
rdfs:label "Goseq" ;
definition: "Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies." .
SCR:017053 a owl:NamedIndividual ;
rdfs:label "COsleep" ;
NIFRID:synonym "Closed and Open loop sleep",
"Closed- and Open-loop Sleep Stimulations with Auditory Stimuli" ;
NIFRID:abbrev "cosleep" ;
definition: "Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton." .
SCR:017054 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellPhoneDB" ;
definition: "Collection of publicly available data of curated receptors, ligands and their interactions. Integrates existing datasets that pertain to cellular communication and new manually reviewed information. Used to search for particular ligand or receptor or to interrogate single cell transcriptomics data." .
SCR:017055 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:clustal2" ;
rdfs:label "Clustal 2" ;
NIFRID:synonym "clustal2",
"clustal X",
"CLUSTAL_X",
"Clustalx",
"clustalx" ;
definition: "Software tool for nucleotide sequence alignment. Graphical version of multiple sequence alignment program for DNA and proteins. Windows interface for ClustalW multiple sequence alignment program. Provides integrated environment for performing multiple sequence and profile alignments and analyzing results. Available on Linux, Mac and Windows." .
SCR:017057 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:prsice",
"OMICS_23656" ;
rdfs:label "PRSice" ;
NIFRID:synonym "Polygenic Risk Score software",
"prsice",
"PRSice1",
"PRSice2",
"PRSice-2" ;
definition: "Software R package for calculating, applying, evaluating and plotting results of polygenic risk scores analysis. Performs simulation study to estimate P value significance threshold for high resolution PRS studies and produces plots for inspection of results. Operating Unix/Linux." .
SCR:017058 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ;
rdfs:label "BioPortainer" ;
NIFRID:synonym "BioPortainer Workbench" ;
definition: "Open source software designed in modular way, aimed at facilitating user interaction with Docker environments in three different computational layers like infrastructure, platform and application." .
SCR:017059 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:HatSPiL" ;
rdfs:label "HaTSPiL" ;
definition: "Software Python tool for high throughput sequencing analysis, focused on high reliability, modularity and customisability." .
SCR:017060 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kinarm | End-Point Lab" ;
NIFRID:synonym "KINARM End-Point Lab",
"Kinesiological Instrument for Normal and Altered Reaching Movements End-Point Lab" ;
definition: "Robotics research tool designed to make quantitative neurological assessments of sensorimotor, proprioception, and cognitive brain function by BKIN Technologies. Robotic manipulandum with display for studying arm movements. Allows to assess coordination of limbs at multiple joints while measuring joint specific force." .
SCR:017062 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Italian Institute for Genomic Medicine; Turin; Italy" ;
NIFRID:abbrev "HuGeF",
"IIGM" ;
definition: "Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience." .
SCR:017063 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "p300db" ;
definition: "Data collection of CBP/p300 regulated acetylome, proteome, and transcriptome in murine embryonic fibroblasts. Composed of Symbol search for quantified acetylation sites, proteins and transcripts abundance in CBP/p300, Domain search for batch query of proteins by specific domain and Conserved sites for acetylation sites that are conserved between mouse and human, and their regulation in KATi treated cells." .
SCR:017064 a NLX:63400,
owl:NamedIndividual ;
definition: "C. elegans RNAi feeding library distributed by Source BioScience Ltd. Designed for genome wide study of gene function in C. elegans through loss of function studies." .
SCR:017065 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D Roi Manager" ;
definition: "Software tool as plugin for ImageJ. Used for 3D objects and image can be segmented directly within plugin via 3D segment button." .
SCR:017066 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D Objects Counter" ;
NIFRID:abbrev "3D-OC" ;
definition: "Software tool as plugin for ImageJ. Counts the number of 3D objects in stack, quantifies for each found object, generates results representations." .
SCR:017067 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GAGE" ;
NIFRID:synonym "gage",
"Generally Applicable Gene-set Enrichment",
"Generally Applicable Gene-set Enrichment for pathway analysis",
"GSEA" ;
definition: "Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies." .
SCR:017068 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "seqNMF" ;
definition: "Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers." .
SCR:017069 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NMF Toolbox" ;
NIFRID:synonym "NMF MATLAB Toolbox",
"Non negative Matrix Factorization Toolbox",
"Non-negative Matrix Factorization toolbox" ;
definition: "Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach." .
SCR:017070 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CDC Diseases & Conditions" ;
definition: "List of diseases and conditions on Centers for Disease Control and Prevention website., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017072 a NLX:63400,
owl:NamedIndividual ;
definition: "Open source scripts for medical image processing. Provides set of scripts in Python shell. These scripts use essentially tools from Anima to perform more complex series like image preprocessing, model estimation, atlas creation." .
SCR:017073 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Source code for analysis of GC-MS data - Rice HxD Project" ;
definition: "Source code used in the analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice exposed to combined drought and heat stress." .
SCR:017074 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Empenn" ;
NIFRID:synonym "Brain" ;
definition: "Project between Inria, Inserm, CNRS, and University of Rennes for biomedical image analysis for understanding neurological disease. Used to diagnose, monitor and deliver treatment for mental, neurological and substance use disorders by establishing multidisciplinary team between information sciences and medicine in medical imaging, neuroinformatics and population cohorts." .
SCR:017075 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RNAmmer" ;
definition: "Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes." .
SCR:017076 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_32746" ;
rdfs:label "cwl-metrics" ;
NIFRID:synonym "common workflow language metrix",
"Common Workflow Language-metrics" ;
NIFRID:abbrev "CWL-metrics" ;
definition: "Software framework to collect and analyze computational resource usage of workflow runs based on common workflow language CWL. Used to share set of tools packaged in containers. Enables users to choose proper cloud instance for workflow runs based on run time metrics data. Operating system Unix/Linux." .
SCR:017077 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:shovill",
"biotools:shovill" ;
rdfs:label "shovill" ;
definition: "Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit." .
SCR:017079 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ML_Repo" ;
rdfs:label "ML Repo" ;
NIFRID:synonym "Machine Learning Repository" ;
NIFRID:abbrev "MLRepo" ;
definition: "Machine learning repository for microbiome datasets." .
SCR:017080 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Gigwa" ;
rdfs:label "Gigwa" ;
NIFRID:synonym "Genotype Investigator for Genome Wide Analysis",
"GIGWA",
"GIGWA2" ;
definition: "Web tool to explore genotyping metdata by filtering it on basis of variant features, including functional annotations and matching genotype patterns. May be deployed on workstation or as data portal. Allows to feed MongoDB database with VCF, PLINK or HapMap files and provides interface to filter data in real time. Used to export filtered data into formats and features connectivity with online genomic tools and with standalone software such as FlapJack or IGV. Gigwa hosted datasets are interoperable via two standard REST APIs such GA4GH and BrAPI." .
SCR:017081 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Signal" ;
NIFRID:synonym "Cambridge Electronic Design Signal",
"CED Signal",
"Signal Version 6" ;
definition: "Software package for sweep based data acquisition and analysis of time based waveform data obtained through CED digital analogue converter by Cambridge Electronic Design System Limited. Used for transient capture, patch and voltage clamp, LTP studies, evoked response and TMS." .
SCR:017082 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Surface Modified Amperometry CMOS IC" ;
NIFRID:synonym "Surface Modified Amperometry Complementary Metal Oxide Semiconductor IC" ;
definition: "Integrated circuit device used as tool for amperometry measurement as replacement of conventional carbon fiber microelectrode. Surface modified structures with SU 8 microwells increases life span of each individual device and achieves single cell measurement efficiency by trapping cells inside microwells." .
SCR:017083 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Prophet" ;
NIFRID:synonym "Prophet Automatic Forecasting Procedure" ;
definition: "Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton." .
SCR:017084 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scikit-Criteria" ;
definition: "Software tool as collection of Multiple Criteria Decision Analysis methods integrated into scientific Python stack." .
SCR:017085 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "metagear" ;
definition: "Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis." .
SCR:017086 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "10.5281/zenodo.1157941" ;
rdfs:label "SciPipe" ;
definition: "Software tool for writing scientific workflows of shell commands that depend on each other in Go programming language. Workflow library for agile development of complex and dynamic bioinformatics pipelines. Used in bioinformatics and cheminformatics, but works for any problem involving pipelines of commandline applications." .
SCR:017087 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Haystack" ;
NIFRID:synonym "haystack",
"haystack_bio" ;
definition: "Software suite of computational tools implemented in Python to study epigenetic variability, cross cell type plasticity of chromatin states and transcription factors motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation. Epigenetic variability and transcription factor motifs analysis pipeline." .
SCR:017088 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_26946" ;
rdfs:label "mzStudio" ;
definition: "Software tool for proteomics data analysis, visualization, and notebook application. Dynamic digital canvas for user driven interrogation of mass spectrometry data. Operating system Unix/Linux, Windows." .
SCR:017089 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CaVEMan" ;
definition: "Software tool as single nucleotide variant expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired tumour and normal cancer samples. Algorithms for calling somatic mutations." .
SCR:017090 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cgpPindel" ;
definition: "Software tool as cancer genome project insertion or deletion detection workflow for Pindel." .
SCR:017091 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BRASS" ;
definition: "Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements." .
SCR:017092 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cgpBattenberg" ;
definition: "Software tool as installation helper, perl wrapper and R program Battenberg which detects subclonality and copy number in matched NGS data." .
SCR:017093 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dndSCV" ;
definition: "Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets." .
SCR:017094 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pagoda2" ;
NIFRID:synonym "PAGODA",
"pagoda" ;
definition: "Software R package for analyzing and interactively exploring large single cell RNAseq datasets." .
SCR:017095 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PseudoFuN" ;
NIFRID:synonym "Pseudogene Functional Networks" ;
definition: "Software as database and query tool for homologous pseudogene and coding gene families. Collection of human pseudogenes and gene associations. Supports search, graphical visualization and functional analysis of pseudogenes and coding genes based on PGG families." .
SCR:017096 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "golang" ;
NIFRID:synonym "GO programming language",
"The Go Programming Language" ;
NIFRID:abbrev "GO" ;
definition: "Software tool as open source programming language to build simple, reliable, and efficient software. Developed by team at Google and many contributors from open source community." .
SCR:017097 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Google",
"Crossref funder ID: 100006785",
"grid.420451.6",
"ISNI",
"Wikidata: Q95" ;
rdfs:label "Google" ;
NIFRID:synonym "Google LLC" ;
definition: "American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook." .
SCR:017098 a NLX:63400,
owl:NamedIndividual .
SCR:017099 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PAGODA" ;
NIFRID:synonym "pagoda",
"Pathway And Gene set OverDispersion Analysis" ;
definition: "Software tool for analyzing transcriptional heterogeneity to detect statistically significant ways in which measured cells can be classified. Used to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells." .
SCR:017101 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aspen Plus" ;
definition: "Software process modeling tool for conceptual design, optimization, and performance monitoring for chemical, polymer, specialty chemical, metals, minerals, and coal power industries." .
SCR:017102 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tidyr" ;
definition: "Software R package for easily tidy data with spread and gather functions. Used for simplifying process of creating tidy data." .
SCR:017103 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miRTarVisPlus" ;
NIFRID:synonym "mirtarvisplus" ;
NIFRID:abbrev "miRTarVis+" ;
definition: "Web based interactive visual analytics tool for miRNA target predictions and integrative analyses of multiple prediction results. Used for sequence based miRNA target prediction by exploiting miRNA-mRNA expression profile data." .
SCR:017104 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "EchoMRI" ;
NIFRID:synonym "EchoMRI™" ;
definition: "International research instruments company that develops, manufactures and markets NMR and CT-based whole body composition and tissue characterization equipment." .
SCR:017105 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Hamamatsu Photonics" ;
NIFRID:synonym "Hamamatsu Photonics K.K." ;
definition: "Manufacturer of optical sensors including, photomultiplier tubes, electric light sources, and other optical devices and their applied instruments for scientific, technical and medical use." .
SCR:017106 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Viagen Biotech" ;
NIFRID:synonym "Viagen Biotech Inc." ;
definition: "Commercial provider of innovative DNA extraction technologies and products for life science research. Reagents for preparation of DNA from mouse tails, ear pieces, yolk sac, and culture cells, DNA extracts, DNA markers." .
SCR:017107 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ponemah" ;
definition: "Software tool for complete physiologic data acquisition and analysis used by physiologists, pharmacologists, and toxicologists to collect, analyze, and summarize preclinical study data. Allows to custom design configuration based on needs, budget and convenience without need for any programming." .
SCR:017108 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iMicrobe" ;
definition: "Portal to provide integrated and federated system that interconnects diverse microbiome data sets, bioinformatics tools, and community resources. Built on guiding principles for FAIR data. Open source, community driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with broader community. Partners with CyVerse and XSEDE." .
SCR:017109 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:comw" ;
rdfs:label "Comparative Metatranscriptomics Workflow" ;
NIFRID:abbrev "CoMW" ;
definition: "Software tool for standardized and validated workflow to functionally classify quality filtered mRNA reads from metatranscriptomic or total RNA studies generated using NGS short reads. Used for classification of these reads using assembled contigs to reference databases." .
SCR:017113 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:BSA4Yeast" ;
rdfs:label "BSA4Yeast" ;
NIFRID:synonym "Bulk Segregant Analysis for Yeast" ;
definition: "Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs." .
SCR:017114 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Data Archive BRAIN Initiative" ;
NIFRID:synonym "DABI",
"Data Archive Brain Initiative" ;
definition: "Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves." .
SCR:017118 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:OrthoFinder",
"biotools:OrthoFinder",
"OMICS_09733" ;
rdfs:label "OrthoFinder" ;
NIFRID:synonym "OrthoFinder2" ;
definition: "Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format." .
SCR:017119 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scanco | Medical microCT 100 system" ;
definition: "Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG." .
SCR:017120 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WinRHIZO" ;
definition: "Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots." .
SCR:017121 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tunable Biclustering Algorithm" ;
NIFRID:abbrev "TuBA" ;
definition: "Software tool as graph based unsupervised biclustering algorithm to identify alterations in tumors based on hypothesis that gene pairs relevant to clinical process share statistically significant number of samples with extreme expression." .
SCR:017122 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:SwiftOrtho",
"OMICS_30890" ;
rdfs:label "SwiftOrtho" ;
definition: "Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets." .
SCR:017123 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Good Calculators" ;
definition: "Web service as calculator for statistics and analysis. Used on variety of browsers as well as mobile and tablet devices.They include Z-score, sample size, t value, One Way ANOVA Calculator, Percentile Calculator, Chi Square, p Value, and more." .
SCR:017124 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Waxholm Space Atlas of the Sprague Dawley Rat Brain" ;
NIFRID:synonym "WHS SD rat atlas",
"WHS-SD-rat-atlas",
"WHS_SD_rat_atlas" ;
NIFRID:abbrev "WHS-SD-atlas" ;
definition: "Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format." .
SCR:017125 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ImmuneDB" ;
definition: "Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features." .
SCR:017126 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CATALYSTLite" ;
definition: "Software tool as interactive Shiny web application that provides user interface to mass cytometry data processing pipeline implemented in CATALYST R Bioconductor package." .
SCR:017127 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:catalyst" ;
rdfs:label "CATALYST" ;
NIFRID:synonym "Cytometry dATa anALYSis Tools" ;
definition: "Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation." .
SCR:017128 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellCycleTRACER" ;
definition: "Software tool as supervised machine learning algorithm that classifies and sorts single cell mass cytometry data according to their cell cycle, which allows to correct for cell cycle state and cell volume heterogeneity. Reveals signaling relationships and cell heterogeneity that were otherwise masked. Computational method to quantify cell cycle and cell volume variability." .
SCR:017129 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nanoPOTS" ;
definition: "Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes." .
SCR:017130 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Constant distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry" ;
NIFRID:synonym "constant-mode nano-DESI MSI" ;
NIFRID:abbrev "nano-DESI MSI" ;
definition: "System to extend constant distance mode mass spectrometry imaging using nanospray desorption electrospray ionization by integrating shear force probe with nano DESI probe to improve imaging capabilities. Used for imaging biological samples of complex topography in their native states. Enables ambient imaging of biological samples with high sensitivity and minimal sample pretreatment." .
SCR:017131 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microfluidic device to attain high spatial and temporal control of oxygen" ;
definition: "Device to control spatial and temporal variations in oxygen tensions to better replicate in vivo biology. Consists of three parallel connected tissue chambers and oxygen scavenger channel placed adjacent to these tissue chambers. Provides consistent control of spatial and temporal oxygen gradients in tissue microenvironment and can be used to investigate important oxygen dependent biological processes present in cancer, ischemic heart disease, and wound healing." .
SCR:017132 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "imctools" ;
NIFRID:synonym "imaging mass spectrometry tools" ;
NIFRID:abbrev "IMCtools" ;
definition: "Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc." .
SCR:017133 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:clustvis",
"OMICS_08539" ;
rdfs:label "ClustVis" ;
definition: "Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps." .
SCR:017135 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CPTAC" ;
NIFRID:synonym "Clinical Proteomic Tumor Analysis Consortium" ;
definition: "Clinical proteomic tumor analysis consortium to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand molecular basis of cancer that is not possible through genomics and to accelerate translation of molecular findings into clinic. Operates through Proteome Characterization Centers, Proteogenomic Translational Research Centers, and Proteogenomic Data Analysis Centers. CPTAC investigators collaborate, share data and expertise across consortium, and participate in consortium activities like developing standardized workflows for reproducible studies." .
SCR:017136 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:panorama" ;
rdfs:label "PanoramaWeb" ;
definition: "Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents." .
SCR:017137 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "stop-signal task resources" ;
definition: "Open source resources to execute stop signal task and analyze resulting data. Simulation code is provided, and can be used in planning stage for investigation of response inhibition and impuls control." .
SCR:017138 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Penn machine learning benchmark repository" ;
NIFRID:synonym "Penn Machine Learning Benchmark" ;
NIFRID:abbrev "PMLB" ;
definition: "Python wrapper for Penn Machine Learning Benchmark data repository. Large, curated repository of benchmark datasets for evaluating supervised machine learning algorithms. Part of PyPI https://pypi.org/" .
SCR:017139 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReBATE" ;
NIFRID:synonym "Relief Based Algorithm Training Environment" ;
definition: "Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity ." .
SCR:017140 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions" ;
NIFRID:abbrev "HIBACHI",
"hibachi" ;
definition: "Software tool that creates data sets with particular characteristics. Method and open source software for simulating complex biological and biomedical data to aid in comparing and evaluating machine learning methods." .
SCR:017141 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TopScan" ;
NIFRID:synonym "TopScan Suite" ;
definition: "Software suite as top view based behavior analysis system by CleverSys Inc. Uses animal body parts to provide behavior analysis results. Used in experiments with animal tracking task." .
SCR:017142 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultima_In_Vitro",
"SCR_019800" ;
rdfs:label "Bruker | Ultima In Vitro Multiphoton Microscope System" ;
NIFRID:synonym "Bruker Ultima In Vitro Multiphoton Microscope" ;
definition: "Fluorescence microscopy system by Bruker. Multiphoton imaging system for intravital imaging applications in neuroscience, oncology and immunology using Bruker Prairie View software to provide turnkey operation for imaging as well as synchronizing Ultima system with external stimulus and experimental control devices." .
SCR:017143 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OMTools" ;
definition: "Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles." .
SCR:017144 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core",
"UKE",
"University Medical Center Hamburg Eppendorf Core" ;
NIFRID:abbrev "UKE Bioinformatics Core" ;
definition: "Core provides bioinformatics services for researchers at University Medical Center Hamburg Eppendorf and related institutions. Focusing on high throughput sequencing data. Services include data analysis, consulting, software development, and bioinformatical training." .
SCR:017145 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Centre for Genome Regulation Bioinformatics Core Facility" ;
NIFRID:synonym "Biocore",
"Bioinformatics Core",
"Centre for Genomic Regulation",
"Core Facility",
"CRG" ;
NIFRID:abbrev "Biocore CRG" ;
definition: "Provides services of consultation and data analysis, with focus on Next Generation Sequencing and other high throughput experiments, software and database development, and training in basic and advanced bioinformatics techniques. Services provided for fee to support collaborative grant funded investigations." .
SCR:017146 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpticalMapping.info" ;
definition: "Platform to provide tutorials and resources in experimental design and data analysis to researchers interested in using optical mapping data." .
SCR:017147 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Tübingen Quantitative Biology Center" ;
NIFRID:synonym "QBiC",
"Quantitative Biology Center",
"University of Tübingen" ;
definition: "Central unit for bioinformatics and omics technologies of University of Tübingen, Medical Faculty and Max Plank for Developmental Biology. Through partnering with on campus core facilities, offers services on full range of omics technologies. Data generation is complemented by integrated bioinformatics analyses, and all high throughput data is managed centrally." .
SCR:017148 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Babraham Institute Babraham Bioinformatics Core Facility" ;
NIFRID:synonym "Babraham Bioinformatics",
"Babraham Institute",
"Core Facility" ;
definition: "Provides bioinformatics services to research groups in Babraham Institute, United Kingdom and external commercial consultancy service. Provides assistance in genomics, proteomics, statistics, microarrays, and custom software development." .
SCR:017150 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Whitehead Institute Bioinformatics and Research Computing Core Facility" ;
NIFRID:synonym "BaRC",
"Bioinformatics",
"Research computing",
"Whitehead Institute" ;
definition: "Core provides consultation, training, software and educational tools in bioinformatics and graphics." .
SCR:017151 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Edinburgh Wellcome Trust Centre for Cell Biology Bioinformatics Core Facility " ;
NIFRID:abbrev "University of Edinburgh WTCCB Bioinformatics Core Facility" ;
definition: "Facility provides regular training sessions, tools, advice and data analysis services to Centre members." .
SCR:017152 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility" ;
NIFRID:synonym "BCF",
"Bioinformatics",
"Core Facility",
"Rikshospitalet-Radiumhospitalet",
"University of Oslo" ;
definition: "Core facility provides high throughput sequencing data analysis, metagenomics data analysis, proteomics data analysis, protein structure analysis, functional genomics, programming, scripting, and database or web services." .
SCR:017153 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Israel Weizmann Institute of Science Bioinformatics Unit Core Facility" ;
NIFRID:synonym "Bioinformatics and Biological Computing Unit" ;
definition: "Core promotes and supports adoption, use, and development of bioinformatics tools for advancing biological research. Organizes and teaches courses and workshops for all services needed by Weizmann researchers." .
SCR:017154 a owl:NamedIndividual ;
rdfs:label "University of Cambridge Bioinformatics and Computational Biology Services Core Facility" ;
NIFRID:synonym "Bioinformatics",
"Computational Biology",
"Computational Biology Services",
"Core Facility",
"Services",
"University of Cambridge" ;
definition: "Provides assistance in characterization and analysis of genomic variants, next generation sequencing data processing and analysis, computational systems biology, HPC and big data software development for genome scale data analysis, machine learning and data mining, cloud based solutions to process and manage large amounts of data, databases and genome scale data visualization." .
SCR:017156 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.13648.38",
"ISNI:0000 0001 2180 3484",
"Wikidata:Q316207" ;
rdfs:label "University Medical Center Hamburg-Eppendorf" ;
NIFRID:abbrev "UKE" ;
definition: "Teaching hospital of University of Hamburg located in Eppendorf, Hamburg, Germany." .
SCR:017157 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University (BGU) of the Negev, Israel, Bioinformatics Core Facility" ;
NIFRID:synonym "Ben-Gurion",
"Bioinformatics",
"Core Facility",
"Israel",
"National Institute for Biotechnology",
"Negev",
"NIBN",
"The Bioinformatics Core",
"University of the Negev" ;
definition: "Provides customized data analysis services and consultation to scientists at BGU and all over Israel from academia and industry. Goal to help scientists advance their research using bioinformatics methodologies, to design and analysis of experiments that use genomic technologies like next generation sequencing, mass spectrometry proteomics and metabolomics profiling, microarrays as well as mining and reanalysis of publicly available datasets. Facility develops software tools for automation of data analysis workflows like NeatSeq-Flow, Microbe-Flow." .
SCR:017158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Cape Town Centre for Proteomic and Genomic Research (CPGR) Core Facility" ;
NIFRID:synonym "Center for Proteomic and Genomic Research",
"Centre for Proteomic and Genomic Research",
"core facility",
"CPGR",
"University of Cape Town" ;
NIFRID:abbrev "CPGR Core" ;
definition: "Services to life science and biotech communities in South Africa. Based in Cape Town, combine information about genomic and proteomic technologies with bio computational pipelines to create fit for purpose offerings for customers in academia and industry." .
SCR:017159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nbdocker" ;
definition: "Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment." .
SCR:017160 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core Facility",
"Bioinformatics Facility",
"Core Facility",
"Epigenetics",
"Max Planck Institiute of Immunobiology" ;
definition: "Core provides assistance in primary analysis of sequencing data and other large scale biocomputing. For our internal users we host extensive web services, workflows and customized tools that help with data management, visualizations, standardized analyses and data sharing." .
SCR:017161 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mayo Clinic Rochehster Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core",
"Core Facility",
"Division of Biomedical Statistics and Informatics",
"Mayo Clinic",
"Rochehster" ;
NIFRID:abbrev "Mayo Clinic Bioinformatics Core" ;
definition: "Core assists in genomics, proteomics and metabolomics data acquisition, management, analyses and interpretation to Mayo investigators. Participates in Basic science research, Clinical trials, Population health, and Translational science to execute analytical workflows and manage large omics data sets. Provides support to Mayo Clinic Center for Individualized Medicine and Mayo Clinic Cancer Center. Has its academic home in Department of Health Sciences Research within Division of Biomedical Statistics and Informatics." .
SCR:017162 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioViz3D" ;
NIFRID:synonym "BioVis3D New Version 3.1" ;
definition: """Software for 3D reconstruction from serial slices. Used to create 3D model to analyse organs, tissues and cells, create photos and videos to help scientists in life science, biology and medicine, visualize, analyze and exploit information from serial slices
and get accurate quantitative information from reconstructed 3D models.""" .
SCR:017163 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Liege Interdisciplinary Cluster for Applied Genoproteomics Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core Facility",
"Bioinformatics Facility",
"GIGA",
"Interdisciplinary Cluster for Applied Genoproteomics",
"University of Liege" ;
definition: "Core provided by interdisciplinary center of biomedical research of Liege University. Develops and applies computational methods to extract information from large sets of biological and biomedical data." .
SCR:017164 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Cambridge Department of Plant Sciences Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics",
"Core Facility",
"Department of Plant Sciences",
"University of Cambridge" ;
NIFRID:abbrev "University of Cambridge Bioinformatics Core Facility" ;
definition: "Core provides assistance in data analysis to support members of Plant Sciences." .
SCR:017165 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2841",
"SCR_025534" ;
rdfs:label "Indiana University Center for Genomics and Bioinformatics Core Facility" ;
NIFRID:synonym "Indiana University Bloomington Center for Genomics and Bioinformatics" ;
NIFRID:abbrev "CGB" ;
definition: "CGB offers range of genomic services, including high-throughput DNA/RNA extraction, library preparation, next-generation sequencing, and bioinformatic analysis." .
SCR:017166 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Oxford Computational Biology Research Group Core Facility" ;
NIFRID:synonym "CBRG",
"Computational Biology",
"Core Facility",
"Oxford University",
"Research Group" ;
definition: "Core provides bioinformatics training and analysis tools. Supports bioinformatics analysis at University of Oxford." .
SCR:017167 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Idaho IBEST Institute for Bioinformatics and Evolutionary Studies Core" ;
NIFRID:synonym "IBEST",
"ibest",
"institute for Bioinformatics and Evolutionary Studies",
"UI",
"University of Idaho" ;
definition: "Genomics, Computational and Northwest Knowledge Network core facilities for researchers from University of Idaho and their collaborators." .
SCR:017168 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility" ;
NIFRID:synonym "Bioinformatics Center",
"Core Facility",
"Little Rock",
"MBC",
"MidSouth",
"UA",
"UALR",
"University of Arkansas" ;
NIFRID:abbrev "MidSouth Bioinformatics Center" ;
definition: "Core provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure for faculty, students, and researchers in region with their bioscience computational needs. Offers private sessions, workshops and training on specialty topics. Computing resources including software, computing cluster, technical advice." .
SCR:017169 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Malaga Andalusian Platform of Bioinformatics Core Facility" ;
NIFRID:synonym "Plataforma Andaluza de Bioinformatica",
"SCBI",
"scbi",
"Supercomputing and Bioinnovation Center",
"UMA",
"Universidad de Malaga",
"University of Malaga" ;
definition: "Provides assistance in computing, nanotechnology, and biological fields. Provides scientific support and resources to the UMA research groups, public institutions and private companies." .
SCR:017170 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.429509.3",
"ISNI 0000 0004 0491 4256",
"Wikidata Q1912076" ;
rdfs:label "Max Planck Institiute of Immunobiology and Epigenetics; Freiburg; Germany" ;
definition: "Interdisciplinary research institute that conducts basic research in modern immunobiology, developmental biology and epigenetics." .
SCR:017171 a owl:NamedIndividual ;
rdfs:label "University of Manchester Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core Facility",
"Bioinformatics Facility",
"University of Manchester" ;
NIFRID:abbrev "Manchester Bioinformatics Facility" ;
definition: "Core provides assistance in integrative analysis of genomic datasets to support faculty." .
SCR:017172 a "Research",
owl:NamedIndividual ;
rdfs:label "Johns Hopkins Medicine Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core Facility" ;
NIFRID:synonym "Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core" ;
NIFRID:abbrev "JHMI",
"JHU",
"SCTC" ;
definition: "Core provides assistance with Single Cell RNA and DNA Sequencing, Spatial Transcriptomics, Next-Generation Sequencing libraries." .
SCR:017173 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Oxford Medical Sciences Division Computational Genomics: Analysis and Training Core Facility" ;
NIFRID:synonym "CGAT",
"Computational Genomics Analysis and Training Core Facility",
"Computational Genomics: Analysis and Training Core Facility",
"Medical Sciences Division",
"University of Oxford" ;
definition: "Core provides genomics training, as well as assistance in next generation sequencing analyses." .
SCR:017174 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Duke University Omics Data Analysis Core Facility" ;
NIFRID:synonym "Analysis Core",
"Core Facility",
"Duke University",
"Genomic Analysis and Bioinformatics",
"Omics Data",
"Resource" ;
definition: "Genomic Analysis and Bioinformatics core for data analysis associated with performing complex and data intensive projects in life science research of Duke University and Duke Medical School. Provides expertise, training, data analysis in next generation sequencing, array and proteomic based technologies." .
SCR:017175 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vall dHebron Institut de Recerca Statistics and Bioinformatics Unit Core Facility" ;
NIFRID:synonym "Barcelona",
"Statistics and Bioinformatics Unit",
"Support Unit in Methodology for Biomedical Research",
"UEB",
"USMIB",
"Vall dHebron Institut de Recerca" ;
definition: "Core at Vall dHebron Institut de Recerca, Barcelona, Spain to provide data analysis, softwares and training programs in statistics and bioinformatics for clinical research at VHIR." .
SCR:017176 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Montreal Clinical Research Bioinformatics Core Facility" ;
NIFRID:synonym "BIF",
"Bioinformatics Core Facility",
"Institute of Clinical Research of Montreal",
"IRCM" ;
NIFRID:abbrev "IRCM BIF" ;
definition: "Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses." .
SCR:017177 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility" ;
NIFRID:synonym "Bio Information Technologies Lab",
"BIT",
"Canada",
"Department of Plant Science",
"Fritensky Lab",
"University of Manitoba" ;
NIFRID:abbrev "University of Manitoba BIT Core Facility" ;
definition: "BIT Core at University of Manitoba, Manitoba, Canada, provides bioinformatics services, resources and collaborations. Support for Genome assembly and annotation, Microarray and Transcriptomics, Systems Biology and Pathway analysis, Databases, Data pipelines, Bioinformatics software, Custom software and programming, Project Wikis, Lab group computer management." .
SCR:017178 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCSF Gladstone Institutes Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core",
"Gladstone Core Services",
"Gladstone Institutes",
"UCSF",
"University California San Fransisco" ;
NIFRID:abbrev "UCSF Gladstone Institutes Bioinformatics Core" ;
definition: "Core provides consulting services, sequencing, data analysis, and programming assistance. Used for Experimental Design and Power Analysis Consultation, RNA-seq, ChIP-seq, ATAC-seq analysis, Statistics consulting, Variant calling, Data normalization across multiple projects, General programming, Custom Figures for publication, tutorials for learning common software tools." .
SCR:017179 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Michigan School of Medicine Center of Computational Medicine and Bioinformatics Core Facility" ;
NIFRID:synonym "CCMB",
"Computational Medicine and Bioinformatics",
"School of Medicine",
"UM",
"University of Michigan" ;
NIFRID:abbrev "Center of Computational Medicine and Bioinformatics",
"UM School of Medicine Computational Medicine and Bioinformatics" ;
definition: "University interdisciplinary academic center for bioinformatics, biomedical data science, and translational precision health informatics. Core provides training programs." .
SCR:017180 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Illinois Urbana-Champaign High Performance Biological Computing Core Facility" ;
NIFRID:synonym "High Performance Biological Computing",
"HPCBio",
"University of Illinois",
"Urbana-Champaign" ;
definition: "Core provides infrastructure for bioinformatics, combining hardware, software, databases, training, consulting and services for all campus researchers at University of Illinois requiring computational resources and expertise for biomedical research." .
SCR:017182 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of North Carolina Charlotte Bioinformatics Services Division" ;
NIFRID:synonym "Bioinformatics Services Division",
"BiSD",
"Charlotte",
"UNC",
"University of North Carolina" ;
NIFRID:abbrev "UNC Charlotte BiSD" ;
definition: "Core to assist with analyzing and interpreting data produced by genomic technologies." .
SCR:017183 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nutil - Neuroimaging utilities" ;
NIFRID:synonym "Neuroimaging utilities" ;
NIFRID:abbrev "Nutil" ;
definition: "Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems." .
SCR:017184 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReproIn: The ReproNim image input management system (featuring DataLad)" ;
NIFRID:abbrev "ReproIn" ;
definition: "Software tool for automatic generation of shareable, version controlled BIDS datasets from MR scanners." .
SCR:017185 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sainsbury Laboratory Bioinformatics Core Facility" ;
NIFRID:abbrev "TSL Bioinformatics" ;
definition: "Core develops tools for high throughput sequence data to study non reference, non model organisms." .
SCR:017186 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cambridge Institute for Medical Research Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics",
"CIMR",
"Core",
"Core Facility",
"University of Cambridge" ;
definition: "Core provides biological data handling and analysis in differential expression analysis, next generation sequencing, networks, protein architecture, and motif searching for in house researchers." .
SCR:017187 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harvard School of Public Health Microbiome Analysis Core Facility" ;
NIFRID:synonym "Core",
"facility",
"Harvard School of Public Health",
"HSPH",
"Microbiome Analysis" ;
NIFRID:abbrev "HSPH Microbiome Analysis Core" ;
definition: "Core assists with consultation for microbiome project development, provides validated meta omic analysis of microbial community data, and supports fully collaborative grant funded investigations." .
SCR:017188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core Facility",
"City of Hope",
"IGBC",
"Integrative Genomics and Bioinformatics Core",
"National Medical Center" ;
definition: "Core provides genomic and bioinformatics services to City of Hope Comprehensive Cancer Center (COHCCC) investigators." .
SCR:017189 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Gothenburg Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core Facility",
"GU",
"University of Gothenburg" ;
NIFRID:abbrev "GU Bioinformatics Core Facility" ;
definition: "Core assists with statistical and bioinformatics consultation and data analysis." .
SCR:017190 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gulbenkian Institute of Science Bioinformatics and Computational Unit Core Facility " ;
NIFRID:synonym "Bioinformatics and Computational Unit",
"core facility",
"Gulbenkian Institute of Science",
"IGC",
"Instituto Gulbenkian de Ciencia" ;
definition: "IGC Core in Oeiras, Portugal, promotes use of computational methods in biological research, through training and development of resources and materials, supports biological data analysis using computational methods, conducts research and development in bioinformatics, in particular in data flows, data warehousing and data analyses." .
SCR:017191 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ot-tools" ;
definition: "Software tools for analysis of cellular cryo-ET data." .
SCR:017192 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core Facility",
"Center for Trophoblast Research",
"Centre for Trophoblast Research",
"University of Cambridge" ;
NIFRID:abbrev "CTR Bioinformatics Core Facility" ;
definition: "Core provides assistance with experimental design, RNA sequencing, whole genome and targeted sequencing, methylation sequencing, protein alignment, microscopy image analysis, and training." .
SCR:017193 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genome Institute of Singapore Scientific and Research Computing Core Facility" ;
NIFRID:synonym "Core Facility",
"Genome Institute of Singapore",
"GIS",
"Scientific & Research Computing",
"Scientific and Research Computing" ;
NIFRID:abbrev "GIS Scientific and Research Computing" ;
definition: "Core provides research computing resources including bioinformatics, application development, data management and IT infrastructure to support next generation sequencing technologies, human genotyping, high throughput screening and computational biology researchers." .
SCR:017194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Edinburgh College of Medicine and Veterinary Medicine MRC Institute of Genetics and Molecular Medicine Bioinformatics Analysis Core Facility" ;
NIFRID:synonym "Bioinformatics Analysis",
"College of Medicine & Veterinary Medicine",
"College of Medicine and Veterinary Medicine",
"Core Facility",
"IGMM",
"Institute of Genetics and Molecular Medicine",
"MRC",
"The University of Edinburgh" ;
NIFRID:abbrev "MRC Institute of Genetics and Molecular Medicine BAC" ;
definition: "Core provides advice, training, provision of computational tools and collaborative expertise to all IGMM researchers." .
SCR:017195 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "T1D Exchange Biobank" ;
definition: "Collection of biological samples linked to participant medical data from individuals living with type 1 diabetes. Unifies samples and data from eight different clinical studies related to type 1 diabetes." .
SCR:017196 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_26560" ;
rdfs:label "CWL-Airflow" ;
NIFRID:synonym "Common Workflow Language-Airflow",
"CWL-Airflow v 1.0.16" ;
NIFRID:abbrev "CWL DAG" ;
definition: "Software Python package to extend Airflow functionality with Common Workflow Language support. Lightweight pipeline manager supporting Common Workflow Language. Can be used to run workflows on standalone MacOS/Linux servers, on clusters, or on cloud platforms." .
SCR:017199 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "matemaker" ;
NIFRID:synonym "matemaker v1.0.0" ;
definition: "Software tool to make artificial mate pairs from long sequences for scaffolding." .
SCR:017200 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FastqSifter" ;
NIFRID:synonym "FastqSifter v1.1.1" ;
definition: "Software tool to separate contaminating reads from FASTQ files." .
SCR:017201 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:VETA",
"biotools:VEtA" ;
rdfs:label "VETA" ;
definition: "Software suite of functions for EMG data visualization and processing. Open source Matlab toolbox for electromyography combined with transcranial magnetic stimulation. MATLAB toolbox for the collection, analysis, and visualization of EMG and TMS." .
SCR:017202 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Keyence | BZ X-710 fluorescent microscope" ;
definition: "All in one fluorescence microscope BZ-X710 by Keyence, Japan." .
SCR:017203 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Ephys | Pulse Pal" ;
NIFRID:synonym "Pulse Pal v2" ;
definition: "Open source pulse train generator that allows users to create and trigger software defined trains of voltage pulses with high temporal precision. Generates precisely timed pulse sequences for use in research involving electrophysiology or psychophysics." .
SCR:017204 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rice_HxD_Recovery_Metabolomics" ;
definition: "Software tool as source code used in analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice collected during rewatering after exposure to combined drought and heat stress." .
SCR:017205 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BZ Analyzer software" ;
definition: "Software tool as analysis application BZ-H1A by Keyence, Japan for fluorescence microscope BZ-8100 series." .
SCR:017206 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2565CA",
"SCR_019384" ;
rdfs:label "Agilent | G2565CA Microarray Scanner" ;
definition: "Microarray Scanner is part of microarray analysis solution from Agilent Technologies. Laser induced fluorescence scanner designed to read microarrays printed on standard slides. Measures fluorescence intensity of labeled sample nucleic acid bound to microarrays." .
SCR:017207 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Roadmap" ;
definition: "Software tool to display surface of macromolecule and its properties. Uses projections to map van der Waals or solvent accessible surface of macromolecule onto plane., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017208 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100006377",
"GRID grid.169077.e",
"ISNI 0000 0004 1937 2197",
"Wikidata Q217741" ;
rdfs:label "Purdue University; West Lafayette; Indiana" ;
definition: "Public research university in West Lafayette, Indiana, and flagship campus of Purdue University system. University was founded in 1869 after Lafayette businessman John Purdue donated land and money to establish college of science, technology, and agriculture in his name." .
SCR:017209 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kidney Interactive Transcriptomics" ;
NIFRID:abbrev "KIT" ;
definition: "Software tool as analyzer for kidney single cell datasets. Allows users to query gene expression from mouse or human kidney and human kidney organoid single cell datasets. For details about datasets visit ReBuilding a Kidney website." .
SCR:017210 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PIVOT software" ;
NIFRID:synonym "KimLabIDV",
"PIVOT",
"Platform for Interactive analysis and Visualization Of Transcriptomics" ;
definition: "Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows." .
SCR:017211 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RSRef" .
SCR:017212 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IBM® MarketScan® Research Databases" ;
definition: "Software suite of proprietary databases that contain one of longest running and largest collection of privately and publicly insured, de identified patient data in USA. Family of data sets that fully integrate many types of data for healthcare research." .
SCR:017214 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Marshall Scientific | PTC-150 MiniCycler" ;
definition: "Mini Thermal Cycler PCR is compact thermal scanner, catalog number PTC-150 Cycler with Hot Bonnet heated lid for oil free cycling by MJ Research." .
SCR:017215 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PennAI" ;
NIFRID:synonym "Accessible artificial intelligence from University of Pennsylvania" ;
definition: "Open source software tool to leverage supervised machine learning techniques to analyze data. Can assist with tasks such as choosing appropriate models for data. Data science assistant for generating results from large and complex data problems." .
SCR:017216 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RNAstructure" ;
definition: "Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program." .
SCR:017217 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_30185" ;
rdfs:label "CytExpert Software" ;
definition: "Software program that controls instrument operation, data collection and analysis. Software for CytoFLEX Platform by Beckman Coulter." .
SCR:017218 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bonsai" ;
definition: "Software event based framework for processing and controlling data streams. Visual language designed for making software systems that require rich and rapid interaction with external world." .
SCR:017219 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:modmatcher" ;
rdfs:label "proMODMatcher" ;
NIFRID:synonym "probabilisticMulti Omics DataMatcher" ;
definition: "Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles." .
SCR:017220 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:SeQuiLa-cov" ;
rdfs:label "SeQuiLa" ;
definition: "Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals." .
SCR:017221 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "exRNA Atlas" ;
definition: "Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data." .
SCR:017222 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MeshView" ;
NIFRID:synonym "MeshView for brain atlases" ;
definition: "Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases." .
SCR:017224 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chronos" ;
definition: "Cloud based web platform connecting researchers, research organisations, funders and publishers in automated workflow management tool. Platform provides infrastructure for researchers, funders and publishers participating in Open Access Publishing. Features searchable database of journals compliant with research funders Open Access policies, connects researchers directly to journals submission systems, coordinates open access fee payments for funder with publisher upon acceptance, and supports compliancy by overseeing deposition of papers to designated repositories." .
SCR:017225 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_24025" ;
rdfs:label "WTDBG" ;
NIFRID:synonym "Wtdbg2",
"Wtdgb",
"wtdgb",
"wtdgb2" ;
definition: "Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time." .
SCR:017226 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Juicer" ;
definition: "Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps." .
SCR:017227 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D de novo assembly" ;
definition: "Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly." .
SCR:017228 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:prank",
"OMICS_12425",
"SCR_024174" ;
rdfs:label "prank" ;
NIFRID:synonym "PRANK" ;
definition: "Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences." .
SCR:017229 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PSMC" ;
NIFRID:synonym "Pairwise Sequentially Markovian Coalescent" ;
definition: "Software package for implementation of Pairwise Sequentially Markovian Coalescent model. Infers population size history from diploid sequence." .
SCR:017233 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VasoTracker" ;
definition: "Open source and stand alone software for assessing vascular reactivity. Used in pressure myograph system." .
SCR:017234 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_17554" ;
rdfs:label "Computational Suite for Bioinformaticians and Biologists" ;
NIFRID:synonym "CSBB-v1.0",
"CSBB-v2.0",
"CSBB-v3.0" ;
NIFRID:abbrev "CSBB" ;
definition: "Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments." .
SCR:017236 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013971" ;
rdfs:label "CIS-BP" ;
NIFRID:synonym "Catalog of Inferred Sequence Binding Preferences" ;
definition: "Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs." .
SCR:017237 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IDR" ;
NIFRID:synonym "Irreproducible Discovery Rate" ;
definition: "Software R package to measure reproducibility of findings identified from replicate experiments and to provide highly stable thresholds based on reproducibility." .
SCR:017238 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Case Western Reserve University Cystic Fibrosis Mouse Models Core" ;
NIFRID:synonym "Case Western Reserve University",
"CWR",
"Cystic Fibrosis Mouse Model Core" ;
definition: "Core facility for cystic fibrosis mouse strains. Services include mouse production from current strains and creation of new strains, mouse strain maintenance, tissue acquisition, genotyping and treatment of mice with IACUC approved drugs to test potential therapies. Maintains centralized database that contains breeding history, phenotypes observed and experimental records of various CF mouse strains." .
SCR:017239 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GemPharmatech" ;
NIFRID:synonym "GemPharmatech Co.",
"GPT",
"Ltd" ;
definition: "Contract research organization that provides genetically engineered mouse models (GEMMs) and services to global preclinical Research and Development communities. Specializes in developing animal models using cutting edge gene-editing technologies with large collection of cKO/KO (conditional knockout/knockout) mice, humanized mice, immunodeficient mice, and germ-free mice.Provides preclinical services, including mouse model customization, pharmacology services such as drug efficacy testing and mouse phenotyping, CRISPR/Cas9 gene-editing, cryopreservation, rapid expansion, and customized breeding." .
SCR:017241 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of British Columbia Centre for Molecular Medicine and Therapeutics" ;
NIFRID:synonym "Centre for Molecular Medicine and Therapeutics",
"CMMT",
"University of British Columbia (UBC) Centre for Molecular Medicine & Therapeutics" ;
NIFRID:abbrev "UBC CMMT" ;
definition: "Center is part of University of British Columbia Faculty of Medicine, located at British Columbia Children Hospital Research Institute (BCCHR) in Vancouver, British Columbia, Canada. Research at CMMT is focused on discovering genetic susceptibility to illnesses such as Huntington Disease, Type 2 diabetes and bipolar disorder." .
SCR:017242 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StemID" ;
NIFRID:synonym "StemID2" ;
definition: "Algorithm for derivation of cell lineage trees based on RaceID2 results and predicts multipotent cell identites. StemID2 is algorithm for identification of lineage trees based on RaceID3 analysis. Used for better understanding of differentiation dynamics in variety of systems. Written in R computing language." .
SCR:017244 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:fateid" ;
rdfs:label "FateID" ;
definition: "Software R package for inference of cell fate bias from single cell RNA-seq data. Iterative supervised learning algorithm for probabilistic quantification of cell fate bias in progenitor populations." .
SCR:017246 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Secure Access to Research Data and E-Infrastructure" ;
NIFRID:synonym "SAFE",
"Safe",
"Secure Access to Research Data and E-Infrastructure (EUROPE)" ;
definition: "Platform for Secure Access to Research Data and E-Infrastructure based on European Standards for Health Case information. Used for secure processing of sensitive personal data in research in health and care sector." .
SCR:017247 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCENIC" ;
definition: "Software R package as single cell regulatory network inference and clustering. Used for simultaneous gene regulatory network reconstruction and cell state identification from single cell RNA-seq data." .
SCR:017248 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_18884" ;
rdfs:label "NeuroAnatomy Toolbox" ;
NIFRID:synonym "nat" ;
NIFRID:abbrev "NAT" ;
definition: "Software R package for 3D visualisation and analysis of biological image data, especially tracings of single neurons." .
SCR:017249 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "elmr" ;
definition: "Software tool as support for working with light and electron microscopy fly brain data. Part of suite of R packages based on NeuroAnatomy Toolbox. Provides tools to move between adult brain EM and light level data, emphasising interaction between CATMAID web application and R Neuroanatomy Toolbox package." .
SCR:017250 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "vini: A viewer for fMRI data" ;
definition: "Software Python tool as viewer for MRI data and numpy arrays." .
SCR:017251 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CFX Manager" ;
NIFRID:synonym "CFX Manager software" ;
definition: "Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017252 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ebi_search" ;
rdfs:label "EMBOSSMatcher" ;
NIFRID:synonym "EMBOSS Matcher",
"EMBOSS_Matcher",
"emboss_matcher" ;
definition: "Software tool for pairwise sequence alignment. Identifies local similarities in two input sequences. One of EMBL-EBI search and sequence analysis tools." .
SCR:017253 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:centroidfold",
"OMICS_03449" ;
rdfs:label "CentroidFold" ;
definition: "Web server for RNA secondary structure prediction. Predicts RNA secondary structure from RNA sequence. Based on generalized centroid estimator." .
SCR:017254 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ufboot2" ;
rdfs:label "IQ-TREE" ;
definition: "Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference." .
SCR:017255 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BIDS Validator" ;
NIFRID:synonym "Brain Imaging Data Structure (BIDS) Validator" ;
definition: "Software validation tool that checks submitted folder structure for compliance to BIDS data standard. Validates Brain Imaging Data Structure." .
SCR:017256 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pKiss" ;
NIFRID:synonym "pKISS" ;
definition: "Software tool for folding RNA secondary structures, including two limited classes of pseudoknots. Performs abstract shape analysis for structures holding pseudoknots up to complexity of kissing hairpin motifs. Successor of pknotsRG. Used for secondary structure prediction including kissing hairpin motifs." .
SCR:017257 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ascend" ;
rdfs:label "ascend" ;
NIFRID:synonym "Analysis of Single Cell Expression",
"ASCEND",
"Normalization and Differential expression" ;
definition: "Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions." .
SCR:017258 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adobe Flash" ;
NIFRID:synonym "Adobe Flash Player",
"Flash",
"Flash Player" ;
definition: "Software platform used for production of animations, rich Internet applications, desktop applications, mobile applications, mobile games and embedded web browser video players. Adobe will stop updating and distributing Flash Player in 2020. For existing Flash content, eventual, final version of Flash plug-in will still work after 2020, and Adobe will work with browser makers to ensure security vulnerabilities are patched." .
SCR:017259 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bionitio" ;
rdfs:label "Bionitio" ;
definition: "Open source software tool to provide template for command line bioinformatics tools in various programming languages. Program reads one or more input FASTA files, computes variety of statistics on each file, and prints tabulated output. Used as basis for learning and as foundation for starting new projects." .
SCR:017260 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "brainGraph" ;
NIFRID:synonym "brainGraph - Graph Theory Analysis of Brain MRI Data in R" ;
definition: "Software R package for performing graph theory analyses of brain MRI data." .
SCR:017261 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miRquant" ;
NIFRID:synonym "miRquant 2.0" ;
definition: "Software tool for accurate annotation and quantification of microRNAs and their isomiRs from small RNA-sequencing data. Provides information on quality of sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs and yDRs, prevalence of post transcriptional modifications." .
SCR:017263 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SynapseLocator" ;
definition: "Software tool that combines steps of image processing, non rigid image registration, and spot localisation. Performs registration of 3D imaging data and localization of spots, active synapses in light microscopy images, in semi automatic mode with graphical user interface." .
SCR:017264 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Glomerular Disease Study & Trial Consortium" ;
NIFRID:abbrev "GlomCon" ;
definition: "Consortium to bring together clinicians, pathologists, researchers, and biotech innovators to create scalable network of stakeholders interested in helping patients with glomerular kidney disease. Makes collective expertise of its members available for discussion of individual cases, provides infrastructure for biomarker studies, enables genomic research, and facilitates clinical trials." .
SCR:017265 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:PIRAtE" ;
rdfs:label "PIRATE" ;
NIFRID:synonym "Pangenome Iterative Refinement And Threshold Evaluation" ;
definition: "Software pangenomics toolbox for clustering diverged orthologues in bacteria. Used to identify and classify orthologous gene families in bacterial pangenomes over wide range of sequence similarity thresholds." .
SCR:017267 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BICCN Cell Registry" ;
NIFRID:synonym "BRAIN Initiative Cell Census Network Cell Registry" ;
definition: "Searchable table of datasets. Data generated from projects through BRAIN Initiative Cell Census Network. Datasets can be filtered by species, research investigator, grant number or experimental technique. Includes links to data directories at data archives and links to protocols." .
SCR:017269 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FoXS" ;
NIFRID:synonym "Fast X-Ray Scattering" ;
definition: "Web server for computing theoretical scattering profile of structure and fitting of experimental profile. Computes SAXS profile of given atomistic model and fits it to experimental profile. Used for structural modeling applications with small angle X-ray scattering data." .
SCR:017270 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:complexheatmap" ;
rdfs:label "ComplexHeatmap" ;
definition: "Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns." .
SCR:017271 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCÅTTER" ;
definition: "Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets." .
SCR:017272 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R31NJN9G",
"DOI:10.35077",
"r3d100013956" ;
rdfs:label "Brain Image Library" ;
NIFRID:abbrev "BIL" ;
definition: "Public, NIH-funded repository and analysis ecosystem for brain microscopy data, designed to store, share, and process massive volumetric datasets. It enables researchers to access whole-brain images, neuron morphologies, and spatial data without needing to download, fostering collaborative discovery. Used to deposit, analyze, mine, share and interact with large brain image datasets." .
SCR:017273 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Observatory Storage Service and Database (BossDB)" ;
NIFRID:synonym "Block and Object Storage Service",
"Block and Object Storage Service Database",
"BOSSDB",
"BossDB",
"bossDB",
"Brain Observatory Storage Service",
"Brain Observatory Storage Service and Database" ;
NIFRID:abbrev "BOSS DB" ;
definition: "BossDB (Brain Observatory Storage Service and Database) is a cloud-based ecosystem for the storage and management of public large-scale volumetric neuroimaging and connectomics datasets. This includes volumetric Electron Microscopy and X-Ray Micro/Nanotomography data with support for multi-channel image data, segmentations, annotations, meshes, and connectomes. BossDB integrates with community resources for data access, processing, visualization, and analysis, and includes an API that enables metadata management, rendering, datatype conversions, and ingest." .
SCR:017274 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "AcceGen Biotech" ;
definition: "AcceGen offers most complete human and animal cell products and cell/molecular biology services for life science researchers worldwide. Cell line collections include primary cells, tumor cell lines, transfected stable cell lines, stem cells and immortalized cell lines. miRNA agomir/antagomir, nucleic acid kits, enzymes and custom cell/molecular biology services." .
SCR:017276 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Drosophila induction-based torque compensator" ;
definition: "Compensator measure rotational force of tethered fly around its vertical body axis (yaw torque). Used as behavioral read-out after sensory stimulation or to control various environmental stimuli in different kinds of behavioral experiments. Measurement device uses measurement principle that is based on magnetic induction and compensates for any movement of fly." .
SCR:017277 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ClustalW" ;
NIFRID:synonym "ClustalW of DNA Data Bank of Japan" ;
NIFRID:abbrev "ClustalW of DDBJ" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.Web sevice of ClustalW provided by DNA data bank of Japan." .
SCR:017278 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MoRDa" ;
NIFRID:synonym "Automatic Molecular Replacement Pipeline" ;
definition: "Software package for molecular replacement protein structure solution using X-ray data. Includes database and set of programs for structure solution. Automatic molecular replacement pipeline." .
SCR:017279 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SequelQC" ;
definition: "Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data." .
SCR:017280 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Relacs" ;
NIFRID:synonym "and Stimulation",
"Control",
"Relaxed Electrophysiological Data Acquisition" ;
definition: "Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings." .
SCR:017281 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "spm_auto_reorient_coregister" ;
definition: "Open source cross platform for automatic AC-PC realignment, reorientation and coregistration robust to brain damage in Statistical Parametric Mapping. Set of routines to perform auto reorient and auto coregistration in toolbox SPM12." .
SCR:017283 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Inivation | DVS240 camera" ;
definition: "Retina inspired event based camera for low latency, real time image processing by iniVation. Works with graphical interfaces such as jAER." .
SCR:017284 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UNO R3" ;
definition: "Open source microcontroller board based on Microchip ATmega328P microcontroller and developed by Arduino. Board is equipped with sets of digital and analog input, output pins that may be interfaced to various expansion boards and other circuits." .
SCR:017285 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "redbiom" ;
definition: "Software tool for allowing samples that contain microbiome features to be rapidly identified. Rapid sample discovery and feature characterization system. Integrated with existing analysis tools to enable fast, large scale microbiome searches and discovery of new microbiome relationships. Service for sample metadata and sample data." .
SCR:017286 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:GraphClust2" ;
rdfs:label "GraphClust2" ;
NIFRID:synonym "GraphClust",
"GraphClust-2" ;
definition: "Software tool for scalable clustering of RNAs based on sequence and secondary structures similarities. Implemented within Galaxy framework. Used for studying RNA function." .
SCR:017287 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "peddy" ;
definition: "Software package that evaluates correspondence between stated sexes, relationships, and ancestries in pedigree file and those inferred from genotypes in VCF file resulting from human whole genome sequencing or whole exome sequencing studies. Facilitates both automated and interactive, visual detection of sample swaps, poor sequencing quality, and other indicators of sample problems." .
SCR:017288 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:HmtVar" ;
rdfs:label "HmtVar" ;
definition: "Manually curated database offering variability and pathogenicity information about mtDNA variants. Human mitochondrial variants data of healthy and diseased subjects.Data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information." .
SCR:017289 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HmtPhenome" ;
definition: """Collection of data about variants, genes, phenotypes and diseases involved in mitochondrial functionality.
Users can search for variant position, gene, phenotype or disease and retrieve all related information through integrated network of biological entities.""" .
SCR:017291 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UN-SCAN-IT Gel Analysis Software" ;
definition: "Software package for densitometry measurements of electrophoresis gels by Silk Scientific Inc. Gel analysis software. Turns scanner into gel densitometer. Works with most image formats (TIFF, JPG, BMP, GIF, etc.) from any scanner, digital camera, or other image source. Can quantify Western blots, Agarose gels, PCR gels, TLC." .
SCR:017292 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRspa" ;
NIFRID:synonym "Magnetic Resonance signal processing and analysis" ;
definition: "Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab." .
SCR:017293 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SerialEM" ;
definition: "Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function." .
SCR:017294 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Excel Statistics" ;
definition: "Software tool for statistical analysis by BellCurve that adds statistical analysis methods to Excel menu ." .
SCR:017295 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TOMO3D" ;
definition: "Software tool for fast tomographic reconstruction on multicore computers. Used for electron tomography studies with increasing resolution needs." .
SCR:017296 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Protomo" ;
definition: "Software tool for electron tomography and 3D image processing. Software package used in electron tomography for marker free alignment and 3D reconstruction of tilt series. Tomography software package distributed for linux operating system and developed by Hanspeter Winkler." .
SCR:017298 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TWOSEX-MSChart" ;
definition: "Software tool used to conduct life table analysis focused on development of cohort or population for animal species with two sexes. Parent organization is National Chung Hsing University, Taichung, Taiwan." .
SCR:017299 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "R package inTrees" ;
NIFRID:synonym "inTrees" ;
definition: "Software R package for tree ensembles such as random forests, regularized random forests and gradient boosted trees. Provides functions for extracting, measuring and pruning rules, selecting compact rule set, summarizing rules into learner, calculating frequent variable interactions, formatting rules in latex code." .
SCR:017300 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HomoplasyFinder" ;
definition: "Software tool to identify and annotate homoplasies on phylogeny and sequence alignment. Used to automatically identify any homoplasies present in simulated and real phylogenetic data. Java application that can be used as standalone tool or within statistical programming environment R." .
SCR:017301 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GBM R package" ;
NIFRID:synonym "gbm",
"gbm3",
"generalized boosted models" ;
NIFRID:abbrev "GBM" ;
definition: "Software R package to implement extensions to Freund and Schapire AdaBoost algorithm and Friedman gradient boosting machine. Includes regression methods for least squares, absolute loss, t distribution loss, quantile regression, logistic, multinomial logistic, Poisson, Cox proportional hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and Learning to Rank measures." .
SCR:017302 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_12497" ;
rdfs:label "Phangorn" ;
NIFRID:synonym "Phangorn R package" ;
definition: "Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks." .
SCR:017303 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BASTA" ;
NIFRID:synonym "BAyesian STructured coalescent Approximation",
"BEAST2" ;
definition: "Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations." .
SCR:017304 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TempEst" ;
NIFRID:synonym "Path-O-Gen",
"tempest" ;
definition: "Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019." .
SCR:017307 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BEAST2" ;
NIFRID:synonym "Beast 2.5" ;
definition: "Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager." .
SCR:017308 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Brainreader" ;
NIFRID:synonym "BrainReader",
"brainreader" ;
definition: "Developer of medical software to offer image analysis technologies. Company in Denmark that provides medical image processing software to get quantifiable and accurate insight into brain." .
SCR:017309 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuroreader" ;
NIFRID:synonym "Neuro Reader" ;
NIFRID:abbrev "NeuroreaderTM" ;
definition: "Software application as image segmentation tool. Brain volumetry assessment software. Processes MRI scans and provides self explanatory patient report with total brain volume, hippocampal volume and volumetric data on key segments of brain measured against healthy database." .
SCR:017311 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QtiPlot" ;
definition: "Software tool for data analysis and scientific visualization by IONDEV SRL." .
SCR:017312 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurome Project" ;
NIFRID:synonym "The Neurome Project" ;
definition: "Project to determine organization of neuronal connections between nervous system parts. Source for documented connections in rat brain." .
SCR:017313 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mouse Connectome Project" ;
NIFRID:synonym "The Mouse Connectome Project" ;
NIFRID:abbrev "MCP" ;
definition: "Project to create complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks." .
SCR:017314 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Maps" ;
NIFRID:synonym "Brain maps",
"Brain maps 4.0" ;
definition: "Atlas with global nervous system nomenclature ontology and flatmaps for structure of rat brain. Open access resource for neuroscience community." .
SCR:017316 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IncuCyte® Chemotaxis Software" ;
NIFRID:synonym "IncuCyte Chemotaxis Software" ;
definition: "IncuCyte™ Chemotaxis Cell Migration Software by Essen Bioscience. Add on software module for IncuCyte ZOOM® live cell analysis system. To analyze label free and fluorescently labeled chemotactic cell migration images acquired using ClearView Chemotaxis Plate." .
SCR:017317 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gen5" ;
NIFRID:synonym "5",
"Gen",
"Gen 5" ;
definition: "Software tool for microplate reading. Software supports myriad applications, enabled using BioTek microplate readers." .
SCR:017318 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SleepTrip" ;
NIFRID:synonym "SpiSOP" ;
definition: "Software as branch of FieldTrip with added functionality for sleep analyses, like calculating sleep tables, descriptives, ploting hypnograms, detecting slow waves, sleep spindles, REMS and their cooccurrence etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017319 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BPC Instruments | Biomethane Potential Test" ;
NIFRID:synonym "Automatic Methane Potential Test System",
"Automatic Methane Potential Test System (AMPTS) II",
"Biomethane Potential Test System" ;
NIFRID:abbrev "AMPTS",
"BMP",
"BMP Test" ;
definition: "Automatic Methane Potential Test System (AMPTS) II is analytical tool for conducting various anaerobic batch fermentation tests. This includes performing, with up to 15 test vials, biochemical methane potential (BMP) tests, anaerobic biodegradability studies, specific methanogenic activity (SMA) assays, as well as conducting residual gas potential (RGP) analyses on digested slurry." .
SCR:017320 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vesselucida 360" ;
NIFRID:synonym "Vesselucida" ;
NIFRID:abbrev "VL360" ;
definition: "Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience." .
SCR:017321 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tissue Mapper" ;
NIFRID:synonym "Tissue MapperTM" ;
definition: "Software for comprehensive annotation and delineation of tissue structures by MBF Bioscience. Creates 3D model from image data and annotates regions of interest from customizable ontology list. Map images acquired with brightfield, confocal, two-photon, widefield fluorescence, or light sheet microscopes." .
SCR:017322 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_019005" ;
rdfs:label "TissueMaker" ;
NIFRID:synonym "MBF Bioscience TissueMaker",
"TissueMakerTM" ;
definition: "Software tool to automatically align serial sections and visualize entire 3D organ. Generates full resolution 3D reconstructions from serial sections imaged with whole slide scanners and research microscopes. Used to assist with cell mapping, cytoarchitectonics, and other measures that require visualizing neuronal circuitry to create comprehensive anatomical reference." .
SCR:017323 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cancer Imaging Phenomics Toolkit" ;
NIFRID:abbrev "CaPTk" ;
definition: "Software platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome." .
SCR:017324 a owl:NamedIndividual ;
rdfs:label "Trail Technical Report Archive" ;
NIFRID:synonym "Technical Report Archive and Image Library" ;
NIFRID:abbrev "TRAIL" ;
definition: "Repository of technical reports from US government. Identifies, acquires, catalogs, digitizes and provides unrestricted access to U.S. government agency technical reports. Ensures preservation, discoverability, and persistent open access to government technical publications regardless of form or format. Search interface is hosted by University of Washington and searches all TRAIL content found at HathiTrust and UNT." .
SCR:017326 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref funder ID:501100006565",
"grid.412988.e",
"ISNI:0000 0001 0109 131X",
"Wikidata:Q1972050" ;
rdfs:label "University of Johannesburg; Johannesburg; South Africa" ;
NIFRID:abbrev "UJ" ;
definition: "Public university located in Johannesburg, South Africa. Came into existence on 1 January 2005 as result of merger between Rand Afrikaans University, Technikon Witwatersrand and Soweto and East Rand campuses of Vista University." .
SCR:017327 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fiddle" ;
NIFRID:synonym "file drawer data liberation effort" ;
NIFRID:abbrev "FIDDLE" ;
definition: "Software interactive tool to help researchers to identify most appropriate publication format for their dataset that may be hard to publish in traditional journals. Formats include data repositories, micropublications, preprints, data journals, publishing platforms and journals that are open to null results. Users can search for publication format that meets their needs, compare and contrast formats, and find links to publishers. Open source tool to combat publication bias by getting research out of file drawer and into scientific community." .
SCR:017328 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OntoSoft" ;
definition: "A repository for geosciences software. Registry for software for geoscientists. Part of NSF EarthCube OntoSoft project." .
SCR:017329 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sample Size Matters" ;
definition: "Ten hour course describing sample size calculations, when they can and should be used. Online program for graduate students and research professionals. Participants learn to apply knowledge and skills gained to improve rigor, transparency and reproducibility in their own research." .
SCR:017330 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SynGO" ;
NIFRID:synonym "Synaptic Gene Ontologies" ;
definition: "Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms." .
SCR:017331 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:proovread" ;
rdfs:label "Proovread" ;
definition: "Software tool for PacBio hybrid error correction through iterative short read consensus." .
SCR:017332 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GCE" ;
NIFRID:synonym "Genomic Characteristics Estimation" ;
definition: "Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics." .
SCR:017333 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PILER" ;
definition: "Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats." .
SCR:017334 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:trimal" ;
rdfs:label "trimAl" ;
definition: "Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses." .
SCR:017335 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NOVOPlasty" ;
definition: "Software package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data." .
SCR:017336 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:geseq" ;
rdfs:label "GeSeq " ;
definition: "Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes." .
SCR:017337 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OGDraw" ;
NIFRID:synonym "Draw Organelle Genome Maps",
"OrganellarGenomeDRAW" ;
NIFRID:abbrev "OGDRAW" ;
definition: "Software package for graphical visualization of organellar genomes. Converts annotations in GenBank format into graphical maps. Used to create visual representations of circular and linear annotated genome sequences provided as GenBank files or accession numbers." .
SCR:017338 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scmap" ;
definition: "Software tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments." .
SCR:017339 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scfind" ;
definition: "Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed." .
SCR:017340 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Horos" ;
definition: "Software tool as open source medical image viewer. Enables to browse and visualize medical imaging libraries." .
SCR:017341 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ITK-SNAP" ;
definition: "Software as open source, multiplatform tool used to segment structures in 3D medical images." .
SCR:017342 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Connectome Computation System" ;
NIFRID:abbrev "CCS" ;
definition: "Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies." .
SCR:017343 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ape" ;
rdfs:label "ape" ;
NIFRID:synonym "Analysis of Phylogenetics and Evolution",
"ape 3.0",
"ape 5.0" ;
definition: "Software R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R." .
SCR:017344 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Ranger " ;
definition: "Software tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics." .
SCR:017345 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Diffusion Toolkit" ;
NIFRID:abbrev "DTK" ;
definition: "Software as set of commandline tools with GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. It does preparation work for TrackVis. Software Package for diffusion imaging data processing and tractography." .
SCR:017346 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroInfo" ;
definition: "Software for automatic identification and delineation of brain regions within experimental mouse brain sections. NeuroInfo registers serial section images of any orientation to Allen Mouse Brain Atlas, corrects for distortion due to histological processing, delineates anatomies in experimental section, and detects and reports on cell number within selected anatomies." .
SCR:017348 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurolucida Explorer" ;
definition: "Companion analytical software for Neurolucida and Neurolucida 360, designed to perform extensive morphometric analysis on neuron reconstructions, serial section reconstructions, and brain maps." .
SCR:017350 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SBFSEM-tools" ;
definition: "Data analysis and 3D visualization for connectomics and serial electron microscopy. This toolbox provides missing 3D visualization and analysis tools for cylinder-based annotations. Integration with contour, skeleton based annotations and common morphology file formats is also supported." .
SCR:017351 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fastMNN" ;
NIFRID:synonym "Fast Mutual Nearest Neighbors" ;
definition: "Software tool to correct for batch effects in single-cell expression data using fast version of mutual nearest neighbors (MNN) method." .
SCR:017352 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TissueAtlas" ;
definition: "Human miRNA tissue atlas. Database showing distribution of miRNA expression across human tissues." .
SCR:017353 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PathwayNet" ;
definition: "Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks." .
SCR:017354 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:diana-mirpath",
"SCR_017495" ;
rdfs:label "DIANA-mirPath" ;
NIFRID:synonym "DIANA-miRPath v2.0",
"DIANA-miRPath v3.0",
"miRPath",
"miRPathv2",
"miRPathv3" ;
definition: "Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017355 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miRTarBase" ;
NIFRID:synonym "microRNA-Target interactions Base" ;
definition: "Web based manually curated experimentally validated database of microRNA-Target interactions. Collection of MTIs data validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs." .
SCR:017356 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:miRPathDb" ;
rdfs:label "miRpathDB" ;
NIFRID:synonym "miRNA Pathway Dictionary Database" ;
definition: "Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are." .
SCR:017357 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CoMeTa Website" ;
NIFRID:synonym "Co-expression Meta-analysis of miRNA Target" ;
NIFRID:abbrev "CoMeTa" ;
definition: "Interactive database of miRNA targets and miRNA-regulated gene networks to integrate expression data from hundreds of cellular and tissue conditions. Website includes CoMeTa corank lists and additional targets for all of human miRNAs, their associated pathways resulting from COOL analysis, and miRNA communities with their corresponding enriched functional categories. Website is searchable by miRNA, target gene, or biological function of interest, and represents unique resource to gain insight into miRNA-controlled gene networks and functions." .
SCR:017358 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National High Magnetic Field Lab DC Field Core Facility" ;
NIFRID:synonym "DC Field Facility",
"NHMF Lab Facility" ;
NIFRID:abbrev "NHMFL DC Field Laboratory" ;
definition: "Facility located at MagLab headquarters near Florida State University in Tallahassee. Contains 14 resistive magnet cells connected to 56 megawatt DC power supply and 15,000 square feet of cooling equipment to remove heat generated by magnets. Includes several superconducting magnets operating at millikelvin temperatures. Among these instruments is 45-tesla hybrid magnet, which offers scientists strongest continuous magnetic field in world. Research is supported by magnet plant and cryogenic system operators. Technicians design, build and repair instruments for user research." .
SCR:017359 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National High Magnetic Field Laboratory Electron Magnetic Resonance Core Facility" ;
NIFRID:synonym "Electron Magnetic Resonance Facility",
"EMR Instruments",
"NHMFL EMR facility" ;
NIFRID:abbrev "EMR" ;
definition: "EMR Facility offers home-built, high-frequency and high-field continuous-wave instruments providing frequency coverage from 9 GHz to 1 THz, with additional frequencies available up to 2.5 THz using molecular gas laser. EMR covers variety of magnetic resonance techniques associated with electron like Electron Paramagnetic/Spin Resonance (EPR/ESR). EPR/ESR can be performed on any sample that has unpaired electron spins and used in applications in physics, materials science, chemistry and biology, including studies of impurity states, molecular clusters, antiferromagnetic, ferromagnetic and thin film compounds, natural or induced radicals, optically excited paramagnetic states, electron spin-based quantum information devices, transition-metal based catalysts; and for structural and dynamical studies of metallo-proteins, spin-labeled proteins and other complex bio-molecules and their synthetic models." .
SCR:017360 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National High Magnetic Field Laboratory High B/T Core Facility" ;
NIFRID:synonym "High B/T (magnetic field / temperature) Facility",
"High B/T Facility",
"NHMF Laboratory High B/T Facility" ;
NIFRID:abbrev "B/T" ;
definition: "Facility to conduct experiments in high magnetic fields up to 15 tesla and at very low temperatures down to 0.4 mK simultaneously. Located at University of Florida in Gainesville, it is operated as part of Physics Department Microkelvin Laboratory." .
SCR:017361 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National High Magnetic Field Laboratory Ion Cyclotron Resonance Core Facility" ;
NIFRID:synonym "Ion Cyclotron Resonance Facility",
"National High Magnetic Field Laboratory Ion Cyclotron Resonance Facility",
"NHMF Laboratory Cyclotron Resonance Facility" ;
NIFRID:abbrev "FT-ICR",
"ICR" ;
definition: "Facility provides service operations for sample analysis that requires ultrahigh resolution and high mass accuracy of Fourier Transform Ion Cyclotron Resonance. Used for research in biomolecular analysis, hydrogen-deuterium exchange and environmental and petrochemical analysis. Four FT-ICR mass spectrometers feature high magnetic fields including the world-record 21 tesla and are compatible with multiple ionization and fragmentation techniques." .
SCR:017362 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National MagLab University of Florida McKnight Brain Institute Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Core Facility" ;
NIFRID:synonym "Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Facility" ;
NIFRID:abbrev "AMRIS" ;
definition: "National High Magnetic Field Laboratory (MagLab) site. It provides researchers with advanced NMR, MRI, and spectroscopy tools (human/animal imaging) for biomedical studies, specializing in high-field magnetic resonance technology. Hosts spectrometers and scanners, including high-field NMR (up to 1.5 GHz), MR microscopy, and human/animal MRI systems (e.g., 3T and 900 MHz). Offers expertise in high-resolution solution NMR, solid-state NMR, and specialized imaging for in vivo animal models and humans.Features an RF coil lab that designs, builds, and tests custom MRI/NMR coils to optimize data collection. Supports research into Alzheimer's, cancer, metabolism, and brain development." .
SCR:017364 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Communication Power Corporation" ;
NIFRID:abbrev "CPC" ;
definition: "Commercial organization located in New York, USA which provides amplifiers. designs and manufactures standard or custom RF/Microwave Power Amplifiers/Accessories for military (CPC is ITAR registered), industrial, scientific and medical applications." .
SCR:017365 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Bruker Corporation" ;
definition: "Commercial organization located in Massachusetts, USA, for scientific instruments and analytical and diagnostic solutions. Bruker equipment can be used in life science molecular research, in applied and pharma applications,microscopy, nano-analysis and industrial applications. Provider of high-performance systems for cell biology, preclinical imaging, clinical phenomics and proteomics research, clinical microbiology, and for molecular pathology research." .
SCR:017366 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Oxford Instruments" ;
definition: "Commercial organization located in Abingdon, United Kingdom for high technology products. Manufactures instruments for agriculture, astronomy, automotive, aerospace, bio-imaging, life science, chemical and catalysis, energy generation and storage, forensics, environmental industries, geology, metallurgy, pharmacy, photonics, polymers, quantum technology, data storage, and microelectronics. Products are divided into atom force microscopy, electron microscopy, deposition and etch tools, low temperature systems, optical imaging, nuclear magnetic resonance, MRI and CT servicing, Modular optical spectroscopy, and X-Ray." .
SCR:017367 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "SP Scientific" ;
definition: "Commercial organization located in Warminster, Pennsylvania, USA, part of SP Industries, Inc. Provides VirTis, FTS Systems, Hotpack, Hull, Genevac, and PennTech scientific equipment. Manufactures freeze drying/lyophilization, centrifugal evaporation and concentration, temperature control/thermal management, glassware washers, controlled environments, vial washing and tray loading machines., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017368 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.504161.7",
"ISNI: 0000 0004 0566 6119" ;
rdfs:label "SP Industries" ;
definition: "Commercial organization located in Warminster, Pennsylvania, USA is manufacturer of specialty equipment, scientific glassware, laboratory and lab safety supplies, and home healthcare products serving pharmaceutical, biotechnology, educational, industrial, OEM, and commercial markets under market leading brand names. Products include pharmaceutical, scientific research, industrial, aeronautic, semiconductor and healthcare. Flagship brands are SP Scientific, SP Scienceware, and SP Ableware." .
SCR:017369 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.422860.a",
"ISNI: 0000 0004 4911 2169",
"Wikidata: Q30283966" ;
rdfs:label "Tecmag" ;
NIFRID:synonym "Technology for Magnetic Resonance" ;
definition: "Commercial organization, located in Houstion, Texas, USA, for products for magnetic resonance spectroscopy. Manufactures NMR, NQR and amp, MRI instrumentation including nuclear magnetic resonance spectrometers and full consoles, system upgrades, and solid-state NMR / NQR probes. Tecmag was acquired by Avingtrans PLC and became subsidary of Scientific Magnetics Ltd. (UK)." .
SCR:017370 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Scientific Magnetics" ;
definition: "Commercial organization, located in Houston, Texas, USA. Scientific Magnetics is trading name of Space Cryomagnetics Ltd. and specializes in cryogen free super conducting magnets. Products including cryogen free horizontal superconducting magnets, UHV compatible magnets, magnetic separation products, MRI site planning, and liquid helium filling." .
SCR:017371 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Avingtrans PLC" ;
definition: "Machine industry company located in Chatteris, Cambridgeshire, United Kingdom and engaged in provision of highly engineered components, systems and services to energy, medical and traffic. Has investment in Energy Divisions, Medical Division, and Aerospace Industries." .
SCR:017372 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "grid.482350.8",
"ISNI: 0000 0004 0482 3442",
"Wikidata: Q30343843" ;
rdfs:label "Varian Medical Systems, Inc." ;
NIFRID:synonym "Varian" ;
definition: "Manufacturer located in Palo Alto, California, USA, that has made developments in fields of radiotherapy, radiosurgery, X-ray tube technology, digital image detectors, cargo screening, and non-destructive testing. Varian technology and software for processing diagnostic X-ray images is being used in radiotherapy and analysis." .
SCR:017373 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Agile Microwave Technology Inc." ;
NIFRID:synonym "Agile Mwt" ;
definition: "Manufacturer, located in Cary, North Carolina, USA, of amplifiers, RF/microwaves, and other electrical components which come in boards, modules, or systems." .
SCR:017374 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Physiome Model Repository" ;
NIFRID:synonym "Physiome Repository",
"PMR2" ;
NIFRID:abbrev "PMR" ;
definition: "Repository of mainly CellML models powered by collection of software tools and libraries with PMR2 software suite as core power. Third party integration suites are RICORDO, Virtuoso, BiVeS/BudHat, OpenCOR, CombineArchive Web, WebCAT, Morre/MaSyMoS." .
SCR:017375 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BZ-H3A analyzer software" ;
definition: "Software tool as analysis application BZ-H3A by Keyence, Osaka, Japan for fluorescence microscope BZ-X series." .
SCR:017376 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Primer Express Software" ;
NIFRID:synonym "Primer Express Software v3.0.1",
"Primer Express™ Software v3.0.1",
"Primer Express™ Software v3.0.1 License" ;
definition: "Software tool by Applied Biosystems to design primers and probes using TaqMan and SYBR Green I dye chemistries for gene quantitation and allelic discrimination (SNP) real-time PCR applications. Developed for use with StepOne, StepOnePlus, 7300, 7500, 7500 Fast, 7900HT, ViiA 7, and QuantStudio real-time PCR systems. Provides customized application specific documents for absolute⁄relative quantitation and allelic discrimination." .
SCR:017377 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LSM_700" ;
rdfs:label "Zeiss | LSM 700 microscope" ;
NIFRID:synonym "LSM 700 Laser Scanning Microscope" ;
definition: "Laser scanning confocal microscope designed for high-quality imaging of biological and material samples. Member of the seventh generation of confocal microscopes from Carl Zeiss. Point scanning confocal microscope., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017380 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4078" ;
rdfs:label "Florida State University Chemistry and Biochemistry Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "Florida State University Chemistry and Biochemistry NMR Laboratory" ;
NIFRID:abbrev "FSU-NMR" ;
definition: "Facility provides NMR spectroscopy services for FSU campus. Has spectrometers to perform experiments ranging from protein structure determination to solid state characterization of inter-metallic species and nearly all experiments in between." .
SCR:017381 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Image analysis of V1 ocular dominance patterns" ;
definition: "Software tool to quantify ocular dominance patterns of primary visual cortex in different animals." .
SCR:017382 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Florida Department of Chemistry Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "UF Department of Chemistry NMR Facility" ;
NIFRID:abbrev "NMR Facility",
"UF NMR Facility" ;
definition: "Facility serves students and faculty of University of Florida, and researchers from industry who use facility instruments to check outcome of reactions or characterize compounds. Instruments include Inova 500 MHz magnet with 2 RF Channels, Inova 500 MHz magnet with 3 RF Channels, Mercury 300 MHz (m4n and m8n), Mercury 300 MHz Broadband, Agilent 600 MHZ Magnet, and several NMR probes." .
SCR:017383 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biospecimen Repository Access and Data Sharing" ;
NIFRID:synonym "BRADS" ;
definition: "Access to data from the Division of Intramural Population Health Research (DIPHR) of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) from completed studies, including biospecimens and ancillary data." .
SCR:017384 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Medical Information Mart for Intensive Care-III" ;
NIFRID:synonym "Medical Information Mart for Intensive Care",
"MIMIC",
"MIMIC 3",
"MIMIC-III" ;
definition: "Collection of comprising deidentified health related data associated with patients who stayed in critical care units of Beth Israel Deaconess Medical Center between 2001 and 2012. Database includes information such as demographics, vital sign measurements made at bedside (~1 data point per hour), laboratory test results, procedures, medications, caregiver notes, imaging reports, and mortality (both in and out of hospital)." .
SCR:017385 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Science of Behavior Change Research Network" ;
NIFRID:synonym "Science of Behavior Change (SOBC) Research Network",
"SOBC Measures Repository" ;
NIFRID:abbrev "SOBC" ;
definition: "Repository for behavioral science measures that have been validated or are in process of being validated in accordance with SOBC Experimental Medicine Approach." .
SCR:017386 a "Software",
owl:NamedIndividual ;
rdfs:label "Morpheus by Broad Institute" ;
definition: "Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis." .
SCR:017387 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Suiplus | SSA-II sperm analysis system" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 1, 2023. System developed under guidance of experts in reproduction and andrology from Andrological Branch of Chinese Medical Association and Research Institute of National Health Planning Commission. Designed according to standard of 5th edition of World Health Organization laboratory manual for examination and processing of human semen." .
SCR:017389 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Glimma" ;
definition: "Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data." .
SCR:017390 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ROSE" ;
NIFRID:synonym "Rank Ordering of Super Enhancers",
"RANK ORDERING OF SUPER-ENHANCERS" ;
definition: "To create stitched enhancers, and to separate super enhancers from typical enhancers using sequencing data given file of previously identified constituent enhancers ." .
SCR:017391 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LDMatrix" ;
definition: "Software tool to create interactive heatmap matrix of pairwise linkage disequilibrium statistics." .
SCR:017393 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggrepel" ;
definition: "Software tool to provide text and label geoms for ggplot2 that help to avoid overlapping text labels. Labels repel away from each other and away from data points." .
SCR:017394 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Galaxy_scater" ;
rdfs:label "Galaxy scater" ;
definition: "Software tool as Galaxy based training resource for single cell RNA-seq quality control and analyses." .
SCR:017395 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DAQCORD" ;
NIFRID:synonym "Data Access Quality and Curation for Observational Research Designs" ;
definition: "Software tool for practical self assessment and reporting method for clinical research studies, to capture key information about data acquisition and quality control measures. Linked to dataset so that potential research collaborators can determine if data meets their needs and expectations." .
SCR:017396 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CLC Genomics Server" ;
definition: "Commercially available software tool for high throughput sequencing analysis, designed for use on central compute cluster or server. Can handle data volumes beyond capacity of desktop systems and manages submission of many jobs via its own queuing system or through submission of jobs to third party grid scheduler." .
SCR:017397 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Connection-set algebra" ;
NIFRID:synonym "Connection Set Algebra" ;
NIFRID:abbrev "CSA" ;
definition: "Software tool for description of connectivity in small and large scale neuronal network models. It provides operators to form more complex sets of connections from simpler ones and also provides parameterization of such sets. Can be used as component of neuronal network simulators or other tools." .
SCR:017398 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NiMARE" ;
NIFRID:synonym "Neuroimaging Meta Analysis Research Environment",
"Neuroimaging Meta-Analysis Research Environment" ;
definition: "Software Python package for coordinate and image based meta analysis of neuroimaging data." .
SCR:017399 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IBIS Network" ;
NIFRID:synonym "Infant Brain Imaging Study",
"The Infant Brain Imaging Study" ;
NIFRID:abbrev "IBIS" ;
definition: """Research study of brain development in infants and children with autism. Consortium of researchers across North America that work together to discover early changes in brain development of young children with autism. Participants will travel to their closest study location to receive developmental and behavioral assessments, MRI scan of the brain. Participants will be reimbursed for travel and related expenses. Families of children at high risk for developing symptoms of autism will receive assistance with referrals for local services.
check if data repository is in the papers""" .
SCR:017400 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "phyloscanner" ;
definition: "Software tool for analysing pathogen genetic diversity and relationships between and within hosts at once, in windows along genome. Inferring transmission from within and between host pathogen genetic diversity." .
SCR:017401 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:AbCD_database",
"SCR_019000" ;
rdfs:label "ExPASy ABCD database" ;
NIFRID:synonym "AntiBodies Chemically Defined",
"AntiBodies Chemically Defined Expert Protein Analysis System database",
"ExPASy ABCD (AntiBodies Chemically Defined) Database",
"ExPASy ABCD Database",
"The ABCD database",
"The AntiBodies Chemically Defined Database" ;
NIFRID:abbrev "ABCD ExPASy" ;
definition: """Repository of sequenced antibodies, integrating curated information about antibody and its antigen with cross links to standardized databases of chemical and protein entities.
Manually curated repository of sequenced antibodies, developed by Geneva Antibody Facility at University of Geneva, in collaboration with CALIPHO and Swiss Prot groups at SIB Swiss Institute of Bioinformatics. Database provides list of sequenced antibodies with their known targets. Each antibody is assigned unique ID number that can be used in academic publications to increase reproducibility of experiments.""" .
SCR:017402 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioDepot-workflow-builder" ;
NIFRID:abbrev "Bwb" ;
definition: "Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results." .
SCR:017403 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuron Phenotype Ontology" ;
NIFRID:abbrev "NPO" ;
definition: "An ontology for describing the complex phenotypes of neurons." .
SCR:017404 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TSE Systems | IntelliCage" ;
definition: "Behavior instrument, cage allows for assess to home cage behavior and cognitive performance of up to 16 individual mice or rats separately while they are living in social environment. This unique experimental setup fosters natural social behavior in biologically relevant, enriched but highly standardized home cage context. Minimizes need for handling and human intervention, thereby increasing task validity, data reproducibility and ensuring high level of animal welfare." .
SCR:017405 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "neuropredict" ;
definition: "Software tool for assessment of predictive power, with support for neuroimaging features. Easy machine learning and standardized predictive analysis of biomarkers." .
SCR:017406 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "graynet" ;
definition: """Software tool for subject wise networks from morphometric features and structural MRI. Single subject morphometric networks for
neuroscience connectivity applications.""" .
SCR:017407 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iNSCOPIX | nVista" ;
definition: "Miniature microscope for imaging calcium activity in neural circuits by Inscopix, Inc." .
SCR:017408 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mosaic" ;
definition: "Mosaic software features apps designed to help you derive deeper insights from videos of large scale circuit dynamics by Inscopix Inc." .
SCR:017410 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mass spectrometry imaging workbench" ;
definition: "Software tool for analysis of mass spectrometry imaging data implemented in Galaxy framework. Provides options to analyze mass spectrometry imaging data in imzML file format, including quality control, visualization, preprocessing, statistical analysis, image co-registration and feature identification.Galaxy docker container for mass spectrometry imaging." .
SCR:017411 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StatView Version 5.0" ;
definition: "Software package for statistical analysis by SAS Institute Inc, Cary, NC." .
SCR:017412 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dMRIPrep" ;
definition: "Software tool as preprocessing pipeline for diffusion MRI. Pipeline used for preprocessing of diverse dMRI data. Workflow dispenses of manual intervention, thereby ensuring reproducibility of results." .
SCR:017413 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Plant Phenotyping Annotation Toolbox" ;
definition: "Software tool as graphical user interface designed to assist with manual annotation of different parts of the inflorescence. Used in deep plant phenotyping. Works with DeepPod." .
SCR:017414 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:RepeatFiller",
"biotools:RepeatFiller" ;
rdfs:label "RepeatFiller" ;
definition: "Software tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences." .
SCR:017415 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Predomics" ;
definition: "Software package for metagenomics data. Discovers accurate predictive signatures and provides unprecedented interpretability. Package contains three methods for suppervised learning based on ternary coefficients. Used to discover classification models for quantitative metagenomics data." .
SCR:017416 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Corneal Diseases Classification" ;
definition: "Software based on deep learning model for auto detect corneal diseases. Sample may contain multiple categories. After learning thousands of corneal images, you can make automatic judgments on subtypes of cornea." .
SCR:017417 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IKAP" ;
NIFRID:synonym "Identifying K mAjor cell Population" ;
definition: "Software tool for identifying K mAjor cell population groups in single-cell RNA-seq analysis. Algorithm identifying major cell groups that improves differentiating by tuning parameters for clustering. Using multiple datasets improves identification of major cell types and facilitates cell ontology curation." .
SCR:017420 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011560" ;
rdfs:label "SICAS Medical Image Repository" ;
NIFRID:synonym "Medical Image Repository",
"SICAS" ;
definition: "Medical image repository to store medical research data." .
SCR:017421 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012435" ;
rdfs:label "Image Data Resource (IDR)" ;
NIFRID:synonym "IDR",
"Image Data Resource" ;
definition: "Public repository of reference image datasets from published scientific studies. Platform for publishing, mining and integrating bioimaging data, following FAIR principles and Euro-BioImaging/ELIXIR imaging strategy using OMERO and Bio-Formats open source software built by Open Microscopy Environment. Deployed on OpenStack cloud running on EMBL-EBI’s Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super resolution microscopy, and digital pathology." .
SCR:017422 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R3536N",
"DOI:10.22011",
"DOI:10.25504/FAIRsharing.ekj9zx",
"r3d100012329" ;
rdfs:label "STRENDA " ;
NIFRID:synonym "Beilstein-Institut",
"Standards for Reporting Enzymology Data",
"STRENDA" ;
definition: "Storage and search platform supported by Beilstein-Institut that incorporates STRENDA Guidelines. For authors who prepare manuscript containing functional enzymology data, STRENDA DB provides means to ensure that data sets are complete and valid before submitting them to journal." .
SCR:017423 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011562" ;
rdfs:label "Kinetic Models of Biological Systems (KiMoSys)" ;
NIFRID:synonym "KiMoSys",
"KInetic MOdels of biological SYStems" ;
definition: "Web application for quantitative KInetic MOdels of biological SYStems. Platform includes public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. Designed to search, exchange and disseminate experimental data and associated kinetic models for systems modeling community." .
SCR:017424 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "The Decoding Toolbox" ;
NIFRID:abbrev "TDT" ;
definition: "Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data." .
SCR:017425 a "Research",
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:eva" ;
rdfs:label "European Variation Archive (EVA)" ;
NIFRID:synonym "European Variation Archive",
"EVA" ;
definition: "Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser." .
SCR:017426 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurodocker" ;
definition: "Software tool to generate Dockerfiles and Singularity recipes for neuroimaging with simple command-line interface. Command line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers. Supports AFNI, ANTs, Convert3D, Dcm2niix, FreeSurfer, FSL, Matlab Compiler Runtime, MINC, Miniconda, MRtrix3, NeuroDebian, PETPVC, and SPM12." .
SCR:017427 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HeuDiConv: a heuristic-centric DICOM converter" ;
NIFRID:synonym "heudiconv",
"heuristic-centric DICOM converter" ;
NIFRID:abbrev "HeuDiConv" ;
definition: "Software tool as flexible DICOM converter for organizing brain imaging data into structured directory layouts." .
SCR:017428 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100010890" ;
rdfs:label "Protein Circular Dichroism Data Bank (PCDDB)" ;
NIFRID:synonym "PCDDB",
"Protein Circular Dichroism Data Bank" ;
definition: "Public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. For authors to deposit experimental data as well as detailed information on methods and calculations associated with published work. Includes links for each entry to bioinformatics databases. Data are freely available to accessors either as single files or as complete data bank downloads." .
SCR:017429 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100010085" ;
rdfs:label "Inorganic Crystal Structure Database (ICSD)" ;
NIFRID:synonym "ICSD",
"Inorganic Crystal Structure Database" ;
definition: "Database for completely identified inorganic crystal structures. Collection of known inorganic crystal structures published since 1913, including their atomic coordinates. Includes only data which have passed thorough quality checks. Tool for materials research." .
SCR:017436 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WebMAUS" ;
NIFRID:synonym "Web Munich AUtomatic Segmentation" ;
definition: "Web service for automatic phonetic transcription of non-prompted speech. Ludwig Maximilian University of Munich, Munich, Germany is parent organization." .
SCR:017437 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:HNN",
"SCR_017678" ;
rdfs:label "Human Neocortical Neurosolver" ;
NIFRID:abbrev "HNN" ;
definition: "Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data." .
SCR:017438 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Gene Expression Analysis toolbox" ;
NIFRID:synonym "Analysis",
"Brain",
"Expression",
"Gene",
"toolbox" ;
definition: "Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain." .
SCR:017439 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "clusterExperiment" ;
definition: "Software open source R package for executing, evaluating and visualizing different clusterings of experimental data, including data from single cell RNA-Seq studies. Software for running and comparing different clusterings of single cell sequencing data." .
SCR:017441 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioWheel" ;
NIFRID:synonym "bio wheel",
"biowheel" ;
definition: "Software tool for interactive graphs of high dimensional data. Interactive cloud based software tool by DIBSVIS." .
SCR:017442 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mediation Analysis of Causality under Confounding" ;
NIFRID:synonym "macc" ;
NIFRID:abbrev "MACC" ;
definition: "Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method." .
SCR:017443 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "microMS" ;
NIFRID:synonym "microscopy guided Mass Spectrometry" ;
definition: "Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing." .
SCR:017444 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MIIVsem " ;
NIFRID:synonym "Model Implied Instrumental Variable Estimation of Structural Equation Models" ;
definition: "Software R package for estimating structural equation models using instrumental variables." .
SCR:017446 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MountainSort" ;
definition: "Neurophysiological spike sorting software." .
SCR:017447 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:myriads" ;
rdfs:label "Myriads" ;
NIFRID:synonym "SGoF+" ;
definition: "Software package for p value based multiple testing that also implements dependence test and p-value simulation." .
SCR:017448 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neural Ideal" ;
definition: "Software package for extracting neural activity codes." .
SCR:017449 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NEURON" ;
definition: "Software for computational neurophysiology. Simulation environment is used for building and using computational models of neurons and networks of neurons. NEURON Users Group can participate in collaborative development of documentation, tutorials, and software." .
SCR:017450 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuron Tools" ;
definition: "Software tools for converting data files into persistence diagrams and distance matrices." .
SCR:017451 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PetaVision" ;
NIFRID:abbrev "OpenPV" ;
definition: """Open source software neural simulation toolbox. C++ library for designing and deploying large scale neurally inspired computational models.
Object oriented neural simulation toolbox optimized for high performance multi core, multi node computer architectures.""" .
SCR:017452 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyNWB" ;
definition: "Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information." .
SCR:017453 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyRayleighCuda" ;
definition: "Python Rayleigh-Sommerfeld integral for acoustics with optional CUDA graphics processing unit (GPU) implementation." .
SCR:017454 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scope" ;
definition: "Two photon microscope control software with multi area capabilities." .
SCR:017455 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Seizure-Waves" ;
NIFRID:synonym "Seizure Waves",
"SeizureWaves" ;
definition: "Analysis and modeling code for waves of seizure activity." .
SCR:017456 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Silver Lab Microscopy Software" ;
definition: "Software for use with compact Acousto-Optic Lens Microscope (AOLM) developed in the Silver Lab at UCL. Written in LabVIEW. Performs multiple imaging modes and protocols including Z-stacks, multi-plane, single-plane, sub-volume, patches and points. It comes with tools for visualising data acquired with system." .
SCR:017457 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StimVision" ;
NIFRID:synonym "Stim Vision" ;
definition: "Software tool to facilitate tractography based deep brain stimulation (DBS) electrode targeting within patient specific stereotactic coordinate system used in operating room." .
SCR:017458 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TReNA" ;
definition: "Methods for reconstructing transcriptional regulatory networks." .
SCR:017460 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Arteria StackStorm Pack" ;
definition: "Software tool to automate sequencing center operations. This pack provides re-usable units for automating tasks at sequencing core facility using StackStorm event-driven automation platform." .
SCR:017462 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:fastproject" ;
rdfs:label "FastProject" ;
definition: "Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored." .
SCR:017463 a owl:NamedIndividual ;
rdfs:label "ALICE" ;
NIFRID:synonym "Automatic Localization of Intra-Cranial Electrodes" ;
definition: "Software tool for automatic localization of intra-cranial electrodes for clinical and high density grids. Software for coregistering high density ECoG grids to MRI anatomy." .
SCR:017464 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Autopatcher" ;
definition: "Software tool for neuronal recording in intact brain." .
SCR:017465 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cytoNet" ;
definition: "Cloud based analysis software for cell population microscopy images. Network Analysis of Cell Communities cytoNet image analysis software designed to quantify structure of cell communities from microscope images, using principles of graph theory." .
SCR:017466 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DiffuserCam" ;
definition: "Software tool as processing code. Alternating direction method of multipliers (ADMM) algorithm for recovering 3D volumes from 2D raw data captured with DiffuserCam." .
SCR:017467 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gene Expression Analysis Resource" ;
NIFRID:abbrev "gEAR" ;
definition: "Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data." .
SCR:017468 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hemodialysis Pilot Studies Consortium" ;
NIFRID:abbrev "HDPSC" ;
definition: "Consortium to design and conduct pilot and feasibility studies of novel therapies to reduce morbidity and mortality for patients treated with maintenance hemodialysis. Data Coordinating Center (DCC) for consortium provides scientific expertise and operational support for pilot studies that will be conducted at HDPSC Participating Clinical Centers. Data Coordinating Center for Hemodialysis Pilot Studies Consortium." .
SCR:017469 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Analysis, Visualization, and Informatics Lab-space (AnVIL)" ;
NIFRID:synonym "Analysis",
"Analysis Visualization and Informatics Lab-space",
"and Informatics Lab-space",
"AnVIL",
"Visualization" ;
definition: "Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces." .
SCR:017470 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Knowing what you know (kwyk) - Bayesian Brain Parcellation" ;
NIFRID:synonym "knowing what you know" ;
NIFRID:abbrev "kwyk" ;
definition: "Software tool as deep neural network for predicting FreeSurfer segmentations of structural MRI volumes. This tool is implemented as both Docker and Singularity containers. Used for brain parcellation and uncertainty estimation." .
SCR:017471 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "refine.bio" ;
definition: "Software tool to uniformly process and normalize large amounts of data. Harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists." .
SCR:017472 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Data Information System - DAISY" ;
NIFRID:synonym "DAta Information SYstem" ;
NIFRID:abbrev "DAISY" ;
definition: "Open source web application that allows biomedical research institutions to map their data and data flows in accordance with GDPR's accountability requirement." .
SCR:017476 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Italian Twin Registry" ;
NIFRID:synonym "National Register of Twins" ;
definition: "Portal with information about twins in Italy." .
SCR:017477 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Finnish Twin Cohort Study" ;
definition: "Twin panel consists of three nationwide samples of Finnish twin pairs. Major studies include nicotine dependence, eating disorders and brain imaging and alcohol use." .
SCR:017478 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Swedish Twin Registry" ;
definition: "Registry contains information about twin pairs for which zygosity is known, both mono- and dizygotic pairs. Registry covers older, middle, and younger cohorts. There are approximately 30 projects ongoing based on data from this registry." .
SCR:017479 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ABA Mouse Brain: Atlas" ;
NIFRID:synonym "Allen Brain Atlas Mouse Brain: Atlas",
"Allen Brain Atlas: Mouse Brain" ;
definition: "Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain." .
SCR:017480 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cardiff Study of all Wales and North West of England Twins" ;
NIFRID:abbrev "CaStANET" ;
definition: "Study of twins and their families provides tool for disentangling genetic and environmental origins of traits. Study collected behavioral and psychopathological information using self-, parent and teacher reports, and focused on contributions of genetic and environmental risk factors to psychological health of young people." .
SCR:017481 a "Research",
owl:NamedIndividual ;
rdfs:label "National Twin Registry of Sri Lanka" ;
NIFRID:synonym "Sri Lankan Twin Registry" ;
NIFRID:abbrev "NTR" ;
definition: "Independent academic and research institution to establish registration for twins in Sri Lanka , to facilitate study of twins. Center for twin, sibling, family and genetic studies for South Asian Region." .
SCR:017482 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Danish Twin Registry" ;
NIFRID:abbrev "DTR" ;
definition: "Twin registry to studying causes of cancer, gene inheritance and environment. Contains information on twins born in Denmark. Comprises twins born through more than 125 years." .
SCR:017484 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mid-Atlantic Twin Registry" ;
NIFRID:abbrev "MATR" ;
definition: "Organization of twins and their families who are willing to consider taking part in twin-based, health-related research. For twins of any age, ethnicity, and zygosity (identical or fraternal), as well as higher order multiples such as triplets, quadruplets and quintuplets. Most of twins registered in MATR are from Virginia, North Carolina, and South Carolina, but twins from all over the country and all around the world are welcome to register. MATR repository containing DNA samples provided by twins and allows to study twin data collected by studies along with their DNA." .
SCR:017485 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Twins Research Australia" ;
NIFRID:synonym "Australian Twin Registry" ;
definition: "Portal for Twins Research Australia. Brings twins and researchers together for vital health research in twins." .
SCR:017487 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:MethBase",
"biotools:Methbase" ;
rdfs:label "MethBase" ;
NIFRID:synonym "MethBase: a reference methylome database" ;
definition: "Central reference methylome database created from public BS-seq datasets. Provides methylation level at individual sites, regions of allele specific methylation, hypo- or hyper-methylated regions, partially methylated regions, and detailed meta data and summary statistics." .
SCR:017489 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012282" ;
rdfs:label "4D Genome" ;
definition: "Repository for chromatin interaction data. Records can be queried by genomic regions, gene names, organism, and detection technology. Database is continuously updated by curators. Contributions from scientific community." .
SCR:017490 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Deep Blue Epigenomic Data Server" ;
definition: "Central data access hub for large collections of epigenomic data. It organizes data from different sources using controlled vocabularies and ontologies. Data Server for storing, organizing, searching, and retrieving genomic and epigenomic data, handling associated metadata, and to perform different types of analysis." .
SCR:017491 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Canadian Epigenetics, Environment and Health Research Consortium Network" ;
NIFRID:synonym "CEEHRC Network" ;
definition: "Network to connect Canadian epigenetics researchers and expand their reach to broader health research community in Canada and beyond. Curated epigenomics sequence focused on common human diseases." .
SCR:017492 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Accessible Resource for Integrated Epigenomics Studies" ;
NIFRID:synonym "ARIES" ;
definition: "Portal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time." .
SCR:017494 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Epigenie" ;
definition: "Collection of epigenetic data browsers and repositories. Repository of epigenetics tools and databases by EpiGenie team." .
SCR:017496 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miRanda" ;
NIFRID:synonym "MicroRNA.org. microrna.org" ;
definition: "Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017498 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DIANA-mirExTra" ;
NIFRID:synonym "Mirextra 2.0" ;
definition: "Software tool for analysis of expression data for microRNA function." .
SCR:017499 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:transmir" ;
rdfs:label "TransmiR" ;
NIFRID:synonym "TransmiR v2.0" ;
definition: "Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data." .
SCR:017500 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PsychENCODE Knowledge Portal" ;
definition: "Portal of PsychENCODE Consortium to study role of rare genetic variants involved in several psychiatric disorders. Database of regulatory elements, epigenetic modifications, RNA and protein in brain." .
SCR:017501 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Compilation of Genetics Resource Databases" ;
definition: "Portal provides list of genetic resources such as Brain Atlases and genomes for various species provided by National Institute of Drug Abuse." .
SCR:017505 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GO Gene Ontology Consortium and Knowledgebase" ;
NIFRID:synonym "Gene Ontology Consortium",
"GO Consortium" ;
NIFRID:abbrev "GOC" ;
definition: "Consortium integrates resources from variety of research groups, from model organisms to protein databases to biological research communities actively involved in development and implementation of Gene Ontology. Mission to develop up to date, comprehensive, computational model of biological systems, from molecular level to larger pathways, cellular and organism level systems." .
SCR:017506 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atlas of Drosophila Development" ;
definition: "Collection of color illustrations that follow main events of embryogenesis and post embryonic development of Drosophila." .
SCR:017507 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Drosphila Brain Lineage Atlas" ;
definition: "Atlas providing structure and development of Drosophila brain lineages. Used to learn about projection pattern of lineages as first step towards reconstructing and understanding all neurons." .
SCR:017508 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Optogenetics Resource at JAX" ;
definition: "Mouse lines expressing proteins that activate, inhibit or detect neuronal activity are available from The Jackson Laboratory Repository. Many of these strains have been generated by HHMI Janelia Farm GENIE Project or by Allen Institute for Brain Science." .
SCR:017509 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gensat Cre-Mice" ;
NIFRID:synonym "Gene Expression Nervous System ATlas Cre-Mice" ;
definition: """Project provides transgenic BAC-Cre recombinase driver lines that allow for cell-specific gene manipulations in central nervous system of mouse. Gene Expression Nervous System Atlas Project provides Cre driver lines that will target selected neuronal or glial populations in brain and spinal cord.
Cells can be ordered from MMRRC.""" .
SCR:017510 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allen Brain Atlas expression map of Cre and other drivers " ;
NIFRID:synonym "Allen Brain Atlas Data Portal Transgenic Characterization" ;
definition: "Data detailing transgene expression in Cre and other driver lines for adult and developing brain. Experiments include colorimetric in situ hybridization, fluorescent in situ hybridization and other histological methods. Expression maps of transgenic Cre and other driver lines in mice." .
SCR:017511 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nomenclature" ;
definition: "Authoritative source of official names for mouse genes, alleles, and strains. Nomenclature follows rules and guidelines established by International Committee on Standardized Genetic Nomenclature for Mice." .
SCR:017512 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Knockout Mouse Project Repository at JAX" ;
definition: "Information from JAX about their contributions to KOMP project coordinated by International Mouse Phenotyping Consortium. National Institutes of Health has funded three KOMP2 centers in United States, including one at Jackson Laboratory, to work together on task of producing and phenotyping mice to establish resource of knockout mice and related database of gene function." .
SCR:017513 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Optogenetics Resource Center" ;
definition: "Database of different optogenetics resources like hardware, protocols, sequence information." .
SCR:017514 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VGNC" ;
NIFRID:synonym "Vertebrate Gene Nomenclature Committee" ;
definition: "Software resource for vertebrate gene nomenclature. Database of gene symbols. Coordinates with vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), AGNC (Anole green lizard), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs." .
SCR:017515 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Batch Data and Analysis Tool" ;
definition: "Software tool to access various mouse genome information in batch format. Batch data and analysis tools." .
SCR:017517 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vertebrate Homology" ;
definition: "MGI contains homology information for mouse, human, rat, chimp, dog and other species. Complete set of human, chimpanzee, rhesus macaque, dog, cattle, rat, chicken, western clawed frog and zebrafish Homology Classes for mouse genes. Report includes Chromosome and EntrezGene and OMIM IDs. Report of Human and Mouse Homology Classes sorted by HomoloGene ID includes associated nucleotide and protein sequences, Chromosome and OMIM IDs. Report of Human and Mouse Homology with phenotype annotations. Several additional MGI reports are available, including those for Gene Ontology, Phenotypes and Nomenclature." .
SCR:017518 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Strains, SNPs and Polymorphisms" ;
definition: "MGI integrates comparative data on inbred strain characteristics including SNPs, polymorphisms, and quantitative phenotypes." .
SCR:017519 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Functional Annotation" ;
definition: "MGI GO project provides functional annotations for mouse gene products using Gene Ontology. Functional annotation using Gene Ontology (GO)." .
SCR:017521 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Functional Mapping and Annotation of Genome Wide Association Studies" ;
NIFRID:synonym "FUMA",
"Functional Mapping and Annotation of Genome-Wide Association Studies" ;
NIFRID:abbrev "FUMA GWAS" ;
definition: "Platform that can be used to annotate, prioritize, visualize and interpret GWAS results. To submit your own GWAS, login is required for security reason. You can browse public results of FUMA from Browse Public Results without registration or login." .
SCR:017522 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Mouse Disease Connection" ;
NIFRID:synonym "Human - Mouse: Disease Connection" ;
NIFRID:abbrev "HMDC" ;
definition: "Collection of published and potential mouse models of human disease, discovery of candidate genes and investigation of phenotypic similarity between mouse models and human patients. Mouse mutation, and phenotype and disease model data from Mouse Genome Informatics database are integrated with human gene to disease relationships from the National Center for Biotechnology Information and Online Mendelian Inheritance in Man and human disease to phenotype relationships from the Human Phenotype Ontology." .
SCR:017523 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phenotypes and Mutant Alleles" ;
NIFRID:synonym "Alleles & Disease Models",
"Phenotypes" ;
definition: "Enables comparative phenotype analysis, searches for human disease models, and hypothesis generation by providing access to spontaneous, induced, and genetically engineered mutations and their strain-specific phenotypes." .
SCR:017524 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genes, Genome Features and Maps" ;
definition: "Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models." .
SCR:017525 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D Genome" ;
definition: "Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017528 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KOMP2" ;
NIFRID:synonym "Knockout Mouse Phenotyping Project" ;
definition: "Knockout Mouse Phenotyping Project, JAX information about their contributions to KOMP2 project. Project to generate and phenotype single gene KO mouse strains from KOMP ES cell lines. Strains are phenotyped using protocols in pipeline designed by International Mouse Phenotyping Consortium. There are three NIH-funded phenotyping centers in United States: JAX, BaSH Consortium (Baylor College of Medicine, the Wellcome Trust Sanger Institute and MRC Harwell), and the DTCC Consortium (University of California at Davis, the Toronto Center for Phenogenomics, Children’s Hospital Oakland Research Institute (CHORI) and Charles River )." .
SCR:017531 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tree-Based Pipeline Optimization Tool" ;
NIFRID:synonym "Tree based Pipeline Optimization Tool" ;
NIFRID:abbrev "TPOT" ;
definition: "Software Python package to automate building of ML pipelines by combining flexible expression tree representation of pipelines with stochastic search algorithms such as genetic programming." .
SCR:017533 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rhesus Macaque Brain Atlases" ;
definition: "Atlases enable alignment of individual scans to improve localization and statistical power of results, and allow comparison of results between studies and institutions. Set of multi subject atlas templates is constructed specifically for functional and structural imaging studies of rhesus macaque." .
SCR:017534 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nonhuman Primate Reference Transcriptome Resource" ;
NIFRID:abbrev "NHPRTR" ;
definition: "Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species." .
SCR:017535 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Macaque Brain Resource" ;
definition: "Project to facilitate primate research by enabling neuroscience researchers to access collections either on-site or via the web for use in their own research programs. Collections of macaque brain tissue available to investigators worldwide to provide cost effective means for researchers to conduct de novo studies on non-human primate brain." .
SCR:017536 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pharmacogenetics of Nicotine Addiction Treatment" ;
NIFRID:synonym "Nicotine addiction treatment",
"Pharmacogenetics" ;
definition: "To identify role of pharmacokinetic and pharmacodynamic gene variation in nicotine dependence phenotypes, with focus on prospective smoking cessation and medication response." .
SCR:017537 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Whole Tale" ;
definition: "Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility." .
SCR:017538 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Project DARE" ;
NIFRID:synonym "Delivering Agile Research Excellence on European e-Infrastructures",
"project-dare" ;
NIFRID:abbrev "DARE" ;
definition: "EU data infrastructure with workflow connectivity layer. Common Workflow Language. Project pioneers methodologies and integrated set of supporting technologies that will transform European RIs productivity and rate of innovation when three challenges – extreme data, extreme computation and extreme complexity – are faced simultaneously." .
SCR:017541 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dynamo" ;
NIFRID:synonym "pyDynamo",
"python Dynamo" ;
definition: "Software tool for neuron timelapse reconstruction, registration and analysis for Dynamic Morphometrics." .
SCR:017543 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | CM1520 Cryostat" ;
definition: "Cryostat for routine histology and cryosectioning including critical applications such as Mohs surgery. Brain sectioning. Actively cooled quick freezing shelf with defrost function and refrigeration system are provided." .
SCR:017544 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Epigenomics_Workflow_on_Galaxy_and_Jupyter" ;
rdfs:label "Epigenomics Workflow on Galaxy and Jupyter" ;
NIFRID:synonym "REA pipeline" ;
definition: "Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter." .
SCR:017545 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Transcriptive" ;
definition: "Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results." .
SCR:017546 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Single Cell Developmental Database" ;
NIFRID:synonym "Single-Cell Developmental Database" ;
NIFRID:abbrev "SCDevDB" ;
definition: "Database for insights into single cell gene expression profiles during human developmental processes. Interactive database provides DE gene lists in each developmental pathway, t-SNE map, and GO and KEGG enrichment analysis based on these differential genes." .
SCR:017547 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:biobERt" ;
rdfs:label "BioBERT" ;
NIFRID:synonym "Bidirectional Encoder Representations from Transformers for Biomedical Text Mining" ;
definition: "Pre-trained biomedical language representation model for biomedical text mining. This repository provides fine-tuning codes of BioBERT, language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc." .
SCR:017548 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ALZPEDIA" ;
NIFRID:abbrev "AlzPedia" ;
definition: "Collection of brief summaries of various genes and proteins implicated in pathophysiology of Alzheimer’s disease and other neurodegenerative disorders. It will be expanded over time and updated periodically in order to reflect current state of knowledge." .
SCR:017551 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LabChart Reader" ;
NIFRID:synonym "LabChart Reader software",
"LabChart Reader software 8.1" ;
definition: "LabChart data analysis software creates a platform for all of your recording devices to work together, allowing you to acquire biological signals from multiple sources simultaneously and apply advanced calculations and plots as your experiment unfolds. LabChart Reader is free version of software that allows to analyse with some limitations. LabChart Reader doesn’t allow saving of data - export image only. Has data pad for analysis." .
SCR:017552 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rotor-Gene 6000 series software" ;
NIFRID:synonym "Rotor-Gene 6000 series software 1.7" ;
definition: "Rotor-Gene real-time analysis software system for ROTOR GENE 6000 REAL-TIME PCR machine. Software has been refined to provide an intuitive, Wizard driven interface, enabling flexibility and automation. Build-in extensive analysis, graphing and statistical functions. Unlimited use software license for Windows XP, Pentium IV (2GHz) or higher PC." .
SCR:017553 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MixitWin" ;
NIFRID:synonym "Mixit-Win" ;
definition: "Professional feed formulation software for Windows 10 and Macs by Agricultural Software Consultants Inc. Complete feed formulation solution for professional nutritionists and feed producers. Software offers ingredient databases for various domesticated and wild species." .
SCR:017554 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "vbSPT" ;
NIFRID:synonym "variational Bayes single particle tracking" ;
definition: "Software package for analysis of single particle diffusion trajectories, where diffusion constants switch randomly according to Markov process. Analytical tool to combine information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. Has ability to learn number of diffusive states directly from data, in addition to model parameters such as transition rates and diffusion constants." .
SCR:017555 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gsnap2Augustus" ;
definition: "Software tool to generate hints for Augustus in ab initio gene prediction using 2 step mapping by Gsnap." .
SCR:017556 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoEVM" ;
NIFRID:synonym "Autorun EVidence Modeler" ;
definition: "Software tool as Autorun Evidence Modeler. Requires EVidenceModeler (aka EVM) software which combines ab into gene predictions and protein and transcript alignments into weighted consensus gene structures." .
SCR:017557 a owl:NamedIndividual ;
rdfs:label "ExonerateTransferAnnotation" ;
NIFRID:synonym "Resource" ;
definition: "Software tool as pipeline to make anntotations using cDNA and CDS sequences." .
SCR:017558 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ATACseqMappingPipeline" ;
definition: "Software tool as pipeline to map ATAC-seq data to large genome, for example, for wheat. It splits large genome files into parts and do mapping and then finally merge them." .
SCR:017559 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HomoeologPrimer" ;
definition: "Software tool as script used to design primers for homoeologs, to amplify either homoeolog specific or all homoeologs." .
SCR:017560 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:parsmurf" ;
rdfs:label "parSMURF" ;
definition: "Open source software package as high performance computing imbalance aware machine learning tool for genome wide detection of pathogenic variants." .
SCR:017561 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Data Browser" ;
definition: "National research resource to provide interactive views of publicly available All of Us Research Program participant data including electronic health record data, biospecimens, surveys, and other measures taken at time of participant enrollment. Data platform will be open to researchers all over world and show data for groups of de-identified participants. Data is updated periodically." .
SCR:017562 a owl:NamedIndividual ;
rdfs:label "Willoughby–Hoye Python Scripts A-D" ;
definition: """Warning this group of python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain a bug. Please see PMID:31591889.
Script A. Write a Gaussian input file for each structure (local minimum) obtained from operation I (write-g09-inputs.py and variants thereof that use different functional and basis set combinations).
Script B. Check for redundant conformers or any that has an imaginary frequency (duplicate_conf_and_imag_freq-check.py).
Script C. Extract the NMR shielding tensor for a DFT-computed reference compound of interest (get-ref-shifts.py).
Script D. Perform the Boltzmann analysis to generate the weighted-averaged, referenced chemical shifts for each proton and carbon in the candidate structure (nmr-data_compilation.py).""" .
SCR:017563 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "MagVenture" ;
definition: "Danish, privately owned company specializing in non-invasive stimulation systems for treatment of major depressive disorder and neuroscience research based on use of transcranial magnetic stimulation." .
SCR:017564 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Olympus" ;
definition: "Japanese manufacturer of optics and reprography products specializing in microscopes and thermometers." .
SCR:017565 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TIGS" ;
NIFRID:synonym "Tumor Immunogenicity Score" ;
definition: "Repository to share analysis procedure, data and help readers or reviewers to know more detail of this work, reproduce or make use of results they are interested in." .
SCR:017566 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MIITRA atlas" ;
NIFRID:synonym "Multichannel Illinois Institute of Technology and Rush University Aging atlas" ;
definition: "Atlas for studies of older adult brain. Includes T1-weighted template of older adult brain and tissue probability maps. Exhibits high image sharpness, provides higher inter-subject spatial normalization accuracy compared to other standardized templates and similar normalization accuracy to well-constructed study-specific templates." .
SCR:017567 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Transcriptomics Explorer" ;
definition: "Software tool to visualize and analyze transcriptomics data and transcriptomic cell types for mouse and human, all directly in web browser. To explore gene expression heatmap across cell types in datasets, search for genes of interest, explore tSNE visualization, colored by cell types or expression of genes of interest, visualize dataset’s sampling strategy to see how cells and nuclei were sampled across brain areas, cortical layer, and other dimensions, find cell type of interest in one visualization and see its characteristics in different visualization.Used for Allen Brain Map Cell Types Database to Browse Data: Human - Multiple Cortical Areas, and Mouse - Cortex and Hippocampus." .
SCR:017568 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Federal University of Parana Center for Electron Microscopy core facility" ;
NIFRID:synonym "Brazil",
"Center for Electron Microscopy of the Federal University of Paraná" ;
NIFRID:abbrev "CME UFPR" ;
definition: "Laboratory to support scientific research in system of multi user operation of UFPR. Available equipment in electron microscopy." .
SCR:017569 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss | Stemi SV6 Stereomicroscope" ;
definition: """Carl Zeiss Stemi SV6 Stereomicroscope. Manufacturer: ZEISS.
Model: Stemi SV6 Stereomicroscope. This equipment is out of production. Available from the third party sellers.""" .
SCR:017571 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.25504/FAIRsharing.f2c119",
"DOI:10.48324",
"r3d100013638" ;
rdfs:label "Distributed Archives for Neurophysiology Data Integration" ;
NIFRID:abbrev "DANDI" ;
definition: "Free, cloud-based platform for publishing, sharing, and processing standardized neurophysiology data, primarily using the Neurodata Without Borders (NWB) format. Supported by the BRAIN Initiative, it enables researchers to collaborate, reuse datasets, and adhere to FAIR data principles." .
SCR:017572 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stress Mice Portal" ;
definition: "Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data." .
SCR:017573 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rjags" ;
NIFRID:synonym "RJAGS library" ;
definition: """Software package provides interface from R to JAGS library for Bayesian data analysis. Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
simulation.""" .
SCR:017574 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Refgenie" ;
rdfs:label "refgenie" ;
NIFRID:synonym "reference genome manager" ;
definition: "Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis." .
SCR:017575 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mysamplesize" ;
NIFRID:synonym "MySampleSize" ;
definition: "Software tool for experimental design, sample size determination and analysis by Tempest Technologies." .
SCR:017576 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciGraph" ;
definition: "Software tool to represent ontologies and data described using ontologies as Neo4j graph. Ontology serving middleware tool using Neo4J as base server, able to ingest ttl files, and serve them to quickly create services that can underpin autocomplete, term lookup and tree traversal." .
SCR:017577 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneATLAS" ;
NIFRID:synonym "Gene ATLAS",
"Gene Atlas" ;
definition: "Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits." .
SCR:017578 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "immuneXpresso" ;
definition: "Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions." .
SCR:017579 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Michigan Imputation Server" ;
NIFRID:synonym "Next Generation Genotype Imputation Service" ;
definition: "Web server to implement whole genotype imputation workflow for efficient parallelization of computationally intensive tasks. Service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity. Used to find haplotype segments and reference panel of sequenced genomes, assign genotypes at untyped markers, improve genome coverage, facilitate comparison and combination of studies that use different marker panels, increase power to detect genetic association, and guide fine mapping." .
SCR:017580 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH Figshare Archive" ;
NIFRID:synonym "Fig Share",
"Figshare",
"National Institute of Health",
"NIH",
"NIH Fig share",
"NIH Figshare" ;
definition: "Repository to make datasets resulting from NIH funded research more accessible, citable, shareable, and discoverable. Data submitted will be reviewed to ensure there is no personally identifiable information in data and metadata prior to being published and in line with FAIR -Findable, Accessible, Interoperable, and Reusable principles. Data published on Figshare is assigned persistent, citable DOI (Digital Object Identifier) and is discoverable in Google, Google Scholar, Google Dataset Search, and more.Complited on July,2020. Researches can continue to share NIH funded data and other research product on figshare.com." .
SCR:017581 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Computer Vision System Toolbox" ;
NIFRID:synonym "Computer Vision Toolbox",
"MATLAB Computer Vision System Toolbox" ;
definition: "Software tool to provide algorithms, functions, and apps for designing and testing computer vision, 3D vision, and video processing systems for MATLAB. You can perform object detection and tracking, as well as feature detection, extraction, and matching. For 3D vision, toolbox supports single, stereo, and fisheye camera calibration; stereo vision; 3D reconstruction; and lidar and 3D point cloud processing. Computer vision apps automate ground truth labeling and camera calibration workflows." .
SCR:017582 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Geneshot" ;
rdfs:label "Geneshot" ;
definition: "Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations." .
SCR:017583 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "HIRN Human Pancreas Analysis Consortium" ;
NIFRID:synonym "Human Pancreas Analysis Consortium" ;
NIFRID:abbrev "HIRN HPAC" ;
definition: "Consortium is investigating physical and functional organization of human islet tissue environment, cell-cell relationships within pancreatic tissue ecosystem, and contributions of non endocrine components (acinar, ductal, vascular, perivascular, neuronal, lymphatic, immune) to islet cell function and dysfunction. HPAC consists of research grants as well as the Human Pancreas Analysis Program (HPAP)." .
SCR:017584 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rayyan QCRI" ;
definition: "Software tool for screening papers for systematic reviews. Web and mobile app to help to expedite initial screening of abstracts and titles using process of semi automation while incorporating high level of usability." .
SCR:017585 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spyder " .
SCR:017586 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IMOTIONS | SMI RED500 Eye Tracker" ;
definition: "Screen based eye tracker that combines high-speed capabilities at 500 Hz." .
SCR:017588 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D DART" ;
NIFRID:synonym "3DNA-Driven DNA Analysis and Rebuilding Tool" ;
definition: "DNA structure modelling server. Web server for generating custom 3D structural models of DNA with control over local and global conformation." .
SCR:017589 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:patchdock" ;
rdfs:label "PatchDock" ;
definition: "Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles." .
SCR:017590 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RAMPAGE" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2021.Web based structural analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB. Used to visualize dihedral angles ψ against φ of amino acid residues in protein structure." .
SCR:017591 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:yasara" ;
rdfs:label "YASARA" ;
NIFRID:synonym "Yasara",
"Yet Another Scientific Artificial Reality Application" ;
definition: "Software tool to obtain structural guidance in biocatalytic investigations. Program for molecular visualising, modelling, and dynamics. Initial stage YASARA View is for free while higher stages YASARA Model, YASARA Dynamics, YASARA Structure require license fee. Program for Windows, Linux, MacOS and Android. YASARA View is available for free and contains all functions to explore macromolecular structure interactively." .
SCR:017592 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:amoebadb",
"r3d100012457" ;
rdfs:label "AmoebaDB" ;
definition: "Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers." .
SCR:017593 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biotite" ;
definition: "Software Python package bundling popular tasks in computational molecular biology, from sequence analysis to structural bioinformatics. Comprehensive library for computational molecular biology. Package features sequence and structure data analysis and editing functionality, support for common sequence and structure file formats, visualization capabilities, interfaces to external software (MSA software, BLAST, DSSP). Operating system(s): Windows, OS X, Linux." .
SCR:017594 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioAssay Express" ;
definition: "Web based tool for annotating bioassay protocols using semantic web terms. Enables searching, sorting, clustering and analyzing of assays without needing to read through original text. Exploits Common Assay Template based on underlying vocabularies and semantic standards from BioAssay Ontology, Drug Target Ontology, Cell Line Ontology and others. Users can identify similar assays and examine similarity of assays between and within organizations." .
SCR:017595 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JWatcher" ;
definition: "Software Java tool for quantitative analysis of behavior. Used to address any theoretical problem that requires complex sequence of actions to be scored by human observer. Runs on microcomputer providing Java Virtual Machine[TM] and has been tested on Windows[TM] and Macintosh[TM] systems. Legacy version (version 0.9) works on older systems (Macintosh OS-9 and Windows-98), while Version 1.0 works well on Macintosh OS-X and Windows XP systems. JWatcher Video works best on Windows XP systems and has reduced functionality running in Macintosh OS-X. JWatcher-Palm can be used to acquire data on Palm OS[TM] equipped device and analyze it on your main computer." .
SCR:017596 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Macquarie University; Sydney; Australia" ;
definition: "Public research university based in Sydney, Australia, in suburb of Macquarie Park. Founded in 1964 by New South Wales Government, it was third university to be established in metropolitan area of Sydney." .
SCR:017597 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CiteAs" ;
definition: "Software toool as search engine for academic software. Used to get correct citation for diverse research products including, software, datasets, preprints, and traditional articles to help creators of such products get full credit for their work." .
SCR:017598 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.25937" ;
rdfs:label "CoMSES Net" ;
NIFRID:synonym "Network for Computational Modeling in Social and Ecological Sciences" ;
definition: "Open community of researchers, educators, and professionals with goal of improving way we develop, share, use, and re-use agent based and computational models for study of social and ecological systems. Develops and maintains CoMSES Model Library, digital repository that supports discovery and good practices for software citation, digital preservation, reproducibility, and reuse." .
SCR:017599 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clowder" ;
definition: "Web based data management system that allows users to share, annotate, organize and analyze large collections of datasets. Software tool for creating some metadata about software tools automatically. Open source data management for long tail data. Provides support for extensible metadata annotation and distributed analytics for automatic curation of uploaded data. Open source software that can be customized and deployed on your own cloud." .
SCR:017600 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DOE CODE" ;
definition: "Software repository for DOE funded software tools. DOE software services platform and search tool for DOE-funded code – DOE CODE. Provides functionality for collaboration, archiving, and discovery of scientific and business software. DOE CODE replaces OSTI old software center, Energy Science and Technology Software Center (ESTSC).US Department of Energy new open source software services and search platform for sharing research software between national institutes." .
SCR:017601 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "code.gov" ;
definition: "Code repository for all government funded software. Designed to support reuse and public access to custom developed Federal source code. It requires new custom developed source code developed specifically by or for Federal Government to be made available for sharing and re-use across all Federal agencies. Provides tools to help government and public collaborate on open source projects." .
SCR:017602 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R3sw99",
"DOI:10.22002",
"DOI:10.25504/FAIRsharing.S09se7",
"r3d100012384" ;
rdfs:label "CaltechDATA" ;
definition: "Data and software repository from CalTech." .
SCR:017603 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID: grid.20861.3d; ISNI: 0000 0001 0706 8890; Crossref Funder ID: 100006961; Wikidata: Q161562;" ;
rdfs:label "California Institute of Technology; Pasadena; USA" ;
NIFRID:abbrev "CalTech",
"Caltech",
"CIT",
"Instituto de Tecnología de California" ;
definition: "Private doctorate granting research university in Pasadena, California. Known for its strength in natural science and engineering." .
SCR:017604 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Astrophysics Source Code Library" ;
NIFRID:abbrev "ASCL" ;
definition: "Registry for source codes of interest to astronomers and astrophysicists, including solar system astronomers, and lists codes that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. ASCL is indexed by SAO/NASA Astrophysics Data System (ADS) and Web of Science and is citable by using unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net ." .
SCR:017605 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:shinygeo" ;
rdfs:label "shinyGEO" ;
definition: "Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets." .
SCR:017606 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Eastern Connecticut State University; Connecticut; United States" ;
definition: "Public liberal arts university in Willimantic, Connecticut." .
SCR:017607 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100014573" ;
rdfs:label "swMath" ;
definition: "Repository of math software. Information service for mathematical software. Provides access to database of information on mathematical software and includes systematic linking of software packages with relevant mathematical publications. Database for references on mathematical software." .
SCR:017608 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ShinyLearner" ;
rdfs:label "ShinyLearner" ;
definition: """Software framework for performing benchmarks of machine learning classification algorithms.
Containerized benchmarking tool for machine-learning classification of tabular data.""" .
SCR:017609 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChemRICH" ;
definition: "Software tool for chemical similarity enrichment analysis of metabolomics datasets. Used in studies to uncover biological mechanisms in organisms under genetic or environmental stress in system biology manner or finding risk factors for chronic diseases in exposome wise association studies using blood specimens. Allows users to realize pathway analysis." .
SCR:017610 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:blood-exposome-db" ;
rdfs:label "Blood Exposome Database" ;
NIFRID:synonym "exposome",
"The Blood Exposome Database" ;
definition: "Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields." .
SCR:017611 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MoTrPAC Data Hub" ;
NIFRID:synonym "Molecular Transducers of Physical Activity Consortium Data Hub" ;
definition: "National research consortium designed to discover and perform preliminary characterization of range of molecular transducers that underlie effects of physical activity in humans. Used to study molecular changes that occur during and after exercise and to advance understanding of how physical activity improves and preserves health. Six year program into mechanisms of how physical activity improves health and prevents disease led by NIH Office of Strategic Coordination, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute on Aging, and National Institute of Biomedical Imaging and Bioengineering." .
SCR:017612 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EBRAINS Knowledge Graph" ;
NIFRID:synonym "EBRAINS Knowledge Graph (KG)",
"HBP Knowledge Graph",
"New Enabling Infrastructure for Neuroscience Knowledge Graph" ;
definition: "Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems." .
SCR:017613 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StatPackets" ;
definition: "Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together." .
SCR:017614 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PoloPlus USB Drive software" ;
NIFRID:synonym "PoloPlus USB Drive",
"Probit Or LOgit Plus USB Drive" ;
definition: "Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB." .
SCR:017616 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Purge_haplotigs" ;
definition: "Pipeline for reassigning primary contigs that should be labelled as haplotigs. Used for third generation sequencing based assemblies to automate reassignment of allelic contigs, and to assist in manual curation of genome assemblies." .
SCR:017617 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gene-conservation-informed-contig-alignment" ;
NIFRID:abbrev "GCICA" ;
definition: "Software tool for separation haplotigs from genome assembly. Method to separate haplotigs based on sequence similarity." .
SCR:017618 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:blobtools" ;
rdfs:label "Blobtools" ;
NIFRID:synonym "BlobTools" ;
definition: "Software tool as modular command line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Used for interrogation of genome assemblies. Assists in primary partitioning of data, leading to improved assemblies, and screening of final assemblies for potential contaminants." .
SCR:017619 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:sniffles" ;
rdfs:label "Sniffles" ;
definition: "Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates." .
SCR:017620 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ngmlr" ;
rdfs:label "Ngmlr" ;
NIFRID:synonym "coNvex Gap-cost alignMent for Long Reads" ;
NIFRID:abbrev "NGMLR" ;
definition: "Software tool as long read mapper designed to align PacBio or Oxford Nanopore reads to reference genome and optimized for structural variation detection." .
SCR:017621 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Marvel " ;
definition: "Software set of tools that facilitate overlapping, patching, correction and assembly of noisy long reads." .
SCR:017622 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:SMARTdenovo",
"biotools:SMARtdenovo" ;
rdfs:label "SMARTdenovo" ;
definition: "Software tool as de novo assembler for PacBio and Oxford Nanopore data. It produces assembly from all-vs-all raw read alignments without error correction stage. Allows to read overlapping, rescue missing overlaps, identify low-quality regions and chimaera and produce better consensus." .
SCR:017623 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LTR_retriever" ;
NIFRID:synonym "Long Terminal Repeat retriver" ;
definition: "Software package for identification of long terminal repeat retrotransposons (LTR-RTs). Removes false positives from initial software predictions. Achieves very high specificity, accuracy, and precision without significantly sacrificing sensitivity, hence significantly outperforming existing methods. Can construct LTR libraries directly from self-corrected PacBio reads prior to genome assembly." .
SCR:017624 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Computing Genome Assembly Likelihoods" ;
NIFRID:abbrev "CGAL" ;
definition: "Software tool for computing genome assembly likelihoods.Computes likelihood of reads with respect to assembly and statistical model which can be used as metric for evaluating assemblies. Novel likelihood based approach to assembly assessment in absence of ground truth." .
SCR:017625 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_04068" ;
rdfs:label "Recognition of Errors in Assemblies using Paired Reads" ;
NIFRID:abbrev "REAPR" ;
definition: """Software tool to identify errors in genome assemblies without need for reference sequence.
Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.""" .
SCR:017626 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:telescope" ;
rdfs:label "Telescope" ;
definition: "Open source web application that tracks progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. Allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted." .
SCR:017628 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NINscope microscope" ;
NIFRID:abbrev "NIN scope" ;
definition: "Miniaturized microscope that allows imaging from two brain regions. Integrates inertial measurement unit (IMU) and optogenetic LED driver. Used to perform dual miniscope recordings in multiple configurations and works with cross-platform software enabling operation on MSWindows, MacOS and Linux." .
SCR:017629 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LAN toolbox" ;
NIFRID:synonym "EEG Toolbox",
"Laboratory of Analysis in Neurosciences Toolbox" ;
NIFRID:abbrev "LANtoolbox" ;
definition: "Software toolbox for neuroscientist data (EEG and reaction time for time being). Used to create shared language among different algorithms and softwares in this field (e.g. Fieldtrip, Eeglab, Chronux, Brainstorm, etc), in order to facilitate implementation of experimental analysis by users. Code and scripts for EEG analysis for MATLAB." .
SCR:017631 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lab Streaming Layer" ;
NIFRID:abbrev "LSL" ;
definition: "System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording." .
SCR:017632 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iBright Analysis Software" ;
definition: "Software for organizing and analyzing blot and gel images captured on iBright Imaging Systems. Available as desktop version PC and Mac OS compatible and cloud-based version accessible via web browser through Connect platform." .
SCR:017633 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:tGS-GapCloser" ;
rdfs:label "TGS-GapCloser" ;
definition: "Software tool that uses long reads to enhance genome assembly. Fast and accurate gap closing software tool that uses low coverage of error-prone long reads generated by third generation sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs for large genomes." .
SCR:017634 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mBT | mBrainTrain Smarting PRO 32" ;
definition: "24 channel mobile electroencephalographic recording system. Supports synchronization with other sensors and simultaneous multi amplifier streaming via labstreaming layer. Wearable device that features motion sensors so body and head movements can be detected." .
SCR:017636 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Structure Harvester" ;
NIFRID:synonym "StructureHarvester" ;
definition: """Web based program for collating results generated by program STRUCTURE. Provides assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of number of genetic groups that best fit data. Reformats data for use in downstream programs, such as CLUMPP.It is complement for using software Structure in genetics population.
Website and program for visualizing STRUCTURE output and implementing Evanno method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.""" .
SCR:017637 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:structure",
"SCR_002151",
"SCR_021634" ;
rdfs:label "STRUCTURE" ;
NIFRID:synonym "Structure",
"structure" ;
definition: "Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms." .
SCR:017638 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Webcutter" ;
NIFRID:synonym "Webcutter 2",
"Webcutter 2.0" ;
definition: """Software tool to find restriction endonucleases. Helps restriction map nucleotide sequences.
Tool with customizable interface, platform independent accessibility, interfaces to NCBI's GenBank, DNA sequence database, and NEB's REBase, and restriction enzyme database. In addition to restriction site mapping, Webcutter 2 also performs degenerate digests, including option of finding restriction sites that can be introduced into sequence by silent mutagenesis.""" .
SCR:017639 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LeafCutter" ;
definition: "Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs)." .
SCR:017640 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_017675" ;
rdfs:label "MonkeyCBP" ;
NIFRID:synonym "Monkey Connectivity Based Parcellation; MonkeyCBP: A toolbox for connectivity-based parcellation of monkey brain" ;
definition: "Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community." .
SCR:017641 a owl:NamedIndividual ;
rdfs:label "paint.net" ;
NIFRID:synonym "Paint.NET",
"paint.net 4.2.8" ;
definition: "Software tool as image and photo editor for PCs that run Windows. Features user interface with support for layers, unlimited undo, special effects, and variety of useful and powerful tools." .
SCR:017642 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:Racon",
"biotools:Racon",
"OMICS_25714" ;
rdfs:label "Racon" ;
definition: "Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies." .
SCR:017643 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:hic-pro" ;
rdfs:label "HiC-Pro" ;
definition: "Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps." .
SCR:017644 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LACHESIS" ;
NIFRID:synonym "Ligating Adjacent Chromatin Enables Scaffolding In Situ" ;
definition: "Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies." .
SCR:017645 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:PAStEClassifier" ;
rdfs:label "PASTEClassifier" ;
NIFRID:synonym "PASTEC",
"Pseudo Agent System for Transposable Elements Classification" ;
definition: "Software tool for automatic transposable element classification. Used for searching for structural features and similarity to classify transposable elements." .
SCR:017646 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:gemoma" ;
rdfs:label "GeMoMa" ;
NIFRID:synonym "Gene Model Mapper" ;
definition: "Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species." .
SCR:017647 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:transDecoder",
"OMICS_10852" ;
rdfs:label "TransDecoder" ;
NIFRID:synonym "Find Coding Regions Within Transcripts" ;
definition: "Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV." .
SCR:017648 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:GeneMarkS-t" ;
rdfs:label "GeneMarkS-T" ;
definition: "Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark." .
SCR:017650 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:MCScan" ;
rdfs:label "MCScan" ;
NIFRID:synonym "Multiple Collinearity Scan" ;
definition: "Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format." .
SCR:017651 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Multiple_Myeloma_survival_prediction" ;
rdfs:label "Multiple Myeloma survival predictor" ;
definition: "Dockerized environment for winning algorithm in 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3." .
SCR:017654 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CaseViewer" ;
NIFRID:synonym "CaseViewer 2.0",
"CaseViewer 2.3" ;
definition: "Software tool from 3DHISTECH Ltd. designed for work with whole slide images. Digital microscope application for supporting histopathological diagnostic workflow and microscope examination process. Advanced slide viewing software for Windows and Mac used in clinical pathology and research." .
SCR:017655 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cancer Dependency Map Portal" ;
NIFRID:synonym "Cancer Dependency Map Project",
"Cancer DepMap",
"Dependency Map Portal",
"Dependency Map portal" ;
NIFRID:abbrev "DepMap Portal" ;
definition: "Portal for identifying genetic and pharmacologic dependencies and biomarkers that predicts them by providing access to datasets, visualizations, and analysis tools that are being used by Cancer Dependency Map Project at Broad Institute. Project to systematically identify genes and small molecule dependencies and to determine markers that predict sensitivity. All data generated by DepMap Project are available to public under CC BY 4.0 license on quarterly basis and pre-publication." .
SCR:017656 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Journal Citation Reports" ;
NIFRID:abbrev "JCR" ;
definition: "Web tool with systematic, objective means to critically evaluate journals, with quantifiable, statistical information based on citation data. Provides information about academic journals in natural sciences and social sciences, including impact factors in database integrated with Web of Science. Sourced from Web of Science Core Collection,citation index on Web of Science platform." .
SCR:017657 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Clarivate Analytics" ;
definition: "Data analytics company that operates a collection of services: Web of Science (EndNote, InCites, Journal Citation Reports, Publons, Kopernio), Cortellis, Derwent, Derwent World Patents Index, CompuMark, MarkMonitor, Techstreet, Publons, EndNote, Kopernio, and ScholarOne. Deliver critical data, information, workflow solutions and deep domain expertise to innovators everywhere." .
SCR:017658 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013680" ;
rdfs:label "GeneLab" ;
NIFRID:synonym "GeneLab Data System" ;
NIFRID:abbrev "GLDS" ;
definition: "Omics database for spaceflight experiments. Interactive, open access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Enables exploration of molecular network responses of terrestrial biology to space environment. Contains curated omics data, metadata and radiation dosimetry for model organisms. Supports standard guidelines for submission of datasets, MIAME for microarray, ENCODE Consortium Guidelines for RNA-seq and MIAPE Guidelines for proteomics." .
SCR:017659 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:Bio2BEL",
"biotools:bio2bEL" ;
rdfs:label "Bio2BEL" ;
definition: "Software Python package enabling Biological Expression Language to act as semantic integration layer for multi modal and multi scale data sets in life sciences. Used for integrating biological databases and structured data sources in BEL. Has ability to support curation of pathway mappings, integration of pathway databases, and machine learning applications." .
SCR:017660 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pybel" ;
rdfs:label "PyBEL" ;
NIFRID:synonym "pybel",
"Python Biological Expression Language" ;
definition: "Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J." .
SCR:017661 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biological Expression Language" ;
NIFRID:abbrev "BEL" ;
definition: "Language for representing scientific findings in life sciences in reusable, shareable, and computable form. Captures causal and correlative relationships in context, where context can include information about biological and experimental system in which relationships were observed, supporting publications cited and process of curation." .
SCR:017662 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bioNix" ;
rdfs:label "BioNix" ;
definition: "Software tool for reproducible bioinformatics that unifies workflow engines, package managers, and containers. Implemented as lightweight library on top of Nix deployment system. Bioinformatics workflows in functional Nix language." .
SCR:017664 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Condor" ;
definition: "Condor project maintains, distributes, and supports variety of computing systems that are deployed by commercial and academic interests world wide. Explores social and technical problems of cooperative computing on scales ranging from desktop to world wide computational Grid." .
SCR:017666 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BrainMaker" ;
definition: "Software tool to automatically align sections to visualize brains in 3D. Assists with cell mapping, cytoarchitectonics and other areas requiring characterization of neuronal circuitry to create comprehensive anatomical reference. Automatically creates full resolution, 3D reconstructions of entire brain or any organ from serial sections of whole slide images. Allows to view cells, structures, and lesions, locate neurons expressing particular gene or visualize axonal projections of specific neurons with full anatomical context." .
SCR:017667 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stereo Investigator - Whole Slide Edition " ;
definition: "Software tool for quantitative analysis using stereology on whole slide images. Used to analyze whole slide image data. Includes number, length, area and volume analyses." .
SCR:017668 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stereo Investigator - Cleared Tissue Edition" ;
definition: "Software tool for unbiased stereology to be used on cleared tissue. Used to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes. Includes number, length, area and volume analyses." .
SCR:017669 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Worm Lab" ;
definition: "Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays." .
SCR:017670 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vesalius" ;
definition: "Software tool as ultra fast, multi channel resonant scanning laser confocal microscope system for rapid 2D and 3D slide scanning, and cleared tissue imaging. System for imaging of slide mounted specimens and cleared tissue imaging. Utilizes strip mosaic scanning process to rapidly and accurately collect fluorescent image data while stage moves specimen continuously in y-axis." .
SCR:017671 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MicroDynamix" ;
definition: "Software tool for dendritic spine analysis that enables to visualize and quantify spine morphology over time. After loading image data acquired at different time points from in vivo and in vitro imaging sessions, automatically aligns images in 3D, then reconstructs dendritic branches, detects dendritic spines, and identifies important metrics such as length, thickness, and overall number, for accurate quantitative comparison." .
SCR:017672 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SQLite" ;
definition: "Relational database management system contained in C library. SQLite is not client server database engine but it is embedded into the end program." .
SCR:017673 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BootstrappingWithoutReplacement" ;
NIFRID:synonym "Bootstrapping coupled with DESeq2" ;
definition: "Software tool to dig out more robust and reliable differentially expressed genes between two groups. Samples from different groups will be re-sampled randomly associated with total number of samples." .
SCR:017674 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vesselucida Explorer" ;
definition: "Vesselucida Explorer is Vesselucida 360 companion analysis software, to perform analyses. Provides vasculature specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more." .
SCR:017676 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:PEMA" ;
rdfs:label "PEMA " ;
NIFRID:synonym "Pipeline for Environmental DNA Metabarcoding Analysis" ;
definition: "Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution." .
SCR:017677 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cytoHubba" ;
NIFRID:synonym "cytoHubba 1.6" ;
definition: "Software tool for identifying hub objects and sub-networks from complex interactome. Predicts and explore nodes and subnetworks in given network by several topological algorithms. Provides interface to analyze topology of protein-protein interaction networks, such as human, yeast, rat, mouse, fly etc. Plugin works with Cytoscape 2.6 or above, which requires Java 1.5 or above." .
SCR:017679 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Google Sheets" ;
NIFRID:synonym "Spreadsheets" ;
definition: "Spreadsheet program included as part of free, web-based software office suite offered by Google within its Google Drive service. Service also includes Google Docs and Google Slides, word processor and presentation program respectively." .
SCR:017680 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:GADMA" ;
rdfs:label "GADMA" ;
NIFRID:synonym "Genetic Algorithm for Demographic Model Analysis" ;
definition: "Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data." .
SCR:017681 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ISB Cancer Genomics Cloud" ;
NIFRID:synonym "Institute for Systems Biology Cancer Genomics Cloud" ;
NIFRID:abbrev "ISB-CGC" ;
definition: "Web tool as flexible cloud-based platform for cancer genomics research. Platform that serves as large-scale repository and provides computational infrastructure necessary to carry out cancer genomics research at unprecedented scales. ISB-CGC is providing access to TCGA data and computation on Google Cloud Platform." .
SCR:017682 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hMRI-toolbox" ;
definition: "Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis." .
SCR:017683 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TCGAbiolinks" ;
NIFRID:synonym "Cancer Genome Atlas (TCGA) biolinks" ;
definition: "Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R." .
SCR:017684 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "webchem" ;
NIFRID:synonym "Chemical Information from Web" ;
definition: "Open source software package for R programming language that is used to acquire chemical information from online data sources. Package contains functions that allow programmer to interact with webpages and APIs to retrieve chemical information." .
SCR:017685 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3" ;
rdfs:label "Rhode Island INBRE Molecular Informatics Core Facility" ;
NIFRID:synonym "Rhode Island INBRE Molecular Informatics",
"RI-INBRE Bioinformatics Core; RI Genomics and Sequencing Center" ;
definition: "Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research." .
SCR:017686 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_8",
"SCR_017707" ;
rdfs:label "Vermont University Genetics Network Bioinformatics Core Facility" ;
NIFRID:synonym "Vermont Genetics Network Bioinformatics Core" ;
definition: "Core provides expertise in biostatistics, microarray data analysis, proteome informatics, next generation sequencing data analysis, functional analysis, database development and information technology, including data storage infrastructure and high performance computing. Working closely with VGN Proteomics Facility, offers investigators experimental design consultations, comprehensive data analysis, data management and publishing, and manuscript and grant support. Core personnel also engage in teaching and training activities for data analysis and compute resources necessary for VGN network investigators. Our goal is to provide network researchers with bioinformatics expertise." .
SCR:017687 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_63",
"SCR_017706" ;
rdfs:label "New York State Advanced Genomic Technology Core Facility" ;
NIFRID:synonym "Advanced Genomic Technologies" ;
definition: "Advanced Genomic Technologies Cluster provides next-generation sequencing and Sanger sequencing. Next-generation sequencing services are provided using Illumina MiSeq and NextSeq sequencers. Services are available for amplicon re-sequencing, viral or microbial whole genome sequencing and 16S microbiome sequencing. Sanger DNA Sequencing can be performed on DNA templates such as PCR products and plasmids using ABI 3730xl and ABI3130xl instruments." .
SCR:017688 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_11",
"SCR_017704" ;
rdfs:label "Vermont University Center for X-Ray Crystallography Core Facility" ;
NIFRID:synonym "Center for X-Ray Crystallography" ;
NIFRID:abbrev "CXX" ;
definition: "Core for high resolution structural biology at the University of Vermont. X-ray crystallography allows biological and biomedical researchers to visualize proteins, RNA, DNA and their complexes at atomic resolution. The molecular details of specimens as small as DNA binding domains and as large as the ribosome have been elucidated via this powerful method. The CXX provides resources for all stages of macromolecular structure determination." .
SCR:017689 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_71",
"SCR_017711" ;
rdfs:label "Yale University DNA Analysis on Science Hill Core Facility" ;
NIFRID:synonym "DNA Analysis Facility on Science Hill" ;
definition: "Core supports DNA Sequencing of PCR, Plasmid, BAC and Fosmid templates, Fragment Analysis of Microsatellites, AFLP, t-RFLP, SHAPE Experiments and Human Cell Line Authentication." .
SCR:017690 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_79",
"SCR_017708" ;
rdfs:label "Brown University Transgenic and Gene Targeting Core Facility" ;
NIFRID:synonym "Mouse Transgenic and Gene Targeting Facility" ;
NIFRID:abbrev "MTGTF" ;
definition: "MTGTF is to support the investigators in using genetically modified mouse models in Brown University, affiliated hospitals and academic institutions in Rhode Island and other states. Provides services of molecular design and generation of transgenic and knock-out mouse models as well as general advice on use and management of such models. Conventional ES cell gene-targeting system is employed to serve as alternative or to fill the limitations of CRISPR/Cas9 system. Routine services include genotype analysis, sperm or embryo cryopreservation and storage, rederivation, in vitro fertilization (IVF). Other services, such as mouse vasectomy, embryo transfer, colony scale-up, intracytoplasmic sperm injection (ICSI) are also available. New services requiring MTGTF resources can be created through request." .
SCR:017691 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_51",
"SCR_017709" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Antibody and Bioresource Core Facility" ;
NIFRID:synonym "Antibody and Bioresource Core Facility" ;
NIFRID:abbrev "ABCF" ;
definition: "ABCF can provide MAbs from established hybridomas for RESEARCH PURPOSES ONLY, can assist in generating MAbs, offers a weekly mycoplasmal contamination screening service for tissue culture samples, distributes cell lines developed at Memorial Sloan Kettering Cancer Center and Rockefeller University." .
SCR:017692 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_105",
"ABRF_822",
"SCR_017713",
"SCR_017925" ;
rdfs:label "NYU School of Medicine Rodent Genetic Engineering Laboratory Core Facility" ;
NIFRID:synonym "New York University Langone Medical Center Rodent Genetic Engineering Laboratory",
"New York University School of Medicine Langone Health Rodent Genetic Engineering Laboratory Core Facility",
"NYU Langone Rodent Genetic Engineering Laboratory" ;
definition: "Core to apply advanced molecular genetic techniques in rodent models of physiology and disease. Generates novel mutant mouse strains by using gene targeting in embryonic stem cells (ESCs) and by developing novel methods of modifying rodent genomes and assaying genetically modified cells in vivo.Offers sperm and embryo cryopreservation and storage technologies for strain preservation and recovery." .
SCR:017693 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_111",
"SCR_017714" ;
rdfs:label "Weill Cornell Medical College Microscopy and Image Analysis Core Facility" ;
NIFRID:synonym "Imaging Core Facility",
"Microscopy and Image Analysis Core Facility" ;
definition: "Core sassist users with all their microscopic imaging needs, from the conception of idea, to final image analysis and presentation. Offers regular widefield microscopes for fluorescence and brightfield imaging, laser scanning microscopes (confocal and multiphoton), super-high resolution microscope (Zeiss Airyscan), automated high content optical microscopy, and electron microscopy.Provides access to several image analysis software packages, and image analysis workstations that are optimized for handling large amounts of imaging data. Available software include MetaMorph, MetaXpress and Imaris, Fiji/ImageJ." .
SCR:017694 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_102",
"SCR_017710" ;
rdfs:label "Rockefeller University Flow Cytometry Resource Center Core Facility" ;
NIFRID:synonym "Flow Cytometry Resource Center" ;
NIFRID:abbrev "FCRC" ;
definition: "Core offers researchers multi laser and multi color flow cytometry sorters and analyzers, including spectral and imaging flow cytometers." .
SCR:017695 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_113",
"SCR_017715" ;
rdfs:label "Albany University RNA Epitranscriptomics and Proteomics Resource Core Facility" ;
NIFRID:synonym "RNA Epitranscriptomics and Proteomics Resources" ;
NIFRID:abbrev "REPR" ;
definition: "Resource offers range of mass spectrometry instrumentation, expertise in analysis of RNA, RNA modifications, and proteins involved in RNA metabolism/regulation, supports projects involving analysis of biomolecules, metabolites, and small synthetic molecules, provides consulting on experimental design, sample preparation and data interpretation, whole project development and grant writing contributions." .
SCR:017696 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_82",
"SCR_017712" ;
rdfs:label "University of Delaware CBCB Bioinformatics Data Science Core Facility" ;
NIFRID:synonym "CBCB Bioinformatics Core",
"Center for Bioinformatics and Computational Biology Bioinformatics Core" ;
definition: "CBCB Bioinformatics Data Science Core builds upon infrastructure of the Center for Bioinformatics and Computational Biology. Delaware Biotechnology Institute , Delaware Data Science Institute, and Protein Information Resource. Core helps with planning your research or analyzing your current data. Services:Consultation and Collaboration, Proposal Assistance,Training, Bioinformatics Software, Computational Hardware, Database and Web Services, Next Gen Analysis, Custom Analysis." .
SCR:017697 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_118",
"SCR_017719" ;
rdfs:label "McGill University Advanced BioImaging Facility (ABIF)" ;
NIFRID:synonym "Advanced BioImaging Facility",
"McGill University Advanced BioImaging Core Facility" ;
NIFRID:abbrev "ABIF" ;
definition: "Core offers light microscopy platforms providing guidance to researchers with their projects from sample preparation to data analysis, expertise in cellular imaging including live cell imaging, FRAP, Fluorescence Lifetime Imaging Microscopy (FLIM), FRET, FCS, image correlation spectroscopy, TIRF, spectral imaging, lattice lightsheet, stimulated emission depletion (STED), high content screening, cellular image analysis, and custom image analysis, consultations, image processing, image analysis and preparation of data for publication." .
SCR:017698 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_125",
"SCR_017717" ;
rdfs:label "Connecticut University Health Center Flow Cytometry Core Facility" ;
NIFRID:synonym "UConn Health Flow Cytometry Core" ;
definition: "Facility provides flow cytometric analysis and cell sorting services. Located on 6th floor of E building in room E6014, consists of lab space, complete with fume hood, centrifuge, and sink space and has instruments available for cellular analysis and cell sorters." .
SCR:017699 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_132",
"SCR_017720" ;
rdfs:label "Massachusetts University Medical School Xray Crystallography Core Facility" ;
NIFRID:synonym "X-ray Crystallography Core" ;
definition: "Core provides instrumentation for determination of crystal structures using X-ray diffraction techniques. System in Biotech II is comprised of RU300HR X-ray generator, Osmic optics, MAR Image Plate System and Oxford liquid nitrogen cryogenic crystal cooler. LRB includes MicroMax-007 HF Microfocus rotating anode X-ray generator, Osmic optics and Saturn HG CCD detector mounted on AFC11 4-axis goniometer. Sample crystals can be cooled to -180˚C with CSCOBRA Cryogenic system. This system permits very rapid and accurate diffraction data collection." .
SCR:017700 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_62",
"SCR_017705" ;
rdfs:label "Albert Einstein College of Medicine Analytical Imaging Core Facility" ;
NIFRID:synonym "Analytical Imaging Facility" ;
NIFRID:abbrev "AIF" ;
definition: "Analytical Imaging Facility provides state of art methods in modern light and electron microscopy imaging to biomedical scientists with all levels of expertise. Available techniques include Electron microscopy: TEM, SEM, and sample preparation , Light microscopy: confocal, multiphoton, fluorescence, and bright-field imaging , Image analysis: Volocity, Imaris, Imod, Quant Center and ImageJ." .
SCR:017701 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_129",
"SCR_017716" ;
rdfs:label "Massachusetts University Medical School Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core" ;
NIFRID:abbrev "BioCore" ;
definition: "Core to evaluate, select, and implement computational solutions for analysis of biological data." .
SCR:017702 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_133",
"SCR_017721" ;
rdfs:label "Massachusetts University Medical School Deep Sequencing Core Facility" ;
NIFRID:synonym "Deep Sequencing Core Facility" ;
definition: "Facility offers high throughput sequencing and library building services for UMass campuses and outside customers. Operates several types of Illumina next gen sequencers, and is closely integrated with PacBio Core Enterprise and Molecular Biology Core Labs." .
SCR:017703 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_115",
"SCR_017718" ;
rdfs:label "CES Genome Quebec Core Facility" ;
NIFRID:synonym "Genome Quebec Center of Expertise and Services" ;
definition: "Core for full DNA and RNA analysis services. Canada's largest integrated provider of sequencing, genotyping and biochips services. Offers scientific community around the world genomic services in support of research in human health, agrifood, forestry and sustainable development." .
SCR:017724 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_145" ;
rdfs:label "Massachusetts University Medical School Machine Shop Core Facility" ;
NIFRID:synonym "Machine Shop" ;
definition: "Core includes three shops: Custom Machine, Harvard Medical School SEAS Scientific Instrument and WPI Manufacturing Labs. Service include consultation, design, manufacturing, modifications, and instrument repairs." .
SCR:017725 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_143" ;
rdfs:label "Massachusetts University Medical School Drosophila Resource Core Facility" ;
NIFRID:synonym "Drosophila Resource Facility" ;
definition: "Facility provides labs with media necessary for Drosophila research. Includes Low Yeast Brown Food, High Yeast Brown Food, and Yellow Food media available in narrow vials, wide vials, and bottles." .
SCR:017726 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_150" ;
rdfs:label "Massachusetts University Medical School Morphology Core Facility" ;
NIFRID:synonym "Morphology Core" ;
definition: "Histology lab that provides histology services in support of investigators at UMass Medical School, including routine histological preparations,special stains,immunohistochemistry,frozen sections." .
SCR:017727 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_151" ;
rdfs:label "Massachusetts University Medical School RNAi Core Facility" ;
NIFRID:synonym "RNAi Core Facility" ;
NIFRID:abbrev "RNAi Core" ;
definition: "Facility houses complete collections of human and mouse lentiviral short hairpin RNA (shRNA) libraries from Open Biosystems/GE Dharmacon, Mammalian Gene Collection (MGC) cDNA Library, and human and mouse CRISPR/Cas9 GeCKO v2 libraries from Addgene." .
SCR:017728 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_147" ;
rdfs:label "Massachusetts University Medical School Radio Labeling Small Animal Translational Imaging Core Facility" ;
NIFRID:synonym "UMMS Radio Labeling Small Animal Imaging Core Facility" ;
definition: "Core provides consultation services to assist researchers in designing imaging studies, limited labeling services and data acquisition and analysis.Core offers following services:Single Photon Computerized Tomography (SPECT),Positron Emission Computerized Tomography (PET), X-Ray Computerized Tomography (CT),NIR Optical Imaging of small animals." .
SCR:017729 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_146" ;
rdfs:label "Massachusetts University Medical School Transgenic Animal Modeling Core Facility" ;
NIFRID:synonym "Transgenic Animal Modeling Core" ;
NIFRID:abbrev "TAMC" ;
definition: "Core to produce genetically modified mice, rats, and stem cells for the UMMS Scientific Community.Composed of two facilities: Animal Modeling Facility and Gene Targeting and Stem Cell Facility." .
SCR:017730 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_170" ;
rdfs:label "Maine Medical Center Research Institute Proteomics and Lipidomics Analysis Core Facility" ;
NIFRID:synonym "MMRC Proteomics and Lipidomics Analysis" ;
definition: "Core provides protein and small molecule structural and functional analysis, and quantitation using technologies and software applications. Services in Nano-liquid chromatography,Protein identification and quantitation using SWATH,Protein post translational modification identification,Lipid profiling and identification (MS/MSALL),Targeted multiple reaction monitoring (MRM) for lipids." .
SCR:017731 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_186" ;
rdfs:label "University of Texas MD Anderson Cancer Center Proteomics Core Facility" ;
NIFRID:synonym "Proteomics Facility" ;
definition: "Facility provides mass spectrometry analysis of proteins. Provides access to mass spectrometry based proteomics technologies and services including Protein Identification, Molecular Weight Determination, Quantitative Protein Analysis, Post-translational Modification Analysis, LC or LC-MS Analysis, Equipment Usage, Additional Data Analysis:Bioinformatics, statistics, pathway analysis and Assistance preparing materials for manuscripts or grants.Consultations for custom assays for other MS Services are also available." .
SCR:017732 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_179" ;
rdfs:label "Rockefeller University Structural Biology Resource Center Core Facility" ;
NIFRID:synonym "Structural Biology Resource Center" ;
NIFRID:abbrev "SBRC" ;
definition: "Core for protein expression and purification as well as all equipment needed for determination of three dimensional structures of biological macromolecules via X-ray crystallography. Houses Rigaku/MSC microMax 007HF generator for X-ray diffraction data collection, equipped with Varimax optics, X-stream 2000 cryosystems and two RaxisIV++ detectors.Also available is stereomicroscope, Nikon SMZ18, for crystal tray observations and crystal mounting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017733 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_184" ;
rdfs:label "University of North Dakota School of Medicine and Health Sciences Imaging Core Facility" ;
NIFRID:synonym "Imaging Core" ;
definition: "Provides advanced instrumentation for researchers interested in investigating biological processes at cellular, sub cellular and molecular level.Instrumentation include Confocal Microscope Systems :Zeiss LSM-510 Meta Confocal Microscope, Olympus FV1000 MPE Basic Multiphoton Microscope;Brightfield/Fluorescence: Nikon Eclipse TE300 (inverted) Fluorescent Microscope, Nikon Eclipse 80i (upright) Fluorescent Microscope, Leica Thunder Imager; TIRF Systems:Olympus TIRF Microscope; Transmission Electron Microscopy:Hitachi 7500 TEM, RCM MTX Ultramicrotomes;Scanning Electron Microscopy:Hitachi 4700 Field Emission SEM, Denton Desk II Sputter and Turbo-sputter Coaters.Light and electron microscopic facilities, complete with ancillary support equipment, are located in close proximity to each other within suite of rooms housed in medical school." .
SCR:017734 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_188" ;
rdfs:label "Idaho University IBEST Computational Resources Core Facility" ;
NIFRID:synonym "IBEST Computational Resources Core" ;
NIFRID:abbrev "CRC" ;
definition: "Provides evolutionary and computational biology investigators with computing and large data storage capacity for use in analyzing and managing large volumes of research data. Core contains advanced mix of high performance computing clusters, servers and data storage components, knowledge and technical skills required to compress years of analysis into days." .
SCR:017735 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_193" ;
rdfs:label "Beth Israel Deaconess Medical Center Mass Spectrometry Core Facility" ;
NIFRID:synonym "BIDMC Mass Spectrometry" ;
definition: "Provides servies in mass spectrometry, proteomics, metabolomics and lipidomics. Services include Thermo Orbitrap Elite and Thermo QExactive HF Orbitrap microcapillary LC-MS/MS:Protein identification, Post-translational modification site mapping,Relative quantification: Label-free, SILAC, TMT, etc.;AB/SCIEX 5500 QTRAP LC-MS/MS:Polar metabolomics profiling,13C/15N metabolic flux analysis;Thermo QExactive Plus/HF Orbitrap LC-MS/MS:Untargeted Lipidomics profiling, Untargeted Metabolomics Profiling." .
SCR:017736 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_203" ;
rdfs:label "Nebraska University Medical Center Flow Cytometry Research Core Facility" ;
definition: "Provides central location for flow cytometry instrumentation and education. Services include Flow Cytometry,Cell sorting, data analysis, training. Software packages to analyze data include ModFit LT, BD FACSDiva v6, Cell Quest Pro, and FlowJo vX, from facility workstations." .
SCR:017737 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_213" ;
rdfs:label "MIT KIICR Biopolymers and Proteomics Core Facility" ;
NIFRID:synonym "KI Swanson Biotechnology Center Biopolymers and Proteomics Core Facility" ;
definition: "Facility provides integrated synthetic and analytical capabilities for biological materials, including proteins, peptides, and nanoparticles, range of technical expertise and instrumentation. Access is available to all members of MIT community. Priority access is given to KI members, NCI-funded research projects and other contributing user groups in recognition of funding support. In special circumstances, access may be available to non-MIT users." .
SCR:017738 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_221" ;
rdfs:label "West Virginia University Flow Cytometry and Single Cell Core Facility" ;
NIFRID:synonym "FCSCCF",
"WVU Flow Cytometry and Single Cell Core Facility" ;
definition: "Facility provides instrumentation and scientific support for single cell analysis and sorting. Routinely performs analysis of both eukaryotic and prokaryotic cells for expression of intracellular and extracellular proteins, cell cycle, cell proliferation, cytokine production, and cell sorting based on expression of cell surface antigen(s) and/or expression of genetically engineered intercellular fluorescent proteins." .
SCR:017739 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_222" ;
rdfs:label "Maryland University Proteomics Core Facility" ;
NIFRID:synonym "Proteomics-Bioscience Cores" ;
definition: "Facility is equipped withThermoFisher Orbitrap Fusion Lumos Tribrid mass spectrometer that is interfaced to Dionex Ultimate3000 RSLCnano HPLC system. Facility also maintains 2 separate data stations dedicated for proteomics data processing, database searching, and generation of reports." .
SCR:017740 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_197" ;
rdfs:label "University of California Davis DNA Technologies and Expression Analysis Core Facility" ;
NIFRID:synonym "DNA Technologies and Expression Analysis Core at the UC Davis Genome Center" ;
definition: "Genomics and transcriptomics core at the UCD Genome Center provides high throughput sequencing, genotyping, single-cell multi-omics and spatial transcriptomics services, training and consultation. Initial consultations are free. The lab uses liquid handling robots to minimize sample handling variation and to provide fast turnaround times." .
SCR:017741 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_215" ;
rdfs:label "Arkansas University College of Medicine Flow Cytometry Core Facility" ;
NIFRID:synonym "Biopolymers and Proteomics Core Facility" ;
definition: "Core provides flow cytometry instrumentation and analysis. Instruments include Fortessa, FacsAria and Image Stream." .
SCR:017742 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_204" ;
rdfs:label "Zurich University Functional Genomics Center Core Facility" ;
NIFRID:synonym "Functional Genomics Center Zurich" ;
NIFRID:abbrev "FGCZ" ;
definition: "Laboratory performs services in proteomics, genomics and metabolomics by FGCZ personnel without need for user to access labs. Services include Proteomics:Protein identification,quantification,characterization,Glycan/glycoprotein analyses, Analysis of Biomolecules, Fractionation; Genomics:DNA sequencing, RNA sequencing; Metabolomics/Biophysics services." .
SCR:017743 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_224" ;
rdfs:label "South Dakota University SD BRIN Proteomics Core Facility" ;
NIFRID:synonym "Proteomics Core" ;
definition: "Core provides proteomics services to researchers from South Dakota and the surrounding region to rapidly analyze and identify protein expression patterns in their experimental systems.Develops experimental design, protocols, data analysis and interpretation.Provides consulting and advice in grant proposal, as well as data preparation to be submitted to proteomics journal according to requirements.Offers training in use of common equipment such as scanner, spot cutter, imaging software, technique and protocol issues, and sample preparation." .
SCR:017744 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_232" ;
rdfs:label "West Virginia University Transgenic Animal Core Facility" ;
NIFRID:synonym "Transgenic Animal Core Facility" ;
NIFRID:abbrev "TACF" ;
definition: "Core serves as central molecular biology resource for conception and execution of new projects and provide resources to help offset high costs of developing genetically engineered mice. Ensures better quality control, turn-around time, and cost effectiveness than commercially available services. TACF staff is available for education, assistance and consultation during all stages of project development and production.Serves research staff at West Virginia University, Blanchette Rockefeller Neuroscience Institute and National Institute of Occupational Safety and Health." .
SCR:017745 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_243" ;
rdfs:label "Rensselaer Polytechnic Institute Center for Biotechnology and Interdisciplinary Studies BioImaging Core Facility" ;
NIFRID:synonym "Bioimaging" ;
definition: "Core provides equipment with support of research technicians. Research animals are cared for in transient housing rooms. Multiple anesthesia systems and telemetry equipment are available. All procedures are reviewed by Rensselaer Institutional Animal Care and Use Committee (IACUC) and attending veterinarian. Fully outfitted sample and subject preparation workspaces also are available. Additional fees may be incurred for bioresearch animal technician assistance." .
SCR:017746 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_230" ;
rdfs:label "Delaware Biotechnology Institute Protein Characterization Core Facility" ;
NIFRID:synonym "DBI protein characterization Facility" ;
definition: "Facility consists of a Beckman Coulter ProteomeLab XL-I analytical ultracentrifuge is configured with a scanning UV/Vis detection system and Rayleigh Interference Optics. Used to characterize variety of biophysical properties of macromolecules such as molecular weight, sedimentation coefficient, diffusion coefficient, equilibrium constant and stoichiometry. Can assess sample heterogeneity (aggregation and purity), molecular conformation (folded or unfolded), composition (assembled or unassembled) and thermodynamic properties of interacting systems. Provides spectrum of data for protein characterization in solution." .
SCR:017747 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_248" ;
rdfs:label "Columbia University Quantitative Proteomics and Metabolomics Core Facility" ;
NIFRID:synonym "Quantitative Proteomics and Metabolomics Center" ;
definition: "Core provides identification of proteins and metabolites with differential quantitative expression in cells, tissues or in protein affinity purifications. Particular emphasis is on quantitative analysis of posttranslational modifications such as phosphorylation." .
SCR:017748 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_263" ;
rdfs:label "Duke University Sequencing and Genomic Technologies Core Facility" ;
NIFRID:synonym "Duke Cancer Institute Sequencing and Genomic Technologies Shared Resource" ;
definition: "Basic research oriented core provides genomic services.Services include Next Generation Sequencing Solutions,DNA and RNA sequencing, Illumina, PacBio, NGS Library preparation including single-cell RNA-seq, Nucleic Acid Extraction Services, total RNA extraction from blood samples in PAXgene tubes, total RNA extractions from cell pellets and miRNA extraction from serum/plasma." .
SCR:017749 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_249" ;
rdfs:label "Kansas University at Lawrence Protein Production Group Core Facility" ;
NIFRID:synonym "KU COBRE Protein Production Group" ;
NIFRID:abbrev "PPG" ;
definition: "Core focuses on cloning, expression and purification of prokaryotic and eukaryotic proteins for COBRE and other investigators in Kansas and region. Laboratory maintains equipment to support production of properly folded proteins in quantities suitable for structural studies (X-ray and NMR), functional studies (catalytic or biological), label-free binding studies (SPR) and/or high throughput (HTP) screening studies." .
SCR:017750 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_255" ;
rdfs:label "Kansas University at Lawrence Synthetic Chemical Biology Core Facility" ;
NIFRID:synonym "Synthetic Chemical Biology Core" ;
NIFRID:abbrev "SCB" ;
definition: "Core provides synthetic chemistry expertise. Includes novel and commercially unavailable small molecules, fluorescent molecules and peptides. Assists in identifying hits for medicinal chemistry optimization in infectious disease targets and provides synthesis capabilities for structure activity studies. Core staff will work with investigators to design and synthesis novel molecular probes. Core provides access to model organism Danio rerio (zebrafish), and allows investigators to image embryonic and adult zebrafish treated with molecular probes for phenotypic drug discovery and other projects, encompasses Purification and Analysis Laboratory that provides purification, analysis and quality control of compounds via HPLC-MS, utilizes automated mass directed fractionation for purification in both reversed and normal phases (including chiral separations), provides relative purity analysis by UPLC coupled to high-resolution mass spectrometer for structure confirmation." .
SCR:017751 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_252" ;
rdfs:label "Kansas University at Lawrence Applied Bioinformatics Laboratory Core Facility" ;
NIFRID:synonym "Molecular Graphics and Modeling Laboratory" ;
NIFRID:abbrev "ABL" ;
definition: "Research oriented service laboratory providing informatics support to research community. Services include data analysis and mining in proteomics, genomics and chemistry, systems biology approaches such as pathway, network and interaction analyses, large scale statistical and machine learning studies, protein structure, function and stability prediction, sequence and domain analyses,d esign and implementation of relational databases and software programs, consultation on experimental design involving data acquisition, management and analysis, report, grant, and manuscript preparation." .
SCR:017752 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_254" ;
rdfs:label "Kansas University at Lawrence High Throughput Screening Laboratory Core Facility" ;
NIFRID:synonym "High Throughput Screening Laboratory at KU" ;
NIFRID:abbrev "KU-HTSL" ;
definition: "Core offers high throughput screening of large chemical libraries of compounds to identify novel chemical entities that target biological system of interest.Provides target identification and validation, assay development, high throughput screening, hit confirmation, data mining and medicinal chemistry to facilitate hit to lead development." .
SCR:017753 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_267" ;
rdfs:label "Hawaii University School of Medicine Mouse Phenotyping Core Facility" ;
NIFRID:synonym "JABSOM Mouse Phenotyping Core Facility" ;
definition: "Core provides murine echocardiography, blood pressure determinations, surgical procedures and phlebotomy, as well as assistance with mouse husbandry and genotyping." .
SCR:017754 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_265" ;
rdfs:label "Darthmouth College Electron Microscope Core Facility" ;
NIFRID:synonym "EM Facility" ;
definition: "Provides electron microscopy services for faculty, staff and students of Dartmouth College community, including College, Thayer School of Engineering, Dartmouth Medical School, and Dartmouth-Hitchcock Medical Center. Provides training about how to use instruments and service assistance available for those unable to spend time on microscopes, and for processing of biopsy samples from DHMC." .
SCR:017755 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_277" ;
rdfs:label "Nebraska University Medical Center Mouse Genome Engineering Core Facility" ;
NIFRID:synonym "UNMC Mouse Genome Engineering Core Facility" ;
definition: "Core Facility provides expertise and advice for experimental design of transgenic or gene knockout experiments, including DNA construct production and genotyping assays, makes reagents available for generation of transgene or gene targeting constructs, and performs all experimental aspects, which include pronuclear injection of transgene constructs, generation of recombinant mouse ES cells, blastocyst injection, and embryo transfer surgeries, for generation or rederivation of genetically manipulated mouse strains. Transgenic founder mice or chimeric animals with targeted alleles are then transferred to individual investigator for analysis." .
SCR:017756 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_278" ;
rdfs:label "Darthmouth Geisel School of Medicine DartMouse Core Facility" ;
NIFRID:synonym "DartMouse" ;
definition: "Core dedicated to facilitation and development of congenic mice for pre clinical projects across United States. Provides genotyping, background checks to verify purity of mice DNA." .
SCR:017757 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_287",
"SCR_019325" ;
rdfs:label "Wisconsin-Madison University Biotechnology Center Gene Expression Center Core Facility" ;
NIFRID:synonym "Gene Expression Center",
"UWBC Gene Expression Center" ;
NIFRID:abbrev "GEC" ;
definition: "Core provides RNA library preparation services for Illumina, PacBio and Oxford Nanopore sequencing platforms. Single Cell RNA and Spatial Transcriptomics services are available with 10X Genomics technology. Provides RNA extraction, RNA QC and SNP genotyping and methylation bead array services. Provides support from project design through downstream analysis.Service facility, from hypothesis to publication.Microarray: expression and genotyping Affymetrix, Agilent, Nimblegen. Sequencing: RNA, gDNA, ChIP, Capture, 16SNovaSeq, HiSeq 2500, 3000, MiSeq." .
SCR:017758 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_268" ;
rdfs:label "Wyoming University Jenkins Microscopy Core Facility" ;
NIFRID:synonym "Jenkins Microscopy Facility" ;
definition: "Core to assist researchers and students in their imaging needs of fluorescence and electron microscopy and to increase use of microscopes in science education. Consultation, training or touring facility is also available by appointment." .
SCR:017759 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_294" ;
rdfs:label "Wisconsin-Madison University Biotechnology Center DNA Sequencing Core Facility" ;
NIFRID:synonym "UWBC DNA Sequencing Facility" ;
definition: "Core provides sequencing resources. Service support for Illumina Next Generation and Sanger sequencing projects, from project design and sample preparation through downstream analysis. Provides DNA extraction, SNP genotyping, and fragment analysis services, and can facilitate custom projects upon request." .
SCR:017760 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_293" ;
rdfs:label "Chicago University Cytometry and Antibody Technology Core Facility" ;
NIFRID:synonym "Cytometry and Antibody Technology Core Facility" ;
NIFRID:abbrev "CAT Facility" ;
definition: "Core offers services in cytometry and antibody technology, helps to design projects, data acquisition, analysis and/or interpretation beyond routine practices,critical drafting and/or revision of manuscript for intellectual content purposes." .
SCR:017761 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_281",
"SCR_011043" ;
rdfs:label "University of Nevada at Reno Nevada Proteomics Center Core Facility" ;
NIFRID:synonym "Mick Hitchcock",
"Ph.D. Nevada Proteomics Center" ;
definition: "Core offers mass spectral proteomic analysis. Assists with qualitative and quantitative characterization of proteins in biological matrices such as plasma/serum, tissue, cell lines and other biological material to gain understanding of physiological pathways, molecular interactions and regulatory signaling." .
SCR:017762 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_298" ;
rdfs:label "Vermont University Vermont Advanced Computing Core Facility" ;
NIFRID:synonym "UVM Vermont Advanced Computing Core" ;
NIFRID:abbrev "VACC" ;
definition: "Core provides access to computing infrastructure while offering technical support. Provide tools and instruction allowing for inclusion of high performance computing in classroom." .
SCR:017763 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_295" ;
rdfs:label "University of Illinois at Chicago Electron Microscopy Core Facility" ;
NIFRID:synonym "Electron Microscopy Core" ;
NIFRID:abbrev "RRC EMC" ;
definition: "Core provides electron microscopy imaging and analytical characterization, surface analysis by XPS or Raman, access to instrumentation, training, and service for using scanning (SEM), transmission (TEM) and scanning transmission (STEM) electron microscopy, surface analysis and vibrational spectroscopy, specimen preparation." .
SCR:017764 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allen Human Reference Atlas, 3D, 2020" ;
definition: "Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas." .
SCR:017765 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_303" ;
rdfs:label "Northwestern University Behavioral Phenotyping Core Facility" ;
NIFRID:synonym "Behavioral Phenotyping Core" ;
NIFRID:abbrev "BPC" ;
definition: "Facility dedicated to help to determine behavioral effects of genetic manipulations, potential pharmaceuticals, aging, and other manipulations upon normal behavior, and learning and memory capacities of rodents used as model systems. Provides mouse and rat stereotaxic surgery, helps design behavioral studies." .
SCR:017766 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_315" ;
rdfs:label "Northwestern University Cancer Center Flow Cytometry Core Facility" ;
NIFRID:synonym "Robert H. Lurie Comprehensive Cancer Center Flow Cytometry Core Facility" ;
definition: "Provides 6 cell sorters and 5 benchtop analyzers. Helps investigators to define their projects in the early stages of development to make optimal and efficient use of flow cytometry. Educates ALL users (faculty and staff) in the science and technology of flow cytometry." .
SCR:017767 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_306",
"ABRF_725",
"ABRF_855",
"SCR_017875",
"SCR_018269" ;
rdfs:label "Northwestern University Biological Imaging Core Facility" ;
NIFRID:synonym "Advanced Molecular Imaging Facility",
"Northwestern University Biological Imaging Facility" ;
NIFRID:abbrev "BIF" ;
definition: "Shared use and training facility. Servies include Confocal Laser Scanning Microscopy, DIC (Differential Interference Contrast Microscopy), FCS (Fluorescence Correlation Spectroscopy), FLIP (Fluorescence-Loss-In-Photobleaching), FRAP (Fluorescence Recovery After Photobleaching),FRET (Fluorescence/ Forster Resonance Energy Transfer),Live-cell Imaging,Phase Contrast Microscopy,Widefield Fluorescence Microscopy,Image Processing and Analysis. Services include poster printing, and specimen preparation. Provides training for most instruments. Instruments include Leica DM6B Fluorescent Microscope (Hogan 5-112), Leica TCS SP8 Confocal Microscope (Hogan 5-128),Leica SP5 II Confocal Microscope (Hogan 5-114),Leica Spinning Disk Confocal Microscope (Hogan 5-113),DeltaVision Deconvolution Microscope (Hogan 5-111),Olympus IX83 Inverted Fluorescent Microscope (Silverman Hall 1-567),Olympus IX53 Inverted Color Microscope (Silverman Hall 1-567), LionHeart Automated Microscope BioTeck (Hogan 5-110)." .
SCR:017768 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_326" ;
rdfs:label "Northwestern University Mary Beth Donnelley Clinical Pharmacology Core Facility" ;
NIFRID:synonym "Mary Beth Donnelley Clinical Pharmacology Core Facility" ;
definition: "Core provides quantitative mass spectrometry based support for in vitro studies and both preclinical and clinical studies of variety of small molecules, including cancer chemotherapeutic agents, analgesics, and antidepressants. Expertise includes optimizing design, conduct, analysis, interpretation, and reportage of pharmacokinetic studies. Helps with biological sample preparation, quantitative mass spectrometric drug concentration measurement, and drug concentration versus time data modeling. Small molecule concentrations in plasma and other body fluids are measured using Sciex 6500 QTrap with UPLC and nano LC or an Agilent HPLC system linked to Applied Biosystems API 3000 triple quadrupole mass spectrometer after sample preparation by, for example, solid-phase extraction. Drug concentration versus time relationships are fitted to various compartmental pharmacokinetic models using commercially available and specialized software." .
SCR:017769 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_333" ;
rdfs:label "Northwestern University School of Medicine Lurie Cancer Center Pathology Core Facility" ;
NIFRID:synonym "Pathology Core Facility" ;
NIFRID:abbrev "PCF" ;
definition: "Centralized, comprehensive, core laboratory providing histology, immunohistochemistry, molecular analysis and extraction and microscopic evaluation services for human tissue-based studies. Serves integral marker studies that require biomarker-based treatment arm assignment. Performs procurement of fresh biospecimens for clinical trials and biobanking." .
SCR:017770 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_311",
"ABRF_726",
"SCR_017884" ;
rdfs:label "Northwestern University Center for Atom Probe Tomography Core Facility" ;
NIFRID:synonym "Northwestern University Center for Atom-Probe Tomography" ;
NIFRID:abbrev "NUCAPT" ;
definition: "Facility specializes in high resolution chemical imaging by three dimensional atom probe tomography. APT produces three-dimensional (3D) atom-by-atom elementally and isotopically resolved image with sub-nanometer spatial resolution of sample volume typically 100 x 100 x 300 nm^3, by simultaneous high resolution direct-space imaging and atom-by-atom time of flight mass spectrometry. APT is particularly suited to study nano- or nanostructured materials." .
SCR:017772 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_339" ;
rdfs:label "Northwestern University School of Medicine Transgenic and Targeted Mutagenesis Laboratory Core Facility" ;
NIFRID:synonym "Transgenic and Targeted Mutagenesis Facility" ;
definition: "Shared resource designed to produce genetically engineered mice for investigators." .
SCR:017773 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_017876" ;
rdfs:label "Northwestern University Quantitative Bulk-Elemental Information Core Facility" ;
NIFRID:synonym "Quantitative Bio-element Imaging Center" ;
NIFRID:abbrev "QBIC" ;
definition: "Provides imaging and quantification instrumentation for analyzing metal quotas at scales ranging from subcellular level to entire ecosystems shaping global biogeochemical cycles. Instruments are capable of quantitatively imaging biologically essential elements in individual cells. Used for research in co-evolution of microbial and eukaryotic life within broad range of challenging chemical environments. Services including instrument training, sample preparation and analysis, experiment design, and grant proposal assistance." .
SCR:017774 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_347" ;
rdfs:label "Hunter College Digital Bio-Imaging Core Facility" ;
NIFRID:synonym "BioImaging Facility" ;
definition: "Core provides access to instruments, ranging from simple white light wide field microscopes to fluorescent multidimensional super resolution and confocal imaging systems. Provides expertise in areas of microscopy including laser scanning confocal microscopy, super resolution microscopy, two photon microscopy. Helps with image analysis software packages, including, Imaris, Volocity, Autoquant, MetaMorph, and NIS-Elements." .
SCR:017775 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_353" ;
rdfs:label "Texas University Health Science Center at San Antonio Biomolecular NMR Core Facility" ;
NIFRID:synonym "Biomolecular NMR Core" ;
definition: "Core offers high field NMR instrumentation for structural studies of biological macromolecules. Instrumentation includes four-channel Bruker Avance 500, 600, and 700 MHz NMR spectrometers, ultra high sensitivity 5mm 1H-13C-15N triple-resonance cold probe for 600 MHz spectrometers. Service include acquisition and analysis of required spectra for elucidation of small molecule structures (includes synthetic molecules, natural products, cofactors, lipids, and short peptides (30 amino acids or less)). Types of projects conducted collaboratively include determination of three-dimensional structures of biological macromolecules, including proteins and nucleic acids, both alone and as complexes with various ligands." .
SCR:017776 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_360" ;
rdfs:label "Stowers Institute for Medical Research Molecular Biology Core Facility" ;
NIFRID:synonym "Molecular Biology Facility" ;
definition: "Core services include DNA sequencing, site directed mutagenesis, genome engineering (TALENs & CRISPRS), plasmid preparations and distributing clones/vectors from in house collections. Supports real time quantitative PCR through instrument training, troubleshooting and experimental design. Stowers researchers also have access to Illumina Next Generation Sequencing technology. Constructs libraries, performs sequencing and assists with high throughput genome sequencing, RNA-seq and ChIP-seq projects. Utilizes liquid handling and colony manipulation robots to automate many of services. Provides automation expertise and collaborate with researchers on custom automation projects." .
SCR:017777 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_361" ;
rdfs:label "Iowa State University Genomic Technologies Core Facility" ;
NIFRID:synonym "Genomic Technologies Facility" ;
NIFRID:abbrev "GTF" ;
definition: "Provides expertise and equipment to conduct high throughput research. Services and equipment include:Next Generation Sequencing Services,Ion Torrent Proton sequencing,High Throughput Nucleic Acid Manipulation,Qiagen BioSprint 96 high-throughput DNA/RNA extraction system,Eppendorf AF2200 Plate Reader (absorbance and fluorescence based quantification),Lyophilization and Tissue Grinding,PCR Instruments,Two MJ Research 384 well 4 block DNA engine tetrads,Two Applied Biosystems 384 well 2 block Gene Amp PCR,Roche Lightcyler 480 RealTime thermocycler,Miscellaneous Services and Instruments,Blue Pippin and E-gel size selection systems,Agilent Bioanalyzer,Eppendorf epMotion M5073 liquid handling system." .
SCR:017778 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_363" ;
rdfs:label "University of Missouri Genomics Technology Core Facility" ;
NIFRID:synonym "Genomics Core Facility",
"University of Missouri Genomics Technology Core" ;
NIFRID:abbrev "GTC" ;
definition: "Core research facility providing services in high-throughput DNA sequencing that includes staff experience in the construction of libraries for targeted amplicons, miRNA analysis, transcriptome profiling (RNA-Seq), whole exome sequencing (WES), epigenomic and genomic DNA analysis. Services in single cell library preparation are available using the 10x Genomics Chromium X system. In addition, spatial transcriptomics services using Visium HD arrays are provided. The GTC maintain and operate Illumina sequencing platforms; NovaSeq X Plus and MiSeq i100 instruments." .
SCR:017779 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_329" ;
rdfs:label "Northwestern University Micro/Nano Fabrication Core Facility" ;
NIFRID:synonym "Micro/nano fabrication facility",
"Northwestern University micro/nano fabrication facility",
"NUFAB Northwestern University micro/nano fabrication facility" ;
NIFRID:abbrev "NUFAB" ;
definition: "Central micro/nano fabrication facility of Northwestern University. Provides range of nanofabrication equipment and technical expertise. Supports research in all areas of science, engineering, medicine, and interdisciplinary fields." .
SCR:017780 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_359" ;
rdfs:label "Iowa State University Office of Biotechnology Protein Core Facility" ;
NIFRID:synonym "Protein Facility of the Iowa State University Office of Biotechnology" ;
definition: "Core offers protein/peptide sequencing, large and small scale peptide synthesis (Fmoc), matrix assisted laser desorption/ionization (MALDI) mass spectrometry, SDS-PAGE/electroblotting, 2-D gel electrophoresis, isoelectric focusing (IEF), in-gel and solution digestion, tandem mass spectrometry (LC-MS/MS), ion mobility mass spectrometry (IM-MS), digital image acquisition and analysis using Typhoon imaging system and 2D gel documentation/analysis system, and semi-preparative, analytical and micro-analytical high performance liquid chromatography (HPLC). MALDI, HPLC, SDS-PAGE/blotting, IEF, 2D gel electrophoresis, 2D gel documentation/analysis and Typhoon imaging system are all available for user operation after appropriate training." .
SCR:017781 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_368" ;
rdfs:label "Brigham Young University College of Life Sciences DNA Sequencing Center" ;
NIFRID:synonym "Brigham Young University DNA Sequencing Center" ;
NIFRID:abbrev "DNASC" ;
definition: "Core services include Custom DNA Sequencing (3730xl for dideoxy sequencing chemistry, or Illumina HiSeq 2500 for large scale sequencing projects),DNA Fragment Analysis,Sequencing and PCR troubleshooting and training,SNP analysis,Primer walking, Contig assembly and editing." .
SCR:017782 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_371" ;
rdfs:label "Boston University Microarray and Sequencing Resource Core Facility" ;
NIFRID:synonym "Boston University Microarray & Sequencing Resource" ;
definition: "Core provides analysis of gene expression using Affymetrix GeneChip platform. Offers next generation sequencing via Illumina NextSeq and Ion Torrent PGM and Proton instruments, analysis of RNA and DNA using Agilent Bioanalyzer." .
SCR:017783 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_348" ;
rdfs:label "Donald Danforth Plant Science Center Tissue Culture and Transformation Core Facility" ;
NIFRID:synonym "Plant Tissue Culture and Transformation Facility" ;
definition: "Facility operates as full service facility delivering transgenics and cell cultures to researchers and self service facility providing high quality space for researchers to use for their own specific project needs. Services available include transformations and cell/ tissue culture in many different plant species, project consultation, training workshops, self-service hood usage and offering high quality growth space. Facility staff has developed portfolio of transformation and tissue culture systems such as: Setaria, tobacco, petunia, tomato, Arabidopsis, soybean, Indian mustard, maize, rice and various different cell cultures. Within the facility, researchers have also produced cassava, sweet potato, and potato. Transformation systems will be added, developed, inherited, or modified as needed." .
SCR:017784 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_365" ;
rdfs:label "Buffalo University Genomics and Bioinformatics Core Facility" ;
NIFRID:synonym "UB Genomics and Bioinformatics Core" ;
definition: "Core sequencing services include Illumina Sequencers, Single-Cell RNA-Seq,Single-Cell Immune Profiling,Single-Cell ATAC-Seq,Linked-Read Sequencing. Provides bioinformatic analysis including Single-Cell RNA Analysis,Linked-Read Genome Analysis,ChIP-Seq Analysis Package,RNA-Seq Analysis Package,miRNA Analysis Package,Custom Project Requests,A La Carte Bioinformatics. Provides services including QX100 Droplet Digital PCR Machine (Biorad),Nucleic acid extractions from bio-specimens, Sample QC,Realtime PCR." .
SCR:017785 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_395" ;
rdfs:label "Quebeck Sherbrooke University Genomic Core Facility" ;
NIFRID:synonym "Laboratoire de genomique fonctionnelle de l'University de Sherbrooke" ;
NIFRID:abbrev "LGFUS" ;
definition: "Provides system for Splicing isoform Annotation. This LISA platform allows high throughput annotation and functional analysis of Alternate Splicing in humans." .
SCR:017786 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_394" ;
rdfs:label "Massachusetts University Medical School Quantitative Methods Core" ;
NIFRID:synonym "Quantitative Methods Core" ;
NIFRID:abbrev "QMC" ;
definition: "Provides University of Massachusetts Medical School investigators with clinical research support in biostatistics, experimental design, and data management." .
SCR:017787 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_397" ;
rdfs:label "Stanford University Cell Sciences Imaging Core Facility" ;
NIFRID:synonym "Cell Sciences Imaging Facility" ;
NIFRID:abbrev "CSIF" ;
definition: "Provides high resolution, light and electron microscopy technologies for imaging and analyzing molecular and structural organization of cells, tissue and bioengineered materials. Operates two sites at Stanford University: SOM Beckman Center CSIF and SOE Shriram Center CSIF." .
SCR:017788 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_398" ;
rdfs:label "Stanford University Shared FACS Core Facility" ;
NIFRID:synonym "Stanford Shared FACS Facility" ;
definition: "Provides flow cytometry instrumentation and expertise. Provides operator assisted analyzer and sorter use, as well as training and support for user instrument operation." .
SCR:017789 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_407" ;
rdfs:label "Nebraska-Lincoln University Metabolomics and Proteomics Core Facility" ;
NIFRID:synonym "Metabolomics and Proteomics Core Facility" ;
definition: "Provides tools of modern functional proteomics and metabolomics. Facility is equipped with chromatography and mass spectrometry based technologies for proteomics and metabolomics (Clinical and non clinical), personalized experimental design consultation and comprehensive, individualized bioinformatics support.Services include:Small molecule exact mass determination or quantitation using positive or negative ion mode;Protein identification using LC/MS/MS analysis and MASCOT and SEQUEST database search;Shot gun proteome analysis of biological samples;Biomarker discovery from biological fluid;Drug protein or drug nucleic acid protein interaction;Protein complex isolation and identifying interacting partners and its quantitation;Protein differential expression analysis and quantitation by 2D-LC MS/MS (MudPIT);Global PTM analysis and quantitation;Specialization in phosphorylation and oxidation analysis;Coomassie Blue and Silver Stained Gel analysis; de novo peptide sequencing by tandem mass spectrometry;Confirmation of mutations in protein ;Customized sequence search of in-house proteins that are not available in database; Post translational modifications (phosphorylation, sumoylation, ubiquitination, oxidation, etc.); Determination of oxidation state of cysteine (disulfide bonds);Intact proteins and peptides mass determination." .
SCR:017790 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_422" ;
rdfs:label "Iowa State University Genome Informatics Core Facility" ;
NIFRID:synonym "Genome Informatics Facility" ;
NIFRID:abbrev "GIF" ;
definition: "Provides help with grant review, information on data management plans,suggestion best practices for bionformatics analyses, advise on experimental design for Next Gen Sequencing (NGS) projects.Services include:Genome assembly and annotation,Transcriptome assembly and annotation,SNP/InDel calling,RNA-Seq analysis,ChiP-seq,Introgression mapping,novel gene discovery,Personalized GBrowse instances for data visualization,Access to high performance computing, Custom big data projects." .
SCR:017791 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_426" ;
rdfs:label "Rockefeller University Bio-Imaging Resource Center Core Facility" ;
NIFRID:synonym "Frits and Rita Markus Bio-Imaging Resource Center" ;
NIFRID:abbrev "BIRC" ;
definition: "Provide members of University and their visitors with wide spectrum of optical microscopy equipment and extensive training in its use." .
SCR:017792 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_427" ;
rdfs:label "Rockefeller University Electron Microscopy Resource Center Core Facility" ;
NIFRID:synonym "Electron Microscopy Resource Center" ;
NIFRID:abbrev "EMRC" ;
definition: "Provides support to University researchers for transmission- and scanning-electron microscopy. Based on center capacity, support is also available to researchers from other not-for-profit institutions." .
SCR:017793 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_440" ;
rdfs:label "Nebraska-Lincoln University Center for Virology Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core at Nebraska Center for Virology" ;
definition: "Facility is equipped with high performance computers, bioinformatics related software, biological databases, and data storage. Provides bioinformatics and computational services in virology, molecular biology, genomics, proteomics, next generation high throughput sequencing, and other biological related fields. For special requirements, can design and develop new algorithms, and implement programs and customize data processing pipelines. Core promotes education in bioinformatics to students and researchers, develops and delivers training material, including workshops that facilitate practical application of bioinformatics knowledge by students, postdoctoral fellows, and faculties in NCV community." .
SCR:017794 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2460",
"SCR_023235" ;
rdfs:label "Stanford University School of Medicine High Throughput Bioscience Center Core Facility" ;
NIFRID:synonym "High Throughput Bioscience Center" ;
NIFRID:abbrev "HTBC" ;
definition: "Core provides fully automated high throughput screening (HTS) of Compound Libraries (130,000+ compounds) for both enzyme/protein-based assays and cell-based assays, using Caliper Life Sciences Staccato system;Genomic siRNA screening with siARRAY whole human genome siRNA library from Dharmacon targeting 21,000 genes, using Agilent Bravo system;High-Content Screening using ImageXpress Micro automated fluorescent microscope with live cell, bright field, phase contrast and integrated plate handling with Thermo Catalyst CRS, and image analysis using MetaXpress software;High Throughput Molecular Biology reagents and services, including access to cDNA libraries (Human ORFeome collection, 15,000 genes) and 96 and 384-well bead clean-ups and PCR setup (Biomek FX and Agilent Bravo), and other automation steps in collaboration with SFGF;High-throughput assay development assistance with cell culture, experiment design, robotic programming and Standard Operating Procedure drafting;Screening data analysis assistance with protocols, hit determination and structure activity analyses using MDL chemical database ISIS/HOST, Plate Manager, Assay Explorer and Report Manager. Use of microplate reader detection systems, including Tecan Infinite M1000 and Infinite M1000 PRO and Molecular Devices Analyst GT for fluorescence; fluorescence polarization; time-resolved fluorescence; absorbance and luminescence (with injectors and AlphaScreen); and Flexstation II 384, for kinetic fluorescence reads to measure calcium mobilization and ion channels.Use of liquid-handling robots, including Sciclone ALH3000 (96- and 384-well pipetting), Agilent Bravo (96- and 384-well pipetting), Velocity11 VPrep (96-well pipetting), Bio-Tek plate washers/dispensers, Matrix Wellmate and Titertek/Labsystems Multidrop microplate dispensers, and Velocity11 PlateLoc plate heat sealer;Training for most of these services." .
SCR:017795 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_437" ;
rdfs:label "Oklahoma Medical Research Foundation Human Antibody Core Facility" ;
NIFRID:synonym "Human Antibody Core Facility" ;
definition: "Core produces fully human, full length, antigen specific antibodies for use in studying human immune responses. Produces high affinity protective antibodies to influenza, anthrax lethal toxin, and various S. pneumonia polysaccharides. Helps quantify antibody secreting cell responses after vaccination and by generating human monoclonal antibodies to be characterized. Pathogen specific human monoclonal antibodies are also available for licensing agreements and other forms of commercial development. Services include to define temporal human immune responses after vaccination and to generate human monoclonal antibodies to supplement research,development of novel methods to produce human monoclonal antibodies after acute infection and other immune events, investigation of new technologies for characterization of human monoclonal antibodies produced by core." .
SCR:017796 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_439" ;
rdfs:label "Delaware University Surface Analysis Core Facility" ;
NIFRID:synonym "Surface Analysis Facility" ;
definition: "Core provides consulting and services in X-ray Photoelectron Spectroscopy (XPS or ESCA), Time-of-Flight Secondary-Ion Mass Spectrometry (TOF-SIMS), X-ray Photoelectron Imaging, Auger Electron Spectroscopy (AES), Scanning Auger Microscopy or Imaging (SAM), Secondary-Electron Microscopy (SEM), Ion-Scattering Spectroscopy (ISS or LEIS), Scanning Probe Microscopy (STM and AFM)." .
SCR:017797 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_443" ;
rdfs:label "The Rockefeller University Proteomics Resource Center Core Facility" ;
NIFRID:synonym "Proteomics Resource Center",
"Rockefeller University Proteomics Resource Center",
"Rockefeller University Proteomics Resource Center Core Facility" ;
definition: "Core provides analysis of proteins, peptides, lipids, polar metabolites and small molecules by high resolution/high mass spectrometry. Targeted and hypothesis free analysis are offered combined with relative quantitation based on either label free, tandem mass tags or metabolic labelling. Acquisition tools include Data Dependent (DDA) and Data Independent (DIA)." .
SCR:017798 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_441" ;
rdfs:label "Nebraska-Lincoln University Morrison Microscopy Core Facility" ;
NIFRID:synonym "Morrison Microscopy Core Research Facility" ;
definition: "Core provides imaging systems including light/fluorescence microscopes, confocal laser scanning microscopes and electron microscopes.Provides services, teaching, training and technical support for multi disciplinary research." .
SCR:017799 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_469" ;
rdfs:label "Wisconsin-Madison University Biotechnology Center Bioinformatics Resource Center Core Facility" ;
NIFRID:synonym "Bioinformatics Resource Center" ;
NIFRID:abbrev "BRC" ;
definition: "Facility within UW Biotechnology Center (UWBC) for assisting researchers with their data analysis needs. Helps with variety of common sequencing related projects, DNA-seq, ChIP-Seq, RNA-Seq, 16S metagenomics, and small RNA analyses." .
SCR:017800 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_458" ;
rdfs:label "Nebraska University Medical Center Epigenomics Core Facility" ;
NIFRID:synonym "Epigenomics Core Facility" ;
NIFRID:abbrev "ECF" ;
definition: "Core assists with epigenetic analysis including DNA Methylation, Chromatin Immunoprecipitation and Real Time Quantitative PCR gene expression analysis. Services include DNA Methylation Analysis, Specific Genomic Location Analysis:Methylation Specific PCR,Bisulfite Sequencing,Bisulfite Pyrosequencing,Qiagen PyroMark Pyrosequencer Instrumentation;Genome Wide Analysis:High Throughput Sequencing Methylation Analysis, Methyl-Sensitive Cut Counting (MSCC),Methyl CpG Binding Domain - Isolated Genome Sequencing (MiGS);Chromatin Immunoprecipitation Analysis (ChIP):Analysis of Histone Modifications,DNA-Protein Interactions,Chromatin Positions analyzed using:Quantitative PCR Analysis (Real-Time QPCR),High Throughput Sequencing Analysis (ChIP-Seq);Gene Expression Analysis (QPCR):Real-Time Quantitative PCR Gene Expression." .
SCR:017801 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_489" ;
rdfs:label "Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility" ;
NIFRID:synonym "Vincent Coates Foundation Mass Spectrometry Laboratory" ;
definition: "Core mass spec and proteomic services include open access lab for trained users with GC/MS, LC/MS, high resolution LC/MS, and MALDI-TOF instruments, help with intact protein analysis, targeted quantitation, drug discovery support, pathway analysis, protein interactions, FFPE tissue analysis, both labeled and label-free proteomics, and more. Please contact SUMS to discuss these and other custom projects including new application development." .
SCR:017802 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_462" ;
rdfs:label "Nevada University at Reno Nevada Bioinformatics Center Core Facility" ;
NIFRID:synonym "Nevada Bioinformatics Center",
"Nevada Center for Bioinformatics" ;
definition: "Provides bioinformatics research resources, services and training in support of existing research programs and in development of new programs and grant applications. Provides next-generation sequencing data analysis including RNA-Seq and QuantSeq analysis, de novo transcriptome assembly, whole-genome sequencing, genome resequencing, single-cell sequencing, metagenomics, microbiome, mass spectrometry proteomic analysis of label-free (DIA) and TMT data, analysis of metabolomics, microbiome, multi-omics data, data mining, modeling, and visualization. Provides customized bioinformatics and statistical services including data quality control, power studies, hypothesis tests, regression, clustering, network analysis, function annotation, pathway analysis including iPathwayGuide." .
SCR:017803 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_445" ;
rdfs:label "Maine University DNA Sequencing Core Facility" ;
NIFRID:synonym "DNA Sequencing Facility" ;
definition: "Provides services in sequencing using ABI model 3730 DNA Sequencer with the XL Upgrade,design and have synthesized primers for primer walking experiments, DNA fragment analysis such as microsatellites, AFLP, SNP analysis." .
SCR:017804 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_507" ;
rdfs:label "Concordia University Center for Microscopy and Cellular Imaging Core Facility" ;
NIFRID:synonym "Centre for Microscopy and Cellular Imaging" ;
NIFRID:abbrev "CMCI" ;
definition: "Services include advise on microscope to use for research project, image acquisition, optimization image analysis and sample preparation, free of charge access to 500GB per laboratory on CMCI server in order to store data for project. Facility houses four wide-field, near-field (TIRF), three confocal (swept-field and laser-scanning) microscopes and laser capture microdissection system." .
SCR:017805 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_490" ;
rdfs:label "Arkansas University Biodosimetry Diagnostic Core Facility" ;
NIFRID:synonym "Biodosimetry Diagnostic Core" ;
definition: "Core using ultrahigh performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) offers high-throughput analytical services for determining diagnostic amino acids and their precursors or metabolic products. Available biomarkers include citruilline and tetrahydrobiopterin. Determination of other small molecules is possible." .
SCR:017806 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_515" ;
rdfs:label "Virginia Commonwealth University Chemical and Proteomic Mass Spectrometry Core Facility" ;
NIFRID:synonym "Chemical and Proteomic Mass Spectrometry Core Facility" ;
NIFRID:abbrev "CPMSC" ;
definition: "Core provides mass spectrometric services, from basic mass measurement to complex proteome analyses.Services include basic mass measurement, ESI-MS/MS,LC-MS,Exact mass measurement,Protein identification." .
SCR:017807 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_508" ;
rdfs:label "University of Texas Southwestern Medical Center Moody Foundation Flow Cytometry Core Facility" ;
NIFRID:synonym "Moody Foundation Flow Cytometry Facility" ;
definition: "Core provides flow cytometry services to scientists, offers analytical cytometry and high-speed sorting either in investigator operated format or facility staff assisted format, offers training for research personnel interested in learning how to design flow cytometry experiments, operate instrumentation and analyze data. Services include experimental design, protocol development, sample staining, instrument operation, data analysis, graphical production, sample processing as a Service (SpaaS). Facility is equipped with three cell sorters and four cell analyzers." .
SCR:017808 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_518" ;
rdfs:label "Stanford University School of Medicine Magnetic Resonance Laboratory Core Facility" ;
NIFRID:synonym "Stanford Nuclear Magnetic Resonance Laboratory" ;
NIFRID:abbrev "SMRL" ;
definition: "Core provides instrumentation in area of solution phase, high resolution NMR spectroscopy and expertise. Primary solution state spectroscopy of bio molecules including, but not limited to, studies of polymers, minerals, soils, and extracts. Equipment includes: 800MHz Varian Inova Spectrometer, 600MHz Varian Inova Spectrometer, 500MHz Varian Inova Spectrometer, and staff assistance/consultation is available." .
SCR:017809 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_536" ;
rdfs:label "Johns Hopkins University School of Medicine Transgenic Mouse Core Facility" ;
NIFRID:synonym "Transgenic Core Laboratory" ;
definition: "Core provides complete CRISPR services, design, production of gRNAs & Cas9 mRNA, and injection." .
SCR:017810 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_553" ;
rdfs:label "Charite - Universitatsmedizin Berlin 7T Experimental MRIs Core Facility" ;
NIFRID:synonym "7T Experimental MRIs" ;
definition: "Core provides two experimental 7 Tesla magnetic resonance imaging machines which were purchased by Center for Stroke Research CSB (Device 1) and Cluster of Excellence NeuroCure (Device 2) with aim of creating experimental platform for small animal imaging. Services projects in areas of experimental neuroimaging and molecular imaging, but projects in other fields of research are explicitly encouraged." .
SCR:017811 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_564" ;
rdfs:label "Saint Louis University School of Medicine Protein Core Facility" ;
NIFRID:synonym "Protein Core Facility" ;
definition: "Core facility that supports expression, purification, and analysis of reagent and preclinical proteins by providing instrumentation and consultation for protein production from small to large scale. Available equipment includes shaking incubators, 5 L fermentor, high pressure cell disruptor, hollow fiber concentrator, Maxwell16 magnetic bead purification system, AKTA Purifier chromatograph, analytical ultracentrifuge, analytical HPLC, and MALDI-QIT-TOF mass spectrometer." .
SCR:017812 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_568" ;
rdfs:label "Princeton University Confocal Microscopy Core Facility" ;
NIFRID:synonym "Confocal Microscopy Core Facility" ;
definition: "Core provides researchers with ability to visualize samples, from monolayers and small organisms, such as developing fly and fish embryos, to very thick sections from brain and other organ tissues by using instruments including laser point (LSCM) and field scanning confocal (CSU), Total Internal Reflectance Fluorescence (TIRF), Multi Photon (MP), and Widefield (WF). Services in imaging in mammalian cells, yeast cells, Drosophila and Zebrafish embryos and ovaries, bacteria, sections of brain and other tissues, in both fixed and live specimens, Quantitative imaging methods such as FRAP, FLIP, and FRET, software packages for image processing, analysis, and 3D image reconstruction." .
SCR:017813 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_528" ;
rdfs:label "UTSW Proteomics Core" ;
definition: "Core provides seven mass spectrometry platforms, for shotgun and targeted analyses, run by core staff. Services include protein and peptide identification from gels and solutions, identification and localization of post translational modifications, relative and absolute quantitation of peptides and proteins, intact mass analysis of proteins in solution." .
SCR:017814 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_537" ;
rdfs:label "University of Delaware BioImaging Center Core Facility" ;
NIFRID:synonym "Delaware University BioImaging Center Core Facility",
"University of Delaware Bio-Imaging Center" ;
definition: "Microscopy facility that houses equipment including confocal microscopes: LSM780 confocal microscope (Located at CBBI),LSM880 confocal microscope (Located at DBI 117),electron microscopes and their accessory instrumentation:Thermo Scientific Apreo VS SEM microscope,Hitachi S-4700, Leica EM ACE600 and Tousimis Autosamdri-815B,CX7 high content analysis system. Our staff has technical expertise across different microscopy platforms and methodologies." .
SCR:017815 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_580" ;
rdfs:label "Albert Einstein College of Medicine Molecular Cytogenetics Core Facility" ;
NIFRID:synonym "Molecular Cytogenetics Core Albert Einstein College of Medicine" ;
NIFRID:abbrev "MC" ;
definition: "Core provides tools for preparation of human and murine samples suitable for molecular genetic and cytogenetic analysis of entire genome. These tools include establishment of EBV transformed cell lines; isolation of DNA and mRNA from variety of tissue culture samples as well as primary biopsies; preparation of metaphase chromosomes suitable for fluorescence in situ hybridization (FISH) and Spectral Karyotyping (SKY) or whole chromosome paints for human and mouse genome. Core personnel is trained to hybridize commercial probes and to designed locus specific probes for regions of interest to investigators. All probes are custom designed and in house generated." .
SCR:017816 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_582" ;
rdfs:label "University of Miami Hussman Institute for Human Genomics Biorepository Core Facility" ;
NIFRID:synonym "Biorepository at the CGT",
"University of Miami Miller School of Medicine Biorepository Core Facility",
"University of Miami School of Medicine Biorepository Core" ;
definition: "Core provides services and houses samples collected over the last 30 years. Biorepository processes, archives, and retrieves biological samples for genomic research. Offers variety of sample processing options including but not limited to automated DNA extraction using Autogen FLEXSTAR+ instrument, automated DNA/RNA extraction using Qiagen QIASymphony, peripheral blood mononuclear cell (PBMC) isolation, serum, plasma and buffy coat isolation, creation of blood cards, DNA/RNA quantitation and qualitation, whole genome amplification, cell-line lymphoblast immortalization and primary fibroblast tissue culture. Offers sample solutions tos uit customized needs.Services also include DNA/RNA Extraction,Sample archiving, retrieval and allocation,Unique and custom labels printing,DNA/RNA quantitation and qualitation,Tissue culture,Whole genome amplification." .
SCR:017817 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_572" ;
rdfs:label "Miami University SCCC Flow Cytometry Core Facility" ;
NIFRID:synonym "Flow Cytometry Shared Resource" ;
NIFRID:abbrev "FCSR" ;
definition: "Core provides analytical and preparative flow cytometers, to facilitate range of experiments in biology of both normal and cancer cells. Experimental analyses, including:Complex, 19 fluorescence parameter immuno-phenotyping;DNA content, ploidy and cell cycle analysis; 17 fluorescence parameter cell sorting and single-cell flow cloning; High speed (10,000 � 30,000+ cells per second) and efficiency (95%+ purity) cell sorting;Assessment of apoptosis;Molecular cytogenetics;Cell function studies;Micro-biological applications;Multiplexed and micro-particle-based analysis;Mass cytometry analysis and imaging;Fluidigm Helios plasma mass cytometer. Cells are labeled with antibodies conjugated to heavy metal markers, vaporized in plasma and detected with time-of-flight mass spectrometry;Fluidigm Hyperion solid tissue imager provides simultaneous imaging of labeled solid tissue sections, for mass cytometry analysis. FCSR has bank of metal reagent kits (for custom antibody conjugation), available for purchase at favorable rates compared to those available commercially. The bank has 35 unique labeling metals, for users to create custom reagents and panels. Please contact FCSR for further information and pricing. Robotic automated cell transfer A.L.S. CellCelector automated cell transfer robot. For automated transfer of single cells and colonies from culture plates, without pre-treatment. Integral bio-safety cabinet for BSL-2 cultures." .
SCR:017818 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_570" ;
rdfs:label "Kansas University Medical Center Mass Spectrometry/Proteomics Core Facility" ;
NIFRID:synonym "KUMC Mass Spectrometry/Proteomics Core Laboratory" ;
NIFRID:abbrev "MSPCL" ;
definition: "Core provides access to mass spectrometry based proteomics applications, customizes mass spectrometry designs that fit individual needs. Used for general proteomics evaluations and protein identification designs, quantitation techniques, hydrogen/deuterium exchange, and oxidative footprinting. Equipment includes Orbitrap Fusion Lumos." .
SCR:017819 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_595" ;
rdfs:label "Miami University Mass Spectroscopy Laboratory Core Facility" ;
NIFRID:synonym "Mass Spectrometry Laboratory" ;
definition: "Core provides two mass spectrometers at UM Department of Chemistry, Bruker MicroQ-TOF ESI, and Agilent Technologies 5975C GC/MS with autosampler." .
SCR:017820 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_596" ;
rdfs:label "University of Miami Hussman Institute for Human Genomics Genotyping Core Facility" ;
NIFRID:synonym "Genotyping at the CGT",
"University of Miami Miller School of Medicine Genotyping Core Facility" ;
definition: "Core provides services in analyzing genetic variation, performing genome-wide association studies, conducting non-human genotyping. Offers flexible platforms from low to high throughput, tailored to research needs. Specializes in Illumina Genotyping Arrays and TaqMan Allelic Discrimination Assays, with fully automated processing using Tecan EVOs and BioMek liquid handlers and Genologics LIMS for reliable data tracking.Applications include: GWAS – Identify genetic variants linked to traits and diseases; PRS Analysis – Assess genetic risk for complex diseases; Pharmacogenomics – Study genetic factors in drug response; Population Genetics – Explore ancestry and genetic diversity; CNV Analysis – Detect large-scale genomic variations; Methylation Analysis." .
SCR:017821 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_588" ;
rdfs:label "Neural Stem Cell Institute NeuraCell Core Facility" ;
NIFRID:synonym "NeuraCell" ;
definition: "Core facility provides neural stem cells (NSC) and everything you need to grow them, custom lentiviral shRNA and over-expression vectors, consult based characterization service where we can assess how your products or reagents affect stem cell performance and behavior. Services include:Cell Supply,Adult SVZ Neural Stem Cells,Any Age Embryonic stem cells from any region of the brain,Human Retinal Pigmented Epithelial cells,RPE iPSCs,iPSCs,Neural Progenitor Cells (NPCs),Custom Orders,Media/ Dissociation Reagents,High-performance Media formulated according to optimal cell growth conditions,Complete Defined Media for Neural Stem Cell Culture,Complete Defined Media for Human Retinal Pigmented Epithelial Culture,Cell characterization. Performs assays to verify how stem cell populations behave in response to certain environments, plastics, reagents, etc., using trade secret assays via FACS and cell culture techniques. This can be used for neural stem cells as well as embryonic stem cells.Cell banking solutions shall ensure that their integrity is maintained, and that sufficient supply is readily available. We will also expand cells, harvest cells, generation the freezing medium and thaw cells to test performance. Provides Generation of custom lentiviral shRNA constructs,Generation of custom lentiviral over-expression constructs,Supply of NSC lines already expressing these shRNA or over-expression constructs." .
SCR:017822 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_585" ;
rdfs:label "Miami University Veterinary Clinical Pathology Laboratory Core Facility" ;
NIFRID:synonym "Comparative Pathology Laboratory" ;
definition: "Full service veterinary reference laboratory directed by members of faculty of University of Miami Miller School of Medicine. Offers clinical pathology and histopathology services to meet needs of avian, exotic, lab animal, and wildlife veterinarians. Services include Acute Phase Protein Laboratory. Provides recent diagnostic testing developments which may not yet be available in other veterinary diagnostic testing environments." .
SCR:017823 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_604" ;
rdfs:label "Howard Hughes Medical Institute at Janelia Research Campus Advanced Imaging Center Core Facility" ;
NIFRID:synonym "Advanced Imaging Center" ;
definition: "Facility provides imaging methods and instruments, microscopes that reveal biological processes in three-dimensional detail and behavior of single molecules in high resolution. Welcomes proposals with high-risk/high-gain projects. AIC will cover lodging and basic experimental cost for scientists whose proposals have been accepted to come to Janelia to perform their experiments." .
SCR:017824 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_603" ;
rdfs:label "Miami University X-Ray Crystallography Resources Core Facility" ;
NIFRID:synonym "X-Ray Crystallography Resources" ;
definition: "Core provides upgraded Bruker SMART 1000 CCD single crystal diffractometer to SMART APEX II CCD Area Detector, and its low-temperature LT3 device to KRYO-FLEX low-temperature device. Instrument which is equipped with Mo radiation source is used for small molecule crystal structure determination." .
SCR:017825 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_598" ;
rdfs:label "University of Miami Miller School of Medicine Gene Expression Core Facility" ;
NIFRID:synonym "Gene Expression at the CGT" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 27,2025. CGT gene expression core utilizes Affymetrix GeneChip Arrays and Illumina BeadChips to identify gene expression variation in single genes, targeted set of genes, or entire genomes. Affymetrix GeneChip Arrays Human Gene ST,Human Transcriptome Array 2.0, Human Exon ST, Human miRNA, Illumina Expression, HumanHT-12 v4 BeadChip." .
SCR:017826 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_612" ;
rdfs:label "University of California Davis Flow Cytometry Shared Resource Laboratory Core Facility" ;
NIFRID:synonym "UC Davis Flow Cytometry Shared Resource Laboratory",
"University of California Davis Health Flow Cytometry Shared Resource Laboratory Core Facility" ;
definition: "Core provides access to expertise and instrumentation for analytical flow cytometry, cell sorting and laser scanning cytometry.Cell sorting and analytical cytometers are located at three sites in Davis and Sacramento for research use on recharge basis. Provides cell sorters for assisted sorting on appointment basis and provides training to investigators in acquiring data on analytic cytometers.Can advise on experiment design for flow cytometry, provides training to enable independent use of analytical cytometers, and familiarize investigators with popular data analysis software tools such as BD Diva and CellQuest, FlowJo, ModFit and iBrowser." .
SCR:017827 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_616" ;
rdfs:label "Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Genomics Core Facility" ;
NIFRID:synonym "Genomics Core",
"Genomics Core at Scripps Research Florida",
"Scripps Research Institute - Florida Genomics Core Facility",
"UF Scripps Genomics Core" ;
definition: "Core provides services in Next Generation Sequencing (NGS), library preparation, consultation on sample preparation and procedures." .
SCR:017828 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_597" ;
rdfs:label "University of Miami Hussman Institute for Human Genomics Sequencing Core Facility" ;
NIFRID:synonym "Sequencing at the CGT",
"University of Miami Miller School of Medicine Sequencing Core Facility" ;
definition: "Core Facility offers services utilizing Illumina Novaseq X Plus, Pacific Biosciences Revio, ONT Promethion, and 10x Genomics platforms. The core has extensive knowledge of DNA/RNA library preparation for short-read, long-read and single cell sequencing. Sample preparation is fully automated on Perkin Elmer robotic workstations and tracked via the Clarity LIMS. Services include, but are not limited to, whole genome, exome and custom capture protocols, as well as, bulk RNAseq, small RNAseq, and single cell RNA sequencing." .
SCR:017829 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_611" ;
rdfs:label "University of Virginia School of Medicine Flow Cytometry Core Facility" ;
NIFRID:synonym "Flow Cytometry Facility",
"UVA Flow Cytometry Core Facility",
"Virginia University School of Medicine Flow Cytometry Core Facility" ;
definition: "Services include unassisted and assisted sample acquisition, cell sorting, mass cytometry (CyTOF), Luminex cytokine assays, antibody conjugation and data analysis." .
SCR:017830 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_615" ;
rdfs:label "Scripps Research Institute - Florida Flow Cytometry Core Facility" ;
NIFRID:synonym "Flow Cytometry" ;
definition: "Flow cytometry core to measure phenotypic, biochemical and molecular characteristics of individual cells or particles suspended in fluid stream.Flow Cytometry Core on Jupiter, Florida campus of Scripps Research provides services including Cell Sorting, Analytical Cytometry,Data Analysis,Microdissection and Imaging. Hematology services including:Cell Sorting on ARIA: violet, blue, green and red lasers and on FUSION: violet, blue, green and red lasers; Cell Analysis on LSR2: ultra-violet, violet, blue, green and red lasers, GALLIOS: violet, blue, green and red lasers,CANTO: violet, blue and red lasers;Laser Microdissection and Fluorescence Imaging using LEICA LMD 7000;Hematology using HEMAVET 950FS." .
SCR:017831 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_617" ;
rdfs:label "Penn State College of Medicine Mass Spectrometry and Proteomics Core Facility" ;
NIFRID:synonym "Penn State College of Medicine's Mass Spectrometry & Proteomics Core" ;
definition: "Core provides mass spectrometry analyses and identification of proteins, peptides, oligonucleotides, carbohydrates and small molecules.Other services include separations of complex protein and/or peptide mixtures; protein expression analysis (iTraq, SILAC, SWATH/DIA label-free); quantitation of protein, cytokine, amino acid and other small-molecule levels; bioinformatics; spot-cutting and robotics; and gel imaging and analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017833 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_614" ;
rdfs:label "Princeton University Macromolecular Crystallography Core Facility" ;
NIFRID:synonym "Macromolecular Crystallography Core Facility" ;
definition: "Facility helps with structure determination and analysis on service basis, but also encourages users with prior experience to use facilities independently. Offers services for setting up crystallization trials, x-ray data collection, structure determination and structure analysis. Assists in interpretation of existing structures available in Protein Data Bank and assists in homology modeling." .
SCR:017834 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_621" ;
rdfs:label "Scripps Research Institute - Florida Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "Research Services Nuclear Magnetic Resonance Facility" ;
definition: "Core provides NMR spectroscopy to researchers in Scripps Research, as well as spectral service to local biotech communities.Facility houses six NMR spectrometers:Bruker AVIII HD 600 NMR spectrometer equipped with 5 mm CPQCI (H-C-N-P) CryoProbe This spectrometer also has 1.7 mm CPTCI (H-C-N) CryoProbe which can be installed upon requested for experiments on micro-gram scale compounds;Bruker AVIII HD 600 NMR spectrometer equipped with 5 mm CPDCH (C-H) CryoProbe. This CryoProbe provides high sensitivity for C-13 NMR experiments;Bruker AV NEO 500 NMR spectrometer with 5 mm BBFO Smart Probe;Bruker AVIII 400 NMR spectrometer equipped with 5 MM BBFO probe ;Bruker AV NEO 399 spectrometer equipped with 5 mm BBFO Smart Probe. All BBFO probes have capabilities to perform NMR experiments on nuclei with resonance frequencies between Ag-109 and P-31, as well as H-1, and F-19.Bruker DPX-400 NMR spectrometer equipped withQ NP (H-F-P-C) probe and B-ACS 120 sample changer." .
SCR:017835 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_620" ;
rdfs:label "Scripps Research Institute - Florida X ray Crystallography Core Facility" ;
NIFRID:synonym "Macromolecular X-ray Crystallography Core facility" ;
definition: "Core provides equipment and resources for crystallographic analysis of target macromolecules and small inorganic or organic molecules. Performes crystallization, X-ray diffraction data collection (both in-house and synchrotron sources) processing, phasing, crystallographic refinement, model building, and visualization. Structural data provide information including biological functions, 3D-folding, ligand binding (small molecule or protein), or mutational effect of target macromolecules. Services include Crystallization Screening; Data Collection Service: Diffraction experiments will be performed at in-house X-ray facility as well as synchrotron beam lines; Structure Determination and Analysis: complete data set collected at home or synchrotron will be processed for inorganic, organic, protein or nucleic acid structure determination, model building and crystallographic refinement. Other Structural Biology Related Services: core facility offers thorough analysis of macromolecular structure for publication or grant applications, also provides computational experiments such as homology modeling and in silico ligand docking." .
SCR:017836 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_628" ;
rdfs:label "North Carolina University at Chapel Hill R.L. Juliano Structural Bioinformatics Core Facility" ;
NIFRID:synonym "R. L. Juliano Structural Bioinformatics Core facility at UNC-Chapel Hill" ;
definition: "Core provides consultations and collaborations on research studies requiring computational structural biology methods. Analyses available are to study of static structures, molecular dynamics studies for analyzing contribution of dynamic and collective motions to macromolecular functionality. Trains researchers in computational structural biology techniques, or works in collaborative manner with researchers.Provides access to software tools for protein and DNA sequence analysis, protein fold determination, homology modeling, active site identification, and analysis of effects of various mutations on structure and function of protein, along with additional computational analyses." .
SCR:017837 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_626" ;
rdfs:label "North Carolina University at Chapel Hill School of Medicine High Throughput Peptide Synthesis and Array Core Facility" ;
NIFRID:synonym "UNC High-Throughput Peptide Synthesis and Array Facility" ;
definition: "Core offers services for: High quality synthetic peptides, stable isotope labeled peptides, peptides with PTM and fluorescent and affinity tags, synthesis of peptide libraries. Analysis of synthetic peptides. Purification, lyophilization and aliquoting of synthetic peptides." .
SCR:017838 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_623" ;
rdfs:label "Wisconsin University Great Lakes Genomics Center Core Facility" ;
NIFRID:synonym "Great Lakes Genomics Center" ;
definition: "Core provides services which include massively parallel sequencing on Illumina MiSeq, traditional Sanger sequencing, fragment analysis, quantitative PCR, nucleic acid extractions and QC, and digital PCR. Offers various level of service for Sanger sequencing and qPCR from full service to ready to load plates. Trains researchers in laboratory techniques and provide protocols. Each MiSeq sequencing project and qPCR project is unique and specifically designed so experimental design should be discussed before collecting samples." .
SCR:017839 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_629" ;
rdfs:label "North Carolina University at Chapel Hill School of Medicine Macromolecular X-Ray Crystallography Core Facility" ;
NIFRID:synonym "Macromolecular X-Ray Crystallography" ;
NIFRID:abbrev "MX Facility" ;
definition: "Core provides support and infrastructure necessary to initiate and successfully complete structural biology or structural chemistry project. Offers services in Crystallization,X-Ray DiffractionData Collection,Structure Determination and Refinement." .
SCR:017840 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_631" ;
rdfs:label "Steve and Cindy Rasmussen Institute for Genomic Medicine Clinical Laboratory Core Facility at Nationwide Children�s Hospital" ;
NIFRID:synonym "Institute for Genomic Medicine Clinical Laboratory" ;
NIFRID:abbrev "IGM" ;
definition: "Core performs and analyzes integrated clinical genomic, molecular, microarray, FISH, and cytogenetic analyses to diagnose broad range of inherited diseases and cancer. Serves as centralized clinical testing laboratory for Children Oncology Group leukemia, Wilms tumor, medulloblastoma, and rhabdomyosarcoma studies. Emphasizes collaborative interactions between clinicians, physician-scientists, and basic science investigators to quickly transition cutting edge research results into cutting edge diagnostics, using technology platforms. Services include Whole Exome Sequencing (WES),cytogenetic chromosome analysis,Fluorescence in situ Hybridization,Chromosomal microarray analysis,Molecular Genetic Testing - Inherited Diseases,Molecular Genetic Testing - Cancer." .
SCR:017841 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_625" ;
rdfs:label "North Carolina University at Chapel Hill School of Medicine Biomolecular NMR Laboratory Core Facility" ;
NIFRID:synonym "NMR Spectroscopy",
"UNC Biomolecular NMR Laboratory" ;
definition: "Core to support academic and industrial users. Spectrometer time is available to trained users for an hourly fee. Lab manager trains new users, consults to determine whether NMR will be useful in their research, and helps design experimental plan to obtain information they need. Manager also operates spectrometer for users whose experiments do not justify time and expense of individual training." .
SCR:017842 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_638" ;
rdfs:label "Max-Planck-Institute for Molecular Cell Biology and Genetics High Throughput Technology Development Studio Core Facility" ;
NIFRID:synonym "High-Throughput Technology Development Studio" ;
NIFRID:abbrev "TDS" ;
definition: "Provides expertise in assay development towards high-throughput applications and high content screening services, provides technologies for cell-based screening such as robotic liquid handling stations, plate readers and several automated microscopes. Services include developing complex automated image analysis pipelines and multi-parametric analysis of high content imaging applications.Equipment:Flexible liquid handling work stations Biomek FXp (Beckman), Freedom Evo 200 (TECAN);Multilabel microtiter plate readers Envision (Perkin Elmer), GENios Pro (TECAN);Acoustic dispensing (Labcyte Echo 550);CellVoyager CV7000 automated live cell confocal microscope (Yokogaw);Perkin Elmer OPERA;Operetta widefield microscope (Perkin Elmer);Automated confocal microscopy OPERA (Perkin Elmer);Washers, dispensers;96-well electroporation system (amaxa nucleofector)." .
SCR:017843 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_627" ;
rdfs:label "North Carolina University at Chapel Hill School of Medicine Protein Expression and Purification Core Facility" ;
NIFRID:synonym "Protein Expression and Purification" ;
definition: "Core specializes in production of pure, functional proteins for structural, biophysical, and biochemical studies. Facility offers three categories of service:Protein Expression,Protein Purification,Scientific Consultation, Mentoring, and Training; Offers Isotope labeled proteins for NMR;High production scales for immunizations, drug discovery, structural biology;Endotoxin-free protein production;Stable cell line generation;Expert baculovirus expression;Custom packages to efficiently suit your needs." .
SCR:017844 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_641" ;
rdfs:label "Centre for Cellular and Molecular Platforms High Throughput Screening and Imaging Core Facility" ;
NIFRID:synonym "High Throughput Screening" ;
definition: "Core assists in developing and performing high-throughput assays involving NCEs, siRNA, shRNA and dsRNA.Core also houses High Content image-based platform for chemical and biology research using both live and fixed cells. Services include High Throughput Screening,Assay development and validation (Cell-based/ Biochemical),siRNA screens,Small molecules screens,Proof of concept with validation." .
SCR:017845 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_634" ;
rdfs:label "Indiana University - Bloomington Electron Microscopy Center Core Facility" ;
NIFRID:synonym "IUB EMCenter" ;
NIFRID:abbrev "EMC" ;
definition: "Core provides access to electron microscopy equipment and services which includes AFS 2 Freeze Substitution robot,Denton DV502 Carbon Evaporator,JEOL JEM 1010,JEOL JEM 1400plus,JEOL JEM 3200FS,Polaron E5100 sputter coater,Vitrobot Mk3,Wohlwend High Pressure Freezer. Users have to be included on user e-mail lists and have iLab account in order to use core." .
SCR:017846 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_654" ;
rdfs:label "Albert Einstein College of Medicine shRNA Core Facility" ;
NIFRID:synonym "shRNA Core Facility" ;
definition: """Core Facility was closed in November 2016. Services of shRNA Core were redistibuted to other existing facilities at Einstein.Gene Modulation Services: CRISPR, RNAi and ORF. CRISPR-Cas9 services for cell lines will now be performed in Gene Modification Facility. Gene Modification Facility already offers CRISPR services for genetic modification of mice and will utilize this scientific expertise to provide CRISPR services for the gene modification of cell lines as well. You can access these services through core's site in iLab.The human and mouse whole genome shRNA library has been relocated to the Molecular Cytogenetic Core. The core staff will pull requested shRNA and ORF clones from our collection for investigators. You can access this service through the core's site in iLab.Access and operation of the Operetta instrument for high-content imaging will now be coordinated through the Macromolecular Therapeutics Development Facility (MTDF). You can access this service through the core's site in iLab.
Lentivirus prep from shRNA and CRSPR constructs can be obtained from our Gene Therapy Core from clones obtained from the Molecular Cytogenetic Core. You can access this service through the core's site in iLab.""" .
SCR:017847 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_643",
"SCR_016327" ;
rdfs:label "Rockefeller University Antibody and Bioresource Core Facility" ;
NIFRID:synonym "Antibody and Bioresource Core Facility" ;
definition: "Core used to develop custom monoclonal antibodies and obtain large scale quantities of existing ones for experiments. Core provides cell line distribution service and tests samples for mycoplasma contamination." .
SCR:017848 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_622" ;
rdfs:label "Scripps Research Institute - Florida Core Microscopy Core Facility" ;
NIFRID:synonym "California Campus",
"Core Microscopy Facility at Scripps Research",
"La Jolla" ;
definition: "Core provides researchers with equipment and expertise required for multi-dimensional imaging of cells and tissues at high resolution and to perform quantitative image analysis. Resources include widefield, confocal, multi-photon, TIRF, super-resolution and electron microscopy, as well as equipment for live cell imaging and image analysis. Services include sample preparation, imaging, molecular localization, and image analysis. Provides training, technical support, sample preparation, imaging assistance, collaboration and consultation." .
SCR:017849 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_656" ;
rdfs:label "Garvan Institute of Medical Research Molecular Genetics Core Facility" ;
NIFRID:synonym "Garvan's Genetics Core Facility" ;
definition: "Core facility for high throughput services covering the areas of Capillary Sequencing, Mouse Genotyping, SNP Genotyping, Clinical Diagnostic Sequencing, Cell Line Identification, Gene Expression Analysis and DNA/RNA extraction." .
SCR:017850 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_642" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Molecular Cytogenetics Core Facility" ;
NIFRID:synonym "Molecular Cytogenetics" ;
definition: "Core supports cytogenetic analysis of cells from human and research animal sources. Range of chromosome analysis techniques are ranging from basic G-banded karyotyping, to 24-color Spectral Karyotyping (SKY), as well as Fluorescence in situ Hybridization (FISH) mapping of cloned DNAs.Services include:Karyotype characterization of new cell lines,Confirmation of cell line identity or stability,Karyotype screening of ES cells prior to transgenesis,Mapping of transgene integration sites,Chromosome or locus copy number enumeration,Publication-quality illustrations.Cytogenetic techniques available:Short-term cell culture,Metaphase chromosome preparation,G-banded karyotyping.FISH techniques available:DNA labeling for custom probe generation (for FISH projects),DNA amplification by DOP-PCR,Chromosome painting,FISH mapping (on chromosomes, interphase nuclei or DNA fibers),Tissue FISH (paraffin or frozen sections),Immuno-FISH (DNA FISH combined with fluorescent immunostaining) , Spectral karyotyping (SKY),Q-FISH (measurement of telomere lengths)." .
SCR:017851 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_660" ;
rdfs:label "University of California-Davis Mouse Biology Program CRISPR Based Genome Editing Service Core Facility" ;
NIFRID:synonym "UC Davis Mouse Biology Program" ;
NIFRID:abbrev "MBP" ;
definition: "Core located on campus of UC Davis, providing fully customized support for scientific research using genetically altered mice. Provides access to develop, plan, execute, and analyze research project involving genetically-altered mice. Provides description of project, including alternative approaches, accurate timelines, and cost estimates.Provides regular and informative communication throughout project, including email updates on completion of each milestone. Project progress can be followed at each stage by viewing detailed information anytime by accessing our online and secure project tracking system (PTS) available 24 hours a day." .
SCR:017852 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_659" ;
rdfs:label "University of California at Berkeley Cancer Research Laboratory Molecular Imaging Center Core Facility" ;
NIFRID:synonym "CRL Molecular Imaging Center" ;
NIFRID:abbrev "MIC" ;
definition: "Microscopy core specializing in laser based fluorescence techniques. Offers training and expertise in 20 different microscope systems, including live cell and in vivo imaging, laser scanning (LSM) and spinning disk (SDC) confocal, multi-photon (2p), fluorescent lifetime imaging (FLIM), light-sheet microscopy (SPIM), super resolution (Airyscan), slide scanning and patterned illumination for optogenetic manipulation and readout. Provides offline computer analysis workstations for image processing, visualization and analysis, including GPU workstations. MIC operates in 3 different buildings on campus, with primary locations in Life Sciences Addition (LSA), North-side core in Barker Hall, and small outpost in Li Ka Shing Center for Biomedical and Health Sciences (LKS).Provides equipment in categories:Confocal and multi photon laser scanning microscopes,Spinning disk confocal microscopes,Lightsheet (SPIM) microscopes,Epifluorescence/widefield scopes and Computer workstations." .
SCR:017853 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_657" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Investigantional Products Support Core Facility" ;
NIFRID:synonym "Investigational Products Facility" ;
definition: "Core mission is to ensure quality and regulatory compliance of Memorial Sloan Kettering Cancer Center�s clinical trials investigational products and Investigational New Drug (IND) applications, and to promote efficiency in our drug development projects, through combination of advisory, project management, and quality assurance (QA) oversight services." .
SCR:017854 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_662" ;
rdfs:label "Nemours/A.I.duPont Hospital for Children Cell Science Core Facility" ;
NIFRID:synonym "Cell Science Core" ;
NIFRID:abbrev "CSC" ;
definition: "Core specializes in cell, protein, and small molecules analysis as well as cell culture techniques. Services include:2-D gel electrophoresis, 2-D DIGE, LC-MS/MS, HPLC, flow cytometry, fluorescence-activated cell sorting (FACS), cell and tissue culture, and immortalization of cell lines. Our staff works closely with investigators to help design, perform, and analyze experiments.Offers training and assistance in flow cytometry, tissue culture, and operation many of our walk-up instruments.Instruments:Cell Sorter: FACS Aria III, BD Biosciences;Flow Cytometers, analyzers:C6, Accuri/BD Biosciences;Novocyte 3000, ACEA Biosciences;software for analysis: FSC Express, DeNovo software;LC-MS/MS: 6460 Triple Quadrupole, Agilent;Typhoon Trio Scanner, GE Lifesciences;Blood Analyzer: Hemavet 950, Drew Scientific.Plate Readers:;Victor Nivo 5F, Perkin Elmer;Luminometer: Centro XS, Berthold.Services:Cell Sorting (FACS);2-D gel electrophoresis/2D-DIGE;LC-MS/MS analysis of compounds; Cell immortilization." .
SCR:017855 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_677" ;
rdfs:label "Washington University Histology and Imaging Core Facility" ;
NIFRID:synonym "HISTOLOGY AND IMAGING CORE" ;
NIFRID:abbrev "HIC" ;
definition: "Core provides servises including:Immunohistochemistry,Image analysis,Quantitative microscopy,Histology,Luminex cell based multiplex assay,Comparative pathology consultation.Offers experience, expertise and instrumentation across all platforms. HIC utilizes automated immunohistochemistry stainers which provide efficiency and consistency as well as standardization of protocols across studies of all sizes." .
SCR:017856 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_671" ;
rdfs:label "Baylor College of Medicine RNA In Situ Hybridization Core Facility" ;
NIFRID:synonym "RNA In Situ Hybridization" ;
definition: "Core performs non-radioactive, RNA in situ hybridization (ISH) on tissue sections. Provides services including: collecting animal tissue specimens, preparation of frozen and paraffin sections, preparation of RNA probes from customer templates, conducting high-throughput ISH, and documentation and quantification of expression patterns by microscopy. We also do X-gal and Cresyl Violet staining on sections. For human studies, customers must provide tissue sections." .
SCR:017857 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_678" ;
rdfs:label "Loyola University Genomics Core Facility" ;
NIFRID:synonym "Loyola Genomics Facility" ;
NIFRID:abbrev "LGF" ;
definition: "Core provides next-generation sequencing capabilities using Illumina MiSeq. Helps with experimental design, quality control analysis, library preparation, and data analysis. MiSeq desktop sequencer allows to access applications such as targeted gene sequencing, metagenomics, small genome sequencing, targeted gene expression, amplicon sequencing, and HLA typing.MiSeq is capable of delivering up to 15 Gb of output with 25 million sequencing reads and 2x300 basepair read lengths." .
SCR:017858 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_674" ;
rdfs:label "University of Massachusetts Boston Advancing Personalized Cancer Medicine Through Research Genomics Core Facility" ;
NIFRID:synonym "CPCT Genomics Core" ;
definition: "Center for Personalized Cancer Therapy Genomics Core offers sequencing services on Illumina HiSeq 2500 (v4; 1TB enabled) and Illumina MiSeq platforms, library preparation from DNA and RNA and sample QC services.Please create an iLab account to be able to use services." .
SCR:017859 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_676" ;
rdfs:label "Washington University In Vivo Services (IVS) Core Facility" ;
NIFRID:synonym "In Vivo Services Core in the Department of Comparative Medicine" ;
NIFRID:abbrev "IVS" ;
definition: "Core provides rodent colony management. IVS staff oversee maintenance, breeding, weaning, identification, and record keeping of mouse and rat colonies. Core offers sample collection, sample administration, and testing of drug compounds in rodents. Services include Colony Management,Technical Procedures,Drug Testing." .
SCR:017860 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_682" ;
rdfs:label "Duke University Molecular Genomics Core Facility" ;
NIFRID:synonym "Molecular Genomics Core" ;
NIFRID:abbrev "MGC" ;
definition: "Core offers variety of experimental platforms to facilitate genomics research. Accredited as Duke Shared Resource facility offers experience with genetic, genomic and epigenomic study design and technology, working closely with researchers to customize experiments to meet their needs. Applications include 10x Genomics NGS library generation for both single cell and gDNA experiments, DNA methylation microarrays, SNP genotyping and copy number microarrays, and Taqman targeted SNP genotyping." .
SCR:017861 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_684" ;
rdfs:label "Brown University Leduc Bioimaging Core Facility" ;
NIFRID:synonym "Leduc Bioimaging Facility" ;
definition: "Core provides equipment and training dedicated to high resolution imaging in life sciences. Facility includes Transmission Electron Microscope, a Scanning Electron Microscope, three Fluorescence Microscopes, Fluorescence Stereomicroscope, four Confocal Laser Scanning Microscopes,Multiphoton Microscope, and software for image analysis.Maintains equipment for sample preparation, including critical point dryer, sputter coater, and microtomes for ultrathin sectioning. Listed within CoresRI.org." .
SCR:017862 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_680" ;
rdfs:label "University of California at San Francisco, Nikon Imaging Center Core Facility" ;
NIFRID:synonym "Nikon Imaging Center at UCSF" ;
definition: "Core provides light microscopy instrumentation, microscopy training and education and can provide assistance with experiment design, data acquisition, and image analysis. Provides training for users.Services include:Fluorescence imaging (up to 5 colors) Brightfield, phase contrast, and DIC imaging;High speed imaging (over 100 frames per second);Automated imaging, including multiwell plates;Super-resolution imaging (SIM / STORM / PALM);Single molecule imaging;3D confocal imaging;Gigapixel image stitching;Live cell time lapse imaging;Photoactivation and photobleaching;Light sheet imaging of cleared tissues." .
SCR:017863 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_675" ;
rdfs:label "University of Washington Transgenic Resources Program Core Facility" ;
NIFRID:synonym "Transgenic Resources Program",
"University of Washington Transgenic Resources Program" ;
NIFRID:abbrev "TRP" ;
definition: "Core facility that creates transgenic and gene-targeted mice using pronuclear microinjection, targeted ES cell microinjection, and CRISPR/Cas9 gene editing. Offers mouse rederivation services to create specific pathogen free mice or to rederive cryopreserved mouse lines. Additionally, embryo and sperm cryopreservation services are available to provide long-term storage of valuable mouse strains or stocks. Services include:Pronuclear Microinjection,ES Cell Microinjection,ES Cell Electroporation CRISPR/Cas9,In Vitro Fertilization,Sperm Cryopreservation,Embryo Cryo,Embryo Rederivation." .
SCR:017864 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_691" ;
rdfs:label "Nebraska University Medical Center Electron Microscopy Core Facility" ;
NIFRID:synonym "University of Nebraska Medical Center Electron Microscopy Core Facility" ;
NIFRID:abbrev "EMCF" ;
definition: "Core provides instrumentation and technical assistance to research programs utilizing Transmission Electron Microscopy (TEM) and Scanning Electron Microscopy (SEM). Available for consultation and service." .
SCR:017865 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_690" ;
rdfs:label "London Regional Genomics Centre Core Facility" ;
NIFRID:synonym "London Regional Genomics Centre" ;
definition: "Core provides Next Generation Sequencing and Bioinformatics services.Services include:RNA assessment using Agilent 2100 Bioanalyzer,Next Generation Sequencing:Single cell RNA-seq,DNA-seq,RNA-seq,miRNA-seq,ChIP-seq,Microbiome (16S rRNA),ATAC-seq,Data Analysis (Partek Flow, Transcription Analysis Console)." .
SCR:017866 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3229" ;
rdfs:label "Northwestern University Jerome B. Cohen X-ray Diffraction Core Facility" ;
NIFRID:synonym "Jerome B.Cohen X-Ray Diffraction Facility" ;
NIFRID:abbrev "X-RAY" ;
definition: "Core provides general purpose x-ray equipment for diffraction and fluorescence studies. Examples of current measurements are: powder diffraction, single-crystal diffraction, thin-film reflectivity, thin-film diffraction, crystal truncation rod scattering, small angle scattering, Laue diffraction, residual stress, pole figures, EDX-ray fluorescence, x-ray standing waves, high-resolution x-ray diffraction, and grazing incidence small angle scattering." .
SCR:017867 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_683" ;
rdfs:label "Mayo Clinic Immunochemical Core Facility" ;
NIFRID:synonym "Immunochemical Core at Mayo Clinic",
"Immunochemical Core Lab (ICL) - Mayo Clinic" ;
definition: "Provides immunochemical, chemistry and immune testing to clinical and basic science researchers, develops and validates new assays, and improves current assay methodology. Services include Assay development, Automated chemistry analysis, Immunoassay analysis, Small molecule analysis,Mass Spectrometry, LC-MS/MS and HRAM LC-MS,Enzyme-linked immunosorbent (ELISA), Meso Scale Discovery (MSD), Luminex, and radioimmunoassay (RIA) procedures for various analytes." .
SCR:017868 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_698" ;
rdfs:label "Northwestern University Surface Science Core Facility" ;
NIFRID:synonym "Surface Science Facility" ;
definition: "Core provides multiple technique characterization of variety of surfaces with regard to atomic structure, surface chemical composition, and chemical bonding characteristics. Equipment includes:AFM/Nanoindentor for high resolution imaging and nanoindentation studies;Laser writing for generating controlled surface roughness and patterns;Optical profilometers: Two optical interferometers (Zygo and Aliconia) are available for surface topographic imaging;Three-target magnetron sputter-deposition system. Provides Training Seminars/Workshops.Provisions have been made to accommodate routine short term measurements by user groups as well as more extended studies. User and research groups are encouraged to work with facility staff to tailor facility resources to research project." .
SCR:017869 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_700" ;
rdfs:label "Northwestern University Cryogenics Core Facility" ;
NIFRID:synonym "Cryogenics Facility" ;
definition: "Facility provides liquid helium and liquid nitrogen to researchers and laboratories at Northwestern University." .
SCR:017870 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_702" ;
rdfs:label "Northwestern University Mouse Histology and Phenotyping Laboratory Core Facility" ;
NIFRID:synonym "Mouse Histology and Phenotyping Laboratory" ;
NIFRID:abbrev "MHPL" ;
definition: "Core provides assistance with standard and customized research specific histology services for variety of tissues (i.e., mouse, rat, sheep, pig, zebrafish, etc.) for routine histology, and immunohistochemistry. Provides Pathologist consultation to help develop strategies to elucidate phenotypes and gain mechanistic insight regarding biologic actions of targeted molecule(s) or toxicity of exogenously administered substances.Provides training opportunities for learning histology techniques and phenotyping analysis.Services include Immunohistochemistry (IHC) . Using tyramide signal amplification (TSA) and ABC methods (automated), with DAB chromogenic substrate; Immunofluorescence (IF)- Single and multiple staining;TUNEL assay; Freezing and embedding of tissues for histology;Frozen sections;Paraffin block processing and Paraffin sections;Hematoxylin and Eosin staining of sections;Specialized histochemical staining of sections (e.g. Trichrome, PAS, Luxol fast blue, Cresyl violet, and many other stains);Dissection and tissue collection;Histopathology (slide interpretation);Histopathology toxicity evaluation;Training in necropsy techniques including perfusion of mice and special tissue dissection;Assistance with development of animal pathology protocols." .
SCR:017871 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_697" ;
rdfs:label "Northwestern University Comprehensive Metabolic Core Facility" ;
NIFRID:synonym "Comprehensive Metabolic Core" ;
definition: "Core provides hormone analyses for both human and animal studies for scientific community at Northwestern, small rodent metabolic phenotyping resources for diabetes, obesity and other metabolic research.Maintains quality control and standardize internal references for hormone assays.Maintains reference database information on mouse metabolic phenotyping models from Northwestern University community.Services include:Immunoassays for endocrine hormones, assays using technology from Luminex,Lipid and glucose chemical analyeses,Roche Cobas e 411 analyzer employing sophisticated electrochemiluminescence (ECL) technology to deliver excellent low-end sensitivity and broad dynamic range of assays including metabolic and reproductive hormones, thyroid function test, cardiac markers, maternal care, tumor markers and bone turnover markers.,TSE LabMaster Automated Phenotyping system is a state-of-the-art system for studying energy metabolism at whole animal level." .
SCR:017872 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_716" ;
rdfs:label "Northwestern University Recombinant Protein Production Core Facility" ;
NIFRID:synonym "Recombinant Protein Production Core" ;
NIFRID:abbrev "rPPC" ;
definition: """Core provides quality controlled recombinant proteins. rPPC operates based on the two service models: Training model where Northwestern researchers use specialized bioreactor systems and participate in hands-on-training activities and Production model where staff carry out expression (mg to gm scale) and purification of recombinant or synthetic biologics, including potential therapeutic proteins and peptides, among others. Main focus of rPPC is to be user-facility;facility has parallel bioreactor systems for multiplexed lab-scale cultivation of microbial, insect, and mammalian cells. rPPC also serves as a production facility, providing low-cost recombinant biologics for researchers at Northwestern University.Services include: TRANSFECTION/TRANSFORMATION, ANALYTICAL (SMALL SCALE) EXPRESSION IN E.COLI AND MAMMALIAN CELLS,PROTEIN EXPRESSION IN E. COLI (LARGE SCALE),PROTEIN EXPRESSION IN MAMMALIAN CELL SYSTEM (LARGE SCALE),PROTEIN EXPRESSION IN INSECT CELL SYSTEM,GENERATION OF MOUSE HYBRIDOMA, PRODUCING MONOCLONAL ANTIBODIES, per one fusion,RESCUING AND CULTIVATING EUKARYOTIC CELLS,DOWNSTREAM PROCESSING OF GROWN CULTURE (BEFORE PROTEIN PURIFICATION),RECOMBINANT PROTEIN PURIFICATION,TAG CLEAVAGE WITH TEV. PROTEASE,LARGE SCALE mAb PRODUCTION ,DNA PLASMID PROPAGATION AND PURIFICATION,SDS-PAGE ANALYSIS,WESTERN BLOT ANALYSIS, INSTRUMENT TIME SHARING
TECHNICAL/INSTRUMENT ASSISTANCE TIME,PROTEIN RECOVERING FROM INCLUSION BODIES.""" .
SCR:017873 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_714" ;
rdfs:label "Northwestern University Stem Cell Core Facility" ;
NIFRID:synonym "Stem Cell Core" ;
definition: "Core provides iPSC technology services.Specialize in creating custom patient-derived iPSCs, providing training in stem cell culture, project consultation, CRISPR gene editing services, cell banking, and facility usage." .
SCR:017874 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_722" ;
rdfs:label "Northwestern University Integrated Molecular Structure Education and Research Center Core Facility" ;
NIFRID:synonym "Integrated Molecular Structure Education and Research Center at Northwestern" ;
NIFRID:abbrev "IMSERC" ;
definition: "Core provides access to NMR, mass spectrometry, X-Ray crystallography instruments and education on use of instrumentation needed for molecular structure characterization." .
SCR:017877 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_727" ;
rdfs:label "Northwestern University Central Laboratory for Materials Mechanical Properties Core Facility" ;
NIFRID:synonym "Central Laboratory for Materials Mechanical Properties" ;
NIFRID:abbrev "CLaMMP" ;
definition: "Core provides mechanical testing machines and accessories for conducting educational, research, and outreach experiments on most solid materials." .
SCR:017878 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_719" ;
rdfs:label "Northwestern University Center for Translational Imaging Core Facility" ;
NIFRID:synonym "Center for Translational Imaging" ;
NIFRID:abbrev "CAMRI",
"CTI" ;
definition: "Core is Northwestern Radiology research facility providing translational imaging capabilities that promote pre-clinical and clinical research efforts. CTI occupies space in basement of Olson building housing imaging equipment along with research staff. Services include Cardiovascular Imaging for development, analysis and application of MRI methods providing insights into structure and function of cardiovascular system,NeuroImaging for functional MRI using spectroscopy and diffusion-weighted imaging to studying human anatomy and physiology during development and disease,Small Animal Imaging for molecular and functional imaging of biological processes in living animal models to study diseases and responses to intervention." .
SCR:017879 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_724",
"SCR_017771" ;
rdfs:label "Northwestern University High Throughput Analysis Laboratory Core Facility" ;
NIFRID:synonym "Northwestern Highthroughput Analysis Laboratory" ;
NIFRID:abbrev "NU-HTA" ;
definition: "Core provides expertise and resources for large scale biology. Helps to set up, run, gather data and perform analysis in drug discovery research, biochemistry, cell and organismal biology, functional genomic screening, and synthetic genetic. Works with proteins, nucleic acids, small model organisms, and microbial strains. Provides tissue culture,produces and uses lentivirus particles, screens compound libraries, does experiments for investigators,generates preliminary data to figure out if idea is workable, discusses project development. Services include Macromolecular binding, biochemical, and cell-based assays,High content screening with widefield or confocal optics,Nanoliter liquid handling up to 1536-well density,Whole-plate kinetic assays (ion currents, GPCR signaling),Compound library screening,CRISPR/Cas9 screening (multiplexed libraries),Analysis of large data sets,Fluorescence Thermal Shift assay (measures protein melting),Complex liquid handling work flows." .
SCR:017881 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_737" ;
rdfs:label "Northwestern University and Northwestern Memorial Health Mathews Center for Cellular Therapy Core Facility" ;
NIFRID:synonym "Mathews Center for Cellular Therapy" ;
NIFRID:abbrev "MCCT" ;
definition: "Core offers researchers, clinicians and biotech companies regulatory compliant labs and services to manufacture minimally manipulated and complex biotechnology products." .
SCR:017882 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_756" ;
rdfs:label "Maine Medical Center Research Institute Viral Vector Core Facility" ;
NIFRID:synonym "Viral Vector Core" ;
definition: "Core provides viral vector services dedicated to development and production of viral vectors for angiogenesis, stem cell and regenerative medicine and clinical renal research. Viral vectors are produced in dedicated BL2 facility within MMCRI building. Vector systems currently being used include adenovirus, retrovirus and lentivirus. Services Available:Transfection and transduction of gene-specific viral DNA provided by principal investigators;Small, large and custom scale production of adenovirus;retrovirus and lentivirus (2nd and 3rd generation packaging);TCID50 titration of adenovirus;Titration of retrovirus and lentivirus (fluorescence marker or antibiotic resistance);Test for replication competent virus (RCV) in lentivirus preparations." .
SCR:017883 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of New England In Vivo Behavior Core Facility" ;
NIFRID:synonym "In Vivo Behavior Core" ;
definition: "Core provides technical expertise, training, instrumentation and related services for assessing behavior in animals to help to gain insight into function of nervous system and mechanisms of acute and chronic pain. Services include Behavioral Testing; General Behavioral Phenotyping: Observational Screens, Motor Function; Pain/Sensory Testing: Thermal, Mechanical, Chemical; Additional Neurobehavioral Tests: Psychiatric, Addiction, Learning and Memory;Miscellaneous Systems: GI Transit, Cardiovascular and Respiration. Other Services: Assistance choosing behavioral test and statistical tests for assessing results; Training in surgical techniques for small animal surgeries; Staff expertise includes surgical methods for producing pain models; dosing of drugs/anesthetics including central, systemic and localized administration; and tissue extractions." .
SCR:017885 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_748" ;
rdfs:label "University of New England COBRE Histology and Imaging Core Facility" ;
NIFRID:synonym "Histology and Imaging Core" ;
definition: "Core provides access to expertise, training and specialized instrumentation related to tissue processing, sectioning, staining, immunohistochemistry and microscopy. Offers services and training related to image analysis and image analysis software to guide investigators in choosing best methods for presenting their data.Services include Trimming of wet tissues,Tissue processing into paraffin, OCT and paraffin embedding, Sectioning of paraffin-embedded/frozen tissues, Routine and special histochemical staining, Immunohistochemistry/Immunofluorescence, Antibody optimization, Brightfield/ widefield/ confocal microscopy, Image capture and image analysis.Core has cryostats, microtomes and microscopes available for reservation." .
SCR:017886 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_759" ;
rdfs:label "Brown University Flow Cytometry and Sorting Core Facility" ;
NIFRID:synonym "Flow Cytometry and Sorting Facility" ;
definition: "Core provides technical assistance to Brown researchers by performing flow cytometry-based analysis and sorting. Facility has 4-laser, 19-parameter BD FACSAria IIIu for flow and sorting applications, as well as 3-laser, 15-parameter BD FACSCelesta equipped with high throughput system for analysis of samples from 96 well plates." .
SCR:017887 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_754" ;
rdfs:label "Washington University Gnotobiotic Animal Core Facility" ;
NIFRID:synonym "Gnotobiotic Animal Core" ;
NIFRID:abbrev "GNAC" ;
definition: "Core at University of Washington (UW) is managed by Department of Comparative Medicine and open to investigators with research needs to maintain mice free of any microorganisms (germ-free), or with known population of microorganisms (gnotobiotic).Services provided include Rederivation, Germ-Free (GF) Mice, Isolator Maintenance of GF Mice, Experimental Study Support, Diet Sterility Testing, Technical Procedures." .
SCR:017888 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_763" ;
rdfs:label "Kansas University Medical Center Analytical Core Facility" ;
NIFRID:synonym "Analytical Core Laboratory" ;
NIFRID:abbrev "ACL" ;
definition: "Core provides access to advanced chromatographic and mass spectrometry instrumentation. Main analytical focus is quantitative analysis of small molecules (drugs, drug metabololites, endogenous metabolites, xenobiotics and toxicants) and intact large molecules (biologics, intact proteins, and biopolymers like hyaluronan). Provides analytical instruments including Liquid Chromatography and Mass Spectrometry, Microbalances, Quantitative PCR (qPCR or Real-Time PCR), Sample Preparation Aids, Pharmacology Department Shared Instruments." .
SCR:017889 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_746" ;
rdfs:label "Northwestern University Pulsed Laser Deposition Core Facility" ;
NIFRID:synonym "Pulsed Laser Deposition" ;
NIFRID:abbrev "PLD" ;
definition: "Core provides means to grow thin films of metals and metal oxides. Facility contains two state of art deposition chambers PVD PLD/MBE 2300 and a PVD nanoPLD 1000. PLD provides convenient way to make thin films of materials heretofore studied in bulk by pressing and sintering target from bulk material; facilities are available at Northwestern for pressing and sintering of targets." .
SCR:017890 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_761" ;
rdfs:label "Kansas University at Lawrence Computational Chemical Biology Core Facility" ;
NIFRID:synonym "Computational Chemical Biology Core" ;
NIFRID:abbrev "CCB" ;
definition: "Core provides computational resources and expertise to enhance productivity of researchers studying infectious diseases. Assists with virtual screening, protein-small molecule docking, binding site prediction, protein modeling and design, prediction of protein stability changes upon mutation, fragment based probe design, as well as preparation of presentation graphics.Specializes in initial hit identification of non-traditional drug targets such as protein-protein or protein-RNA interfaces by offering high-throughput virtual screening via pocket optimization with exemplar screening at protein-protein interfaces and hotspot pharmacophore mimicry of protein-RNA interactions.CCB works in collaboration with Molecular Graphics and Modeling Laboratory." .
SCR:017891 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_749" ;
rdfs:label "New England University Microscopy Core Facility" ;
NIFRID:synonym "Microscope Core Facility" ;
definition: "Core Facility provides access to Atomic Force Microscope and Leica SP5 Scanning Laser Confocal Microscope, located in Room 122 of Pickus Center for Biomedical Research on Biddeford Campus." .
SCR:017892 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_765" ;
rdfs:label "Massachusetts Institute of Technology Koch Institute Flow Cytometry Core Facility" ;
NIFRID:synonym "Swanson Biotechnology Center Flow Cytometry Facility" ;
definition: "Core provides technical expertise, training and access to instrumentation, enabling and supporting use of flow cytometry techniques. Allows simultaneous multiparametric analysis of many thousands of cells per second, enabling trained researchers to rapidly analyze complex cell populations using benchtop analysis flow cytometers. High-speed assisted cell sorting services provide researchers with fast, objective and quantitative recording of fluorescent signals from individual cells combined with physical separation of cells of particular interest.Services include High-end, staff assisted cell sorting, using four different high speed sorters;Unassisted bench-top analysis available 24/7;Assisted bench-top analysis available by appointment;Extensive training on bench-top analyzers;Extensive training on FACS Aria sorters;Consultation on experimental design and data interpretation." .
SCR:017893 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_764" ;
rdfs:label "North Carolina University School of Medicine Histology Research Core Facility" ;
NIFRID:synonym "Histology Research Core Facility" ;
definition: "Facility offers histological services including Tissue Sectioning:Paraffin embedding and frozen embedding in OCT;Paraffin section serial, random, serial interrupted;Frozen section thaw mount cold/warm, serial, free floating,thick slice, random and serial interrupted, CryoJane tape transfer;Vibratome section;Routine staining, i.e., H+E, Nuclear Fast Red Special staining, Alcian Blue, Cresyl Violet, PAS, Oil Red , Toluidine Blue, Von Kossa, Combined Massons Elastin, Picrosirius Red, Sudan IV, Thionin, Prussian Blue, Movats Pentachrome, Masson Trichrome, Alcian Blue/Phloxine/Tartrazine, others available upon request. Immunohistochemistry/Enzyme:ABC method (direct/indirect);Fluorescence;Biocytin detection;HRP;Single and multiple-labeling;Edu/Brdu,in situ Hybridization,RNAScope,BaseScope." .
SCR:017894 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_769",
"SCR_017155" ;
rdfs:label "Massachusetts Institute of Technology Koch Institute Bioinformatics and Computing Core Facility" ;
NIFRID:synonym "Barbara K. Ostrom Bioinformatics Facility",
"The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility" ;
definition: "Core provides support, assistance and training in wide range of bioinformatics topics. Maintains high-performance computing resource offering many bioinformatics applications, substantial processing power and secure storage. Provides support for desktop computing and poster printing. Services include Data Analysis, Software Support (access to proprietary bioinformatics resources Ingenuity Pathway Analysis and GeneGO MetaCore, Training sessions covering various bioinformatics topics, Linux compute cluster, data storage." .
SCR:017895 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_768" ;
rdfs:label "Massachusetts Institute of Technology Koch Institute Flow Cytometry Core Facility" ;
NIFRID:synonym "Flow Cytometry: Nanowell Cytometry" ;
definition: "Nanowell Cytometry platform is shared resource housed in Flow Cytometry Core that provides Koch Institute and MIT researchers access to Microengraving and SeqWell technologies, developed in Love and Shalek Laboratories at Koch Institute. Microengraving platform enables measurement of multiple traits from individual cells derived from wide array of tissues or cell types, such as immune cells either in their native condition or upon stimulation. Platform allows simultaneous assessment from small or large numbers of cells. Additionally, it is possible to obtain genetic information from individual cells of interest. Platform has been employed in projects related to antibody discovery, tumor profiling from various cancer tissues, and immune cell functions in various allergic, infectious or auto-immune diseases.Core offers access to CellCelector, tool which enables users to isolate single cells using ultra-precise robotic micromanipulator. Offers access to nanowell microplates which enable automated isolation of monoclonal and viable clones. Seq-Well is portable, low-cost platform for massively-parallel single-cell RNA-Seq. Barcoded mRNA capture beads and single cells are sealed in array of subnanoliter wells using semi-permeable membrane, enabling efficient cell lysis and transcript capture." .
SCR:017896 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_760" ;
rdfs:label "Purdue University Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core" ;
definition: "Core to facilitate, amplify, and accelerate biological research and discovery through application of bioinformatics. Provides bioinformatic analysis services for Next Generation Sequencing (NGS) data." .
SCR:017897 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_771" ;
rdfs:label "Texas A&M University Integrated Metabolomics Analysis Core Facility" ;
NIFRID:synonym "Integrated Metabolomics Analysis Core" ;
NIFRID:abbrev "IMAC" ;
definition: "Open access core facility available to all TAMU users for Metabolomics service and research. Provides different levels of service from drop-off to collaborative projects.Training for TAMU postdoctoral fellows and students to use instrumentation in support of specific projects.Short courses and workshops on advances in metabolomics. Instrumentation for targeted and untargeted metabolomics analysis.Provides mass spectrometers that are coupled to liquid chromatography (LC) or gas chromatography (GC) separation systems." .
SCR:017898 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_772" ;
rdfs:label "Brown University Molecular Pathology Core Facility" ;
NIFRID:synonym "Molecular Pathology Core" ;
definition: "Core provides equipment and technical expertise for evaluation of molecular and morphological changes in cells, tissues, and organs following exposure to complex environmental contaminants. Provides equipment, including automated tissue processor, paraffin embedding center, two automated microtomes, cryostat, vibratome for soft-tissue sectioning, multiheaded light microscope with projection capabilities, system for laser capture microdissection, and slide scanner with analysis software for identification and quantification of morphological structures.Offers expertise in histopathological and immunocytochemial methods, including fixation, dehydration, embedding, sectioning, histological staining, immunolabeling, high-resolution imaging, and quantitative image analysis. Services in sample preparation, offers assistance in imaging and image analysis and provides consultation for ongoing or future research projects, training program for students and investigators who use centrally available equipment." .
SCR:017899 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_766" ;
rdfs:label "Massachusetts Institute of Technology Koch Institute Preclinical Modeling Core Facility" ;
NIFRID:synonym "Preclinical Modeling Facility" ;
definition: "Core provides service support to all MIT investigators who utilize specialized in vitro cells such as stem cells, organoids, or primary cell lines and/or novel mouse models to study human diseases such as cancer. Projects involve generation of new model system, such as CRISPR-mediated gene editing in mouse to introduce mutation that mimics one found in patients. Helps with projects required optimization of finicky cell cultures and other challenges.Provides customizable set of service options to match specific needs of each project, including consultative advice and troubleshooting, complete tissue culture and microinjection services within our facilities or hands-on training to enable investigators to perfom these experiments either at their own laboratory or within our facilities.Services Include:Gene Targeting genomic modification through traditional or CRISPR/Cas9 locus targeting, assistance with targeting strategies and vector designs;Embryonic Stem Cells generation of new ES lines from mouse strains, importation and testing of lines from outside sources, differentiation of ES lines into specific cell lineages or cell types and more;Microinjection injection of mouse ES cells into blastocysts to generate chimeras and injection of DNA, RNA or CRISPR RNPs into the pronucleus of fertilized mouse eggs to generate transgenic and edited mice;Specialized Tissue Culture establishemnt of new primary cell cultures from a tumor, tissue or organ; Isolation of fibroblasts (MEFs) from mice for culture and analysis;Tissue Culture for Xenograft and Syngenic Modeling optimization, validation and testing of cell lines for orthotopic placement into mice, coordinated with Preclinical Testing Facility;Repository of Reagent Mice Commonly used wild type mice such as C57BL/6j as well as KrasG12D-based models of cancers are maintained on campus for efficient distrubution;Training and Troubleshooting for all aspects of embryonic stem cells, primary cultures, animal breeding etc.;Serum, DMEM, LIF and other media components that have been tested and verified for use with ES cells." .
SCR:017900 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_777" ;
rdfs:label "Brown University Structural Biology Core Facility" ;
NIFRID:synonym "Structural Biology Core Facility" ;
definition: "Core provides equipment used for structural modeling in crystals and in solution, using X-ray diffraction and scattering, as well as magnetic resonance." .
SCR:017901 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_775" ;
rdfs:label "South Florida University College of Medicine Fred Wright Jr Flow Cytometry Core Facility" ;
NIFRID:synonym "USF COM Fred Wright Jr Flow Cytometry Core" ;
definition: "Core is equipped with two benchtop analyzers from BD Immunocytometry Systems (3 laser/8 color BD Canto II and 4 laser/17 color BD LSR II). These instruments support large variety of applications, including multicolor cell phenotyping, apoptosis, cell cycle and bead arrays. After orientation and training, equipment is available for use directly by investigators. Alternatively experiments can be run and analyzed by Core Facility staff.For sorting purposes facility is equipped with high speed BD FacsAria IIu sorter (4 laser/11 colors), as well as magnetic sorter (AutoMacs Pro) from Miltenyi Biotech. FacsAria IIu is enclosed in Baker Bioprotect III to support sort of biohazardous agents level 1 and 2." .
SCR:017902 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_779" ;
rdfs:label "University of California at San Francisco Embryonic Stem Cell Targeting Core Facility" ;
NIFRID:synonym "UCSF ES Cell Targeting Core" ;
definition: "Core provides ES cell services with high probability of germline transmission. Offers ES cell targeting, genomic DNA extraction from 96-well plates, expansion of targeted ES cells, chromosome counts, and preparation of ES cells for microinjection.Prior to initiation of project, consultation is available on entire procedures of generating knockout mice. Core works with Gladstone Transgenic Gene Targeting Core for your microinjections to deliver full-range gene targeting service;CRISPR gRNA cloning,Cell-based functional test to identify best-performing TALENs or sgRNAs for your gene-editing experiment via mismatch-based assays such as Surveyor or T7E1;In vitro RNA synthesis - can help to make RNAs for your zygote injection or RNA transfection. We have TALEN and Cas9 plasmids with either T7 or T3 promoter subcloned in for efficient in vitro synthesis.sgRNAs for CRISPR can be synthesized off T7-sgRNA PCR product. Quality of synthesized RNAs will be checked via bioanalyzer;Custom TALEN to make double-strand breaks in genome;ES cell targeting (feeder-independent).Investigators targeting construct will be electroporated by core personnel. We have two feeder-independent ES cell lines, E14 (129-derived) and JM8A3.N1 (C57BL/6-derived) you can choose from. After drug selection for about one week, up to 300 colonies will be picked. When they are about to be confluent, we will split them as duplicate, one master plate to freeze for future expansion of positive clones and one plate for genotyping to identify targeted ES cell clones. Your plates for genotyping will be ready for pick-up 2-3 weeks after electroporation date.Genomic DNA extraction from ES cells on 96-well plate;Expansion of targeted clones from core targeting (up to 5 clones),A maximum of 5 positive clones will be thawed from 96-well plates and expanded to 6-wells. We will freeze 5 vials (each about 1 million)/clone for future use and give you 1 vial-equivalent cells to validate your genotyping before injection. It takes about 10 days to expand and freeze down cells;Expansion of ES cells from outside resources (per clone) Investigators provide one vial of frozen ES cells with information about culture condition from original resource. We will revive, nurture, and refreeze ES cells (5 vials) when they are ready. In addition, we will give you 1~2 million cells for your genotyping verification;Preparation for microinjection;Chromosome counting;Custom services." .
SCR:017903 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_778" ;
rdfs:label "University of California at San Francisco Division of Experimental Medicine Flow Core Facility" ;
NIFRID:synonym "Flow Cytometry Core" ;
definition: "Flow cytometry facility offering training and services including:Access to two, 17-color BD LSR II analytical instruments with High Throughput Sampler (HTS) module,Configurations:LSRII 1,LSRII 2;Help with Flow Cytometry Panel Design;Fluorofinder (access our cytometers under CFAR Immunology Core);BD Panel designer;SFGH LSRII Flow Core Protocols;LSRII Startup and Shutdown;How to run the CST calibration assay;Access to a 17-color BD FACSAria II for fluorescence-activated cell sorting (FACS);4-way tube sorting;96 well plate sorting;Index sorting;SFGH ARIA Flow Core Protocols and configuration;ARIA Startup;Determining Drop Delay;Side Stream Set Up;Clog Procedure;ARIA Shutdown Protocol;ARIA Configuration;DNA analysis with standard dyes;Analysis of CFP, GFP, YFP, mRFP, mTomato, and mCherry gene expression proteins;Calcium flux measurements using Indo-1;Training of users on the operation of instruments and experimental design through the CIL Flow Cytometry Course;Maintaining and Upgrading Instruments;Research Support Services (study design, assay selection, grant and paper writing support)." .
SCR:017904 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Mousebytes",
"r3d100013886",
"SCR_021549",
"SCR_021598" ;
rdfs:label "Mousebytes" ;
NIFRID:synonym "MouseBytes" ;
definition: "Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available." .
SCR:017905 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RegulomeDB" ;
definition: "Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature." .
SCR:017906 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_780" ;
rdfs:label "University of California at San Francisco Immunology Lab Core Facility" ;
NIFRID:synonym "Core Immunology Lab",
"University of California at San Francisco Core Immunology Lab" ;
NIFRID:abbrev "CIL" ;
definition: "Provides immunology assays, expert consultation, and education to UCSF and global research community. CIL specializes in developing immunology research tools, and initiating and stimulating innovative research projects to address emerging questions in immunologic diseases including HIV pathogenesis.Services include:Isolation of PBMC for staining, cell sorting, or viable cryopreservation;Isolation of mucosal mononuclear cells (MMC) from mucosal tissue biopsies;Immunomagnetic bead isolation of untouched cell populations for functional studies;Immunophenotyping of whole blood, PBMC, MMC and cerebrospinal fluid for: NK, B and T cells percentages, and their subsets, including maturation, trafficking, senescence, activation, in vivo proliferation and chemokine receptor expression;Flow cytometric functional assays, including NK cell function, antigen-specific CD4+ and CD8+ T cell cytokine expression, degranulation and proliferation;Evaluation of T cell signaling by phosflow using monoclonal antibodies specific for phosphorylated protein;Training and Support;Flow Cytometry Training Course;Three-hour lecture and lab course designed to cover basics of flow cytometry including:Fluorescence emission and detection,Fluidics,Operation,Panel design,Controls." .
SCR:017907 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_789" ;
rdfs:label "University of Massachusetts Amherst Genomics Resource Laboratory Core Facility" ;
NIFRID:synonym "Genomics Resource Laboratory" ;
NIFRID:abbrev "GRL" ;
definition: "Core provides services and advanced instrumentation support for nucleic acid (DNA and RNA) analysis, high-throughput next-generation sequencing, including solutions for sample processing such as nucleic-acid isolation, nucleic-acid quantitative and qualitative analysis, NGS library preparation, quantitative-PCR analysis, etc. Provides sample processing and library preparation such as whole genome sequencing, shotgun metagenomics, metatranscriptomics, targeted amplicon sequencing, RNA-Seq, ChIP-Seq, Exome Sequencing, Methyl-seq, Single Cell Genomics, etc. Facility accepts samples and will perform requested analysis. Offers training to users to conduct experimentation." .
SCR:017908 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_788" ;
rdfs:label "Johns Hopkins University School of Medicine Synthesis and Sequencing Core Facility" ;
NIFRID:synonym "Synthesis and Sequencing Facility" ;
definition: "Core provides services including Peptide Synthesis and Purification,Protein/Peptide Sequence Analysis,DNA Synthesis and Purification,Sanger DNA Sequencing,Next Generation Sequencing." .
SCR:017909 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_783" ;
rdfs:label "Oregon State University Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "Nuclear Magnetic Resonance (NMR) Facility" ;
definition: "Facility maintains instrumentation, provides hands-on training to new users, experimental design expertise, assistance with data analysis and support for incorporating NMR into grants and manuscripts. NMR spectrometers are available at 800 MHz, 700 MHz, 500 MHz and 400 MHz (2), corresponding to magnetic field strengths ranging from 18.8 T to 9.4 T. Data processing and analysis software is available on workstations in NMR Facility. The facility supports scientific inquiry in research areas such as structural biology, organic chemistry, natural products analysis and environmental studies." .
SCR:017910 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_791" ;
rdfs:label "Brown University Division of Biology and Medicine Proteomics Shared Resource Core Facility" ;
NIFRID:synonym "NSF/EPSCoR Proteomics Shared Resource Facility" ;
definition: "Core provides instrumentation and proteomics expertise to Brown University and Rhode Island-EPSCoR scientific communities and training in emerging proteomic techniques. Mass Spectrometry proteomics resources and services are provided by COBRE Center for Cancer Research Development (CCRD) at Rhode Island Hospital: Proteomics Core." .
SCR:017911 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_796" ;
rdfs:label "Iowa State University W.M. Keck Metabolomics Research Laboratory Core Facility" ;
NIFRID:synonym "Iowa State University Metabolomics Research Laboratory",
"Iowa State University W.M. Keck Metabolomics Research Laboratory",
"W. M. Keck Metabolomics Research Laboratory" ;
NIFRID:abbrev "MRL" ;
definition: "Core facility that conducts fee for service mass spectrometry-based non-targeted and targeted metabolomic studies. The facility serves and partners with both on- and off-campus clients." .
SCR:017912 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_786" ;
rdfs:label "University of Sheffield Genomic Core Facility" ;
NIFRID:synonym "Core Genomic Facility" ;
definition: "Core provides DNA sequencing services including DNA extraction, cell line identification, microsatellite analysis, and antibody sequencing,DNA Sequencing, Monoclonal Antibody Sequencing,Nucleic Acid Quantification,PCR Machine Hire,Real-Time PCR Robotic Liquid Handling,Taqman SNP Analysis." .
SCR:017913 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_790" ;
rdfs:label "University of North Carolina at Chapel Hill Microscopy Services Laboratory Core Facility" ;
NIFRID:synonym "Microscopy Services Laboratory" ;
NIFRID:abbrev "MSL" ;
definition: "Core provides training, assistance and services in light microscopy, electron microscopy and image analysis. UNC core facility that is part of Department of Pathology and Laboratory Medicine, and are light microscopy core for Lineberger Comprehensive Cancer Center." .
SCR:017914 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_801" ;
rdfs:label "University of Chicago Cellular Screening Center Core Facility" ;
NIFRID:synonym "Cellular Screening Center",
"Cellular Screening Facility",
"University of Chicago Cellular Screening Center" ;
definition: "Facility provides high throughput cell- and non-cell-based screening. Has number of validated cell lines and variety of small molecule or siRNA screening libraries available to investigators." .
SCR:017915 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_802" ;
rdfs:label "Chicago University Biophysics Core Facility" ;
NIFRID:synonym "BioPhysics Core Facilities" ;
definition: "Core provides access to biophysics equipment, integral to research community at University of Chicago.Provides tools, training, and assistance for quantitative analysis of macromolecules and their interactions. Instruments include Seahorse XFe-96 Extracellular Flux Analyzer,Jasco J-1500 CD Spectrometer,Synergy Neo HST Plate Reader,Wyatt DAWN HELEOS II SLS,Wyatt DynaPro Plate Reader DLS,Wyatt DynaPro NanoStar DLS,HORIBA Fluorolog-3,Microcal iTC200,Molecular Imager,Bio-Rad ProteOn XPR to Biacore 8K,Agilent 8453 Spectrophotometer. Core provides staff assistance in conducting experiments." .
SCR:017916 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_804" ;
rdfs:label "University of Chicago Human Immunologic Monitoring Core Facility" ;
NIFRID:synonym "Human Immunologic Monitoring Facility" ;
NIFRID:abbrev "HIM" ;
definition: "Facility serves as specialized laboratory performing correlative assays for cancer-based clinical trials. Participates in project development to assist in assay selection and optimization prior to study initiation. Offers pick-up service for specimens from patients at U of C Hospital or outpatient clinics, and process samples as indicated for assays being performed. For some studies, isolation and freezing of peripheral blood lymphocytes for analysis at later date is performed, while for others immediate staining of whole blood for specific cell surface markers of interest is carried out. Prepares clinical grade products, such as peptide vaccines, for administration into patients.Assays performed include ELISA, ELISPOT, tetramer binding assays, detection of cell surface markers by flow cytometry, and biochemical assays such as Western Blots, RNA extraction from tumor biopsies and either real time RT-PCR for specific transcripts or preparation of samples for gene expression profiling. Facility is equipped with MACSQuant Flow Cytometer, ELISA microplate reader, ELISPOT reader, PCR thermocyclers, CO2 incubators, biosafety cabinets, centrifuges, and equipment for Western blot analysis. Performs assays on human samples but consideration will be given to expanding these services to mouse-model systems." .
SCR:017917 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_797" ;
rdfs:label "Case Western Reserve University Imaging Research Core Facility" ;
NIFRID:synonym "Imaging Research Core" ;
definition: """Core provides preclinical and clinical imaging instrumentation and techniques.Preclinical services include Bioluminescence,Fluorescence,In situ cryoimaging,Magnetic Resonance Imaging (MRI),Positron Emission Tomography (PET),Radiochemistry Synthesis,
Scintigraphy,Ultrasound,X-ray / Computed Tomography (CT) / micro CT,Image Processing / Quantification clinical research imaging systems. Clinical services include Comprehensive MR imaging research services, Dedicated Siemens Skyra 3T MRI scanner, Large animal preclinical studies, or clinical human research may be conducted,Structural and functional brain scanning can be performed with Avotec LCD Projection System, Coodination of access to PET and CT scanners for additional preclinical and human imaging studies. Core includes PET radiopharmaceutical core facility. Core staff provide radiochemistry synthesis.""" .
SCR:017918 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_803" ;
rdfs:label "Chicago University iPSC Core Facility" ;
NIFRID:synonym "IPSC Core Facility" ;
definition: "Core provides training to use latest episomal techniques to reprogram, expand and characterize human and mice iPS cells from skin or blood tissues of healthy subjects and diseased patients. Develops capability to differentiate iPS cells into specific somatic cells, such as neutrons, cardiomyocytes, and hepatocytes." .
SCR:017919 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_800" ;
rdfs:label "University of California San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences NMR Core Facility" ;
NIFRID:synonym "SSPPS NMR Facility" ;
definition: "Core provides access to NMR technology. Users can collect their own data, facility staff can do it all for you, or collaborative projects can be developed. Provides training in instrument operation and can offer advice for data analysis or project feasibility. Facility houses two 600 MHz Bruker Avance III spectrometers with cryogenically cooled probes." .
SCR:017920 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_807" ;
rdfs:label "Kansas University Medical Center Hoglund Brain Imaging Center Core Facility" ;
NIFRID:synonym "Hoglund Brain Imaging Center" ;
NIFRID:abbrev "HBIC" ;
definition: "Core provides imaging capabilities, including magnetic resonance imaging, magnetoencephalolgraphy, electroencephalography, magnetocardiography, and ultrasound,expertise in cognitive neuroscience, neurobiology, biomedical physics, and computing, together with support team of technologists, nurses, research associates, and research assistants. Through strong collaborations, these individuals assist with study design, collection of data, analysis, and interpretation of results. HBIC supports investigators with new technique development, feasibility studies, pilot funding, preparing grant applications and manuscripts, and compliance. Carries out investigator-initiated research and research/clinical trials sponsored by public and private agencies. Offers education and training." .
SCR:017921 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_814" ;
rdfs:label "University of Texas Southwestern Medical Center Mouse Genome Engineering Core Facility" ;
NIFRID:synonym "CRI Mouse Genome Engineering Core" ;
definition: "Core provides production of mouse models to support fundamental and translational research. Provides transgenic, gene targeting,DNA microinjection services, CRISPR/Cas9 microinjection, ES cell manipulation and other microinjection services to generate transgenic mice, knock-in/knock-out mice and chimeric mice harboring select genetic mutations. Other services include mouse sperm cryopreservation and recovery, in vitro fertilization (IVF), rederivation of pathogen free mouse lines and derivation of mouse embryonic stem cell lines. Provides general consultations on experimental designs and vectors for gene modification-related projects, DNA preparation, recombinant ES clones, mouse genotyping, colony breeding and husbandry, customize services as requested to support development of animal models for modeling human diseases." .
SCR:017922 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_815" ;
rdfs:label "Florida State University X-Ray Crystallography Core Facility" ;
NIFRID:synonym "X-Ray Crystallography Facility" ;
NIFRID:abbrev "XRF" ;
definition: "Shared macromolecular x-ray crystallography facility provides instruments and expertise for screening, optimizing, imaging, growing, and storing crystals of biological macromolecules. The X-Ray Facility coordinates single crystal x-ray diffraction data collection at third generation synchrotron x-ray source using FSU's membership at the National Synchrotron Light Source II at Brookhaven National Lab, Upton, NY. XRF also offers custom buffer preparation, optimization, and crystal set-up using multi-well format crystallization blocks and plates.XRF has ARI Crystal Gryphon robot, Formulatrix Rock Imager, Formulator 16, Rock Maker software, RUMED incubator, Cryo storage and shipping dewars, Leica S8 AP0 Zoom microscope and other amenities." .
SCR:017923 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_805" ;
rdfs:label "Chicago University Integrated Small Animal Imaging Research Resource Core Facility" ;
NIFRID:synonym "Integrated Small Animal Imaging Research Resource" ;
NIFRID:abbrev "iSAIRR" ;
definition: "Core offers imaging modalities, techniques, and services for in vivo imaging of small animals and ex vivo imaging of tissue/organ specimens. iSAIRR sub-cores feature magnetic resonance imaging and spectroscopy (MRIS); optical imaging (bioluminescence and fluorescence); positron emission tomography, single photon emission computed tomography, and computed tomography (PET/SPECT/CT).Services include Assistance with experimental design,Assisted and/or independent image acquisition,Veterinary support for all imaging modalities,Assistance with data processing and interpretation." .
SCR:017924 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_816" ;
rdfs:label "University of California, Berkeley Biosciences Divisional Services Cell Culture Core Facility" ;
NIFRID:synonym "Cell Culture Facility" ;
definition: "Core provides cell cultures (mammalian and insect), media, supplies and expertise and consultation regarding cell culture needs, media, and experimental design.Provides tested media, serum, and cell lines at exceptionally low prices, large scale production of cells, expansion and harvesting of hybridoma lines,cryopreservation of cell lines, Cell Authentication by STR analysis provided in conjunction with DNA Sequencing Facility, Mycoplasma screeening,Use of 2 laminar flow hoods for mammalian or insect cell manipulation." .
SCR:017926 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_820" ;
rdfs:label "New York University School of Medicine Langone Health Proteomics Laboratory Core Facility" ;
NIFRID:synonym "New York University School of Medicine Langone Health Proteomics Laboratory",
"Proteomics Laboratory" ;
definition: """Core offers specialized expertise for analysis of proteins and peptides using mass spectrometry. Develops new methods and customized approaches for proteomic analysis and suggests experimental strategies and sample preparation prior to mass spectrometry analysis. Services include:comprehensive protein identification ,analysis of affinity purified complexes,characterizing protein post-translational modifications,de novo sequencing,label and label-free quantitation ,multiplexed quantitation
global phosphorylation and ubiquitin analysis,analysis of laser-capture microdissected formalin-fixed paraffin-embedded tissue,secretome analysis,crosslinking analysis,disulfide mapping.""" .
SCR:017927 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_817" ;
rdfs:label "Children's Hospital Oakland Research Institute Elemental Analysis Core Facility" ;
NIFRID:synonym "Elemental Analysis Facility" ;
NIFRID:abbrev "CHORI-EAF" ;
definition: "Core provides sample preparation, metal extraction, dissolved solids measurement, analytic consultation, and technical writing assistance) in support of wide range of clinical and biomedical research projects.Instruments include Agilent 5100 SVDV Inductively-Coupled Plasma-Optical Emission Spectrometer, SPS3 Robotic Autosampler,MARS5 Microwave Sample Digestion Oven,ICPExpert Advanced Workstation.Analytic Capabilities:Simultaneous, multi-element quantitation over wide dynamic range;Broad elemental detection capability with high precision and sensitivity;Compatible with range of clinical, nutritional, basic research, and pharmaceutical samples;Tolerant of high total dissolved solids and complex matrix components;NIST-traceable calibrants, standards, and other QA/QC controls included in analyses." .
SCR:017928 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_823" ;
rdfs:label "New York University School of Medicine Langone Health Experimental Pathology Research Laboratory Core Facility" ;
NIFRID:synonym "New York University School of Medicine Langone Health Experimental Pathology Research Laboratory",
"NYU Langon Experimental Pathology Research Laboratory" ;
definition: """Core provides services, access to instruments, and training to facilitate production of animal tissue samples for morphological and molecular analyses. Supports multiplex immunofluorescence staining, RNA in situ hybridization (ISH), and imaging analysis.
Services include tissue preparation, processing, and sectioning, as well as histochemistry and immunohistochemistry of fresh, frozen, and fixed animal tissues, can optimize and validate commercial or proprietary antibodies for chromogenic or fluorescence-based immunohistochemistry including seven-color multiplexing.Provides access to database listing antibodies that have been tested in lab to date and are currently in stock.Offers basic imaging resources and digital whole-slide scanning of stained tissue sections, which allows researchers to view their slides online at their convenience.Researchers can also rent our self-service instruments. These include embedding station, microtome, cryostat, and vibratome. Provides access to brightfield and fluorescence upright and dissecting microscopes,laser capture microdissection scope, and high-throughput multispectral imaging system.To reserve time on instrument, faculty, staff, and investigators must be registered in iLab.""" .
SCR:017929 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_824",
"SciEx_41",
"SCR_012514" ;
rdfs:label "New York University School of Medicine Langone Health Genome Technology Center Core Facility" ;
NIFRID:synonym "New York University School of Medicine Genome Technology Center",
"New York University School of Medicine Langone Health Genome Technology Center",
"NYU Langone's Genome Technology Center" ;
NIFRID:abbrev "GTC",
"NYU GTC" ;
definition: "Core provides range of services related to genome, epigenome, and transcriptome analysis. Offers technologies including Illumina deep sequencing and sample preparation for variety of applications, including DNA and RNA sequencing (DNA- and RNA-seq), exome sequencing, targeted capture, chromatin immunoprecipitation sequencing (ChIP-seq), methylation sequencing (Methyl-seq), metagenomics, and many others;Automation of Illumina library and targeted capture preps, including 16S ribosomal RNA (rRNA) sequencing;Oxford Nanopore sequencing (long reads);Bio-Rad Droplet Digita polymerase chain reaction (PCR);Nanostring nCounter;Single-cell RNA- and DNA-seq using the C1 Auto Prep System from Fluidigm, and 10x Genomics Chromium System.Provides expertise on strategies to achieve research goals in any field related to genomics, and can tailor bioinformatics analysis to individual project. If you supply us with nucleic acids, we can perform every step required to help you achieve your desired results." .
SCR:017930 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_825" ;
rdfs:label "New York University School of Medicine Langone Health Center for Biospecimen Research and Development Core Facility" ;
NIFRID:synonym "New York University School of Medicine Langone Health Center for Biospecimen Research and Development",
"NYU Langone Center for Biospecimen Research and Development" ;
definition: "Core mission is to drive scientific discovery through use of human specimens.Helps facilitate translational research, match human specimen resources to scientific needs, foster multi-investigator collaborative projects, and catalyze scientific innovation,improving researcher access to existing biospecimen resources, and enhancing institution-wide tissue-banking efforts and capacity. Another priority is to implement campus-wide policy for human biospecimen collection and storage to ensure regulatory compliance." .
SCR:017931 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_809" ;
rdfs:label "University of Wisconsin-Madison Chemistry Instrumentation Center - Mass Spectrometry Core Facility" ;
NIFRID:synonym "Mass Spectrometry Facility" ;
definition: "Core provides mass spectrometers including Thermo Q Exactive Plus,Bruker impact II ,Bruker microflex LRF,Bruker ULTRAFLEX III,Shimadzu GCMS-QP2010S,Waters Acquity LCMS." .
SCR:017932 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_827" ;
rdfs:label "New York University School of Medicine Langone Health Genotyping Core Laboratory Core Facility" ;
NIFRID:synonym "New York University School of Medicine Langone Health Genotyping Core Laboratory",
"NYU Langone Genotyping Core Laboratory" ;
definition: "Core provides fast, accurate, convenient, and affordable genotyping technologies. We use conventional polymerase chain reaction (PCR) and gel electrophoresis methods. By pooling samples from group of users, we can better ensure accuracy, cost-effectiveness, and quality control." .
SCR:017933 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_837" ;
rdfs:label "Queensland University of Technology Central Analytical Research Facility (CARF) Proteomics and Small Molecule Mass Spectrometry Core Facility" ;
NIFRID:synonym "Proteomics and small molecule mass spectrometry" ;
definition: "Core provides liquid chromatography and gas chromatography mass spectrometry instrumentation for selective identification and reproducible quantification of trace-level biomolecules in complex samples. Services include qualitative, quantitative and structural analysis of proteins, lipids, metabolites, pesticides, pharmaceuticals and volatile organic compounds. Tests can be performed as long as molecules of interest are amenable to ionisation technique employed in source of mass spectrometer. Depending on instrument type, samples may be solid, liquid or gas. Mass spectrometry platforms include Liquid Chromatography Mass Spectrometry (LC-MS) and Gas Chromatography Mass Spectrometry (GC-MS). Analysis include volatile organic compounds (odour analysis),pharmacokinetics (bioavailability, bioefficacy),drug development (determining structures of drugs and metabolites),clinical testing (biomarkers discovery and endogenous compounds),genomics (oligonucleotide sequencing) epigenetics (global DNA methylation analysis),environmental research (testing water, soil, food and air quality)." .
SCR:017934 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_366" ;
rdfs:label "New York University School of Medicine Langone Health Microscopy Laboratory Core Facility" ;
NIFRID:synonym "NYU Langone Microscopy Laboratory" ;
definition: "Core offers comprehensive light and electron microscopy technologies. Our scientists use light microscopes and electron microscopes at resolutions ranging from centimeters to angstroms, providing clear and detailed images.We assist at every stage of your experiment, offering research-design consultation and instrument training, as well as guidance in study execution, analysis, and presentation for publication." .
SCR:017935 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_826" ;
rdfs:label "New York University School of Medicine Langone Health Metabolomics Laboratory Core Facility" ;
NIFRID:synonym "New York University School of Medicine Langone Health Metabolomics Laboratory",
"NYU Langone Metabolomics Laboratory" ;
definition: "Core offers custom metabolomics services,specializes in mass spectrometry based metabolomics, offering global (untargeted) and targeted methods for metabolite identification and quantification.Commonly assayed targets include glycolytic and tricarboxylic acid (TCA) cycle intermediates, amino acids, nucleotides, and lipids. Using custom-targeted method, we can perform absolute or relative quantification, flux analysis, and biotransformation analysis." .
SCR:017936 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_833" ;
rdfs:label "New York University School of Medicine Langone Health Precision Immunology Laboratory Core Facility" ;
NIFRID:synonym "New York University School of Medicine Langone Health Precision Immunology Laboratory",
"NYU Langone Immune Monitoring Laboratory",
"NYU Langone Precision Immunology Laboratory" ;
definition: """THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 20,2025. Core to study immune cell phenotype and function, characterizes antitumor immune responses, determines mechanisms of immune escape and evasion, and develops biomarkers that predict patient outcomes or possible toxicities. Offers services for immune monitoring,provides expert knowledge that guides choice of technologies used for study, coordinates purchase, quality control, and use of reagents. Stand-alone services include high-quality cell processing and storage to support correlative studies. These services allow convenient batched analysis of trial samples.Staff purifies peripheral blood mononuclear cells daily from clinic visits and another staff member is available for on-demand and after-hours processing. Samples are cryopreserved on-site in temperature-monitored LN2 freezers for short-term storage. For long-term storage, samples are transferred to Novare Biologistics,off-site cGMP-compliant, New York State-licensed, and FDA-registered biorepository.
Routinely assess quality of processing and cryopreservation. Core meets performance targets for cell viability and recovery necessary for certification by Integrated Biobank of Luxembourg. Offers service for isolating tumor-infiltrating lymphocytes using dissociation protocols optimized for various tumor tissues. Offers flow cytometry at Perlmutter Cancer Center, along with expert service and training. Sterile fluorescence-activated cell sorting (17 colors) is routinely performed with options for high-speed (50K cells per second), single-cell deposition (into polymerase chain reaction plates), and BSL-3 sorting for unscreened or infected human material. Data analysis workstations are also available.Offers single-cell analysis through our cutting-edge 30-parameter flow cytometry technology and Integrated Molecular Cytometry Platforms (IMCPs).""" .
SCR:017937 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_830" ;
rdfs:label "New York University School of Medicine Langone Health Preclinical Imaging Laboratory" ;
NIFRID:synonym "NYU Langone Preclinical Imaging Laboratory" ;
definition: "Core provides investigators with access to imaging technologies and strategies to image live animals on organ, tissue, cell, or molecular level.Core for studying and monitoring disease in small living subjects.Performs noninvasive and nonlethal three-dimensional imaging. Equipped with instruments for micromagnetic resonance imaging, micropositron emission tomography, X-ray microcomputed tomography, bioluminescence and fluorescence scanning, and high-frequency ultrasound." .
SCR:017938 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_881" ;
rdfs:label "University of Illinois at Urbana-Champaign Core Facilities at IGB" ;
NIFRID:synonym "Core Facilities at IGB" ;
definition: "Core for biological microscopy and image analysis. Offers high-end equipment,user training,ongoing support, including experiment design and data interpretation,twenty-four hour access Services,3D Printing, Transfer Files, Image Analysis,Histology,Instrument Training." .
SCR:017939 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_892" ;
rdfs:label "Northern Arizona University Environmental Genetics and Genomics Laboratory" ;
NIFRID:synonym "NAU Environmental Genetics and Genomics Laboratory" ;
NIFRID:abbrev "EnGGen" ;
definition: "Core facility for genomics research offers range of DNA sequencing, assistance and advising in planning, data acquisition, and data analysis. Provides genetic and genomic support to environmental and biomedical research projects. Creates education and training opportunities for students and professionals." .
SCR:017940 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_872" ;
rdfs:label "Gladstone Institutes Histology and Light Microscopy Core Facility" ;
NIFRID:synonym "Histology and Light Microscopy Core" ;
definition: "Core provides technical assistance, training, consultation and assistance with all aspects of experimental design, sample preparation, image processing, and data analysis to scientists from Gladstone, UCSF, and Bay Area scientific community. Core is equipped with expertise in histological techniques including complex immunolabeling and histological image analysis, high-resolution imaging, confocal microscopy, light-sheet microscopy, spinning disk microscopy, and optical projection tomography and advanced image analysis.Histology Services includeTissue dissection and fixation, Paraffin processing and embedding,Frozen (cryo) processing and embedding,Tissue sectioning,Section staining.Microscopy Services include Epifluorescence, confocal and light sheet microscopy,Whole slide scanning,Microscopy consultation and training,Digital image analysis." .
SCR:017941 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_939" ;
rdfs:label "Northwestern University Materials Research Center Cleanroom Core Facility" ;
NIFRID:synonym "Materials Processing and Microfabrication Facility" ;
NIFRID:abbrev "NUFAB-Cook Hall" ;
definition: "Cleanroom facility is devoted to materials processing, growth, device fabrication, characterization and electronic and photonic materials. Provides microfabrication and thin film processing capabilities. Facility includes class 100 and 1000 cleanrooms.Training of equipment and assisted use within facility is available to provide necessary expertise.Provides centralized resource for deposition of metal, semiconductor and dielectric thin films, photolithography, etching, bonding, dicing, characterization and materials processing." .
SCR:017942 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_831" ;
rdfs:label "New York University School of Medicine Langone Health Rodent Behavior Laboratory" ;
NIFRID:synonym "NYU Langone Rodent Behavior Laboratory" ;
definition: "Core offers equipment, facilities, and expertise to quantitatively assess broad range of behaviors in mice and rats, develop and validate novel paradigms to improve translation of preclinical behavioral results to clinically relevant outcome measures and create better tools for biobehavioral research.Core helped develop novel touch-screen tests to assess rodent attention, working memory, and reinforcement learning." .
SCR:017943 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_945" ;
rdfs:label "Northwestern University Biostatistics Collaborative Center" ;
NIFRID:synonym "Biostatistics" ;
definition: "Core where division members engage in statistical methods development and application, research design and statistical computing for health science research. Faculty interests encompass Bayesian methods, bioinformatics, causal inference, computational biology, clinical trials, diagnostic testing, longitudinal modeling, missing data modeling, observational data methods, semi-parametric models, spatial modeling, statistical genetics and survival analysis." .
SCR:017945 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_944",
"SCR_017880" ;
rdfs:label "Northwestern University Proteomics Core Facility" ;
NIFRID:synonym "Northwestern Proteomics",
"Northwestern University Proteomics Center of Excellence Core Facility" ;
definition: "Core offers multiple types of experiments from simple protein identification to protein quantitation. Performs traditional bottom-up proteomics, where proteins are digested with enzyme prior to analysis and intact, top-down proteomics analyses. Services include proteins identification after in-gel or in-solution digestion, top-down mass spectrometry to preserve post-translationally modified forms of proteins present in vivo by measuring them intact, IP-MS Pulldown,BioID service to identify target of biotin ligase that has been tagged onto their protein via traditional cloning methods,Untargeted Quantitative Peptide Proteomics,Targeted Quantitative Peptide Proteomics,Epiproteomic Histone Modification Panel A,Epiproteomic Histone Modification Panel B,Untargeted Metabolomics,Phosphoproteomics,PTM Scan,ChIP-MS." .
SCR:017946 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_894" ;
rdfs:label "Oregon Health and Science University Bioinformatics and Biostatistics Core Facility" ;
NIFRID:synonym "Bioinformatics and Biostatistics Core",
"Oregon Health and Science University Bioinformatics and Biostatistics Core" ;
NIFRID:abbrev "BBC" ;
definition: "Core provides statistical and big data analysis support. Performs data analysis and manuscript preparation services in Biostatistics, such as statistical genetics, longitudinal, survival, and high-throughput/high-dimensional omics data analysis; and Bioinformatics, such as DNA- and RNA-seq alignment, single cell DNA- and RNA-seq analysis, variant calling, differential expression and pathway analysis, data integration, online data submission, and custom script writing. Provides training to lab staff to enable them to perform future analyses." .
SCR:017947 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_937" ;
rdfs:label "Northwestern University Materials Characterization and Imaging Core Facility" ;
NIFRID:synonym "Materials Characterization and Imaging Facility" ;
NIFRID:abbrev "MatCI" ;
definition: "Core offers characterization and sample preparation equipment. Characterization techniques include optical microscopy, thermal imaging, thermal analysis (DSC, TGA), hardness testing (Vicker, Knoop, Rockwell), electronic characterization (Hall Effect, Impedance Spectroscopy, Kelvin Probe, Charge Transport) and rheological characterization. Sample and surface preparation capabilities include mounting (castable mounts, hot pressure mounting, vacuum impregnation), cutting, sectioning and wafer dicing, polishing/grinding, electropolishing, ion beam milling and cross-sectional polishing. Tube and box furnaces are available with temperature range up to 1700C for thermal processing." .
SCR:017948 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_947" ;
rdfs:label "Northwestern University Developmental Therapeutics Core Facility" ;
NIFRID:synonym "Developmental Therapeutics Core" ;
NIFRID:abbrev "DTC" ;
definition: "Core evaluates therapeutic agents and diagnostics, as well as existing therapeutics being considered for novel uses, through continued development and deployment of relevant animal models and in vitro cell lines and tissue models. Provides services to investigators to suit many needs, including those who may lack laboratory facilities and/or expertise for conducting experiments associated with preclinical therapeutic hypothesis testing.Services include Proliferation and Apoptosis Assays, Therapy-Response Experiments, Exploratory PK and Tox, Device Implantation and Monitoring,PDX Models,Immunization." .
SCR:017949 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_975" ;
rdfs:label "Texas University Southwestern Medical Center Whole Brain Microscopy Core Facility" ;
NIFRID:synonym "Whole Brain Microscopy Facility" ;
NIFRID:abbrev "WBMF" ;
definition: "Core suited to advance study of traumatic brain injury, as well as other neurological and psychiatric disorders.Utilizes microscopy strategies to evaluate neuropathology across micro-, meso-, and macro-scales of inquiry. Provides access to microscopes including TissueCyte 1000 multi-photon microscopes,Hamamatsu NanoZoomer 2.0-HT,Zeiss Axioscan.Z1. Offers access to fluorescence stereomicroscope and upright microscope, both with digital cameras, as well as sectioning equipment (cryostat, microtome, and vibrotome). Provide computer available for use running MicroBrightField Stereo Investigator and Neurolucida software packages for offline stereological analysis, neuron tracing, and 3D rendering of large, whole-brain datasets." .
SCR:017950 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_982" ;
rdfs:label "Beth Israel Deaconess Medical Center Translational MRI Research Core Facility" ;
NIFRID:synonym "Translational MRI Research Core" ;
definition: "Core provides MRI capabilities for imaging human subjects and potentially large animals as part of research studies. Facility operates GE Discovery MR750 3T whole-body scanner and can provide access to 1.5T system. Scanner is FDA cleared for clinical use. It has proprietary software including pulse programming environments and reconstruction programs and customizable software and protocols for applications including functional and structural brain imaging, abdominal perfusion and diffusion, muscle functional imaging and spectroscopy are available to users.Support for fMRI acquisition and visual and auditory stimulus presentation, diffusion tensor imaging, spectroscopy, and high quality anatomic imaging is available. The system has specialized receiver coils for sensitive imaging of particular anatomy. Additional customized coils can be manufactured in our RF lab. The system also has full broadband capability for multinuclear MRI and MRS, including (F-19, C-13, P-31, and Na-23).Our facility can also provide Image Post-processing and computerized image transfer, assistance to ensure MRI equipment safety, and can facilitate Clinical Readings." .
SCR:017951 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_983" ;
rdfs:label "North Carolina University at Chapel Hill Nanomedicines Characterization Core Facility" ;
NIFRID:synonym "Nanomedicines Characterization Core Facility" ;
definition: "Core provides physicochemical characterization of nanoscale entities. Offers characterization of several classes of nanomaterials:Polymer conjugates,Polymeric micelles,Liposomes,Nanogels,Polyion complexes of small drugs and biomacromolecules (proteins, DNA, and RNA),Inorganic/metal nanoparticles,Bio-derived nanoparticles such as exosomes with protein and nucleic acid cargo." .
SCR:017952 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_946" ;
rdfs:label "Northwestern University School of Medicine Structural Biology Core Facility" ;
NIFRID:synonym "Structural Biology Core" ;
definition: """Core provides equipment, training, technical support, and maintenance of equipment for studying structures of biological macromolecules and materials. Serves with expertise in structural and computational biology. Services offered include Macromolecular Structure Determination and Analysis,Macromolecular crystallography at LS-CAT,Robotics equipment for crystallization experiments,UV crystal imaging capabilities,Software for structure analysis,Graphics facilities for visualization/presentation of molecular structures,Computer servers specialized for structural biology calculationss,Support and Training ,X-ray crystallography, from designing crystallization experiments to structure determination and refinemen,Molecular graphics for analysis and presentation,CryoEM and EM training.Resources Available:Crystallography Art Robbins, Inc. Phoenix and Gryphon crystallization robots,TTP Labtech Dragonfly liquid handler for crystal tray setup,Jansi UVEX UV/Vis microscope/imaging system,Stereomicroscopes (camera equipped, at room temperature and 4 degrees C),Incubators for temperature-controlled crystallization,Coordination of access to LS-CAT for Northwestern University users,CryoEM,JEOL 3200FS TEM equipped with in-column energy filter (omega filter), field emission gun capable of operating at 200 or 300 kV and Gatan K2 Summit Direct Electron Detector,JEOL 1400 with Gatan 4k x 4k Ultrascan CCD camera,Solarus Plasma Cleaner and Pelco easyGlow Discharge Cleaning System,Cressington 308R carbon coater,Gatan Cryoplunge 3 and FEI Vitrobot Mark IV,Gatan 626 cryoholders with 655 Turbo pump stations.Resources available Computational:50+ node cluster running Linux including several single- and multi-GPU nodes,7 Quad-core Intel Xeon 3.4GHz workstations (3D stereo equipped for visualization and model building)
3 Dual Quad-core Intel Xeon 3.5GHz workstations with GPU computing capabilities (3D stereo equipped for visualization, model building, and GPU computing),LTO6 writers for quick data backup,45 tape LTO6 system for continuous data backup,Over 200 Tb of disk storage including RAID systems,10 Gigabit fiber Ethernet connection to APS.Software Crystallography,CCP4 suite,PHENIX,SHARP,SOLVE,HKL2000,XDS,CryoEM,CryoSparc,Relion3,Leginon,cisTEM,Appion,NMR,CNS,FELIX,Aria
Modeling, graphics, and simulations,COOT,Pymol,Chimera,APBS,GROMACS,AMBER,VMD/NAMD.""" .
SCR:017953 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_986" ;
rdfs:label "South Carolina Medical University Bioenergetics Profiling Core Facility" ;
NIFRID:synonym "Bioenergetics Profiling Core" ;
definition: "Core provides several technologies that enable researchers to quantify fluxes of these metabolic reactions in cells, tissues, organoids and small animal models such as zebrafish embryos and nematodes.Technologies include high resolution respirometry using XF technology from Seahorse Biosciences/Agilent. Instrumentation utilizes 96-well microplates to provide sufficient sample numbers to provide flux profiles of glycolysis, mitochondrial respiration, fatty acid oxidation, glutamine utilization and other related metabolic processes. Rapid, high-throughput imaging optimized to XF plate architecture provides normalization of cell/tissue numbers, health, and other.Provides training, data analyses support and aid in experimental design." .
SCR:017954 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_988" ;
rdfs:label "South Carolina Medical University Cell and Molecular Imaging Core Facility" ;
NIFRID:synonym "Cell and Molecular Imaging Core" ;
NIFRID:abbrev "CMI" ;
definition: "Core provides COBRE investigators access and assistance for high end laser scanning confocal/multiphoton/super-resolution microscopy and related imaging techniques. Houses confocal/multiphoton systems: Zeiss LSM 880 NLO Quasar confocal/multiphoton microscope with Fast Airyscan super-resolution detector; Olympus FV1200 silicone oil optics multiphoton microscope configured especially for intravital imaging; Olympus FV10i LIV confocal microscope with water immersion optics for live cell imaging; Zeiss LSM 510 META laser scanning confocal microscope for general purpose imaging of live and fixed specimens; BD CARV II disk-scanning confocal microscope for video rate real-time confocal imaging providing sophisticated imaging technologies, expertise and training." .
SCR:017955 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_987" ;
rdfs:label "South Carolina Medical University Analytical Redox Biology Core Facility" ;
NIFRID:synonym "Analytical Redox Biology Core" ;
definition: "Core provides analytical redox biochemistry methods and mentoring support for COBRE junior faculty with goal to advance their research endeavors, publications and fundability. Specific aims are:Provide ROS /RNS identification and quantification, Perform quantitative analysis of ROS/RNS. Provides expertise and technology for in depth biochemical analysis of thiol-centered enzyme activities and define protein:protein interactions." .
SCR:017956 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_990" ;
rdfs:label "Virginia Tech Mass Spectrometry Incubator Core Facility" ;
NIFRID:synonym "Virginia Tech Mass Spectrometry Incubator" ;
NIFRID:abbrev "VT-MSI" ;
definition: "Facility supports Virginia Tech's research infrastructure as mass spectrometry analysis and education center. Provides training in sample preparation, instrument operation and data analysis, with strong emphasis on metadata and analytical requirements for publication of metabolomic and proteomic results." .
SCR:017957 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_949" ;
rdfs:label "Northwestern University DevSci Neurodevelopmental Core Facility" ;
NIFRID:synonym "Developmental Sciencies Neurodevelopmental Core" ;
NIFRID:abbrev "ND Core" ;
definition: "Core provides services in support of research, education, and assessment technology related to neurodevelopmental research methods. Services include Scientific Consultation, Workshops and Training,EEG/ERP,Eye-tracking,Clinical and Behavioral Measure Services.Services include Data Collection, Use of Equipment, Experimental Task Creation and Preparation." .
SCR:017958 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_991" ;
rdfs:label "Virginia Tech Biocomplexity Institute Genomics Sequencing Center Core Facility" ;
NIFRID:synonym "Genomics Sequencing Center" ;
NIFRID:abbrev "GSC" ;
definition: """Core for development and application of Next-Generation Sequencing technologies. Provides experimental design consultation, and genomic, transcriptomic, and functional-genomics services. Specializes in development and application of Next-Generation Sequencing technologies and bioinformatics analyses. Instruments include Illumina NovaSeq 6000, Illumina NextSeq 500,Illumina MiSeq,Thermo Ion S5. Services include mRNA-Seq: Stranded and non-stranded, high levels of multiplexing up to 96 or more samples on NovaSeq;Standard amounts, Stranded-Seq: 500 ng total RNA, RIN 8;Low Input amounts, Stranded-Seq: 5 ng to 100 ng total RNA;Ultra Low Input amounts, Non-Stranded-Seq: 1-1000 cells or 10 pg - 10 ng;Total RNA-Seq - Stranded: 5-250 ng;Small RNA-Seq: 1 ug, multiplexing up to 48 samples/NextSeq run;Partially degraded samples - Stranded and Non-Stranded: LCM, FFPE samples, both stranded and non-stranded, 50 -100 ng;Microbial rRNA depletion and RNA-Seq with amounts as low as 1-5 ug of total RNA;Whole Genome Sequencing;Human / Animal / Plant;Microbial;As low as 1 ng De novo Sequencing;Exome/Targeted capture re-sequencing: Enables high sequencing depths;Agilent and Illumina platforms;Human, Mouse, Canine and other species;Targeted re-sequencing: High levels of multiplexing up to 200 samples / MiSeq run;PCR Amplicon sequencing;Illumina and Agilent platforms;ChIP-Seq;Transcription factor analysis;Histone modifications;DNA Methylation;MeDIP- and MBD-Seq;MethylC-Seq;Agilent SureSelect MethylC-Seq;Nucleosome Mapping;FAIRE-Seq and DNAse I-Seq;16S / 18S / ITS amplicon sequencing;Whole Genome Metagenomic sequencing;Metatranscriptomic analysis;DNA/chromatin fragmentation by Covaris
DNA / RNA quality analysis: BioAnalyzer / TapeStation assay, Qubit (Picogreen) assays;qPCR services.""" .
SCR:017959 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_985" ;
rdfs:label "South Carolina Medical University Mass Spectrometry Core Facility" ;
NIFRID:synonym "MUSC Mass Spectrometry Facility" ;
definition: "Core provides expertise, services, education, and instrumentation to enhance biomedical research through LC-MS/MS-based proteomics. Services are offered for protein identification; characterization of post-translational modifications; and quantitative proteomics to identify differentially expressed/degraded proteins, regulated sites of post-translational modification, protein-protein interactions, and protein targets of drugs identified in phenotypic screens. Analyses include sample preparation, LC-MS/MS, database searching, generation of reports, and assistance with data interpretation. Faculty and staff assist with experimental design and development/optimization of customized methodology for analysis of post-translationally modified peptides (e.g. phosphorylation and O-GlcNAc modification, N- and O-linked glycosylation, Cys modifications including S-glutathionylation, and glycation of Lys and Arg). Quantitative approaches including metabolic labeling (SILAC), isobaric tagging (iTRAQ/TMT), and label free proteomics (LFQ) are performed on Orbitrap Elite or Orbitrap Fusion Lumos Mass Spectrometers. Developes methodology to identify alterations in post-translational modifications that impact signal transduction, transcription, translation, and response to therapeutics with goal of enabling investigators to discover molecular mechanisms underlying disease progression and therapeutic response." .
SCR:017960 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:csa2.6" ;
rdfs:label "Chromosome Scale Assembler" ;
NIFRID:abbrev "CSA" ;
definition: "Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions." .
SCR:017961 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "syGlass" ;
definition: "Software visualization tool for direct volume rendering with no segmentation required. Enables users to view, annotate and analyze 3D data in VR. Data visualization and annotation system that allows rendering of large, volumetric data in its true, three- or four-dimensional form." .
SCR:017962 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JTK_CYCLE" ;
NIFRID:synonym "Jonckheere-Terpstra-Kendall-CYCLE" ;
definition: "Software R package for Detecting Rhythmic Components in Genome-Scale Data Sets. Non-parametric algorithm to identify rhythmic components in large datasets. Identifies and characterizes cycling variables in large datasets." .
SCR:017963 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013202" ;
rdfs:label "Primate Cell Type Database" ;
definition: "Database of intracellular recordings of non-human primates (NHP) cells sampled from the lateral prefrontal cortex. 249 patch clamp recordings for 2 protocols: 1 second current pulse and 3 millisecond pulse. Morphology obtained by biocytin injections and confocal imaging at 63x magnification." .
SCR:017965 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CopyNumber450kCancer" ;
definition: "Software R package baseline correction for accurate copy number calling from 450k methylation array. Baseline correction for copy number data from cancer samples. Implements maximum density peak estimation (MDPE) method together with interactive reviewing to efficiently correct baseline in cancer samples." .
SCR:017966 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Vieworks" ;
definition: "Optics and Imaging Company. Vieworks has developed imaging technologies for various areas and has offered solutions suitable for the digital X-ray detector, industrial camera, and in vivo imaging system." .
SCR:017967 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LESYMAP" ;
NIFRID:synonym "Lesion to Symptom Mapping" ;
definition: "Software R package to conduct lesion-to-symptom mapping from human MRI data.Takes lesion maps and cognitive performance scores from patients with stroke, and maps brain areas responsible for cognitive deficit." .
SCR:017968 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "merge-gbk-records" ;
definition: "Software tool to merge multiple GenBank records using defined spacer sequence.Used to turn multiple GenBank records either in multiple files or single multi-record file into single record." .
SCR:017969 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NEB Tm calculator" ;
definition: "Calculator to estimate appropriate annealing temperature when using NEB PCR products.Tm calculator provided by New England Biolabs." .
SCR:017970 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:crispy" ;
rdfs:label "CRISPy-web" ;
NIFRID:synonym "single guide RNA desing" ;
definition: "Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction." .
SCR:017971 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LINDA" ;
NIFRID:synonym "Lesion Identification with Neighborhood Data Analysis" ;
definition: "Software R package for automated segmentation of chronic stroke lesions. Automated segmentation algorithm capable of learning relationship between existing manual segmentations and single T1-weighted MRI." .
SCR:017972 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fusion software" ;
definition: "Software for analyzing mouse behavior by Omnitech Electronics Inc." .
SCR:017973 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "k-FLBPCM method" ;
definition: "Software tool as novel k-FLBPCM method for detecting morphologically similar crops and weeds based on combination of contour masks and Local Binary Pattern operators." .
SCR:017974 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:CandiMeth" ;
rdfs:label "CandiMeth" ;
NIFRID:synonym "CANDIdate feature METHylation" ;
definition: "Software tool for visualisation and quantification of DNA methylation at candidate features." .
SCR:017975 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:netphos" ;
rdfs:label "NetPhos" ;
NIFRID:synonym "NetPhos 2.0",
"NetPhos 3.1" ;
definition: "Web tool as artificial neural network method that predicts phosphorylation sites in independent sequences. Web application based on determination of activity of protein kinases using in vitro assays with either naturally occurring peptides or synthetic peptides. NetPhos 3.1 server predicts serine, threonine or tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. Generic predictions are identical to predictions performed by NetPhos 2.0. Kinase specific predictions are identical to predictions by NetPhosK 1.0. NetPhos 3.1 is available as stand-alone software package." .
SCR:017976 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:PAFScaff" ;
rdfs:label "PAFScaff" ;
NIFRID:synonym "Pairwise mApping Format reference-based Scaffold" ;
definition: "Software as Pairwise mApping Format reference based Scaffold anchoring and super scaffolding tool. Dsigned for mapping genome assembly scaffolds to closely related chromosome level reference genome assembly." .
SCR:017978 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VisuAlign" ;
definition: "Software tool for applying user guided nonlinear refinements (inplane) to existing, affine 2D-to-3D registration. Used for precise quantitative analysis of residual anatomical variability among test subjects after registration." .
SCR:017979 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BGI | BGISEQ-500" ;
definition: "Desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics sequencing technologies, it generates short reads at large scale. BGI/MGI Sequencer." .
SCR:017980 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MGI | DNBSEQ-G400" ;
NIFRID:synonym "MGISEQ-2000" ;
NIFRID:abbrev "Restricted" ;
definition: "Sequencer developed by MGI Tech Co. Ltd. Next generation sequencing platform. Its sequencing principle relies on DNB and cPAS technologies also used in previous version of BGISEQ-500 device, but reagents for MGISEQ-2000 are refined and platform utilizes updated software. Built with new chip system that can flexibly support variety of different sequencing models." .
SCR:017981 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MGI | DNBSEQ-T7" ;
definition: "Sequencer can generate 1-6Tb of high quality data per day, for wide range of applications including Whole Genome Sequencing, Deep Exome Sequencing, Epigenome Sequencing, Transcriptome Sequencing, and targeted panel projects. Powered by DNBSEQTM Technology, DNBSEQ-T7 makes sequencing more efficient and productive with advances in biochemical, fluidics, and optical systems. Detection and characterization of copy number variants based on whole-genome sequencing by MGI platforms." .
SCR:017982 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Ion Proton System" ;
NIFRID:synonym "Ion Proton™ System" ;
definition: "Thermo Fisher Ion Torrent Sequencer. Ion Proton System for Next-Generation Sequencing. Used for accurate high-throughput sequencing." .
SCR:017983 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Ion Personal Genome Machine System" ;
NIFRID:synonym "Ion Personal Genome Machine (PGM) System",
"Ion Personal Genome Machine System",
"Ion Personal Genome Machine™ (PGM™) System" ;
NIFRID:abbrev "Ion PGM System" ;
definition: "Thermo Fisher Ion Torrent Sequencer. System combines semiconductor sequencing technology with natural biochemistry to directly translate chemical information into digital data. Coupled with Torrent Suite Software performs preliminary reference genome alignment and outputs data in BAM format for easy downstream analysis with optional third party analysis tools. It can also provide access to web portal for data review and sharing." .
SCR:017984 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | HID Ion GeneStudio S5 Prime System" ;
NIFRID:synonym "HID Ion GeneStudio™ S5 Prime System" ;
definition: "Thermo Fisher Ion Torrent Sequencer. Semiconductor based next generation sequencing system that enables simple targeted sequencing workflows. With cartridge based reagents, system is simple to use and offers scalability and flexibility. Uses Ion 5 Series chips to support broad range of forensic applications including mitochondria sequencing, STR analysis, and SNP genotyping." .
SCR:017985 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Oxford | Nanopore Technologies MinION" ;
definition: "Portable, real time device for DNA and RNA sequencing, putting you in control of your sequence data. Portable DNA/RNA sequencing by Oxford Nanopore Technologies." .
SCR:017986 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoporeTech | GridION Mk1" ;
definition: "Benchtop sequencing and analysis device designed to run and analyse up to five individually addressable MinION or Flongle Flow Cells by Oxford Nanopore Technologies. Good for labs with multiple projects that need advantages of nanopore sequencing: simple library preparation, real-time analysis and new biological insights from long reads." .
SCR:017987 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Oxford |Nanopore Technologies | PromethION" ;
NIFRID:synonym "PromethION 24",
"PromethION 48" ;
definition: "System offers real-time, long-read, direct DNA and RNA sequencing by Oxford Nanopore Technologies. System suitable for large scale projects such as population-scale sequencing or plant genomics, or for large scale service offerings. PromethION 24 and PromethION 48 systems offer ability to run 24 and 48 flow cells respectively. System allows on demand sequencing, using any flow cell at any time. Users can start and stop running individual experiments as required, or deploy multiple flow cells onto single experiments for greater speed or throughput." .
SCR:017988 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PacBio | RS II Sequencing System" ;
NIFRID:synonym "RS II Sequencing System",
"RS II System" ;
definition: "Sequencer by Pacific Biosciences. System allows scientists to generate finished genome assemblies, reveal and understand epigenomes, and characterize genomic variation. It achieves longest read lengths and highest consensus accuracy. Finishes microbial genomes and improves assembly of larger organisms with multi-kilobase reads and unbiased coverage regardless of GC content. No amplification is required." .
SCR:017989 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PacBio | Sequel System" ;
NIFRID:synonym "PacBio Sequel™ System",
"Sequel System" ;
definition: "Single Molecule, Real-Time sequencer by Pacific Biosciencies. System provides higher throughput, more scalability, reduced footprint and lower sequencing project costs compared to PacBi RS II System, while maintaining benefits of SMRT technology. Ideal for projects such as generating high quality, whole genome de novo assemblies for larger genomes, such as human, plants, and animals. Provides characterization of wide variety of genomic variation types, including those in complex regions not accessible with short-read or synthetic long-range sequencing technologies, while simultaneously revealing epigenetic information." .
SCR:017990 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PacBio | Sequel II System" ;
definition: "Sequencer by Pacific Biosciencies. System provides advantages of SMRT Sequencing and now makes it more affordable for all scientists to drive discovery with comprehensive views of genomes and transcriptomes. Generates 8 times more data than original Sequel System. Provides access to highly accurate long reads (HiFi reads). Reduces project time for faster results. Makes sequencing more affordable.Supports range of SMRT Sequencing applications." .
SCR:017991 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Prayoga | GenapSys Sequencer" ;
definition: "Compact sequencer for DNA sequencing by GenapSys, Inc. Sequencing is carried out on microfluidic chips that have scalable number of detectors, allowing for applications ranging from targeted sequencing of specific amplicons to genome-scale data collection. System utilizes electrical sequencing chip., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:017992 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Marshall Scientific | Saphyr" ;
NIFRID:synonym "BIONANO SAPHYR® GENOME IMAGING" ;
definition: "Whole genome imaging instrument by Bionano Genomics for high speed, high throughput structural variant detection and analysis with exceptional sensitivity and specificity. Detects structural variations ranging from 500 bp to megabase pairs in length. For mosaic samples or heterogeneous cancer samples, detects all types of structural variants down to 5% Variant Allele Fraction. Calls repeats and complex rearrangements." .
SCR:017993 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Alberta University Diabetes Institute IsletCore Core Facility" ;
NIFRID:synonym "Alberta Diabetes Institute IsletCore",
"University of Alberta Diabetes Institute IsletCore",
"University of Alberta Isletcore" ;
definition: "Core as campus based lab that offers pancreatic islet isolations accompanied by various assays of islet function and metabolism. Provides service for variety of procedures including: Human pancreatic islet isolation, Islet banking, Basal characterization of donor islets, Limited experimental work, Coordination of ethical approvals." .
SCR:017994 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mesquite" ;
NIFRID:synonym "Mesquite 3.04",
"Mesquite 3.61" ;
definition: "Software tool as modular system for evolutionary analysis. Software for evolutionary biology, designed to organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Analyses available depend on modules installed. Comes with many packages already installed." .
SCR:017995 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GE | Phoenix Nanotom S" ;
definition: "System for scientific and industrial nanofocus computed tomography nanoCT and 3D metrology. Realizes unique spatial and contrast resolution on wide sample and application range. Used in material science, precision injection moulding, micromechanics, electronics geology and biology. Used in 3D CT applications. Allows many analysis, e.g. non-destructive visualization of slices, arbitrary sectional views, or automatic pore analysis." .
SCR:017996 a NLX:63400,
owl:NamedIndividual .
SCR:017997 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VG Studio MAX" ;
NIFRID:synonym "VG Studio MAX 3.1",
"VGStudio",
"VGStudio MAX" ;
definition: "Software tool for analysis and processing of µCT data, e.g. compiling virtual 3D models of morphological structures in site by Volume Graphics GmbH. Used for visualization of CT data." .
SCR:017998 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ToupView " ;
definition: """Software tool that controls microscope camera by Touptek Photomics. Provides functions to fully control camera and present video stream processed by Ultra FineTM color engine at high speed, which includes dedicated pipeline to process raw data into realistic scene. Compatible with ToupCam full series of digital cameras. With authorized license, ToupView software could be used with other cameras which support Twain or DirectShow interface.
Used in field of medical microscopic imaging, industrial detection, machine vision, astronomical observation, etc.""" .
SCR:017999 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Drishti" ;
definition: "Open source scientific visualisation software. Multi platform, volume exploration and presentation software. Used for visualising volumetric data, such as tomography data, electron microscopy data, etc." .
SCR:018000 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "arivis Vision4D" ;
NIFRID:synonym "arivis Vision4D 3.1.3" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 20,2024. Modular software for working with multi-channel 2D, 3D and 4D images from high speed confocal, Light Sheet/ SPIM and 2 Photon systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:018001 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Digimeter | DS5 Isolated Bipolar Current Stimulator" ;
definition: "Stimulator allows computer control of stimulus amplitude and timing parameters. Designed to speed up and enhance human peripheral nerve diagnostics by facilitating semi-automated nerve excitability tests. It also has roles in wider aspects of clinical neurophysiology research, including psychological, vestibular system and nociceptive testing. CE marked medical device under European Medical Device Regulation." .
SCR:018002 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mqtldb" ;
NIFRID:synonym "methylation quantitative trait loci database" ;
definition: "Data collection of large scale genome wide DNA methylation analysis of 1,000 mother-child pairs at serial time points across life course (ARIES)." .
SCR:018003 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FlowSorted.Blood.450k R package" ;
definition: "Illumina HumanMethylation data on sorted blood cell populations." .
SCR:018004 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:epidish" ;
rdfs:label "EpiDISH R package" ;
NIFRID:synonym "Epigenetic Dissection of Intra-Sample Heterogeneity" ;
NIFRID:abbrev "EpiDISH" ;
definition: "Software R package provides tools to infer proportions of priori known cell-types present in sample representing mixture of such cell-types. Comparison of reference based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies." .
SCR:018005 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MOON" ;
definition: "Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid." .
SCR:018006 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Illumina | HiSeq 1500 System" ;
NIFRID:synonym "HiSeq 1500 System" ;
definition: "High-throughput sequencing system. Support of instrument and supply reagents will be provided through February 28th, 2023. Other instruments that support same applications as HiSeq 1500 System are available. Use Sequencing Platform Comparison Tool to find the best instrument for your needs." .
SCR:018007 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CNV webstore" ;
NIFRID:synonym "CNV-WebStore",
"CNV-webstore" ;
definition: "Integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Platform to streamline processing and downstream interpretation of microarray data in clinical context. Analysis tools include CNV analysis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases." .
SCR:018008 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BERT" ;
NIFRID:synonym "Bidirectional Encoder Representations from Transformers" ;
definition: "Technique for Natural Language Processing pre-training developed by Google. Pre-training of Deep Bidirectional Transformers for Language Understanding. Language representation model designed to pre-train deep bidirectional representations from unlabeled text by jointly conditioning on both left and right context in all layers." .
SCR:018009 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Google CoLab" ;
NIFRID:synonym "Colaboratory",
"Google Colaboratory" ;
NIFRID:abbrev "Google Colab" ;
definition: "Colaboratory is product from Google Research. Allows anybody to write and execute arbitrary python code through browser, and is especially well suited to machine learning, data analysis and education. Colab is hosted Jupyter notebook service that requires no setup to use, while providing free access to computing resources including GPUs." .
SCR:018010 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VariantDB" ;
definition: "Web based interactive annotation and filtering platform that automatically annotates variants with allele frequencies, functional impact, pathogenicity predictions and pathway information. Allows filtering by all annotations, under dominant, recessive or de novo inheritance models. Flexible annotation and filtering portal for next generation sequencing data." .
SCR:018011 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SonarCloud Vulnerable Code Prospector for C" ;
NIFRID:synonym "SVCP4CDataset" ;
NIFRID:abbrev "SVCP4C" ;
definition: "Software tool to collect vulnerable source code from open-source repositories linked to SonarCloud. Dataset repository with tagged files with BufferOverflow features associated to source code repositories publicly available." .
SCR:018012 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adobe Photoshop Lightroom" ;
definition: "Camera raw data processing software. Cloud-based service to edit, organize, store, and share photos across any device." .
SCR:018013 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LibreOfficeCalc" ;
definition: "Open source software application with data analysis tools and spreadsheet templates used to manage, process and visualize data. LibreOffice Calc is spreadsheet component of LibreOffice software package developed by Document Foundation." .
SCR:018014 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:4see" ;
rdfs:label "4See" ;
definition: "Software tool to visualize 4C data." .
SCR:018015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multiple Mapping Method Server" ;
NIFRID:synonym "Multiple Mapping Method server" ;
NIFRID:abbrev "MMM server" ;
definition: "Web server for modeling protein structure by using Multiple Mapping Method. Approach to sequence-to-structure alignment in comparative protein structure modeling." .
SCR:018016 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "O'Hara | T-maze" ;
definition: "Automatic T-maze setup to quantify various cognitive functions of animals. Single maze system by O'HARA and CO.,LTD." .
SCR:018017 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Amplipex | KJE-1001 amplifier" ;
definition: "Multiplexed biosignal amplifier used to record neural signal by Amplipex Ltd. Related to electrophysiology experiments with multichannel extracellular recordings in freely moving rodents." .
SCR:018018 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "USEDit" ;
NIFRID:synonym "Universal Scientific Equipment Discovery Tool" ;
definition: "Project that attempts to identify instruments used in research by assigning universal unique identifiers and standardized set of information for each piece of equipment." .
SCR:018019 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroNexus | nDrive" ;
definition: "Microdrive for chronic implantation of neural probe by NeuroNexus." .
SCR:018020 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:NeuroChat" ;
rdfs:label "NeuroChaT" ;
NIFRID:synonym "Neuron Characterisation Toolbox" ;
definition: "Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories." .
SCR:018021 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sietraj" ;
definition: "Software tool for binding free energies from Amber-generated MD trajectories. Alternative to MM-PBSA software provided by AMBER distribution. Virtual alanine mutations are also possible. Solvated interaction energies are calculated using parameters that have been fitted to reproduce binding free energies of data set of 99 protein-ligand complexes." .
SCR:018022 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:OPEtH" ;
rdfs:label "Online Peri-Event Time Histogram for Open Ephys" ;
NIFRID:synonym "Online Peri-Event Time Histogram" ;
NIFRID:abbrev "OPETH" ;
definition: "Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them." .
SCR:018023 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Single Read Paired Read Indel Substitution Minimizer" ;
NIFRID:abbrev "SRPRISM" ;
definition: "Software tool as single read paired read indel substitution minimizer." .
SCR:018024 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:VEnCode",
"biotools:VEnCode" ;
rdfs:label "VEnCode" ;
NIFRID:synonym "Versatile Entry Codes" ;
definition: "Software tool to perform intersectional genetics-related operations to find VEnCodes using databases provided by FANTOM5 consortium, namely CAGE enhancer and transcription start site (TSS) databases." .
SCR:018025 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Luminex | 100 Flow Cytometry Analyzer System" ;
NIFRID:synonym "Luminex 100 System" ;
definition: "Flow cytometry analyzer system for individual labs that performs up to 100 different tests in single reaction volume and can use either magnetic beads or plain polystyrene beads." .
SCR:018026 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Rad | Bio-Plex 200 System" ;
NIFRID:synonym "Bio-Plex 200 Suspension Array System",
"Bio-Plex 200 System",
"BioRad suspension array reader" ;
definition: "Suspension array system which offers protein and nucleic acid researchers multiplex assay solution permiting analysis of up to 100 biomolecules in single sample." .
SCR:018027 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_324" ;
rdfs:label "Wafergen | Apollo 324 NGS Library Prep" ;
NIFRID:synonym "Apollo 324 NGS Library Prep Robot",
"Apollo 324 NGS Library Prep System" ;
definition: "Compact benchtop platform that enables rapid and full walk-away automation of next generation sequencing applications. Paired with PrepX reagents, Apollo 324 line offers complete sample-toanswer solution for NGS library prep. Apollo 324 automated protocols and PrepX reagent kits combine liquid handling and proven chemistries to produce high quality libraries for all major NGS platforms. System provides complete, walkaway solution using validated protocols and chemistries that produce consistent libraries for DNA-seq, RNA-seq, and ChIP-seq applications." .
SCR:018028 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_454" ;
rdfs:label "Roche | 454 GS FLX Genome Sequencer" ;
NIFRID:synonym "454 GS FLX",
"Roche 454 GS FLX" ;
definition: "Genetic sequencer that sequences clinically relevant exons and identifies genomic variations in solid tumors treated with antibody-based medicine. Scaled version of Genome Sequencer FLX System for use by individual labs. Features include simple sample preparation workflow, overnight sequencing and data processing, and suite of data analysis software." .
SCR:018029 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018601" ;
rdfs:label "Select Science | Carestream Gel Logic 212 PRO Imaging System" ;
NIFRID:synonym "Bruker BioSpin Gel Logic 212 PRO",
"Carestream Gel Logic 212 PRO Imaging System",
"Carestream Gel Pro 212 Imager",
"Gel Logic 212 PRO" ;
definition: "Automated gel imaging system for imaging fluorescence or colorimetric data in sample formats such as gels (DNA/Coomassie/Silver stain) membranes, and 96 well plates. Features include autofocusing and directed autoexposure." .
SCR:018030 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AGFA_CP1000" ;
rdfs:label "AGFA | CP1000 Automatic Film Processor" ;
NIFRID:synonym "AGFA CP1000 Film Developer" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10,2024. Automatic film processor for low-volume processing or back-up purposes. Its features include fast start up (7 minutes from cold start) and 125-second cycle time. Uses simple, accessible film transport system with fewer rollers than conventional heavy roller racks, infrared dryer instead of hot-air dryer, 400 watts of power when in operation and 100 watts in standby mode, and automatic temperature control and drying." .
SCR:018031 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_840" ;
rdfs:label "Molecular Devices | Molecular Dynamics Storm 840 Molecular Imager" ;
NIFRID:synonym "Molecular Dynamics Storm 840 Phosphorimager Scanner",
"Storm 840 Molecular Imager",
"Storm Gel and Blot Imaging System" ;
definition: "Molecular imager system for performing gel and blot analysis. This system provides both PhosphorImager capabilities along with non-radioactive fluorescent labeling techniques-direct fluorescence and chemifluorescence. It can be used for non-radioactive gel and blot analysis methods or radioisotope techniques. Storm 840 scans storage phosphor screens plus fluorescent gels and chemifluorescent blots in the 35 x 43 cm scanning area." .
SCR:018032 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Storm 860 Imager" ;
rdfs:label "Molecular Devices | Molecular Dynamics Storm 860 Molecular Imager" ;
NIFRID:synonym "Storm 860 Molecular Imager",
"Storm Gel and Blot Imaging System" ;
definition: "Multifunction phosphoimager fluorimager laser scanner that collects fluorescent or storage phosphor images from gels, membranes and phosphor screens. It is equipped with blue (450 nm) and red (635 nm) lasers, can scan at resolutions down to 50 microns. It is able to quantify radioactive gels for commonly used isotopes such as 32P, 33P, 125I, 35S, and 14C. There are three detection modes: phosphor screen mode, red/blue fluorescence, chemifluorescence." .
SCR:018033 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1160" ;
rdfs:label "Leica | EG1160 Embedding Station" ;
NIFRID:synonym "EG 1160 paraffin embedding station" ;
definition: "Paraffin embedding station that provides constant, reproducible paraffin flow at ten different flow rate settings. All instrument functions, including automatic starting time, are individually programmable at press of button. Compact dimensions, ease of operation, and high standards of convenience. Separately-heated paraffin dispensing system with integrated filter provides constant, reproducible paraffin flow at ten different flow rate settings." .
SCR:018034 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_450" ;
rdfs:label "Thermo Fisher: Affymetrix | GeneChip 450 Fluidics Station Microarray Processer" ;
NIFRID:synonym "GeneChip 450 Fluidics station",
"GeneChip Fluidics Station 450" ;
definition: "Microarray processor that washes and stains GeneChip arrays.110V and 220V compatible." .
SCR:018036 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1230" ;
rdfs:label "JEOL | 1230 Transmission Electron Microscope" ;
NIFRID:synonym "JEM 1230 Transmission Electron Microscope" ;
definition: "High performance, high contrast, 40-120kV transmission electron microscope that performs imaging for biological and materials science applications." .
SCR:018037 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | 1200 High Performance Liquid Chromatography System" ;
NIFRID:synonym "1200 HPLC",
"Agilent 1200 Series HPLC",
"Agilent 1200 Series HPLC System" ;
definition: "Liquid chromatography analyzer that achieves high levels of sample throughput by use of either binary or quaternary pumps and interchangeable autosamplers. High pressure operation and use of short columns with small diameter media result in fast, high resolution separations. Features includedu al-lamp design and temperature control of diode array detectors." .
SCR:018038 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2105" ;
rdfs:label "Perkin Elmer | EnVision 2105 Multimode Plate Reader" ;
NIFRID:synonym "Perkin Elmer Envision plate reader" ;
definition: "Multimode microplate reader that provides speed, ultra-high throughput, and maximum sensitivity across all detection technologies. Provides higher sensitivity for time-resolved fluorescence TRF applications, and Enhanced Security software option includes tools to facilitate 21 CFR Part 11 compliance for integration into regulated environments GxP." .
SCR:018039 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LEO_1525" ;
rdfs:label "Zeiss | LEO 1525 Field Emission Scanning Electron Microscope" ;
NIFRID:synonym "LEO 1525" ;
definition: "Field emission scanning electron microscope that performs ultra high resolution imaging and analysis. Designed for requirements of nano-analysis, chamber of LEO 1525 is capable of accommodating both EDS and full-focusing Wavelength-dispersive X-ray spectroscopy WDS spectrometers as well as rage of other accessories. Coincident and short working distances allow signals from these detectors to be acquired simultaneously." .
SCR:018040 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2125" ;
rdfs:label "Leica | RM2125 RTS Manual Microtome" ;
NIFRID:synonym "RM 2125 paraffin microtome" ;
definition: "Manual rotary microtome that sections tissue samples. Features include precise feed mechanism, powerBase that ensures stable operation for vibration-free sectioning, advanced knife holder and specimen clamp securely align cutting edge to block, user-selectable coarse feed wheel turn direction and retraction functions, hand wheel, in-built safety guards and rounded shape with arm rests for fatigue-free sectioning,quick-exchange specimen clamp and orientation system for object head allow rapid set up for any block, and two trim steps." .
SCR:018041 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2265" ;
rdfs:label "Leica | Biosystems RM2265 Fully Automated Rotary Microtome" ;
NIFRID:synonym "Leica RM2265 automated microtome" ;
definition: "Automated rotary microtome that sections tissue samples. Specimen feed system with zero-backlash and maintenance-free cross roller guides and stepper motor operated coarse feed system are located in dust-proof plastic housing. Equipped with safety handwheel with handle that can be centered, as well as mechanical handwheel lock. In manual operation retraction can be adjusted. In motorized operation retraction value varies with selected sectioning speed." .
SCR:018042 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ND_2000" ;
rdfs:label "Thermo Fisher | NanoDrop 2000 Spectrophotometer" ;
NIFRID:synonym "NanoDrop 2000",
"NanoDrop 2000 Spectrophotometer" ;
definition: "Full-spectrum, UV-Vis spectrophotometer used to quantify and assess purity of DNA, RNA, Protein and more. The NanoDrop 2000 is microvolume spectrophotometer with patented sample retention technology that measure sample volumes as small as 0.5L." .
SCR:018043 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2100 Bioanalyzer",
"SCR_019389" ;
rdfs:label "Agilent | 2100 Bioanalyzer Instrument" ;
NIFRID:synonym "2100 Bioanalyzer (Agilent Technologies)",
"Agilent 2100 Bioanalyzer" ;
definition: "Bioanalyzer system is automated electrophoresis tool that provides an analytical evaluation of various samples types in many workflows, including next generation sequencing NGS, gene expression, biopharmaceutical, and gene editing research. Digital data is provided in timely manner and delivers assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for accurate result, and data may be exported in many different formats." .
SCR:018044 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Biacore 3000",
"SCR_018577",
"SCR_019676" ;
rdfs:label "GE | Biacore 3000 Real Time Biomolecular Interaction Analyzer" ;
NIFRID:synonym "BIACORE 3000 GOLDSEAL",
"BiaCore 3000 Surface Plasmon Resonance" ;
definition: "Biacore 3000 processing unit is an established, label-free system for detailed studies of biomolecular interactions. The system delivers comprehensive characterization of the interaction, answers questions about the rate constants, affinity, specificity, and determines the active concentration of components. The ability to recover and transfer interaction partners directly to MALDI targets for identification and further characterization makes the system highly applicable to fast identification of unknown interactants." .
SCR:018045 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2720" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 2720 Thermal Cycler" ;
NIFRID:synonym "ABI 2720 Thermal Cycler" ;
definition: "Personal sized 96-well thermal cycler that performs both basic PCR and cycle-sequencing applications using 0.2 mL reaction tubes or 96-well reaction plates. Its dimensions are 21 cm (8.3 in.) wide and 36 cm (14.2 in.) deep with cooling vents." .
SCR:018046 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_3130" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 3130 Genetic Analyzer" ;
NIFRID:synonym "Applied Biosystems 3130 (4-capillary) Genetic Analyzer",
"Genetic Analyzer (4 capillary)" ;
definition: "Genetic analyzer can run sequencing and fragment analysis applications including microsatellite analysis, AFLP, LOH, SNP validation, and SNP screening. Maintenance time is reduced by eliminating manual syringe washing and filling with automated polymer delivery. Can increase data quality for sequencing and fragment analysis applications by longer read length, and higher resolution with shorter run times. Uses 96- or 384-well plates with four capillary array." .
SCR:018047 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_9410" ;
rdfs:label "GE: Healthcare | 9410 Variable Mode Imager" ;
NIFRID:synonym "Typhoon 9410 Multi-Image scanner (GE Healthcare)" ;
definition: "Variable mode imager that operates in three different modes, including phosphorescence, fluorescence, and chemiluminescence. Can scan in visible range using reflected light. Scanning resolution ranges from 1000um down to 10um. Scanning software is linked to ImageQuant TL 7.0 analysis software. ImageQuant is capable of quantifying Typhoon images such as those from Northern or Western blots. Images can be saved in various formats and imported into Powerpoint slides. Instrument has three excitation lasers (532nm, 633nm, 488nm). Instrument utilizes 536SP, 670BP, 520BP emission filters for fluorescence. For DNA, RNA and protein samples you may choose from: storage phosphor auto-radiography, direct blue-excited fluorescence (457-488 nm), direct green-excited fluorescence (532 nm), direct red-excited fluorescence (633 nm), and chemiluminescence." .
SCR:018048 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_3130xl" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 3130xl Capillary Array" ;
NIFRID:synonym "Applied Biosystems 3130xl capillary fluorescence sequencer" ;
definition: "Genetic analyzer that performs fragment analysis and rapid sequencing applications. Usage per array is 100 runs with use of Applied Biosystems reagents." .
SCR:018049 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4000B",
"SCR_019955" ;
rdfs:label "Molecular Devices | GenePix 4000B Microarray Scanner" ;
NIFRID:synonym "GenePix 4000B Scanner" ;
definition: "Microarray scanner that performs genetic and compound analysis. Coupled with GenePix ProMicroarray Image Analysis Software and Acuity Microarray Informatics Software for acquisition and analysis of data from all types of arrays, including nucleic acids, proteins, tissues, and cells. Scanner flexibility allows to configure scanning and analysis of one slide or many, whether they are all alike or each is different. Slide loader accommodates low- and high-density, opaque, mirrored, or translucent, plastic or glass, commercial or homebrew slides." .
SCR:018050 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5418_R" ;
rdfs:label "Eppendorf | 5418 R Centrifuge" ;
NIFRID:synonym "Eppendorf 5418 Centrifuge (2)" ;
definition: "Refridgerated centrifuge with 18 place capacity rotor that accomdates low to medium capacity in 1.5 or 2.0 mL tubes and Microtainer. Speed allows for standard molecular biology applications. Compact size and quiet operation." .
SCR:018051 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7500" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 7500 Real-Time PCR System" ;
NIFRID:synonym "AB 7500 Fast Real-time PCR System" ;
definition: "Real-time PCR system that performs high performance, multicolor real-time PCR. Has five color platform that is calibrated for broadest range of dyes available: FAM, SYBR Green I, VIC, JOE, NED, TAMRA, Cy3, ROX, Texas Red, and Cy5 dyes. Thermal cycling block is built to reduce environmental exposure and contamination risk." .
SCR:018052 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_3730" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 3730 Genetic Analyzer" ;
NIFRID:synonym "3730 DNA Analyzer" ;
definition: "Medium to high throughput genetic analyzer that performs DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Upgradeable to 96 capillaries." .
SCR:018053 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5600" ;
rdfs:label "SCIEX | TripleTOF 5600+ Mass Spectrometer System" ;
NIFRID:synonym "Sciex 6500 QTRAP" ;
definition: "Mass spectrometry system that combines SCIEX Triple Quad technology with Accelerator TOF Analyzer, to deliver nominal mass and accurate mass benefits in single platform. Integrates comprehensive, qualitative exploration, rapid profiling, and high-resolution quantitation workflows." .
SCR:018054 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Biospec" ;
rdfs:label "Bruker | 9.4T Biospec Biospec Magnetic Resonance Imaging" ;
NIFRID:synonym "9.4T Bruker Biospec MRI" ;
definition: "MRI system that performs preclinical and molecular MR imaging. MRI CryoProbe technology combined with ultra high field USR magnets deliver high spatial resolution in-vivo. Any small animal MR imaging application in life science, biomedical and preclinical research can be conducted." .
SCR:018055 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Canto" ;
rdfs:label "BD Biosciences | FACSCanto Flow Cytometer" ;
NIFRID:synonym "Canto-blue and red lasers" ;
definition: "Flow cytometry system that performs reliable performance, accuracy, and ease-of-use for clinical diagnostic services. System has 10 color capability, optical enhancements, and 4-3-3 configuration deliver high sensitivity and resolution for accurate results." .
SCR:018056 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Canto II" ;
rdfs:label "BD Biosciences | Canto II Flow Cytometer" ;
NIFRID:synonym "Canto II" ;
definition: "Benchtop flow cytometer features reliable performance and accurate results for experiments requiring up to 10 parameters. Fixed alignment flow cell minimizes startup time and improves reproducibility. Patented optical design maximizes signal detection and increases sensitivity and resolution for each color in multicolor assay." .
SCR:018057 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CFX384" ;
rdfs:label "Bio-Rad | CFX384 Real-Time Detection System" ;
NIFRID:synonym "Bio-Rad CFX384 Real-Time System" ;
definition: "Real Time PCR instrument in 384-well format that performs high-throughput data acquisition. System utilizes temperature control and sensitive, 4-color detection optics to deliver qPCR results for singleplex or multiplex reactions. Quickly set up runs and monitor amplification traces in real time on integrated LCD touch screen, or use CFX Maestro Software to design experiment and analyze results from connected computer." .
SCR:018058 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Femto Pulse",
"SCR_019498" ;
rdfs:label "Agilent | Femto Pulse System" ;
NIFRID:synonym "AATI FEMTO Pulse Fragment Analyzer",
"AATI FemtoPulse",
"Advanced Analytical Technologies",
"Inc. FEMTO Pulse Fragment Analyzer" ;
definition: "Femto Pulse System separates large molecular weight DNA fragments and detects nucleic acids into femtogram range.Fragment analyzer that provides pulsed field power supply which allows large molecular weight DNA fragments to be separated and nucleic acids detected into femtogram range. Ability to separate high molecular weight DNA up to 165 kb and detect nucleic acids down to 50 fg per uL input concentration makes system ideal for long-read NGS QC, gDNA, small RNA, or cfDNA analysis from low concentration samples." .
SCR:018059 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_3730xl" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 3730xl Capillary Genetic Sequencer" ;
NIFRID:synonym "Applied Biosystems 3730xl Capillary Sequencer" ;
definition: "96-capillary DNA analyzer that performs DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Has multiple automation features. Performs sequencing and fragment analysis applications including resequencing, microsatellite analysis, AFLP, LOH, SSCP, SNP screening and SNP validation." .
SCR:018060 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7900HT" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 7900HT Fast Real-Time PCR System" ;
NIFRID:synonym "Applied Biosystems 7900HT PCR System" ;
definition: "Real Time quantitative PCR system that combines 96- and 384-well plate compatibility and the TaqMan Low Density Array with fully automated robotic loading and now also offers optional Fast real-time PCR capability. High-throughput Real-Time PCR system that detects and quantitates nucleic acid sequences. Uses fluorescent-based PCR chemistries to provide: Quantitative detection of nucleic acid sequences using real-time analysis and Qualitative detection of nucleic acid sequences using end-point and dissociation-curve analysis." .
SCR:018061 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CM1950" ;
rdfs:label "Leica | CM1950 Cryostat" ;
NIFRID:synonym "10) A Leica CM1950 Cryostat" ;
definition: "Highly adaptable cryostat platform that can be tailor-made for each laboratory. Cryostat with encapsulated microtome and separate specimen cooling features UV disinfection system, optional integrated extraction system for section waste and optional motor for motorized sectioning. Designed to produce frozen sections for biological, medical and industrial applications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:018062 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LSM 510" ;
rdfs:label "Zeiss | LSM 510 Confocal Microscope" ;
NIFRID:synonym "Zeiss LSM-510 META NLO Laser Scanning Confocal Microscope with multiphoton capability" ;
definition: "Versatile laser scanning confocal microscope system that is available in both upright or inverted format. Equipped with ICS-Optics. Selection of dry, water immersion and oil immersion objectives are available. ICS-Optics are infinity color corrected." .
SCR:018063 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LSM 710" ;
rdfs:label "Zeiss | LSM 710 Confocal Inverted Microscope" ;
NIFRID:synonym "LSM-710 with incubation" ;
definition: "Inverted microscope that enables confocal microscopy in cell and developmental biology." .
SCR:018064 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CFX96" ;
rdfs:label "Bio-Rad | CFX96 Real-Time PCR Detection System" ;
NIFRID:synonym "CFX96 Real Time PCR" ;
definition: "Real Time PCR detection system that combines optical technology with temperature control. Six channel, five colors and one FRET channel, real-time PCR instrument for singlexplex or multiplex reactions. Quickly set up runs and monitor amplification traces in real time on integrated LCD touch screen, or use included CFX Maestro Software to design experiment and analyze results from connected computer." .
SCR:018065 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_iCycle" ;
rdfs:label "Bio-Rad | iCycle iQ Real-Time Detection System" ;
NIFRID:synonym "Bio-Rad iCycle Thermal Cycler" ;
definition: "PCR detection system that features broad spectrum light source. Filter based optical design allows selection of optimal wavelengths of light for excitation and emission. Pixel array on CCD detector allows for simultaneous imaging of all 96 wells every second. Simultaneous image collection insures that well-to-well data may reliably be compared. Reports data on PCR in progress in Real Time, allowing immediate feedback on reaction success." .
SCR:018066 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SH800S" ;
rdfs:label "Sony biotechnology | SH800S Cell Sorter" ;
NIFRID:synonym "SH800 cell sorter" ;
definition: "Benchtop cell sorter that sorts wide range of cell sizes for many applications using microfluidic sorting chips. Integrated with comprehensive fluidics controls and advanced automation for set-up, acquisition, sort and analysis. System software supports sorting into tubes and 96- and 384-well plates. Software generates FCS 3.0 and FCS 3.1 files that can be exported to third party analysis tools. For non-clinical research use only. For applications in which cross-contamination is concern, optional e-beam sterilized consumables can be used to replace sample line and sorting chip. Optional class A2 Level II biosafety cabinet provides protection for personnel and products. Biosafety cabinet meets international standards.Optical design offers up to four collinear excitation lasers (488 nm, 405nm, 561nm and 638nm) and six fluorescence detectors. The six free-form PMTs enable detection of fluorescence signals from any laser based on filter selection." .
SCR:018067 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SP6800" ;
rdfs:label "Sony Biotechnology Inc. SP6800 Spectral Cell Analyzer" ;
NIFRID:synonym "1 SP6800 cell analyzer" ;
definition: "Analyzer that uses spectral technology to collect photons from 420nm to 800nm. Global standardization mode automatically sets system to master specification with single click. Sony patented Flowpoint core stability and tracking system and automated QC ensure highest resolution possible of target populations." .
SCR:018068 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Blackfynn Discover" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. Data repository for scientific data. Open data library to explore neuroscience data for neurodegenerative diseases for which there are no disease modifying treatments." .
SCR:018069 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MaRe" ;
NIFRID:synonym "EasyMapReduce" ;
definition: "Software tool to leverage power of Docker and Spark to run and scale your serial tools in MapReduce fashion." .
SCR:018070 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SeqCode" ;
NIFRID:synonym "SeqCode web" ;
definition: "Suite of open software command line tools to develop high-quality pictures from high-throughput sequencing samples. Source code is designed to be integrated into existing bioinformatics pipelines. SeqCode web is web interface implemented to show only selection of features of standalone distribution. Suite of command-line software for high-performance comprehensive analysis of ChIPseq data. Designed to develop high-quality images and perform genome-wide calculations from high-throughput sequencing experiments. Presented into two distinct modes: web tools and command line." .
SCR:018071 a "Resoruce",
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:Warp",
"biotools:Warp" ;
rdfs:label "Warp" ;
definition: "Software tool that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Corrects micrographs for global and local motion, estimates local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. Software includes deep-learning-based models for accurate particle picking and image denoising." .
SCR:018072 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PremierBiosoft Proteo IQ Software" ;
NIFRID:synonym "ProteoIQ" ;
definition: "Software package as comprehensive qualitative and quantitative suite for proteomics. Used to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. Provides customizable interface to support any form of biological annotation. Used to compare protein quantitative results in relation to biological pathways, protein localization, protein function, or to transcript abundance. Every protein identification can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or in-house LIMS." .
SCR:018073 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_OmniGrid 100" ;
rdfs:label "Select Science | Genomic Solutions OmniGrid 100 Microarrayer" ;
NIFRID:synonym "GeneMachines OmniGrid 100 Microarray Printer",
"OmniGrid 100 microarrayer" ;
definition: "OmniGrid 100 microarrayer is high capacity multi axis microarrayer that prints biological samples onto solid substrates with speeds that give high throughput array production. Can be integrated with optional Server Arm 3 for fully automated handling of up to 72 input plates." .
SCR:018074 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QIIME 2 View" ;
NIFRID:synonym "q2view" ;
definition: "Web based serverless viewer of QIIME 2 artifacts and visualizations. Client side interface for viewing QIIME 2 artifacts and visualizations. Not needed working QIIME 2 installation to inspect QIIME 2 results. Supports viewing externally hosted files by automatically downloading and displaying them when links to files are provided." .
SCR:018075 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012695" ;
rdfs:label "Amylotrophic Lateral Sclerosis online Database" ;
NIFRID:synonym "ALSOD",
"ALSOD database",
"ALSOD v2.0" ;
NIFRID:abbrev "ALSoD" ;
definition: "Collection of published Amyotrophic lateral sclerosis associated genes and variants. Database can be searched to look for specific type of mutation like compound, insertion, deletion, substitution or non-pathological variant in ALS gene of interest including SOD1, ALS2, VAPB or NEFH. For each mutation DNA position mutated, original DNA sequence, mutated DNA sequence, original amino acid, mutated amino acid, intron/exon location, zygosity, and link to hypothetical mutant structure, can be identified." .
SCR:018076 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QuB" ;
NIFRID:synonym "Quantify unknown Biophysics" ;
definition: """Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system.
Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.""" .
SCR:018077 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mvp_a" ;
rdfs:label "Multi-omics Visualization Platform" ;
NIFRID:synonym "Galaxy MVP" ;
NIFRID:abbrev "MVP" ;
definition: "Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach." .
SCR:018078 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CircaDB" ;
NIFRID:synonym "Circadian gene expression profiles DataBase" ;
definition: "Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans." .
SCR:018079 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCGC CurveFit" ;
definition: "Large scale dose response curve fitting and curve classification software. Automated curve fitting and classificatoin software. Web deployed software. Algorithm recognizes bell shaped curves, implements standard hill equation, extensible for other models." .
SCR:018080 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R3SB9S",
"DOI:10.25504/FAIRsharing.uovQrT",
"DOI:10.25934",
"r3d100012823" ;
rdfs:label "Vivli" ;
definition: "Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials." .
SCR:018081 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cowplot" ;
NIFRID:synonym "R package cowplot" ;
definition: "Software R package as streamlined plot theme and plot annotations for ggplot2. Provides various features that help with creating publication quality figures with ggplot2, such as set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images." .
SCR:018082 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Applied Biosystems | 3130xl Genetic Analyzer" ;
NIFRID:synonym "3130xl Genetic Analyzer",
"Applied Biosystems 3130xl Genetic Analyzer 16-Capillary Array System" ;
definition: "3130xl Genetic Analyzer is latest generation of 16-capillary electrophoresis instruments by Applied Biosystems." .
SCR:018083 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "readxl" ;
NIFRID:synonym "Read Excel Files into R" ;
definition: "Software R package to import excel files into R. Has no external dependencies for easy installment and use on all operating systems. Designed to work with tabular data." .
SCR:018084 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Deltagraph " ;
definition: "Software tool for statistics and data visualization by Red Rock Software, Inc. Provides unparalleled chart selection, data analysis and graph customization capabilities." .
SCR:018085 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ewas-galaxy" ;
NIFRID:synonym "Epigenome-Wide Association Studies- Galaxy",
"EWAS-Galaxy" ;
definition: "Software suite for population epigenetics integrated into Galaxy. Galaxy Docker repository for population epigenetics data analysis." .
SCR:018086 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Database of genes related to Repeat Expansion Diseases" ;
NIFRID:abbrev "DRED" ;
definition: "Database of genes related to Repeat Expansion Diseases, as comprehensive manually curated database that covers all reported repeat expansion diseases included in PubMed and OMIM. Detailed information about each repeat and its related genes/diseases can be found in database, links to OMIM, NCBI and Ensembl are also provided. Provides list of predicted genes containing unstable tandem repeats that may cause diseases via abnormal repeat expansion by support vector machine and random forest." .
SCR:018087 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:protparam" ;
rdfs:label "ProtParam Tool" ;
NIFRID:synonym "ProtParam" ;
definition: "Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity." .
SCR:018090 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Fcirc" ;
rdfs:label "Fcirc" ;
NIFRID:synonym "Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs" ;
definition: "Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs." .
SCR:018092 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eppendorf | 5920R centrifuge" ;
definition: "Swinging bucket benchtop centrifuge. Eppendorf 5920 R refrigerated centrifuge." .
SCR:018093 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mettler | Toledo BenchSmart 96" ;
NIFRID:synonym "Pipetting System BenchSmart 96" ;
definition: "Semi automated pipetting system by Mettler Toledo. Instrument for semi-automated 96/384-well plate pipetting. Semi-Automated 96/384-Well Pipetting System where pipetting options range from 0.5 uL to 1000 uL." .
SCR:018094 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Beckman Coulter | Biomek i7 Hybrid Automated Workstation" ;
definition: "Liquid handling instrument designed to optimize dependability and walk-away time. Biomek i7 Hybrid with enclosure has up to 45 deck positions and includes both Multichannel and Span-8 pipette heads in enclosed work space." .
SCR:018095 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Qubit fluorimeter" ;
NIFRID:synonym "Qubit 4 Fluorometer" ;
definition: "Benchtop fluorometer designed to accurately measure DNA, RNA, and protein quantity. Measures RNA integrity and quality. Touch screen to select and run assays with results displayed in few seconds." .
SCR:018097 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SnapTools" ;
NIFRID:synonym "Single Nucleus Accessibility Profile Tools",
"Single nucleus accessibility profile Tools" ;
definition: "Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets." .
SCR:018098 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scrublet" ;
NIFRID:synonym "Single Cell Remover of Doublets" ;
definition: "Software tool to detect doublets in single-cell RNA-seq data. Software algorithm to remove doublets. Python code for identifying doublets in single-cell RNA-seq data. Framework for predicting impact of multiplets in given analysis and identifying problematic multiplets." .
SCR:018099 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scrattch.Hicat" ;
NIFRID:synonym "Iterative Clustering for Analysis of Transcriptomics",
"Scrattch Hierarchical" ;
definition: "Software R package as hierarchical, iterative clustering for analysis of transcriptomics data.Used for single cell RNA-seq analysis for transcriptomic type characterization from Allen Institute." .
SCR:018100 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LIGER" ;
NIFRID:synonym "Linked Inference of Genomic Experimental Relationships" ;
definition: "Software R package for integrating and analyzing multiple single-cell datasets. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. Used for analysis of multiple scRNA-seq data sets." .
SCR:018116 a "Resoruce",
owl:NamedIndividual ;
rdfs:label "RTKLIB" ;
definition: "Open source software package for standard and precise positioning with global navigation satellite system. Consists of portable program library and several application programs utilizing library. Program Package for GNSS Positioning." .
SCR:018118 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:raptorx" ;
rdfs:label "RaptorX" ;
definition: "Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model." .
SCR:018119 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agisoft Metashape" ;
definition: "Stand alone software that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales. Successor of PhotoScan and is advanced image-based 3D modeling solution aimed at creating professional quality 3D content from still images." .
SCR:018120 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agisoft Photoscan" ;
definition: "Software tool as advanced image-based 3D modeling solution aimed at creating professional quality 3D content from still images by Agisoft LLC." .
SCR:018122 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "genomics resource for animal lectins" ;
definition: "Resource presents information about animal lectins involved in various sugar recognition processes." .
SCR:018123 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:swiss-model_workspace",
"biotools:swiss_model" ;
rdfs:label "SWISS-MODEL" ;
definition: "Software tool as fully automated protein structure homology modeling server, accessible via ExPASy web server, or from program DeepView Swiss Pdb-Viewer. Structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Used to make protein modelling accessible to all biochemists and molecular biologists." .
SCR:018124 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyMOLWiki RotationAxis" ;
NIFRID:synonym "RotationAxis" ;
definition: "Software tool to draw CGO cylinder representing rotation axis for given transformation. Useful for drawing axes of rotational symmetry in oligomeric assembly." .
SCR:018125 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:dichroweb" ;
rdfs:label "DichroWeb" ;
definition: "Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures." .
SCR:018126 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UltraScan" ;
definition: "Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis." .
SCR:018127 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:halSynteny" ;
rdfs:label "halSynteny" ;
NIFRID:synonym "Hierarchical Alignment Format Synteny" ;
definition: "Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment." .
SCR:018128 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:CLIP-Explorer",
"SCR_018130" ;
rdfs:label "CLIP-Explorer" ;
definition: "Webserver to process, analyse and visualise CLIP-Seq data. Software tools to process and visualise RNA protein interactions. CLIP-Seq data analysis in Galaxy. Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to iCLIP workflows also FLASH, and uvCLAP." .
SCR:018129 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Joinpoint" ;
NIFRID:synonym "Joinpoint Trend Analysis Software" ;
definition: """Software package for analysis of trends using joinpoint models where several different lines are connected together at joinpoints.
There are two versions available. Desktop version has graphical user interface and is for interactive use. Command-line version is for use in batch mode or called from other software, such as SAS or R.""" .
SCR:018132 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "seaborn" ;
definition: "Software Python tool as data visualization library based on matplotlib. Provides interface for drawing attractive and informative statistical graphics. Statistical data visualization using matplotlib." .
SCR:018134 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Metagenomic_read_binning_using_sparse_coding" ;
rdfs:label "lsa_slurm" ;
NIFRID:synonym "Metagenomic_read_binning_using_sparse_coding" ;
definition: "Software tool to implement pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in field of metagenomics." .
SCR:018135 a NLX:63400,
owl:NamedIndividual .
SCR:018136 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:hingeprot" ;
rdfs:label "HingeProt" ;
definition: "Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures." .
SCR:018137 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SAXS Molecular Weight" ;
NIFRID:synonym "SAXSMoW 2.0" ;
NIFRID:abbrev "SAXSMoW2" ;
definition: "Software tool as online calculator of molecular weight of proteins in dilute solution from experimental SAXS data measured on relative scale. Software package for easy processing of small angle X ray scattering data from mono disperse systems in diluted solution." .
SCR:018138 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "astroML" ;
definition: "Software Python package for machine learning, statistics and data mining. Contains library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical data sets, and examples of analyzing and visualizing astronomical data sets. Repository of common tools and routines used for statistical data analysis in astronomy and astrophysics." .
SCR:018139 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:scanpy",
"biotools:scanpy" ;
rdfs:label "scanpy" ;
NIFRID:synonym "Single Cell Analysis in Python" ;
definition: "Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time." .
SCR:018140 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:flowcal" ;
rdfs:label "FlowCal" ;
NIFRID:synonym "Python Flow Cytometry Calibration Library" ;
definition: "Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots." .
SCR:018141 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_03490" ;
rdfs:label "ChromHMM" ;
definition: "Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations." .
SCR:018142 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Drop-seq tools" ;
NIFRID:synonym "Droplet sequencing data analysis software tools",
"Droplet sequencing tools" ;
definition: "Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript." .
SCR:018143 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sleipner" ;
NIFRID:synonym "SLEIPNER",
"Sleipner",
"SLEIPNER 2.1" ;
definition: "Software package as collection of modules implementing methods of analysis that form self-contained and empirically grounded toolbox for handling longitudinal data within person oriented paradigm." .
SCR:018145 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KEGG PATHWAY Database" ;
NIFRID:synonym "KEGG PATHWAY" ;
definition: "Reference database for pathway mapping in KEGG Mapper. Collection of manually drawn pathway maps representing knowledge on molecular interaction, reaction and relation networks for metabolism, genetic information processing, environmental information processing, cellular processes, organisms systems, human diseases, drug development." .
SCR:018146 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Laniakea" ;
rdfs:label "Laniakea" ;
NIFRID:synonym "Galaxy cloud on demand workflow workbench" ;
definition: "Software tool for automatic deployment of virtual Galaxy environments for life science. Can be deployed over common cloud architectures supported both by public and private e-infrastructures. User interacts with Laniakea based service through simple front end that allows general setup of Galaxy instance, then Laniakea takes care of automatic deployment of virtual hardware and software components. User gains access with full administrative privileges to private, production grade, fully customized, Galaxy virtual instance, and to underlying virtual machine." .
SCR:018147 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Anatomography" ;
NIFRID:synonym "BodyParts3D / Anatomography" ;
definition: "Web application that enables users to build and publish own custom manikins. Used to build three dimensional model of human body using parts registered in BodyParts3D. Server returns image of assembled 3D model as still image, rotating animation, interactive image, etc. Each part can be downloaded as polygon mesh file that can be used with 3D printer." .
SCR:018148 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "astropy" ;
definition: "Community software Pyton library for astronomy. Collection of software packages written in Python programming language for use in astronomy. Package contains key functionality and common tools needed for performing astronomy and astrophysics with Python. Core of Astropy Project, which aims to enable community to develop ecosystem of Affiliated Packages covering broad range of needs for astronomical research, data processing, and data analysis." .
SCR:018149 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ECOFFinder" ;
NIFRID:synonym "ECOFFinder for Excel Prior to 2010",
"ECOFFinder XL 2010 v2.1" ;
definition: "Software tool as Microsoft Excel spreadsheet calculator designed to estimate epidemiological cutoff values (ECVs, ECOFFs) for minimal inhibitory concentrations or minimal effective concentrations of wild-type bacterial or fungal populations." .
SCR:018151 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LPSN Database" ;
NIFRID:synonym "List of Prokaryotic names with Standing in Nomenclature Database" ;
definition: "Database lists names of prokaryotes that have been validly published in International Journal of Systematic and Evolutionary Microbiology directly or by inclusion in Validation List, under Rules of International Code of Nomenclature of Bacteria. Has classification of prokaryotes and information on prokaryotic nomenclature and culture collections." .
SCR:018152 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Parker | Picospritzer III" ;
NIFRID:synonym "Picospritzer III - Intracellular Microinjection Dispense Systems" ;
definition: "Intracellular microinjection dispense system by Parker Hannifin. Supplies repeatable pressure pulses. Designed for rapid and reproducible ejections of picoliter and nanoliter volumes used in conjunction with intracellular or extracellular studies while avoiding inherent desensitization of nerve cells which accompanies Iontophoretic methodology. System comes complete with high speed valves and necessary tubing assemblies." .
SCR:018153 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TDT | RZ6 Multi-I/O Processor" ;
definition: "Processor for auditory research delivers processing power, data transfer and sample rate of 200 kHz by Tucker-Davis Technologies . Can be equipped with up to 4 high-performance DSPs to support complex stimulus control, high frequency applications, and real time normalization for speakers and microphones." .
SCR:018154 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dolomite Bio | Nadia High Throughput Cell Analyzer Platform" ;
NIFRID:synonym "Nadia Instrument" ;
definition: "Automated, microfluidic droplet based platform for single cell research that encapsulates up to 8 samples. Instrument has sample temperature control from 4 degrees Celsius to 40 degrees Celsius. System detects single use cartridges for specific applications." .
SCR:018155 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "S2 Genomics | Singulator 100 Automated Single Cell Prep Automated System" ;
NIFRID:synonym "S2 Genomics Singulator",
"S2 Genomics Singulator 100",
"Singulator 100" ;
definition: "Singulator to automate tissue preparation for single cell and single nucleus analyses. Bench top Singulator System and single use cartridge enable tissue dissociations into singulated cells or nuclei suspensions." .
SCR:018156 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mizar Imaging | Tilt High Resolution Light Sheet Imaging System" ;
NIFRID:synonym "Tilt" ;
definition: "Modular light sheet illumination system designed to image living samples with minimal photobleaching or phototoxicity by Mizar Imaging. Enables high spatial and temporal resolution light sheet imaging to be added to existing or new microscope system." .
SCR:018157 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NBRP Medaka Pattern Match" ;
definition: "Web medaka pattern match tool for short sequence and/or pattern. Used to search database of medaka genome on target and off target sites when editing genome with CRISRP-Cas9." .
SCR:018158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Epigenetic Pacemaker " ;
NIFRID:synonym "Epigenetic Pacemaker" ;
NIFRID:abbrev "EPM" ;
definition: "Python implementation of conditional expectation maximization algorithm that estimates epigenetic landscapes and state of individuals and may be used to study nonlinear epigenetic aging. Fast conditional expectation maximization algorithm used to model epigenetic states associated with phenotype of interest. Can model non linear epigenetic trait associations directly without transformation of phenotype of interest." .
SCR:018159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NBRP Medaka CRISPR target site" ;
definition: "Web tool to show micro homology sequences striding over double strand break point created by CRISPR/Cas9 system. Used to search for CRISPR target site with micro-homology sequences. Used to predict deletion pattern." .
SCR:018160 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "liftOver" ;
definition: "Web tool to convert genome coordinates and genome annotation files between assemblies. Used to translate genomic coordinates from one assembly version into another and retrieves putative orthologous regions in other species using UCSC chained and netted alignments." .
SCR:018161 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PROMALS3D" ;
definition: "Web tool as multiple sequence and structure alignment server. Automatically identifies homologs with known 3D structures for input sequences, derives structural constraints through structure based alignments and combines them with sequence constraints to construct consistency based multiple sequence alignments. Aligns sequences of multiple input structures, with output representing multiple structure based alignment refined in combination with sequence constraints." .
SCR:018162 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brainome portal" ;
NIFRID:synonym "Brainome" ;
definition: "Web based analytics environment for genomic data arising from BRAIN Initiative Cell Census Network, based on AnnoJ browser. AnnoJ browser displays epigenomic data, including base resolution DNA methylation, RNA-Seq, ChIP-Seq, as well as annotations." .
SCR:018163 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Black Zen software" ;
NIFRID:synonym "Black Zen software (ZEISS)",
"ZEISS ZEN Microscope Software",
"ZEN Black" ;
definition: "Software used to analyze images obtained from microscope. ZEN Black is software Zeiss uses to run their laser-based instruments." .
SCR:018164 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018244" ;
rdfs:label "NeMO Analytics" ;
NIFRID:synonym "Neuroscience Multi-Omic Analytics" ;
definition: "Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools." .
SCR:018165 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MitoCarta" ;
NIFRID:synonym "MitoCarta2.0" ;
definition: "Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria." .
SCR:018166 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BoneJ" ;
NIFRID:synonym "BoneJ2" ;
definition: "Software plugin for bone image analysis in ImageJ. Used for standard bone measurements. Provides free, open source tools for trabecular geometry and whole bone shape analysis." .
SCR:018167 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Velocyto" ;
NIFRID:synonym "velocyto",
"velocyto.py",
"velocyto.R" ;
definition: "Software package for analysis of expression dynamics in single cell RNA seq data. Enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Estimates RNA velocity in single cell RNA sequencing datasets. RNA velocity estimation in Python or R." .
SCR:018168 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:scVelo" ;
rdfs:label "scVelo" ;
NIFRID:synonym "scvelo",
"single-cell RNA Velocity generalized to transient cell states" ;
definition: "Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling." .
SCR:018169 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TCS_SP8" ;
rdfs:label "Leica | SP8 LIGHTNING confocal microscope" ;
NIFRID:synonym "Leica TCS SP8 system" ;
definition: """Confocal microscope by Leica Microsystems to capture up to five true color channels simultaneously at high speed without need for trade-offs in multicolor experiments. Provides super resolution live cell imaging, simultaneous multicolor imaging,
live specimen imaging thanks to fast acquisition rates, sample protection thanks to low phototoxicity.""" .
SCR:018170 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:finestructure" ;
rdfs:label "fineSTRUCTURE" ;
NIFRID:synonym "FineSTRUCTURE version 2" ;
definition: "Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data." .
SCR:018171 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mummer",
"OMICS_14554" ;
rdfs:label "MUMmer" ;
NIFRID:synonym "MUMmer4",
"MUMmer 3.0" ;
definition: "Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes." .
SCR:018172 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:roary",
"OMICS_09491" ;
rdfs:label "Roary" ;
definition: "Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes." .
SCR:018173 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TreeBeST" ;
NIFRID:synonym "NJTREE",
"Tree Building guided by Species Tree" ;
definition: "Software package to build, manipulate and display phylogenetic trees. Designed for building gene trees with known species tree and is highly efficient and accurate." .
SCR:018174 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:itol" ;
rdfs:label "iTOL" ;
NIFRID:synonym "interactive Tree Of Life" ;
definition: "Web tool for display, annotation and management of phylogenetic trees. Accessible with any modern web browser." .
SCR:018175 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SuperDCA" ;
NIFRID:synonym "Super Direct Coupling Analysis" ;
definition: "Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis." .
SCR:018176 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:SpydrPick" ;
rdfs:label "SpydrPick" ;
definition: "Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree." .
SCR:018177 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:SnpHub" ;
rdfs:label "SnpHub" ;
definition: "Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data." .
SCR:018178 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ChiCMaxima" ;
rdfs:label "ChiCMaxima" ;
definition: "Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling." .
SCR:018179 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bioentity2vec" ;
definition: "Software tool as algorithm that represents nodes as vectors by integrating bioentity attribute such as RNA sequence and bioentity behavior that is relationship between bioentities." .
SCR:018180 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Diversity Outbred Database " ;
definition: "Database provides access to genotype and phenotype data from experiments with Diversity Outbred mice. Data can be searched by publication, investigator, and data type and can be downloaded in zipped CSV or R/QTL2 formats. Users can download full studies or subset of samples, genotypes, clinical phenotypes and molecular phenotypes including transcript, proteomic, and metabolomic profiling data." .
SCR:018181 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:R_qtl2",
"SCR_020965" ;
rdfs:label "R/qtl2" ;
NIFRID:synonym "QTL",
"QTL2",
"qtl2",
"quantitative trait loci 2",
"Quantitative Trait Locus 2",
"R/qtl",
"R/quantitative trait loci" ;
definition: "Software R package for mapping quantitative trait loci with high dimensional data and multiparent populations. Used for analysis of high dimensional data and complex crosses. Interactive software environment for mapping quantitative trait loci in experimental populations.R/qtl2 software expands scope of R/qtl software package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations." .
SCR:018182 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:netmhcpan" ;
rdfs:label "NetMHCpan Server" ;
NIFRID:synonym "NetMHCpan",
"NetMHCpan 1.0",
"NetMHCpan 2.0",
"NetMHCpan 3.0",
"NetMHCpan 4.0",
"NetMHCpan 4.1" ;
definition: "Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs)." .
SCR:018183 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018192" ;
rdfs:label "Allen Software Development Kit" ;
NIFRID:abbrev "AllenSDK" ;
definition: "Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas." .
SCR:018184 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "How many cells" ;
NIFRID:synonym "Satija Lab: How Many Cells" ;
definition: "Web tool for calculating number of cells that must be sampled in order to see at least n cells of each type for single cell genomics experiments." .
SCR:018185 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pLogo" ;
NIFRID:synonym "probability logo" ;
definition: "Web tool as probabilistic approach to visualizing protein or nucleic acid sequence motifs. Used for motif visualization in which residue heights are scaled relative to their statistical significance. Supports real time conditional probability calculations and visualizations." .
SCR:018186 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:CRISPRdirect" ;
rdfs:label "CRISPRdirect" ;
definition: "Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast." .
SCR:018187 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cRAP protein sequences" ;
NIFRID:synonym "common Repository of Adventitious Proteins" ;
NIFRID:abbrev "cRAP" ;
definition: """List of proteins commonly found in proteomics experiments that are present either by accident or through unavoidable contamination of protein samples. List is based on analysis of current version of GPMDB, as well as suggestions by users.
Current version of cRAP in FASTA format can be obtained from the GPM FTP site.""" .
SCR:018188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MaxTRAQ" ;
NIFRID:synonym "Innovision Systems MaxTRAQ software" ;
definition: "Software package for motion capture analysis by Innovision Systems Inc." .
SCR:018189 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSpherix | C-Chamber" ;
NIFRID:synonym "C-Chamber",
"Culture Chamber" ;
definition: "Culture chamber for cell culture by BioSpherix. Functionalized by gas controllers for all bioactive gases, e.g. O2, CO2, CO, NO, etc. Made of clear polycarbonate. Magnetic seal door. Temperature is controlled. Combines with ProOx 110, ProCO2, ProOx C21, OxyCycler Series." .
SCR:018190 a NLX:63400,
owl:NamedIndividual .
SCR:018191 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:deltag_prediction" ;
rdfs:label "ΔG prediction server" ;
NIFRID:synonym "ΔG prediction server v1.0" ;
definition: "Web server to predict ΔGapp for membrane insertion of potential TM helix. Given amino acid sequence of putative transmembrane helix, server gives prediction of corresponding apparent free energy difference for insertion of this sequence into Endoplasmic Reticulum membrane by means of Sec61 translocon." .
SCR:018193 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EphysExtraction" ;
definition: "Software tool as code to extract electrophysiological parameters of neurons. Code is continuously being updated to handle more kinds of voltage traces and extract different kinds of features." .
SCR:018194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Half Life Calculator" ;
definition: "Web tool as basic math calculator to do simple calculation. Can generate any one of values from other three in half life formula for substance undergoing decay to decrease by half." .
SCR:018195 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FlowPy" ;
definition: "Software Python tool for flow cytometry data. Data generated by flow cytometer can be read by FlowPy. Used for data extraction, data visualization, data clustering, histogram subtraction." .
SCR:018196 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:IMGt_HighV-QUESt" ;
rdfs:label "IMGT HighV-QUEST" ;
NIFRID:synonym "IMGT web portal",
"IMGT/HighV QUEST",
"IMGT/HighV-QUEST" ;
definition: "Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing." .
SCR:018197 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SMART-Farm Tool" ;
NIFRID:synonym "smart",
"smart farm",
"SMART tool",
"SMART-Farm tool",
"Sustainability Monitoring and Assessment RouTine" ;
NIFRID:abbrev "SMART",
"SMART-Farm" ;
definition: "Web and offline tool for holistic sustainability assessment of farms. Tool operationalizes Sustainability Assessment of Food and Agriculture Systems Guidelines of Food and Agriculture Organisation of United Nations. Tool consists of questionnaire software, centralized database, pool of indicators and scientifically based assessment methodology. Different stakeholders can use results of this assessment e.g. for comparing different farms, production systems or for strategic development, improvement, monitoring and communication to business partners." .
SCR:018198 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneSyntenyPipeline" ;
definition: "Software pipeline was designed to draw gene synteny plot between genomes and obtain 1 to 1 gene pairs from each genome." .
SCR:018199 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VitalRecorder2" ;
definition: "Sleep recording software by Kissei Comtech Co., Ltd. Can measure signals of up to 32 channels while monitoring wave forms in real time. Addition of video recording option enables simultaneous recording of biological signals and video." .
SCR:018200 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SleepSign" ;
NIFRID:synonym "SleepSign 3.0" ;
definition: "Sleep analysis for animals by Kissei Comtec Co., Ltd. Enables to generate various types of reports which are required as standard in basic sleep research field like sleep quality and sleep quantity. Version 3.0 is much more faster than prior method of sleep scoring." .
SCR:018201 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MascotScan" ;
NIFRID:synonym "MScan" ;
definition: "Software tool for analysis of qualitative data, operating on basis of lists of peptides and proteins identified in samples generated by Mascot database system. Responsible for preparing data for quantitative analysis of proteins both with use of stable isotope labeling and without isotope labeling." .
SCR:018203 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OSHA Occupational Chemical Database" ;
definition: "Chemical inventory for occupational chemical information. Collects information from several government agencies and organizations. Includes information about identification and physical properties, exposure limits, sampling." .
SCR:018206 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1007",
"SCR_015105" ;
rdfs:label "University of California San Francisco Parnassus Flow Cytometry Core Facility" ;
NIFRID:synonym "UCSF Parnassus Flow CoLab",
"University of California San Francisco Diabetes Research Center Cytometry and Cell Sorting Core",
"University of California San Francisco Diabetes Research Center Parnassus Flow Cytometry CoLab" ;
NIFRID:abbrev "PFCC" ;
definition: "Core assists investigators whose research requires molecular marker characterization of cells in suspension as well as isolation of cells based on those markers. Advanced cell sorting and cytometric analyses by Flow or Mass Cytometry are provided." .
SCR:018207 a NLX:63400,
owl:NamedIndividual .
SCR:018208 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "YXLON | FF35 CT" ;
definition: """Computed tomography system designed to achieve precise inspection results for wide range of applications by YXLON.
Available in single or dual tube configuration, it is perfect for very small to medium sized parts inspection in automotive, electronics, aviation, and material science industries.""" .
SCR:018209 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Anndata" ;
NIFRID:synonym "Annotated data" ;
definition: "Software tool that provides scalable way of keeping track of data and learned annotations. Initially built for Scanpy. Used as generic class for handling annotated data matrices. Stores data matrix with annotations of observations (samples, cells) and variables (features, genes), and unstructured annotations." .
SCR:018210 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_33004" ;
rdfs:label "Bustools" ;
definition: "Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks." .
SCR:018211 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GNU Awk" ;
NIFRID:abbrev "GAWK" ;
definition: "Software tool to select particular records in file and perform operations upon them. awk utility interprets special purpose programming language that makes it possible to handle simple data reformatting jobs with few lines of code. Source code for latest release of GNU awk is available from GNU project ftp server and its many mirrors." .
SCR:018212 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GNU Grep" ;
NIFRID:synonym "GNU Grep 3.4",
"Grep" ;
definition: "Software tool to searches one or more input files for lines containing a match to a specified pattern. Prints lines that contain match for one or more patterns. Command-line utility for searching plain-text data sets for lines that match regular expression. When finds match, it copies line to standard output (by default), or produces whatever other sort of output you have requested with options." .
SCR:018213 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "kb_python" ;
definition: "Software Python package that wraps kallisto and bustools single-cell RNA-seq workflow. Used for single-cell RNA-seq pre-processing. Simplifies downloading and running of kallisto and bustools programs. Consists of kb ref and kb count commands. kb ref builds or downloads species specific index for pseudo alignment of reads and must be run prior to kb count and it runs kallisto index. kb count runs kallisto and bustools programs and is used for pre-processing of data from variety of single-cell RNA-seq technologies, and for number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.)." .
SCR:018214 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pandas" ;
definition: "Software Python package for data analysis providing labeled data structures similar to R data. Provides data structures designed to make working with relational or labeled data. Software as building block for doing practical, real world open source data analysis and manipulation tool." .
SCR:018215 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GNU sed" ;
NIFRID:synonym "GNU stream editor" ;
definition: "Software tool as non interactive command line text editor. Command line that works with streams of characters for searching, filtering and text processing. Used for extracting part of file using pattern matching or substituting multiple occurrences of string within file." .
SCR:018216 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GNU Tar" ;
NIFRID:synonym "GNU Tape archiver" ;
definition: "Software tool to create tar archives, as well as various other kinds of manipulation. Used to extract files, to store additional files, or to update or list files which were already stored. Can direct its output to available devices, files, or other programs, can access remote devices or files." .
SCR:018217 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Umap" ;
NIFRID:synonym "Uniform Manifold Approximation and Projection" ;
NIFRID:abbrev "UMAP" ;
definition: "Software package as dimension reduction technique that can be used for visualization similar to t-SNE, but also for general non-linear dimension reduction. Used for dimensionality reduction for visualizing single-cell data." .
SCR:018218 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dune" ;
definition: """Software R Package that provides parameter-free method for optimizing trade-off between resolution of clusters and their replicability across datasets. Dune method takes as input set of clustering results on dataset, and iteratively merges clusters within those clusterings in order to maximize their concordance.
Iterative merging of clusters to improve mean ARI""" .
SCR:018219 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SAVES" ;
NIFRID:synonym "SAVES v5.0",
"Structure Analysis and Verification Server" ;
definition: "Web server for structure validation in homology modeling. Used to validate of obtained crude models. Structure analysis and validation server." .
SCR:018220 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IMGT Repertoire" ;
NIFRID:synonym "IMGT Repertoire (MH)",
"IMGT Repertoire (RPI)",
"ImMunoGeneTics Repertoire",
"Repertoire (IG and TR)" ;
definition: "Web resource for immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system (RPI). Comprises LIGM expertized data on immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system." .
SCR:018221 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyCharm" ;
definition: "Software environment that includes tools and integrations for professional Python and Web development. Integrated Development Environment by JetBrains. Used for development in Python and frameworks like DJango. Can be customized with themes and plugins." .
SCR:018222 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "medRxiv" ;
definition: "Free online archive and distribution server for complete but unpublished manuscripts in the medical, clinical, and related health sciences. Preprints are preliminary reports of work that have not been certified by peer review. They should not be relied on to guide clinical practice or health related behavior and should not be reported in news media as established information. Research articles, systematic reviews and meta analyses, clinical research design protocols and data articles may be posted." .
SCR:018223 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "nextstrain.org" .
SCR:018225 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cheshire Image Processing Software" ;
NIFRID:synonym "Alice/Cheshire" ;
definition: """Discontinued software tool used to analyse images. Documented on March 30, 2020.
Cheshire intended for clinical use for teleradiology, telecardiology, in hospital view stations and image review for referring physicians.""" .
SCR:018226 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:biospytial" ;
rdfs:label "biospytial" ;
definition: "Software package as spatial graph based computing engine for ecological big data. Modular open source knowledge engine designed to import, organize, analyse and visualize big spatial ecological datasets using power of graph theory. Handles species occurrences and their taxonomic classification for performing ecological analysis on biodiversity and species distributions. Data are linked with relationships that are stored in graph database, while tabular and geospatial data are stored in relational database management system." .
SCR:018238 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Beckman Coulter | Ultracentrifuge OPTIMA XPN - 90" ;
NIFRID:synonym "Ultracentrifuge Optima XPN 90" ;
definition: "Floor model preparative ultracentrifuge by Beckman Coulter Inc. with max. speed 90,000 rpm. Offers simplified use, optimized control and security, and increases productivity. Rotors, labware, and services are available." .
SCR:018241 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LabSolutions" ;
NIFRID:synonym "LabSolutions Software" ;
definition: "Software package for data analysis by Shimadzu Oceania." .
SCR:018242 a owl:NamedIndividual ;
rdfs:label "Mycobrowser" ;
definition: "Comprehensive and manually annotated resource for mycobacterial genomes. Genomic and proteomic data repository for pathogenic mycobacteria. Provides manually curated annotations and tools to facilitate genomic and proteomic study of these organisms. Integrates genome details, protein information, drug and transcriptome data, mutant and operon annotation." .
SCR:018243 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:nanosim",
"biotools:trans-nanosim" ;
rdfs:label "NanoSim" ;
definition: "Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software." .
SCR:018245 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Swiss Federal Institute of Technology Lausanne" ;
NIFRID:abbrev "EPFL" ;
definition: "Rsearch institute and university in Lausanne, Switzerland, that specializes in natural sciences and engineering. It is one of the two Swiss Federal Institutes of Technology, and it has three main missions: education, research and technology transfer at the highest international level." .
SCR:018246 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "biomod2" ;
definition: "Software R package for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization." .
SCR:018247 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HAST" ;
NIFRID:synonym "Haplotype-resolved Assembly for Synthetic long reads using a Trio-binning strategy" ;
definition: "Software tool for partition stLFR reads based on trio binning using prenatally unique markers. Haplotype resolved assembly for synthetic long reads using Trio-Binning strategy." .
SCR:018248 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ClusPro" ;
NIFRID:synonym "ClusPro 2.0" ;
definition: "Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results." .
SCR:018249 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LigPlot+" ;
NIFRID:synonym "LIGPLOT",
"LigPlot Plus",
"LigPlot+ v.2.2",
"LigPlotPlus",
"LigPlus" ;
definition: "Software tool for automatic generation of multiple 2D ligand-protein interaction diagrams from 3D coordinates. Diagrams portray hydrogen-bond interaction patterns and hydrophobic contacts between ligand(s) and main-chain or side-chain elements of protein. Used for drug discovery for analyzing series of small molecules binding to same protein target, single ligand binding to homologous proteins, or where both protein and ligand change." .
SCR:018250 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fs-tool" ;
NIFRID:synonym "fraction shared tool" ;
definition: "Software tool to calculate fraction of shared bound peptides between HLA proteins. Command-line tool to calculate fraction of shared bound peptides between HLA alleles from NetMHCpan binding predictions. Compares fraction shared between HLA allele and individual taking into account HLA and KIR genotypes." .
SCR:018251 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100010126",
"SCR_018279",
"SCR_018318" ;
rdfs:label "Global Initiative on Sharing All Influenza Data" ;
NIFRID:abbrev "GISAID" ;
definition: "Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data." .
SCR:018252 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COVID-19 Crowd Generated Gene and Drug Set Library" ;
definition: "Software tool as interface to submit, serve, and analyze COVID19 related gene and drug sets. Collection of gene and drug sets related to COVID-19 research contributed by community." .
SCR:018253 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCBI Virus" ;
NIFRID:synonym "National Center for Biotechnology Information Virus" ;
definition: "Community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories. Integrative, value added resource designed to support retrieval, display and analysis of curated collection of virus sequences and large sequence datasets. Used to increase usability of data archived in GenBank and other NCBI repositories." .
SCR:018254 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GlycoCalyx | GlycoCheck" ;
definition: """Microvascular health measurement system that measures endothelial glycocalyx layer of vessels by MicroVascular Health Solutions. Software automatically identifies measurable micro vessels, below 30 µm thickness, during acquisition by contrast between RBC and background. After acquisition, software undergoes series of quality checks to measure vascular segments that are of good quality.
Video microscope is placed under tongue, showing live movement of red blood cells as they travel through micro vessels.""" .
SCR:018255 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "multcomp" ;
definition: "Software R package for simultaneous inference in general parametric models. Offers interface to perform multiple comparisons in general context. Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models." .
SCR:018256 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biolucida" ;
NIFRID:synonym "Micro File Plus",
"MicroFile",
"MicroFile+" ;
definition: "Enables visualization, storage and sharing of large image data. Cloud based system by MBF Bioscience to help with data from 2D and 3D slide scanners, confocal Z-stacks, lightsheet whole brain images. System for data storage and management, data analysis and visualization. Data is stored in secure and permanent way. Available also is free application named Biolucida Viewer, for viewing public images or images shared by collaborators owning Biolucida." .
SCR:018257 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:qupath" ;
rdfs:label "QuPath" ;
definition: "Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images." .
SCR:018258 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Coronavirus Immunotherapy Consortium" ;
NIFRID:abbrev "CoVIC" ;
definition: "Consortium to unite efforts and resources from experts across globe to advance effective, antibody based therapies against novel coronavirus, SARS-CoV-2. Represents multidisciplinary convergence of structural biology, virologists, immunologists, clinicians and bioinformaticians from academic and industry settings. Collects antibodies for testing as part of CoVICS. Contributed antibodies are blinded and will only be known as code name. Antibody contributors will be able to see performance of their own molecules and take part in analysis. Contributors retain ownership of their antibodies and may continue to publish on them using original antibody names. Goal is to determine relative in vitro potency and in vivo efficacy using centralized standardized assays to identify best individual mAbs and rational combinations of mAbs. Consortium will recommend ideal therapeutic molecules for human use to protect vulnerable populations from COVID-19 disease. CoVIC database (CoVIC-DB) will serve as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them." .
SCR:018259 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Database of Immune Cell Epigenomes" ;
NIFRID:synonym "Database of Immune Cell Expression",
"Expression quantitative trait loci (eQTLs) and Epigenomics" ;
NIFRID:abbrev "DICE" ;
definition: "Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis." .
SCR:018260 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GLYCAM-Web" ;
NIFRID:synonym "GLYCAM" ;
definition: "Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates." .
SCR:018261 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:gps-sumo" ;
rdfs:label "GPS-SUMO" ;
NIFRID:synonym "GPS Small Ubiquitin-like MOdifiers",
"GPS-SUMO 2.0",
"Group-based Prediction System -Small Ubiquitin-like MOdifiers",
"Group-based Prediction System-SUMO",
"Small Ubiquitin-like MOdifiers sp",
"SUMOsp" ;
definition: "Web service for prediction of SUMOylation sites and SUMO-interaction motifs in proteins by CUCKOO Workgroup." .
SCR:018262 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_106" ;
rdfs:label "University at Albany SUNY Center for Functional Genomics Microarray and Next Gen Sequencing Core Facility" ;
NIFRID:synonym "Microarray &HT Sequencing Core",
"UAlbany Center for Functional Genomics Microarray and Next Gen Sequencing Services",
"University at Albany SUNY Center for Functional Genomics" ;
NIFRID:abbrev "CFG" ;
definition: "Provides services for DNA microarrays for large scale analysis of gene expression,gene regulation, exon splicing, epigenetics. Provides instrumentation for scanning of protein arrays.Offers services in RNA sequencing, ChIP-seq, ChIRP-seq, metagenomics and miRNA sequencing.Provides bioinformatics tools for analysis of results of microarray and sequencing experiments. Houses Illumina Nextseq500 and Ion PGM platforms for next generation sequencing. Provides instruments for Next gen sequencing including Illumina, MinIon, Wafergen-Takara, 10x genomics and for DNA microarrays including Affymetrix, Agilent." .
SCR:018263 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_148" ;
rdfs:label "University of Massachusetts Medical School Molecular Biology Core Facility" ;
NIFRID:synonym "Molecular Biology Core Lab (MBCL)",
"Molecular Biology Core Labs (MBCL)",
"University of Massachusetts Medical School - Molecular Biology Core Lab (MBCL)",
"University of Massachusetts Medical School Molecular Biology Core Lab" ;
NIFRID:abbrev "MBCL" ;
definition: "Core services including UMass Oligo Discount Program which provides discounted oligos to researchers, Reagent Program offers discounted pricing on TAQMAN, qPCR reagents, enzymes, etc. from ThermoFisher (Life Technologies/Ambion), and Empirical Biosciences, Fragment Analyzer Service, Sequencing Library Preparation, Sanger Sequencing and GeneMapper/ARISA. Provides DNA fragment analysis, Genotyping, and SPR services on an ABI capillary sequencer, and DNA/RNA fragment analysis on the Advanced Analytical (Agilent) Fragment Analyzer." .
SCR:018265 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_117" ;
rdfs:label "Nemours Biomolecular Core Facility" ;
NIFRID:synonym "Nemours Biomolecular Core Laboratory" ;
definition: "Develops research projects in pediatric genetics and provides essential services in molecular biology and genetics to Nemours clinicians and research staff and to affiliates researchers of University of Delaware and Thomas Jefferson University. Resource for staff of Alfred I. duPont Hospital for Children, Nemours affiliates, COBRE / INBRE investigators and outside customers. Offers expertise in molecular genetics and genomics. Operates according to policies set forth by federal CLIA standards.Services provided include Ion Torrent PGM Next Generation Sequencing, QuantStudio (QS) 3D Digital PCR, Cell Line Authentication, Nucleic Acid Quality Number (AATI Fragment Analyzer),Genotyping including Allelic Discrimination Probes (SNP Real-Time PCR), Affymetrix Microarray (CNV CytoScan, SNP arrays), Fragment Analysis (Capillary Electrophoresis up to 1200 bp), DNA Sequencing (Sanger Sequencing), Expression Analysis including Affymetrix Microarray (global gene expression, transcriptome assays), Pathway-focused Real-Time qPCR (mRNA and miRNA). Shared Instrumentation including Beckman Biomek 3000 Liquid Handler, NanoDrop 2000c, ABI7900 384-well Real-Time Genetic Analyzer, PCR Tamer, Thermocyclers." .
SCR:018266 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_399" ;
rdfs:label "Stanford University Human Immune Monitoring Center Core Facility" ;
NIFRID:synonym "Human Immune Monitoring Center (HIMC)",
"Stanford University - Human Immune Monitoring Center" ;
NIFRID:abbrev "HIMC" ;
definition: "Core designed for immune monitoring services for clinical and translational studies. Goals include providing standardized, state-of-the art immune monitoring assays at RNA, protein, and cellular level, testing and developing new technologies for immune monitoring, archive, report, and mine data from immune monitoring studies. HIMC uses online database for integration of data from standard HIMC assays, along with de-identified clinical and demographic data." .
SCR:018267 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_560" ;
rdfs:label "Pasteur Institute Biophysics of Macromolecules and their Interactions Core Facility" ;
NIFRID:synonym "Centre of Biophysics of Macromolecules and their Interactions",
"Institut Pasteur",
"Paris - Biophysics of Macromolecules and their Interactions",
"Pasteur Institute Centre of Biophysics of Macromolecules and their Interactions" ;
NIFRID:abbrev "PFBMI" ;
definition: "Provides services and instrumentation for characterization of biological macromolecules with technical and methodological expertise. Provides characterization of macromolecules including shape, folding, stability auto-association,and they interactions including stoichiometry,thermodynamic and kinetic parameters." .
SCR:018270 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_997" ;
rdfs:label "Harvard Medical School Center for Macromolecular Interactions Core Facility" ;
NIFRID:synonym "Center for Macromolecular Interactions (CMI) in the department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School",
"Harvard Medical School Center for Macromolecular Interactions" ;
NIFRID:abbrev "CMI" ;
definition: "Core provides scientific consultation, training and access to shared biophysical equipment for characterization and analysis of macromolecules and their complexes. Facility includes instruments measuring molecular interactions and assessing protein quality by Isothermal Titration Calorimetry (ITC), Surface Plasmon Resonance (SPR), Biolayer Interferometry (BLI), MicroScale Thermophoresis (MST), Differential Scanning Fluorimetry (DSF), Circular Dichroism (CD), Analytical Size Exclusion Chromatography with Multi-Angle Light Scattering (SEC-MALS), and Dynamic Light Scattering (DLS)." .
SCR:018271 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_514",
"nif-0000-30014",
"SCR_002914" ;
rdfs:label "Kendrick Labs Core Facility" ;
NIFRID:synonym "Kendrick Labs",
"Private Company - Kendrick Labs" ;
definition: "Contract Research Org. specializing in custom protein analysis. Services Provided include SDS PAGE analysis, Western Blotting, Mass Spectrometry, protein staining ( silver,coomassie) for academia, federal institutions and industry." .
SCR:018272 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_351" ;
rdfs:label "Nevada University Genomics Core Facility" ;
NIFRID:synonym "Las Vegas - Genomics Core Facility",
"University of Nevada",
"UNLV Genomics Core Facility" ;
definition: "Provides development and support of genomics-based research, serving investigators in Nevada and beyond. Staff can be contracted for select services including ABI 3130 DNA sequencing, BD FACSCalibur flow cytometry, Affymetrix microarray processing, Agilent 2100 Bioanalyzer analysis and Qubit analysis. Facility also provides equipment and training for real-time PCR, Western blot/gel/microarray scanning, and analysis of DNA, RNA and protein samples." .
SCR:018273 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Proteomic Data Commons" ;
NIFRID:abbrev "PDC" ;
definition: """Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal.
Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication.""" .
SCR:018274 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018817" ;
rdfs:label "Data and Computational Resources to Address COVID-19" ;
NIFRID:synonym "NIH Open-Access Data and Computational Resources to Address COVID-19",
"Open Access Data and Computational Resources to Address COVID-19" ;
definition: "COVID-19 open access data and computational resources provided by federal agencies, including NIH, public consortia, and private entities. Continuously updated as more information becomes available. These resources are being shared for scientific and public health interests, and content is responsibility of resource organizers." .
SCR:018275 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COVID-19 Open Research Dataset" ;
NIFRID:synonym "CORD-19" ;
definition: "Dataset of scholarly articles, including full text, on COVID-19, SARS-CoV-2, and related coronaviruses. Machine readable resource provided to enable application of natural language processing and other AI techniques. Open resource for global research community. Updated weekly as new research is published in peer-reviewed publications and archival services like bioRxiv, medRxiv, and others." .
SCR:018276 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dimensions COVID-19 publications, datasets and clinical trials" ;
definition: "All Dimensions publications, datasets, and clinical trials related to COVID-19, updated daily." .
SCR:018277 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COVID-19 research data on Figshare" ;
definition: "Portal to discover COVID-19 open research data on Figshare. Figshare collection of COVID-19 related research data." .
SCR:018278 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Broad Terra cloud commons for pathogen surveillance" ;
NIFRID:synonym "Terra" ;
definition: "Broad Terra cloud workspace for best practices with COVID-19 genomics data. Raw COVID-19 sequencing data from NCBI Sequence Read Archive. Workflows for genome assembly, quality control, metagenomic classification, and aggregate statistics." .
SCR:018280 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LitCovid" ;
definition: "NLM curated literature hub for COVID-19. Curated literature hub for tracking up-to-date scientific information about 2019 novel Coronavirus. Provides central access to relevant articles in PubMed. Articles are updated daily and are further categorized by different research topics and geographic locations for improved access." .
SCR:018281 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Modeling Infectious Disease Agents Study online portal for COVID-19" ;
NIFRID:synonym "MIDAS online portal for COVID-19" ;
definition: "Portal for COVID-19 modeling research. Public access data collections with documented metadata.Computational models to study transmission dynamics of broad range of infectious diseases." .
SCR:018282 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "outbreak.info" ;
definition: "Resource to aggregate all outbreak information into single location during outbreaks of emerging diseases, such as COVID-19." .
SCR:018283 a owl:NamedIndividual ;
rdfs:label "Research Data Alliance Working Group" ;
NIFRID:abbrev "RDA Working Group" ;
definition: "Guidelines for data deposition in any common data hub or platform to facilitate data sharing in public health emergencies for scientific research." .
SCR:018284 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UC Health clinical data warehouse" ;
definition: "Data warehouse using Observational Medical Outcomes Partnership standard to integrate patient data across University of California health systems. Data asset created by electronic health records from six health systems as well as claims data from UC self-funded health plans and external sources of data such as Vizient and California Office of Statewide Health Planning and Development. Shared data and analytic environment designed to improve research and patient treatments." .
SCR:018285 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Virus Outbreak Data Network" ;
NIFRID:synonym "VODAN Implementation Network" ;
NIFRID:abbrev "VODAN" ;
definition: "Network as federated AI-ready repository of COVID-19 data adherent to FAIR principles. SARS CoV-2 virus data FAIR, meaning that they are Findable, Accessible, Interoperable and thus Reusable by both humans and machines, during this epidemic of COVID-19." .
SCR:018286 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cloud resources for COVID-19 research" ;
definition: "Cloud resources for COVID-19 research provided by Rescale, Google Cloud, and Microsoft Azure. High performance computing resources immediately available for COVID-19 research." .
SCR:018287 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COVID-19 High Performance Computing Consortium" ;
NIFRID:synonym "COVID-19 High Performance Computing (HPC) Consortium",
"COVID-19 HPC Consortium" ;
definition: "Consortium encompasses computing capabilities from powerful and advanced computers in the world. Used to empower researchers to accelerate understanding of COVID-19 virus and development of treatments and vaccines to help address infections. Teams who receive Consortium access will publish their results in open scientific literature. All supported projects will have name of principal investigator, project title and project abstract posted to COVID-19 HPC Consortium web site." .
SCR:018288 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Data-Against-COVID Team" ;
definition: "Group of volunteer data scientists, machines learning experts, bioinformaticians and professional software developers who have joined together to offer their expertise for any data analysis problems that arise in context of ongoing coronavirus pandemic." .
SCR:018289 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NASEM Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats" ;
NIFRID:synonym "and Medicine Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats",
"Engineering",
"National Academies of Science" ;
definition: "Committee provides expert consultation on data elements and systems design for modeling and decision making for COVID-19 pandemic. Assembled at request of White House Office of Science and Technology Policy and Office of Assistant Secretary for Preparedness and Response in response to COVID-19 outbreak. Provides expert consultations on several topics, such as surface stability and incubation, social distancing, and crisis standards of care." .
SCR:018290 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIAID Overview of Coronaviruses" ;
definition: "Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses." .
SCR:018291 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Schema.org" ;
NIFRID:synonym "Schema.org 7.0" ;
definition: "Portal includes vocabulary to assist global response to Coronavirus outbreak. Creates, maintains, and promotes schemas for structured data." .
SCR:018292 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mendeliht.jl" ;
rdfs:label "MendelIHT.jl" ;
NIFRID:synonym "Mendel Iterative Hard Thresholding",
"Mendel Iterative Hard Thresholding.jl",
"MendelIHT" ;
definition: "Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs." .
SCR:018293 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mnemiopsis Genome Project Portal" ;
NIFRID:abbrev "MGP Portal" ;
definition: "Portal to obtain genomic information on Mnemiopsis. Data available provide annotations and other key biological information not available elsewhere. Used to advance research projects aimed at understanding phylogenetic diversity and evolution of proteins that play fundamental role in metazoan development. Collection of sequenced, assembled, annotated, and performed preliminary analysis of genome of Mnemiopsis." .
SCR:018294 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gene Expression Profiling Interactive Analysis" ;
NIFRID:abbrev "GEPIA" ;
definition: "Web server for cancer and normal gene expression profiling and interactive analyses. Interactive web server for analyzing RNA sequencing expression data of tumors and normal samples from TCGA and GTEx projects, using standard processing pipeline. Provides customizable functions such as tumor or normal differential expression analysis, profiling according to cancer types or pathological stages, patient survival analysis, similar gene detection, correlation analysis and dimensionality reduction analysis." .
SCR:018295 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH COVID-19 Portfolio" ;
NIFRID:synonym "COVID-19 Portfolio",
"COVID-19 Portfolio Tool From the Office of Portfolio Analysis",
"iSearch COVID-19 Portfolio",
"iSearch COVID-19 portfolio" ;
definition: "NIH comprehensive, curated source for publications related to COVID-19. Includes articles from PubMed and pre-prints from arXiv, medRxiv, bioRxiv, and ChemRxiv. Updated daily. NIH Office of Portfolio Analysis has developed this resource to explore and analyze set of advances in COVID‑19 research as they accumulate in real time, and complements efforts by NLM to aggregate full text documents broadly related to COVID-19 and other outbreaks, and articles on COVID‑19 specific to PubMed database." .
SCR:018296 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:crisprcasidentifier" ;
rdfs:label "CRISPRcasIdentifier" ;
definition: "Software tool providing machine learning approach for identification and classification of CRISPR-Cas systems. Combines regression and classification approaches for improving quality of input protein cassettes and predicting their subtypes." .
SCR:018297 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eukaryotic Pathogen CRISPR guide RNA/DNA Design Tool" ;
NIFRID:synonym "CRISPR/Cas gRNA design tool",
"Eukaryotic Pathogen gRNA Design Tool" ;
NIFRID:abbrev "EuPaGDT" ;
definition: "Web tool tailored to design CRISPR guide RNAs for Eukaryotic pathogens. Used to identify gRNAs in input sequence, and then calculate ranked list of those gRNAs based on on-target and off-target hits in selected or uploaded pathogen genome, to predict gRNA activity and to identified microhomology pairs flanking gRNA targeted cut site." .
SCR:018298 a owl:NamedIndividual ;
NIFRID:synonym "CLIMB Lesion Symptom Mapping" ;
NIFRID:abbrev "CLSM" .
SCR:018299 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Track-A-Worm" ;
NIFRID:synonym "Tracker-A-Worm version 1.0",
"Tracker-A-Worm version 2.0" ;
definition: "Open source system for quantitative assessment of C. Elegans locomotory and bending behavior. Used for quantitative behavioral analyses to understand circuit and gene bases of behavior. Constantly records and analyzes position and body shape of freely moving worm at high magnification." .
SCR:018301 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_80" ;
rdfs:label "Pittsburgh University HSCRF Genomics Research Core Facility" ;
NIFRID:synonym "University of Pittsburgh Genomics Research Core",
"University of Pittsburgh HSCRF Genomics Research Core" ;
definition: "Offers high throughput genomics services, technical expertise and support with experimental design and protocol development. Includes Nucleic Acid Services, genetic and genomic DNA analysis with sequencing available in standard, high-throughput and next-generation formats, Genome-wide MicroArray or RNA-seq and targeted RNA analysis, Next Generation Sequencing,Drop Seq." .
SCR:018302 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1008" ;
rdfs:label "Colorado University Boulder BioFrontiers Advanced Light Microscopy Core Facility" ;
NIFRID:synonym "BioFrontiers Advanced Light Microscopy Core",
"University of Colorado Boulder BioFrontiers Advanced Light Microscopy Core" ;
definition: "Facility designed to advance biological discovery through quantitative microscopy techniques. Houses multiple imaging technologies ranging from conventional widefield to state-of-the-art Super Resolution/localization microscopies.Offers N-STORM Super Resolution Microscopy,Laser Scanning Confocal Microscopy, Widefield Fluorescence Microscopy,Spinning Disc Confocal Microscopy,Total Internal Reflection Fluorescence (TIRF) Microscopy,Long-Term Imaging with Temperature, Oxygen, Carbon Dioxide, and Humidity Control,High-Content Screening,Analysis Workstation." .
SCR:018303 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_602" ;
rdfs:label "Miami University Miller School of Medicine Viral Vector Core Facility" ;
NIFRID:synonym "University of Miami Viral Vector Core Facility",
"Viral Vector Core (VVC) Facility (Miami Project to Cure Paralysis)" ;
NIFRID:abbrev "VVC" ;
definition: "Produces high titer lentiviral and AAV viral particles. Stock viruses including GFP-, mCherry-, and LacZ-expressing lentiviral and AAV particles can be purchased. For generating custom viral particles, investigator provides high quality maxiprep of transfer plasmid to be packaged into viral particle of choice. Turn around time is about 2 weeks for lentivirus and AAV viral particles." .
SCR:018304 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_672" ;
rdfs:label "New York University School of Medicine Center for Biospecimen Research and Development Histology Core Facility" ;
NIFRID:synonym "NYU Grossman School of Medicine Center for Biospecimen Research and Development Histology",
"NYU Langone Center for Biospecimen Research and Development" ;
definition: "Assists researchers and clinicians with molecular and morphologic characterization of normal and disease tissues of interest in support of biomarker discovery and translational research. Offers both routine and advanced histology immunohistochemistry, in situ and whole slide scanning services." .
SCR:018305 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ResistomeDB" ;
definition: "Web tool to explore and visualize Antibiotic Resistance Genes found on Tara Oceans samples. Can be explored by individual ARG or grouped by antibiotic class." .
SCR:018306 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:TDimpute",
"biotools:tDimpute" ;
rdfs:label "TDimpute" ;
definition: "Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data." .
SCR:018307 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:smashpp",
"biotools:smashpp" ;
rdfs:label "smashpp" ;
NIFRID:synonym "Smash++" ;
definition: "Software tool to find and visualize rearrangements in DNA sequences." .
SCR:018308 a owl:NamedIndividual ;
rdfs:label "auto_acpc_reorient" .
SCR:018309 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Measurement Control And Data Analysis Software" ;
NIFRID:abbrev "MES" ;
definition: "Software package for measurement control and analysis by Femtonics Ltd. Designed in MATLAB and used in field of cellular and network imaging. New version offers new scanning features and improved overall usability." .
SCR:018310 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPCM" ;
definition: "Software tool as instrument software for SPC- and DPC Modules by Becker and Hickl GmbH." .
SCR:018311 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fluorescent Imaging Analysis Software FIMAS" ;
NIFRID:abbrev "FIMAS" ;
definition: "Software tool to perform basic and specific analysis procedures on fluorescent microscopy and fluorescent lifetime imaging microscopy data. Requires MATLAB with image processing and statistical toolboxes. Can import fluorescent data from Olympus, Biorad, Femtonics, TIFF, Excel, ASCII files." .
SCR:018312 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Generalized Algebraic Modeling System" ;
NIFRID:abbrev "GAMS" ;
definition: "Software tool as modeling system for mathematical optimization by GAMS Development Corporation. GAMS is designed for modeling and solving linear, nonlinear, and mixed-integer optimization problems. Used in genome scale modeling." .
SCR:018313 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Perl Programming Language" ;
NIFRID:synonym "Perl 5",
"Perl 6",
"Raku" ;
definition: "Software tool to accompany existing resources such as Python programming language resource and comprehensive Perl archive network (CPAN) resource. Perl is family of two high level, general purpose, interpreted, dynamic programming languages. Perl refers to Perl 5, but from 2000 to 2019 it also referred to its redesigned sister language, Perl 6, before name was officially changed to Raku in October 2019." .
SCR:018314 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MOLEonline" ;
NIFRID:synonym "MOLEonline 2.0" ;
definition: "Interactive web based tool for analyzing biomacromolecular channels, tunnels and pores. Enables two modes of calculation with one dedicated to analysis of channels and another for transmembrane pores. Can use PDB and mmCIF formats. Can analyze biomacromolecular structures stemming from NMR, X-ray and cryo-EM techniques. Interconnected with PDBe, CSA, ChannelsDB, OPM, UniProt to help setup and analysis of acquired results. Provides analytics for detection and structural characterization of channels and information about their physicochemical features." .
SCR:018315 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Jupyter Notebook" ;
definition: "Open source web application to create and share documents that contain live code, equations, visualizations and narrative text. Used for data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning." .
SCR:018316 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bioconda" ;
rdfs:label "BioConda" ;
NIFRID:synonym "Bioconda" ;
definition: "Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install." .
SCR:018317 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Conda" ;
definition: "Software tool as cross platform, language agnostic binary package manager. Open source package management system and environment management system that runs on Windows, macOS and Linux. Can quickly install, run, and update packages and their dependencies. Package, dependency and environment management for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN, and more. Created for Python programs, but it can package and distribute software for any language. Conda can be combined with continuous integration systems such as Travis CI and AppVeyor to provide frequent, automated testing of your code. Conda package and environment manager is included in all versions of Anaconda and Miniconda." .
SCR:018319 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SARS-CoV-2-Sequences" ;
NIFRID:synonym "Severe Acute Respiratory Syndrome CoronaVirus 2 Sequences" ;
definition: "Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released." .
SCR:018320 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RefLib" ;
NIFRID:synonym "Reflib-Node" ;
definition: "Reference library processing for JavaScript. Reference library processing for NodeJS." .
SCR:018321 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Estimation Stats" ;
NIFRID:synonym "Estimation Statistics" ;
definition: "Web application for data analysis and visualizing effect sizes. Data analysis with estimation graphics." .
SCR:018322 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Itamar | EndoPat" ;
definition: "System for non-invasive vascular function assessment by Itamar Medical Ltd." .
SCR:018323 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ATCOR | SphygmoCor" ;
NIFRID:synonym "SphygmoCor XCEL" ;
definition: "System for measuring pulse wave velocity, pulse wave analysis by ATCOR. System for noninvasive central blood pressure waveform assessment. Provides measures of central arterial pressure waveform and pulse wave velocity as well as assessment of arterial stiffness via waveform analysis e.g. augmentation index, augmented pressure, and reflected wave magnitude." .
SCR:018324 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Complior | Analyse" ;
NIFRID:synonym "Alam Medical Complior Analyse",
"Complior Analyse" ;
definition: "System for arterial assessment and diagnosis by Alam Medical. Device measuring pulse wave velocity and central pressure analysis in single acquisition." .
SCR:018325 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FMD Studio" ;
NIFRID:synonym "Flow Mediated Dilation Studio" ;
definition: """Software tool for analysis of ultrasound data from vascular flow mediated dilation studies. Flow Mediated Dilation software
endothelial function assessment by Quipu.""" .
SCR:018326 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Jittered Boxplots for Toxicological Data" ;
NIFRID:synonym "Jittered boxplots" ;
NIFRID:abbrev "ToxBox" ;
definition: "Web tool for creating box plots with dot plots. Boxplot for grouped and clustered data in toxicology. Jittered boxplots for visualizing grouped and clustered data from toxicological studies together with individual raw values and indications of statistical significance." .
SCR:018328 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Interactive Repeated Experiments Dotplot" ;
definition: "Web tool for creating interactive graphics. Enables authors to create interactive graphics from data obtained with repeated independent experiments. Designed for laboratory studies with repeated experiments." .
SCR:018329 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Interactive Dotplot" ;
definition: "Web-based tool to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of continuous variable across different study groups, visualization of subgroups or clusters of non-independent data. Web visualization tool for creating dot plots, box plots and violin plots for small sample size data sets." .
SCR:018330 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cytosplore Viewer" ;
definition: "Web based interactive visual analysis system for exploration of single cell data published in Allen Cell Types Database and for number of single cell data resources of Brain Initiative Single Cell Network. Allows interactive exploration of hierarchies of cell types, visualization of transcriptome wide gene expression in combination with metadata of individual cells, performing differential analyses and statistics between manual selections of cells, or between pre-defined clusters throughout cellular hierarchy and more." .
SCR:018331 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:PlotTwist",
"biotools:Plottwist" ;
rdfs:label "PlotTwist" ;
NIFRID:synonym "PlotTwist Shiny" ;
definition: """Web application for plotting and annotating continuous data. Open source web app for plotting and annotating time series data.
Used to inspect data and generate publication quality visualizations. Available options for plotting include lineplot, small multiples and heatmap, summary statistics and inferential statistics.""" .
SCR:018332 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Provisional Cell Ontology" ;
NIFRID:abbrev "PCL" ;
definition: "Collection of ontology of provisional cells determined by experimental methods." .
SCR:018333 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PlotsOfData" ;
definition: "Web app for visualizing data together with their summaries. Visualizes data and statistics to enable comparison of experimental conditions. Written in R and uses packages including shiny, ggplot2, dplyr, tidyr, readr, magrittr, ggbeeswarm, readxl, DT. Github page of PlotsOfData can be used to trace changes between different versions." .
SCR:018334 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Interactive Line Graph" ;
definition: "Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions." .
SCR:018335 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Health Data Research UK COVID-19 Initiative" ;
NIFRID:abbrev "HDRUK COVID-19 Initiative" ;
definition: "Initiative to mobilize talent and partnerships across United Kingdom to coordinate and connect national data science driven research efforts related to COVID-19 to address wider impact of COVID-19 pandemic.National Institute for Health Data Science for England, Wales, Scotland and Northern Ireland, is championing use of health data to respond to COVID-19." .
SCR:018336 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COVID-19 Open Research Dataset" ;
NIFRID:synonym "CORD-19",
"COVID-19 Open Research Dataset Challenge",
"COVID-19 Open Research Dataset Challenge (CORD-19)" ;
definition: "Collection of scholarly articles about COVID-19 and coronavirus family of viruses for use by global research community. Dataset is updated on weekly basis." .
SCR:018337 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018816" ;
rdfs:label "EMBL-EBI COVID-19 Portal" ;
NIFRID:synonym "COVID-19 Data Portal",
"EMBL-EBI COVID-19 Data Portal" ;
definition: """EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research.
The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform.""" .
SCR:018338 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018351" ;
rdfs:label "CoronaVIR" ;
definition: "Web based platform on COVID-19 to maintain predicted diagnostic, drug and vaccine candidates and computational resources on novel coronavirus SARS-CoV-2 and its resulting disease COVID-19. Provides collected and organized information from literature and other resources from internet, links to appropriate literature . Integrated multi-omics repository dedicated to current genomic, proteomic, diagnostic and therapeutic knowledge about coronaviruses." .
SCR:018339 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CoVIC-DB Database" ;
NIFRID:synonym "Coronavirus Immunotherapy Consortium Database" ;
NIFRID:abbrev "CoVIC-DB" ;
definition: "Serves as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. Most potent antibodies will guide development of vaccines to stop current outbreak and protect against future pandemics." .
SCR:018340 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Crowdfight COVID-19" ;
definition: "Initiative from scientific community to put all available resources including highly skilled scientists at service of fight against COVID-19." .
SCR:018341 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CORD-19 Explorer" ;
definition: "Software tool as full text search engine for COVID-19 Open Research Dataset. Used to explore dataset and identify potential research efforts." .
SCR:018342 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation" ;
NIFRID:synonym "2019 Novel Coronavirus Resource",
"2019 Novel Coronavirus Resource (2019nCoVR)",
"CNCB 2019 Novel Coronavirus Resource",
"CNCB 2019nCoVR" ;
NIFRID:abbrev "2019nCoVR" ;
definition: "Bioinformation related to COVID-19. Site developed and maintained by China National Center for Bioinformation. Collection of sequences, genome variations, publication, clinical resource data." .
SCR:018343 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EMBL-EBI Pathogens - COVID-19" ;
definition: "Data collection related to COVID-19 held at EMBL-EBI , including sequences of outbreak isolates and records related to coronavirus biology, protein expression, protein sequence, protein structure, proteome and translatome data and literature." .
SCR:018344 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Frontier coronavirus funding monitor" ;
NIFRID:synonym "Coronavirus Funding Monitor" ;
definition: "Curated list of open funding calls and other support for researchers, non profit organizations and commercial organizations, specifically for COVID-19 and coronavirus related research. Non profit and commercial funding opportunities relevant to COVID-19. Updated daily." .
SCR:018346 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "American Diabetes Association COVID-19 Resources and Webinar Series" ;
NIFRID:synonym "COVID-19 and Diabetes" ;
definition: "Web page created by American Diabetes Association. Contains resources and information about COVID-19 for diabetes professionals and patients. ADA also provides online forum, webinar series and podcast. Online forum to exchange questions, answers, and best practices with leading clinicians from diabetes community. All ADA members can contribute, and any interested health professional can read forum and responses." .
SCR:018347 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COVID-19 and Coronavirus plasmids and resources" ;
definition: "Collections of Addgene plasmids, open access articles, protocols, and other resource collections related to COVID-19 that may be of use to scientists. Ordering or depositing plasmids related to COVID-19 research." .
SCR:018348 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NS-Forest" ;
NIFRID:synonym "Necessary and Sufficient Forest",
"NS-Forest v2.0",
"NS-Forest version 1.0",
"NS-Forestversion 1.3" ;
definition: "Software tool as method that takes cluster results from single cell nuclei RNAseq experiments and generates lists of minimal markers needed to define each cell type cluster. Utilizes random forest of decision trees machine learning approach. Used to determine minimum set of marker genes whose combined expression identified cells of given type with maximum classification accuracy." .
SCR:018349 a NLX:63400,
owl:NamedIndividual .
SCR:018350 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HALO" ;
NIFRID:synonym "Indica Labs HALO software" ;
definition: "Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology." .
SCR:018353 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Registration Software Mitra Lab" ;
definition: "Software package to align brain slice images in atlas free manner." .
SCR:018354 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HTStream" ;
definition: "Software tool as quality control and processing pipeline for High Throughput Sequencing data. Uses tab delimited fastq format that allows for streaming from application to application. Interoperable with other standard Linux tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:018355 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Watchdog" ;
definition: "Software workflow management system for automated and distributed analysis of large scale experimental data. Implemented in Java and is thus platform independent." .
SCR:018358 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "org.Rn.eg.db" ;
definition: "Software R tool for genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers." .
SCR:018359 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:go2msig" ;
rdfs:label "GO2MSIG" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2020. Software tool as automated Gene Ontology based multi species gene set generator for gene set enrichment analysis. Used to generate gene sets required for Gene Set Enrichment Analysis for almost any organism for which GO term association data exists.
Gene set collections can be automatically created for wide variety of species." .
SCR:018360 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Positional Gene Enrichment" ;
NIFRID:synonym "PGE analysis" ;
NIFRID:abbrev "PGE" ;
definition: "Web tool implementing positional gene enrichment analysis of gene sets for high resolution identification of over represented chromosomal regions." .
SCR:018361 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biorender" ;
definition: "Web tool for graphical illustrations for biological systems by BioRender. Used for articles and presentations. Collection of pre made icons and templates from life science fields for scientific illustrations. Customized icons possible on request." .
SCR:018362 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "STARANISO" ;
NIFRID:synonym "STARANISO Server",
"STARANISO server",
"The STARANISO Server" ;
definition: "Web server for anisotropy of diffraction limit and Bayesian estimation of structure amplitudes by Global Phasing Limited. Server uses DEBYE and STARANISO software to perform anisotropic cut off of merged intensity data, to perform Bayesian estimation of structure amplitudes and to apply anisotropic correction to data." .
SCR:018363 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PredGPI" ;
definition: "Prediction system for GPI-anchored proteins. Used to predict presence of GPI-anchor and position of omega site. Prediction server based on support vector machine for discrimination of anchoring signal, and on Hidden Markov Model for prediction of most probable omega site. Method for screening whole proteomes." .
SCR:018364 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TinderMIX" ;
NIFRID:synonym "Time-Dose INtegrated moDelling of toxicogenomics data" ;
definition: "Software tool as framework for dose and time dependent gene expression analysis which aims to identify groups of genes that show dynamic dose response behaviour. Software R package to cluster gene expression by contour plots. Used to analyse toxicogenomics data with multiple dose levels and time points and to identify expression patterns with respect to both variables and to cluster molecular features." .
SCR:018365 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SEDFIT" ;
NIFRID:synonym "SEDFIT version 14.7g" ;
definition: "Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly." .
SCR:018366 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COLLECT database" ;
definition: "Collaborative database for pregnancy and placental research studies worldwide by Global Pregnancy Collaboration CoLab . Database for collecting data for pregnancy studies in preeclampsia and other fields. Database has web based data entry platform with study specific user access. Data can also be entered offline using formatted spreadsheet template that can be uploaded to database in bulk or stored locally. Data is property of investigator but with permission can be combined into larger studies across centers and countries. Collaboration is enabled but not required." .
SCR:018367 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nencki-Monash template" ;
NIFRID:synonym "Nencki Monash template",
"Nencki Monash template of common Marmoset cortex",
"Nencki-Monash template of Common Marmoset cortex" ;
NIFRID:abbrev "NM template" ;
definition: "Open access template of young adult marmoset brain, created from three dimensional reconstructions. Histology based average template of marmoset cortex with probabilistic localization of cytoarchitectural areas. Allows direct estimates of most likely coordinates of each cortical area, as well as quantification of margins of error involved in assigning voxels to areas, and preserves quantitative information about laminar structure of cortex.Enables integration with magnetic resonance imaging and tracer based connectivity data. Allows interoperability between NM template and other current digital atlases of marmoset cortex." .
SCR:018369 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_e_411" ;
rdfs:label "Roche | cobas e 411 analyzer" ;
definition: "Fully automated analyzer for immunoassay analysis by Roche. Designed for in vitro assay determinations. Applications including anemia, bone, cardiac and tumor markers, critical care, fertility hormones, and infectious diseases. Available as rack or disk sample handling system." .
SCR:018370 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_UniCel_Dxl_800",
"SCR_019643",
"SCR_019668" ;
rdfs:label "Beckman Coulter | UniCel DxI 800 Access Immunoassay System" ;
NIFRID:synonym "Beckman Coulter UniCel DxI 800 Access Immunoassay System" ;
definition: "Immunoassay analyzer that can run up to 400 tests per hour and has standardized test menus, assay protocols, instrument processes and reference ranges. Sample types include serum, plasma, urine, amniotic fluid, and whole blood." .
SCR:018371 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_i1000sr",
"SCR_019328" ;
rdfs:label "Abbott | ARCHITECT i1000sr System" ;
definition: "Immunoassay analyzer by Abbott for chemiluminescent microparticle immunoassay technology. Sample types include serum, plasma, whole blood, and urine." .
SCR:018372 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_806" ;
rdfs:label "Chicago University Human Imaging Research Office Core Facility" ;
NIFRID:synonym "Human Imaging Research Office" ;
NIFRID:abbrev "HIRO" ;
definition: "Assists University of Chicago investigators and research staff with medical imaging exams performed on human subjects for research purposes. Services include acquisition, analysis, collection, de-identification and distribution of image data for basic science research and clinical trials. Services ensure research-related imaging fulfills protocol requirements and allow investigators to obtain HIPAA- and IRB-compliant clinical research data. Provides services for all types of medical imaging, including x-ray, CT, MRI, ultrasound, nuclear medicine, PET, and most types of specialty imaging." .
SCR:018373 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_856" ;
rdfs:label "Oregon State University Center for Quantitative Life Sciences Core Facility" ;
NIFRID:synonym "Center for Genome Research and Biocomputing",
"CGRB" ;
NIFRID:abbrev "CQLS" ;
definition: "Formerly Center for Genome Research and Biocomputing Core Facility. Functions and facilities include services in genomics, functional genomics, genotyping and imaging.Biocomputing facilities with computing infrastructure, which includes managed cloud and shared resources, data analyses and training are customized to individual needs, including genome assembly and annotation, analysis of RNAseq, GBS, and metagenomics data, and GPU-enabled deep learning analyses." .
SCR:018374 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Image Quant TL" ;
NIFRID:synonym "Image Quant TL array analysis",
"ImageQuant TL 8.2" ;
definition: "Software tool for image analysis by Cytiva. Automated image analysis software for general purpose electrophoresis gel, blot, arrays and colony counting." .
SCR:018375 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FlowCytomix Pro Software" ;
NIFRID:synonym "FlowCytomix Pro2.2.1 software",
"FlowCytomix Pro software",
"FlowCytomixTM Pro Software" ;
definition: "Software tool by eBioscience as part of eBioscience FlowCytomixTM Multiple Analyte Detection System, developed by Bender MedSystems. Used to analyze FlowCytomix assays." .
SCR:018377 a owl:NamedIndividual ;
rdfs:label ;
definition: "Mastermix reagent" .
SCR:018382 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Video Journal of Dementias" ;
NIFRID:abbrev "VJDementia" ;
definition: "Open access online video resource about dementia for researchers dedicated to bringing latest news and education in short form video format. Published by Oxford based Magdalen Medical Publishing." .
SCR:018383 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VariantSpark" ;
definition: "Software toolkit for genome wide association studies optimized for GWAS like datasets by CSIRO. Machine learning framework that creates insights from high dimensional data, including genomics and clinical data." .
SCR:018384 a owl:NamedIndividual ;
NIFRID:abbrev "SOCOPEN" .
SCR:018385 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ODDPub" ;
definition: "Text mining algorithm to screen biomedical publications to find data sharing statements. Algorithm that parses set of publications and detects which publications disseminated Open Data or Open Code together with publication. Tailored towards biomedical literature." .
SCR:018386 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "R scripts for Fly Liquid Food Interaction Counter data analysis" .
SCR:018387 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FLIC Monitor" ;
NIFRID:synonym "Fly Liquid Food Interaction Counter Monitor" ;
definition: "Software tool as user interface for running Fly Liquid Food Interaction Counter experiments." .
SCR:018390 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FoldIndex" ;
definition: "Web tool to predict whether given protein sequence is intrinsically unfolded. Algorithm for predicting ordered and disordered regions in protein based on its primary structure amino acid sequence. Graphic web server to predict if given protein sequence is intrinsically unfolded implementing algorithm of Uversky and co-workers, which is based on average residue hydrophobicity and net charge of sequence." .
SCR:018391 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sphire" ;
NIFRID:synonym "SParx for HIgh Resolution Electron Microscopy",
"SPHIRE",
"SPHIRE 1.3" ;
definition: "Software suite for access to cryo electron microscopy with goal of quality assessment and result reproducibility by statistical resampling. Cryo-EM processing software. Major programs within SPHIRE include Movie, Window, crYOLO, ISAC, VIPER, Meridien, Sort3D, LocalRes, Cinderella." .
SCR:018392 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "crYOLO" ;
NIFRID:synonym "SPHIRE-crYOLO" ;
definition: "Software package for automatic particle picking for cryo-EM using neural networks. Particle picker for electron cryomicroscopy based on deep learning object detection system You Only Look Once YOLO. Distributed as part of image processing workflow in SPHIRE." .
SCR:018393 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Combined Annotation Dependent Depletion" ;
NIFRID:abbrev "CADD" ;
definition: "Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome." .
SCR:018394 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "O" ;
definition: "Software for visualization of macromolecular structures, atomic coordinates, and 3D intensity maps, and for building macromolecular structures." .
SCR:018395 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xiSEARCH" ;
definition: "Software and algorithm for analyzing protein protein cross linking mass spectrometry data. Library of routines for peptide based mass spectrometry. Contains search engine for identification of crosslinked peptides." .
SCR:018396 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MS Amanda" ;
NIFRID:synonym "MS Amanda 2.0",
"Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra" ;
definition: "Software scoring system to identify peptides out of tandem mass spectrometry data using database of known proteins. Universal identification algorithm optimized for high resolution and high accuracy tandem mass spectra. Software tool as peptide and protein identification algorithm developed by Bioinformatics Research Group University of Applied Sciences Upper Austria in close cooperation with group of Karl Mechtler at IMP Vienna, Austria." .
SCR:018397 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Peakjuggler" ;
NIFRID:synonym "apQuant",
"IMP-apQuant" ;
definition: "Software tool to perform label free quantification from shotgun proteomics experiments. Operates as node within Proteome Discoverer workflow environment. Makes use of multi core processors and can process data in parallel threads to speed up data analysis. Provides features such as retention time alignment and peptide identity propagation and more." .
SCR:018398 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pepwheel" ;
rdfs:label "pepwheel" ;
definition: "Web tool to visualise protein sequences as helices. Draws helical wheel diagram for protein sequence. EMBOSS pepwheel displays peptide sequences in helical representation." .
SCR:018399 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EPC 10",
"SCR_020008" ;
rdfs:label "Heka Elektronik | EPC 10 USB Patch Clamp Amplifier" ;
NIFRID:synonym "EPC 10 USB Double",
"EPC 10 USB Patch Clamp Amplifier",
"EPC 10/n USB Patch Clamp Amplifier" ;
definition: "Electrophysiology patch clamp amplifier for collecting electrical signals from tissues and cells. Can be controlled via USB. Designed and manufactured by HEKA Elektronik." .
SCR:018400 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Color Oracle" ;
definition: "Software tool as free color blindness simulator for Windows, Mac and Linux. Design for Color Impaired. Takes guesswork out of designing for color blindness by showing you in real time what people with common color vision impairments will see.Color Oracle is open source, available on GitHub for Mac and Windows/Java." .
SCR:018401 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CuGenDB" ;
NIFRID:synonym "Cucurbit Genomics Database",
"Cucurbitaceae family Genomics Database" ;
definition: "Database to facilitate genomic and genetic data distribution, analysis, mining and integration for cucurbits. To store, mine, analyze, integrate and disseminate Cucurbitaceae family datasets and to provide central portal for cucurbit research and breeding community. Central portal for comparative and functional genomics of cucurbit crops." .
SCR:018402 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Real-time PCR Miner" ;
definition: "Software tool as objective method for quantifying qRT-PCR results using calculations based on kinetics of individual PCR reactions without need of standard curve, independent of any assumptions or subjective judgments which allow direct calculation of efficiency and CT. Algorithm provides objective and noise-resistant method for quantification of qRT-PCR results that is independent of specific equipment used to perform PCR reactions." .
SCR:018403 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Planmeca Romexis" ;
definition: "Software tool as 3D imaging software. Flexible and intuitive all-in-one dental software platform. Provides set of tools to meet imaging needs by any dental facility." .
SCR:018404 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Emerald" ;
rdfs:label "Planmeca | Emerald Intraoral scanner" ;
NIFRID:synonym "Planmeca Emerald",
"Planmeca Emerald TM Intraoral scanner" ;
definition: "Intraoral scanner for taking digital impressions." .
SCR:018405 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SliceScope Pro 2000" ;
rdfs:label "Scientifica | SliceScope Pro 2000" ;
definition: "Electrophysiology system for dual or single patch clamp recording with movable microscope. Consists of SliceScope microscope, motorised XY translation stage, fixed stage platform, and two Patchstar motorised micromanipulators. Manufactured by Scientifica LTD." .
SCR:018406 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nextflow4Metabolomics Suite" ;
NIFRID:synonym "Reproducible Untargeted Metabolomics Data Processing Workflow" ;
NIFRID:abbrev "N4M" ;
definition: "Computational workflows for reproducible untargeted metabolomics data processing pipeline." .
SCR:018409 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Precisionary | Compresstome VF-700" ;
NIFRID:synonym "Compresstome VF-700-0Z" ;
definition: "Vibrotome by Precisionary Instruments designed for cutting fixed tissue slices for histology studies. Offers two point stabilization of blade holder to eliminate unwanted chatter marks on surfaces of tissue slice. Fully automated to section fixed tissues with thickness range of 4 um to 2000 um with adjustable precision of 1 um." .
SCR:018411 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VS120" ;
rdfs:label "Olympus | VS120 microscope" ;
NIFRID:synonym "Olympus VS120",
"VS120 Virtual Slide Microscope" ;
definition: "VS120 Virtual Slide Microscope. Part of slide loader system for manually loading standard slides by Olympus." .
SCR:018412 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Signaling_Pathways_Project",
"r3d100013650" ;
rdfs:label "Signaling Pathways Project" ;
NIFRID:abbrev "SPP" ;
definition: "Web multi omics knowledgebase based upon public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Integrated omics knowledgebase for mammalian cellular signaling pathways. Web browser interface was designed to accommodate numerous routine data mining strategies. Datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available." .
SCR:018413 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Jupyter-client" ;
definition: "Jupyter protocol implementation and client libraries. Part of Project Jupyter which exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages. Jupyter-client contains reference implementation of Jupyter protocol and provides client and kernel management APIs for working with kernels." .
SCR:018414 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Jupyter-console" ;
NIFRID:synonym "Jupyter Terminal Console" ;
definition: "Terminal based console frontend for Jupyter kernels. This code is based on single process IPython terminal." .
SCR:018415 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WPI | DAM50 Extracellular Amplifier" ;
definition: "Battery powered amplifier with high and low pass filtering for recording extracellular signals by World Precision Instruments." .
SCR:018416 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Jupyter-core" ;
definition: "Jupyter core package. Software package on which Jupyter projects rely." .
SCR:018417 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:SymPy" ;
rdfs:label "SymPy" ;
definition: "Software Python library for symbolic mathematics. It aims to become full featured computer algebra system (CAS) while keeping code as simple as possible in order to be comprehensible and easily extensible." .
SCR:018418 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Python Nose" ;
definition: "Software tool to extend unittest to make testing easier. Python unit test framework. Note, Nose has been in maintenance mode for the past several years and will likely cease without a new person/team to take over maintainership. New projects should consider using Nose2, py.test, or just plain unittest/unittest2." .
SCR:018419 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneOverlap" ;
definition: "Software package to test and visualize gene overlaps. Given two gene lists, tests significance of their overlap in comparison with genomic background." .
SCR:018420 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pydot" ;
definition: "Python interface to graph visualization software Graphviz Dot." .
SCR:018421 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Connectivity Toolbox for Python" ;
NIFRID:synonym "bctpy 0.5.2",
"brain connectivity toolbox for python" ;
NIFRID:abbrev "bctpy" ;
definition: "Software brain connectivity toolbox for Python." .
SCR:018422 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pyflakes" ;
NIFRID:synonym "pyflakes 2.2.0" ;
definition: "Software tool to check Python source files for errors. Passive checker of Python programs Used to analyze programs and detect various errors. Works by parsing source file, not importing it, so it is safe to use on modules with side effects." .
SCR:018423 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cycler" ;
definition: "Software tool as composable cycle creator in python." .
SCR:018424 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Geom-matching SRC" ;
NIFRID:synonym "Hera" ;
definition: "Utilities to compute Wasserstein distance between persistence diagrams. Project has been renamed to Hera." .
SCR:018425 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DIANA Tools" ;
definition: "Collection of tools to provide algorithms, databases and software for interpreting and archiving data in systematic framework ranging from analysis of expression regulation from deep sequencing data, annotation of miRNA regulatory elements and targets to interpretation of role of ncRNAs in various diseases and pathways. Includes target prediction algorithms microT v4 and microT-CDS, databases of experimentally verified miRNA targets on coding and non-coding RNAs like TarBase v7.0 and LncBase, and software capable of identifying potentially altered molecular pathways by expression of single or multiple miRNAs , mirPath. Provides Web Server (v5.0) to support series of workflows enabling users to perform miRNA analyses." .
SCR:018426 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FHC | Platinum/Iridium microelectrode" ;
definition: "A platinum/iridium electrode use for stimulating tissue samples. Manufactured by FHC Neural microTargeting Worldwide." .
SCR:018427 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Extending Guilt by Association by Degree" ;
NIFRID:synonym "EGAD Bioconductor",
"Extending guilt by association by degree" ;
NIFRID:abbrev "EGAD" ;
definition: "Software package implements series of highly efficient tools to calculate functional properties of networks based on guilt by association methods. Ultra fast functional analysis of gene networks." .
SCR:018428 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:machado" ;
rdfs:label "Machado" ;
definition: "Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code." .
SCR:018429 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:plantannot" ;
rdfs:label "Plant Co-expression Annotation Resource" ;
NIFRID:synonym "Plantannot v2" ;
NIFRID:abbrev "Plantannot" ;
definition: """Webserver for identifying targets for genetically modified crop breeding pipelines.
Used to find proteins that have no annotation or function assigned and could be related to molecular mechanisms regarding abiotic stresses in plants. System aggregates orthology, coexpression networks and genomic data to filter genomes of plants downloaded from Phytozome and NCBI and select candidate proteins in that regard.""" .
SCR:018430 a owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018441" ;
rdfs:label "Thermo Fisher: Applied Biosystems | ABI 3100 Capillary Genetic Analyzer" ;
definition: "Benchtop capillary genetic analyzer multicolor fluorescence based DNA analysis system with 16 capillaries. It can process 96 or 384 well plates." .
SCR:018431 a owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_3700",
"SCR_018443" ;
rdfs:label "Thermo Fisher: Applied Biosystems | ABI 3700 Genetic Analyzer" ;
definition: "Automated capillary gel electrophoresis genetic analyzer that sequences up to 96 DNA templates per run and is used for PCR sequencing and short tandem repeat genotyping." .
SCR:018432 a owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018445" ;
rdfs:label "Thermo Fisher: Applied Biosystems | ABI Voyager DE Pro MALDI-Mass Spectrometer" ;
definition: "Benchtop MALDI TOF mass spectrometer that has linear and reflector analyzer. It is used to analyze organic and inorganic compounds, protein identification, synthetic peptide validation, and polymer analysis." .
SCR:018433 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018442",
"SCR_019388" ;
rdfs:label "Agilent | 3100 OFFGEL Fractionator" ;
NIFRID:synonym "Agilent 3100 OFFGEL Fractionator" ;
definition: "Agilent 3100 OFFGEL Fractionator performs isoelectric focusing of proteins or peptides in immobilized pH gradient (IPG) gel strips." .
SCR:018434 a owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018451",
"SCR_019570" ;
rdfs:label "American Optical | 860 Sliding Microtome" ;
definition: "THIS REOURCE IS NO LONGER IN SERVICE. Documented on September 29,2023. Sliding microtome used for cutting hard objects such as bone, wood, frozen celloidin, and paraffin preparations. Cutting thickness is adjustable from 1 to 40 microns." .
SCR:018435 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4200 TapeStation",
"SCR_018444",
"SCR_019395",
"SCR_019398" ;
rdfs:label "Agilent | 4200 TapeStation System" ;
NIFRID:synonym "Agilent 4200 TapeStation",
"Agilent 4200 Tapestation Genetic Analyzer" ;
definition: "Benchtop genetic analyzer. Electrophoresis system for DNA and RNA sample quality control. It can be used for next generation sequencing or Biobank workflow." .
SCR:018436 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_9700",
"SCR_018448",
"SCR_019577" ;
rdfs:label "Thermo Fisher: Applied Biosystems | GeneAmp 9700 PCR Thermocycler System" ;
definition: "Automated PCR instrument for automated amplification of nucleic acids with Polymerase Chain Reaction. It has reaction volumes of up to 50 uL and sample temperature range of 4 to 99.9 C." .
SCR:018437 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_API 5000",
"SCR_018450",
"SCR_019569" ;
rdfs:label "SCIEX | | API 5000 Triple Quadrupole Liquid Chromatography Mass Spectrometer System" ;
definition: "Triple quadrupole liquid chromatography mass spectrometer for analysis of bioanalytical samples. It can be used for DMPK and ADME studies.API 5000 LC/MS/MS System delivers the lowest limits of detection for the most demanding DMPK and ADME studies." .
SCR:018438 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_3500xl",
"SCR_018447",
"SCR_019574" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 3500xl Genetic Analyzer" ;
definition: "Applied Biosystems 3500xL 24-capillary Genetic Analyzer is used for the Human Identification application.Genetic analyzer that utilizes capillary electrophoresis for genetic analysis. It has capillary lengths of 50 cm or 36 cm and can use 384 well plates or 96 well plates." .
SCR:018439 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PAL_10S",
"SCR_018449",
"SCR_019583" ;
rdfs:label "Atago | PAL-10S Pocket Refractometer" ;
definition: "Digital hand held pocket refractometer that measures urine specific gravity. It has measurement temperature of 10 to 35 C and sample volume of 0.3ml." .
SCR:018440 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_433A",
"SCR_018446",
"SCR_019575" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 433A Peptide Sequencer" ;
definition: "Automated peptide synthesizer for chain assembly steps in solid phase peptide synthesis or FastMoc chemistry. Data is based on conductance or ultraviolet UV absorbance of reagent, solutions, and solvents in the synthesis cycle." .
SCR:018452 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Precisionary | Compresstome VF-300" ;
NIFRID:synonym "Compresstome VF-300 vibrating microtome" ;
definition: "Vibrating microtome for cutting tissue slices, similar to cryostats and vibrating microtomes. Fully automated for sectioning fixed and live tissues, with down to 1 um precision. Can cut tissue slice thicknesses ranging from 3 um to 2000 um, at 1 um intervals." .
SCR:018453 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | VT1200S vibratome" ;
NIFRID:synonym "Leica VT1200 S vibrating blade microtome",
"Leica VT1200S" ;
definition: "Fully automated Leica VT1200 S vibrating blade microtome designed for sectioning for cutting fresh and fixed tissue in neuroscience by Leica Biosystems." .
SCR:018454 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allied Vision | Mako G-125 camera" ;
NIFRID:synonym "GigE machine vision camera",
"Mako G-125" ;
definition: "GigE camera with Sony ICX445 CCD sensor, 30.3 fps by Allied Vision. 1.2 megapixel GigE machine vision camera that incorporates high quality Type 1/3 (6.0 diagonal) Sony ICX445 CCD sensor with EXview HAD technology. At full resolution, this camera runs frames per second. With smaller region of interest, higher frame rates are possible." .
SCR:018455 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Molecular Devices | MultiClamp 700B Microelectrode Amplifier" ;
NIFRID:synonym "Multiclamp 700B" ;
definition: "Computer controlled amplifier for current clamp and voltage clamp applications from Molecular Devices, LLC. Amplifier used for electrophysiology and electrochemistry." .
SCR:018456 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | SM2000 R Sliding microtome" ;
NIFRID:synonym "Leica SM2000 R",
"Leica SM2000R" ;
definition: "Sliding microtome from Leica Biosystems with low maintenance cross roller bearing slideways designed to easily section either paraffin embedded or fixed, frozen specimens. Features knife holder for both standard knives and disposable blades. Please note: this product is discontinued and no longer available for sale." .
SCR:018457 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | Aperio ScanScope XT" ;
definition: "Automated slide scanner from Leica Biosystems. This product is discontinued." .
SCR:018458 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pilot | 9W Pilot Diode Laser" ;
NIFRID:synonym "PILOT (TM) Diode laser" ;
definition: "Diode laser, 810 nm wavelength with manufacturer from CAO group, USA. Commodity code: 002-00102. Used for rehabilitation procedures to promote healing, reduce pain and inflammation." .
SCR:018459 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stan" ;
definition: "Probabilistic programming language for specifying statistical models. Defines log probability function over parameters conditioned on specified data and constants. Platform for statistical modeling and high performance statistical computation. Provides full Bayesian inference for posterior expectations including parameter estimation and posterior predictive inference by defining appropriate derived quantities of interest." .
SCR:018460 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Campden Instruments | Vibroslice vibrating microtome" ;
NIFRID:synonym "752 vibroslice tissue cutter" ;
definition: "Vibrating microtome manufactured by Campden Instruments. 752 Vibroslice tissue cutter for manual tissue transport." .
SCR:018461 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CurveFitter" ;
NIFRID:synonym "curvefitter" ;
definition: "Software tool for growth curve fitting and visualization. Program allows to fit growth curve using simple GUI or advanced scripting environment. Used to fit growth curves generated for data collected in microtiter plates or elsewhere." .
SCR:018462 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gnumeric" ;
NIFRID:synonym "Gnumeric Spreadsheet",
"Gnumeric version 1.0" ;
definition: "Software tool as open source spreadsheet program that is part of GNOME Free Software Desktop Project. Can do some statistical analysis such as Student t-tests. Spreadsheet application that replicates basic features of popular commercial programs like Microsoft Excel." .
SCR:018463 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kaleidoscope" ;
NIFRID:synonym "Kaleidoscope Pro" ;
definition: "Kaleidoscope Pro analysis software automatically scan field recordings to discover species of interest. Kaleidoscope Viewer enalbes for examining ultrasonic and acoustic sound files visually." .
SCR:018464 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Photometrics | Prime 95B-25MM Camera" ;
definition: "Prime 95B Scientific CMOS camera brings light in from back of sensor. Photons land directly onto light receiving surface, maximizing light collecting capability. Back illuminated sCMOS camera." .
SCR:018466 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:spotyping" ;
rdfs:label "SpoTyping" ;
NIFRID:synonym "SpoTyping-v2.0" ;
definition: "Software tool for fast and accurate in silico Mycobacterium spoligotyping from sequence reads." .
SCR:018467 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReproNim/containers" ;
definition: "Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments." .
SCR:018468 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReproMan" ;
definition: "Software tool to simplify creation and management of computing environments in Neuroimaging." .
SCR:018484 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Big Data Processor " ;
NIFRID:abbrev "BDP" ;
definition: "Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy." .
SCR:018485 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:signor" ;
rdfs:label "SIGNOR" ;
NIFRID:synonym "SIGnaling Network Open Resource",
"SIGNOR 2.0" ;
definition: "Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles." .
SCR:018486 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Context Aware Trainable Segmentation" ;
NIFRID:abbrev "CATS" ;
definition: "Software tool as big image data compatible Fiji plugin for trainable image segmentation." .
SCR:018488 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CLAIRE" ;
NIFRID:synonym "Cell Line A-to-I Rna Editing Database",
"Cell Line Adenosine-to-Inosine RNA editing database" ;
definition: "Cell Line Adenosine-to-Inosine RNA editing database. Searchable catalogue of RNA editing levels across cell lines. Used to facilitate rational choice of appropriate cell lines for future work on A-to-I RNA editing." .
SCR:018490 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:rediportal" ;
rdfs:label "REDIportal" ;
definition: """Comprehensive database of A-to-I RNA Editing Events. Atlas of A-to-I RNA editing events in human and other organisms.
Collection of A-to-I events in body sites of healthy individuals from GTEx project. RNA Editing sites can be searched by genomic region, gene name and other relevant features as tissue of origin. Query results are shown in sortable and downloadable tables in which main characteristics of individual RNA editing events are reported. RNA-Seq and DNA-Seq coverage per site as well as RNA editing levels are provided.""" .
SCR:018491 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:tool_recommender_system_in_galaxy" ;
rdfs:label "Tool recommender system in Galaxy" ;
NIFRID:synonym "Galaxy tool recommendation",
"Tool recommender system in Galaxy using deep learning" ;
definition: "Software developed by analyzing workflows composed by researchers on European Galaxy server, using deep learning approach. Used to recommend tools in Galaxy. Gated recurrent units neural network." .
SCR:018492 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Wikidata_Q2013" ;
rdfs:label "Wikidata" ;
definition: "Open knowledge base that can be read and edited by both humans and machines. Storage for structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. Provides support to many other sites and services beyond just Wikimedia projects." .
SCR:018493 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OntoMate" ;
definition: "Software text mining tool aiding curation at Rat Genome Database. Ontology driven, concept based literature search engine developed at RGD. Tags abstracts with gene names, gene mutations, organism names and terms from ontologies vocabularies used at RGD. Open and fully customizable." .
SCR:018494 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "METAGENOTE" ;
NIFRID:synonym "METAdata of GEnomics studies on a web based NOTEbook" ;
definition: "Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository." .
SCR:018495 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:admixtools" ;
rdfs:label "ADMIXTOOLS" ;
definition: "Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates." .
SCR:018496 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AllerTop" ;
definition: "Web server for in silico prediction of allergens. Alignment free server for in silico prediction of allergens based on main physicochemical properties of proteins. Used to predict the route of allergen exposure: food, inhalant or toxin." .
SCR:018497 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AmberTools" ;
NIFRID:synonym "Amber",
"AmberTools20",
"AmberTools MD software packages" ;
definition: "Software suite that works by themselves, and with Amber20 itself. Can be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models." .
SCR:018498 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JetFighter" ;
definition: "Web tool that automatically screens bioRxiv preprints for rainbow colormaps, which are not colorblind safe. Emails authors information on replacing these colormaps with colorblind safe alternatives. Screens preprints to improve data representation and colour-blind accessibility." .
SCR:018499 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BepiPred-2.0" ;
NIFRID:synonym "BepiPred",
"BepiPred-1.0" ;
definition: "Sequential B-Cell Epitope Predictor. Web server predicts B-cell epitopes from protein sequence. Sequence-based B-cell epitope prediction using conformational epitopes. Sequences of protein of interest should be in fasta format. BepiPred 2.0 is available as stand alone software package, with same functionality as web service., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:018500 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Codon Usage Analyzer" ;
NIFRID:abbrev "Bio-CUA",
"Bio::CUA" ;
definition: "Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems." .
SCR:018501 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioVelocity" ;
definition: "Software tool based on hashing algorithm and approach to genomic reference indices from Noblis. Used to indexing genomic references. Aligns reads on reference genomes at random positions where k-mer indexes are matched with reference genomes." .
SCR:018502 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BisoGenet" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18, 2020. Software package to create, visualize and analyze biological networks. Can include coding relations to distinguish between genes and their products. BisoGenet client is designed to work as Cytoscape plugin for querying server along with graph topology analysis and visualization options for easing interpretation process." .
SCR:018503 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellMarker" ;
definition: "Database provides cell markers for various cell types in tissues of human and mouse. Manually curated resource of cell markers in human and mouse. Provides user-friendly interface for browsing, searching and downloading markers of diverse cell types of different tissues. Summarized marker prevalence in each cell type is graphically presented., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:018504 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Codon and Codon-Pair Usage Tables" ;
NIFRID:abbrev "CoCoPUTs" ;
definition: "Database includes genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome. Facilitates genetic variation analyses and recombinant gene design. Derived from all available GenBank and RefSeq data." .
SCR:018505 a NLX:63400,
owl:NamedIndividual ;
NIFRID:abbrev "AVCpred" .
SCR:018506 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProTox-II" ;
NIFRID:synonym "ProTox-II - Prediction Of Toxicity Of Chemicals" ;
definition: "Web server for prediction of toxicity of chemicals. Virtual lab for prediction of toxicities of small molecules. Used for prediction of multiple toxicological endpoints related with chemical structure." .
SCR:018507 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:QGIS" ;
rdfs:label "QGIS" ;
definition: "Open source cross platform desktop geographic information system application that supports viewing, editing, and analysis of geospatial data. Functions as geographic information system software, allowing users to analyze and edit spatial information, in addition to composing and exporting graphical maps." .
SCR:018508 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Barzooka" ;
definition: "Software automated screening tool that detects bar graphs of continuous data in preprints submitted to bioRxiv. Used for detection of bar graphs for continuous data in BioRxiv preprints." .
SCR:018510 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Waters | Xevo TQ-XS mass spectrometer" ;
NIFRID:synonym "SUMS Xevo",
"TQ-XS Triple Quad Mass Spectrometer",
"Xevo TQ-XS" ;
definition: "Advanced benchtop tandem quadrupole mass spectrometer which expands scope of ultimate sensitivity analysis. Fatures probe design which allows users much easier maintenance, optimization and improved reproducibility between operators. Method transfer onto Xevo TQ-XS is made simple by Xtended Dynamic Range detector which allows six orders of linear dynamic range. Wider compound coverage without changing ionization technique is delivered by the revolutionary UniSpray source option." .
SCR:018511 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CohortMethod" ;
definition: "Software R package for performing new user cohort studies in observational database in OMOP Common Data Model." .
SCR:018512 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "covidcounties.org" ;
NIFRID:synonym "COVID-19 County Tracker" ;
definition: "Interactive web application that depicts daily disease trends at level of US counties using time series plots and maps." .
SCR:018513 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CovidNLP" ;
NIFRID:synonym "Covid Natural Language Processing" ;
definition: "Web Application for distilling systemic implications of COVID-19 pandemic with Natural Language Processing." .
SCR:018514 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VaxiJen" ;
NIFRID:synonym "VaxiJen v2" ;
definition: "Web server for prediction of protective antigens, tumor antigens and subunit vaccines. Alignment free approach for antigen prediction, which is based on auto cross covariance transformation of protein sequences into uniform vectors of principal amino acid properties." .
SCR:018515 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "viral_seq" ;
definition: "Ruby Gem with bioinformatics tools for processing viral NGS data. Specifically for Primer-ID sequencing and HIV drug resistance analysis." .
SCR:018516 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WinBUGS" ;
NIFRID:synonym "Win Bayesian inference Using Gibbs Sampling" ;
definition: "Software package for Bayesian analysis of complex statistical models using Markov chain Monte Carlo methods." .
SCR:018524 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rSPRITE" ;
NIFRID:synonym "rSPRITE beta 0.15",
"Sample Parameter Reconstruction via Iterative TEchniques",
"SPRITE" ;
definition: "Web app to generate possible distributions of data matching given mean, SD, sample size, and range. Used for recovering data from summary statistics. Implementation of SPRITE in R programming environment." .
SCR:018525 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Molinspiration" ;
definition: "Broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation, calculation of various molecular properties needed in QSAR, molecular modelling and drug design, high quality molecule depiction, molecular database tools supporting substructure and similarity searches. Molinspiration tools are platform independent and may be run on any PC, Mac, UNIX or LINUX machine. Software is distributed in form of engines, which may be used as stand-alone computational engines, used to power web-based tools, or incorporated into larger in-house Java applications." .
SCR:018526 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Drug Likeness Tool" ;
NIFRID:abbrev "DruLiTo" ;
definition: "Software as open source virtual screening tool. Calculation is based on various druglikeness rules like Lipinski's rule, MDDR-like rule, Veber rule, Ghose filter, BBB rule, CMC-50 like rule and Quantitative Estimate of Drug-likeness (QED). Uses Chemistry Development Kit (CDK), Java library for descriptor calculation. Used for fast calculation of drug like properties of molecule." .
SCR:018527 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CustomCDF" ;
definition: "Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information." .
SCR:018528 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:dampe" ;
rdfs:label "DAMBE" ;
NIFRID:synonym "DAMBE5",
"DAMBE6",
"DAMBE7",
"Data Analysis in Molecular Biology and Evolution" ;
definition: "Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers." .
SCR:018529 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DiANNA" ;
NIFRID:synonym "DiANNA 1.1" ;
definition: "Neural network and web server, which determines cysteine oxidation state and disulfide connectivity of protein, given only its amino acid sequence. Used to predict disulfide connectivity topology. Predicts which half-cystines are covalently bound to which other half-cystines. DiANNA 1.1 is extension of DiANNA web server for ternary cysteine classification." .
SCR:018530 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DiscoTope" ;
definition: "Web server to predict discontinuous B cell epitopes from protein three dimensional structures." .
SCR:018531 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:galaxyrefine" ;
rdfs:label "GalaxyRefine" ;
definition: "Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation." .
SCR:018532 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SuperSegger" ;
definition: "Software package as automated MATLAB based trainable image cell segmentation, fluorescence quantification and analysis suite. Used for high throughput time lapse fluorescence microscopy of in vivo bacterial cells. Robust image segmentation, analysis and lineage tracking of bacterial cells." .
SCR:018533 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "knitr" ;
definition: "Software R package for dynamic report generation using Literate Programming techniques. Comprehensive software tool for reproducible research in R." .
SCR:018534 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Veritas Microplate Luminometer software" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. Software tool as direct-to-Excel-based software that gives flexibility in data retrieval, storage, and analysis. Software comes preloaded with protocols for Promega luminescent assays. It is also possible to create, store, and retrieve user-defined protocols." .
SCR:018535 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProteomeTools" ;
definition: "Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research." .
SCR:018536 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyTorch" ;
definition: "Open source machine learning library based on Torch library, used for applications such as computer vision and natural language processing. Software Python package that provides tensor computation with strong GPU acceleration and deep neural networks built on tape-based autograd system." .
SCR:018537 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Recombination Detection Program" ;
NIFRID:synonym "RDP3",
"RDP4" ;
NIFRID:abbrev "RDP" ;
definition: "Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes." .
SCR:018538 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:EpiEstim" ;
rdfs:label "EpiEstim" ;
NIFRID:synonym "Estimate Time Varying Reproduction Numbers from Epidemic Curves" ;
definition: "Framework and software to estimate time varying reproduction numbers during epidemics. Tools to quantify transmissibility throughout epidemic from analysis of time series of incidence. Used to estimate time varying instantaneous reproduction numbers from incidence time series." .
SCR:018539 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:epimodel" ;
rdfs:label "EpiModel" ;
definition: "Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics." .
SCR:018540 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:prosa-web" ;
rdfs:label "ProSA-web" ;
NIFRID:synonym "Protein Structure Analysis web" ;
definition: "Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling." .
SCR:018541 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pyrosetta" ;
rdfs:label "PyRosetta" ;
NIFRID:synonym "Python Rosetta" ;
definition: "Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions." .
SCR:018542 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ToxinPred" ;
definition: "Software package for peptides designing and prediction. In silico approach for predicting toxicity of peptides and proteins. Used for predicting peptide toxicity or non toxicity, minimum mutations in peptides for increasing or decreasing their toxicity, toxic regions in proteins." .
SCR:018543 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "missForest" ;
definition: "Software R package to impute missing values particularly in case of mixed type data. Non parametric, mixed type imputation method for any type of data for statistical software R. Predicts missing values." .
SCR:018544 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhyDyn" ;
definition: "Sofware package for performing Bayesian phylogenetic inference under models that deal with structured populations with complex population dynamics. Enables simultaneous estimation of epidemiological parameters and pathogen phylogenies. Epidemiological modelling in BEAST." .
SCR:018545 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21687" ;
rdfs:label "Phyutility" ;
definition: "Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI." .
SCR:018547 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyMC3" ;
definition: "Software Python package for Bayesian statistical modeling and probabilistic machine learning which focuses on advanced Markov chain Monte Carlo and variational fitting algorithms. Allows model specification directly in Python code." .
SCR:018548 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyRx" ;
definition: "Open source virtual screening software for computational drug discovery with intuitive user interface. Runs on operating systems Linux, Windows, and Mac OS. Used to screen libraries of compounds against potential drug targets." .
SCR:018549 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaVolcanoR" ;
definition: "Software R package to combine differential gene expression results. Differential expression meta analysis tool. Gene expression meta analysis visualization tool. Used to identify genes whose expression is consistently perturbed across several studies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:018550 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:minimap2",
"OMICS_31658" ;
rdfs:label "Minimap2" ;
definition: "Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences." .
SCR:018551 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:megahit",
"OMICS_07234" ;
rdfs:label "MEGAHIT" ;
NIFRID:synonym "MEGAHIT v0.1" ;
definition: "Software tool as Next Generation Sequencing assembler. Optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single cell assembly. Can assemble genome sequences from metagenomic datasets of hundreds of Giga base-pairs in time and memory efficient manner on single server." .
SCR:018552 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:maxalign" ;
rdfs:label "MaxAlign" ;
NIFRID:synonym "MaxAlign 1.1",
"MaxAlign 1.1 Server" ;
definition: "Web tool for maximizing usable data in alignment. Maximizes number of characters that are present in gap free columns alignment area by selecting optimal subset of sequences. Removes sequences with many gaps in post process of alignments in order to improve alignment area." .
SCR:018553 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Manubot" ;
definition: "Software workflow and set of tools for scholarly publishing to enable collaborative authoring of scholarly manuscripts. Used to write manuscript in markdown, track it with git, automatically convert it to .html, .pdf, or .docx, and deploy it to destination of choice." .
SCR:018554 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MagicPlot" ;
definition: "Software technical plotting, curve fitting and data analysis application. Provides graphical user interface for data exploration as well as various statistical analysis tools, peak fitting options, raster or vector formats of publishable plots. Graphing software for medical writers." .
SCR:018555 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Loupe Browser" ;
NIFRID:synonym "Loupe Cell Browser 4.0" ;
definition: "Desktop application that provides interactive visualization functionality to analyze data from different 10x Genomics solutions. Used to interrogate different views of 10x data to gain insights into underlying biology." .
SCR:018556 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LASTZ" ;
definition: "Software package for sequence alignment. Pairwise aligner for aligning DNA sequences. Designed to handle sequences size of human chromosomes and from different species. Useful for sequences produced by NGS sequencing technologies." .
SCR:018557 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EMBuilder" ;
definition: "Software tool as model building program for cryo-electron microscopy. Processes cryoEM maps through secondary structure stage and Cα stageA. Template matching based automatic model building program for high resolution Cryo-Electron Microscopy maps." .
SCR:018558 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:galaxyweb" ;
rdfs:label "GalaxyWEB" ;
definition: "Web server for protein structure prediction and refinement. Used to predict protein structure from sequence by template based modeling. Used for refinement after providing starting model structure and locations of loops or termini to be refined." .
SCR:018559 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeoDa" ;
definition: "Software program for spatial analysis for non geographic information systems specialists. Includes functionality ranging from simple mapping to exploratory data analysis, visualization of global and local spatial autocorrelation, and spatial regression." .
SCR:018560 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ggtree" ;
rdfs:label "ggtree" ;
definition: "Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses." .
SCR:018561 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:hpepdock" ;
rdfs:label "HPEPDOCK Server" ;
definition: "Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations." .
SCR:018562 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SAINTexpress" ;
NIFRID:synonym "Significance Analysis of INTeractome Express" ;
definition: "Software tool for upgraded implementation of probabilistic scoring of affinity purification mass spectrometry data. Used for filtering high confidence interaction data from affinity purification mass spectrometry experiments. Used for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments." .
SCR:018563 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SVMTriP" ;
NIFRID:synonym "Support Vector Machine Tri-Peptide" ;
definition: "Web tool to predict linear antigenic epitopes. Predicts antigenic epitope with latest sequence input from IEDB database. Method to predict antigenic epitopes using support vector machine to integrate Tri-Peptide similarity and propensity." .
SCR:018564 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TimeZone" ;
definition: "Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes." .
SCR:018565 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_020961" ;
rdfs:label "Nanotomy" ;
NIFRID:synonym "Anatomy at nanoscale",
"nano-anatomy",
"nanotomy" ;
definition: "Large scale electron microscopy datasets. Large scale electron microscopy database for Human Type 1 Diabetes." .
SCR:018566 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Alberta Diabetes Institute IsletCore database" ;
definition: "Collection of data from all pancreatic islet isolations." .
SCR:018567 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pancreatlas" ;
definition: "Collection of human pancreas data and images. Platform to share data from human pancreas samples. Houses reference datasets from human pancreas samples, achieved through generosity of organ donors and their families." .
SCR:018568 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scite" ;
definition: "Web tool to classify citation statements from scientific articles using deep learning. Used for discovering and evaluating scientific articles via Smart Citations." .
SCR:018569 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Doric Neuroscience Studio" ;
definition: "Software tool which allows to control Doric hardware and acquire all required data simultaneously. Incorporates different modules for each devices connected." .
SCR:018570 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LUNGevity" ;
definition: "Portal dedicated to funding lung cancer research by LUNGevity Foundation. Supports patient focused research and convene multi stakeholder meetings to streamline research process and accelerate progress to patients. Seeks to empower patients to be active decision makers in their treatment process through educational resources, online peer-to-peer support, and in-person survivorship programs." .
SCR:018571 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Custom made 30 kDa microdialysis probe" ;
definition: "Probe uses semi permeable membrane with pore size of 30 kDa which enables small hydrophilic compounds from brain extracellular space to diffuse passively into perfusate. Used to measure extracellular ACh level and glucose metabolites directly without purification." .
SCR:018572 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:lrpath" ;
rdfs:label "LRPath" ;
definition: "Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data." .
SCR:018573 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Intensity Ratio Nuclei Cytoplasm Tool" ;
definition: "Software tool to calculate ratio of intensity in nuclei and cytoplasm. It needs two images as input cytoplasm channel and nuclei channel." .
SCR:018574 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pic" ;
rdfs:label "Protein Interactions Calculator" ;
definition: "Web server for inter residue interaction calculations in single site. Determines accessible surface area and residue depth, which is distance of residue from surface of protein. Recognizes specific kind of interactions, such as apolar–apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near surface or deep inside. Recognizes interactions including disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic- aromatic interactions, aromatic-sulphur interactions and cation interactions within protein or between proteins in complex." .
SCR:018575 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_280A",
"SCR_020143" ;
rdfs:label "Thermo Fisher | Isotemp 280A Vacuum Oven" ;
definition: "Fisher Scientific Isotemp 280A is a Vacuum Oven offers a temperature range from ambient up to 200C with internal dimensions of 11.125\"D x 9.75\"W x 9.75\"H. Front-mounted power indicator and dial thermometer with top-mounted analog vacuum gauge. The 280A's hydraulic thermostat controls temperature. Large glass panel front door and stainless steel chamber." .
SCR:018576 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_n125",
"SCR_019922" ;
rdfs:label "Thermo Fisher | n125 Homogenizer" ;
definition: "Homogenizer with speeds from 8,000 to 30,000 RPM for volumes of up to 100ml. Homogenizer for production of dispersions and emulsions, plant tissues, human tissues, animal tissues, resins, and pigments." .
SCR:018578 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_C1",
"SCR_019930" ;
rdfs:label "Fluidigm | C1 Single-Cell Automated Preparation System" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 14,2023.Automated preparation system that isolates and prepares single cell templates for analysis. It can analyze mRNA and DNA sequencing, epigenetics or miRNA expression. It can extract, reverse transcribe, amplify, and analyze gene expression." .
SCR:018579 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GX_271",
"SCR_019963" ;
rdfs:label "Gilson | GX-271 HPLC System" ;
definition: "HPLC liquid handler with midsize bed capacity and fraction collector. It has maximum flow rates up to 200 mL per min, injection loop volumes of 2 uL to 25 mL, and max sample mass of 15 grams per injection." .
SCR:018580 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_cBot",
"SCR_020129" ;
rdfs:label "Illumina | cBot Genetic Amplifier" ;
definition: "Genetic amplifier that uses amplification to create single molecule DNA templates and dispense reagents. It also controls reaction times, flow rates, and temperatures." .
SCR:018581 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FLA_1500",
"SCR_019925" ;
rdfs:label "Fujifilm | FLA-5100 Scanner" ;
definition: "EImaging scanner that images fluorescent and radioisotopic samples. It can be used for protein electrophoresis, genomics array analysis, fluorescence, radioisotope detection, and chemiluminescence detection by direct detection method." .
SCR:018582 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_StarPlus",
"SCR_020003" ;
rdfs:label "Hamilton | StarPlus Automated Liquid Handler" ;
NIFRID:synonym "Hamilton STARplus" ;
definition: "Liquid handling robot with 8 channel pipetting arm, dual HEPA filter top, and 96 channel pipeting head with 1ml capacity. It can have tube racks, microplate racks, and 50mL temperature controlled tube rack." .
SCR:018583 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NeoPrep",
"SCR_020139" ;
rdfs:label "Illumina | NeoPrep Library Preparation System" ;
definition: "Library preparation system that produces 16 sequencing ready libraries per run. There are steps in NeoPrep workflow run preparation, library card loading, and library collection." .
SCR:018584 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EM" ;
rdfs:label "Molecular Devices | Gemini EM Microplate Reader" ;
definition: "Microplate reader with top and bottom read capability with dual monochromators for fluorescence intensity assays using multiple point well scanning. Temperature sensitive reactions are from ambient to 45 C. Measures fluorescence on variety of sample formats from 6 to 384 well microplates in endpoint, kinetic, spectral scan, and well-scan modes." .
SCR:018585 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kent Scientific | Coda Blood Pressure System" ;
definition: "CODA mouse rat tail-cuff system was designed to allow accurate blood pressure measurement in mice and rats. Blood pressure is measured in the tail of the mouse or rat using Volume Pressure Recording (VPR) sensor technology. Using the included software allows you to continuously view data in real-time." .
SCR:018586 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_300",
"SCR_020200" ;
rdfs:label "JPK Instruments | 300 Force Robot Automated Force Spectroscope" ;
definition: "Force spectroscope that automates routine procedures, data acquisition and evaluation. Force curves without events are filtered out before processing." .
SCR:018587 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_020203" ;
rdfs:label "Labconco | CentriVap Refrigerated Centrifugal Concentrator" ;
definition: "Refrigerated centrifugal concentrator that concentrates heat sensitive samples using centrifugal force, vacuum, and controlled temperature. Concentrator has heater and refrigeration systems have temperature range of negative 4 C to 100 C." .
SCR:018588 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_C2400",
"SCR_020204" ;
rdfs:label "Labnet | C2400 Spectrafuge 24D Microcentrifuge" ;
definition: "Microcentrifuge with brushless drive that accelerates rotor to maximum speed of 13,300 rpm and 16,000 x g. Features precise digital microprocessor control. Speed knob sets speed in either rpm or g-force. Timer knob sets time parameter." .
SCR:018589 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ImageStreamX_MkII",
"SCR_020142",
"SCR_020244" ;
rdfs:label "Luminex | Amnis ImageStreamX Mk II System" ;
NIFRID:synonym "Luminex Amnis ImageStream MkII Multispectral Imaging Flow Cytometer",
"Luminex ImageStream MkII Flow Cytometer",
"Luminex ImageStream MkII Multispectral Imaging Flow Cytometer",
"MkII imaging flow cytometer" ;
definition: """Bench top multispectral imaging flow cytometer designed for the acquisition of
up to 12 channels of cellular imagery. It combines per cell information with statistical significance of sample sizes of standard flow cytometry.""" .
SCR:018590 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ITC 200",
"SCR_020260" ;
rdfs:label "Malvern Panalytical | Microcal ITC 200 Isothermal Titration Calorimeter" ;
NIFRID:synonym "MicroCal iTC200" ;
definition: "Isothermal titration calorimeter for label free, in solution, study of biomolecular interactions. It delivers measurement of binding parameters with minimum of 10 ug sample." .
SCR:018591 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Life Technologies | Countess Automated Cell Counter" ;
definition: "Invitrogen benchtop automated cell counter. Can perform cell counts, viability calculations, hemocytometry, fluorescent protein expression, and measure fluorescence capabilities. There are also reusable slides, fluorescence capabilities, and brightfield fluorescence channels." .
SCR:018592 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PB303_S",
"SCR_020255" ;
rdfs:label "Mettler | PB303-S Milligram Balance" ;
definition: "Miligram balance that is used for weighing, tarring, percent weighing, and dynamic weighing for unstable samples. Has maximum capacity of 310 grams. Lab balance utilizes mono block weighing technology with permanent shock protection and built in overload protection as well as automatic calibration." .
SCR:018593 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GX_II",
"SCR_020135" ;
rdfs:label "Illumina | LabChip GXII Touch protein characterization system" ;
NIFRID:synonym "LabChip GXII Touch" ;
definition: "LabChip GXII Touch is a protein characterization system that provides reproducible quantitation, molecular weight sizing and percent purity analysis of protein samples. Leveraging microfluidic electrophoretic separation technology, the LabChip GXII Touch system enables rapid characterization with minimal sample preparation setup and sample input volume." .
SCR:018594 a owl:NamedIndividual ;
rdfs:label "Malvern Panalytical | Microcal VPViewerTM Differential Scanning Calorimeter VP--DSC" ;
definition: "Differential scanning calorimeter for study of samples in solution. It measures intramolecular stability of proteins, nucleic acids, oligomeric proteins, nucleic acid duplexes, lipid and detergent micellar system." .
SCR:018595 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HM505E",
"SCR_020257" ;
rdfs:label "Microm | HM505E Cryostat" ;
definition: "Electronic microtome cryostat upright standing with open top working area that can cut temperature to negative 35 degrees Celsius. Equipped with automatic 24 hour defroster with interrupt key and handwheel brake.Provides protection for knife and specimen as it retracts specimen at the end of the cut. Motorized coarse feed system allows sample to be moved forward and backward.Two knife carriers are available. Standard knife carrier is for knives to be easily clamped in place and adjusted, and the disposable blade holder EC for high- and low-profile blades." .
SCR:018596 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_020261" ;
rdfs:label "Miltenyi | AutoMACS Magnetic Cell Sorter" ;
definition: "Benchtop manager cell sorter for cell isolation in automated workflows. Sorts cells directly from whole blood or bone marrow without density gradient centrifugation or erythrocyte lysis." .
SCR:018597 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_020262" ;
rdfs:label "MILabs | U Spect Nuclear Imager" ;
definition: "Nuclear imager for quantitative 3D functional imaging of SPECT tracers down to 0.12 mm ex vivo and 0.25 mm in vivo. Used for quantitative sub mm imaging of higher energy and theranostic isotopes such as 131I, 188Re, 213Bi, 225Ac, and 223Ra." .
SCR:018598 a owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Plus_384" ;
rdfs:label "Molecular Devices | Spectramax Plus384 Microplate Reader" ;
definition: "Microplate reader that can read one sample or up to 384 in single plate read using any standard cuvette, 12 x 75 mm test tube, or 96 or 384 well microplate. It can run standard spectrophotometer and microplate reader applications." .
SCR:018599 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FastPrep24",
"SCR_020301" ;
rdfs:label "MP Biochemicals | FastPrep24 Sample Preparation" ;
definition: "Sample disruption instrument that can homogenize, grind, or lyse biological samples. Samples are added to individual lysing matrix tubes and shaken in tridimensional motion." .
SCR:018600 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NanoDrop_8000",
"SCR_020315" ;
rdfs:label "Thermo Fisher | NanoDrop 8000 Spectrophotometer" ;
definition: "Microvolume UV Vis spectrophotometer for nucleic acid and protein quantification that can measure multiple samples using 1 to 2 uL of samples. Can analyze spectrum of 220nm to 750nm and measure 96 samples in less than six minutes. Can measure multiple samples in one measurement cycle, up to eight samples at one time. Has single sample mode. Can analyze the full spectrum from 220 to 750nm and calculates sample purity ratios 260/280." .
SCR:018602 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PTC100",
"SCR_020292" ;
rdfs:label "Marshall Scientific | MJ Research PTC-100 PCR Thermocycler" ;
definition: """Thermocycler that operates with 96 well and 60 well microplates. Has temperature configurations from 0 C to 105 C and pressure and height adjustment via thumbwheel.
Comes with 14 pre-programmed protocols.""" .
SCR:018603 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AZ100",
"SCR_020325" ;
rdfs:label "Nikon | AZ100 Confocal Microscope" ;
definition: "Nikon Instruments AZ100 C1si is macro confocal microscope system combining stereo and compound microscopes into single hybrid imaging system for dynamic imaging of single cells or whole specimens.System covers range of magnifications from 5x to 400x. Has triple nosepiece that can switch magnifications. AZ100 C1si boasts simultaneous 32 channel spectral image acquisition over spectral range of 320 nm in single scan. Simultaneous 32 channel acquisition at 10 nm, 5 nm or 2.5 nm bandwidths, all software controlled, is possible." .
SCR:018604 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IX70",
"SCR_020348" ;
rdfs:label "Olympus | IX70 Inverted Fluorescence Microscope" ;
NIFRID:synonym "Olympus IX70 Inverted Fluorescence Tissue Culture Microscope" ;
definition: "Inverted fluorescence tissue culture microscope capable of imaging specimens in brightfield, darkfield, phase contrast, Hoffman modulation contrast, fluorescence, and differential interference contrast modes.TIRFM-IX illuminator is this microscope accessory which attaches to the rear lamphouse port and contains FC connector for external laser source and port for mercury or xenon lamp housing." .
SCR:018605 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SMZ1500",
"SCR_020314",
"SCR_020327" ;
rdfs:label "Nikon | SMZ1500 Zoom Stereoscope" ;
NIFRID:synonym "Nikon 1500 Fluorescence Dissection Microscope" ;
definition: "SMZ1500 stereoscopic zoom microscope is system with apochromatic objectives, zoom ratio of 15 to 1, range of magnifications from 0.75x to 11.25x for total magnifying capability of 3.75x up to 540x, and is best for in depth imaging.Zoom knob allows to zoom from 1x to 11x at 1x-intervals without interrupting observations. Other facets include high eyepoint eyepieces with built-in diopter adjustments, wide field of view, and built-in aperture diaphragm for achieving optimal depth of focus and improved photomicrography.Provides options of either low eye-level viewing tube or tilting eyepiece tube, with or without eye-level risers. Three different diascopic stands with built-in power supplies may also be utilized with instrument, or standard stand that features low profile for increased clearance." .
SCR:018606 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_E600",
"SCR_018858",
"SCR_020322",
"SCR_020330" ;
rdfs:label "Nikon | Eclipse E600 Fluorescence Microscope" ;
NIFRID:synonym "Nikon Eclipse E600 Microscope" ;
definition: "Microscope equipped with CFI60 infinity optical system, providing images in all applications. Incorporates specifications adopted for CFI60 series objectives, including 60 millimeter parfocal distance, 25 millimeter thread size, and standard 22 millimeter field of view. Main components of CFI60 infinity optical system include objective, tube lens to converge light beam, and eyepiece lens to enlarge intermediate image. Fluorescence microscope that has detachable substage, 12 volt 100 watt tungsten halide lamp, filter magazine, and choice of sextuple nosepiece or sextuple DIC nosepiece.Has objectives for brightfield, darkfield, Nomarski DIC, epi fluorescence, or phase contrast techniques." .
SCR:018607 a "Supercategory",
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IV-100",
"SCR_020342" ;
rdfs:label "Olympus | IV-100 Intravital Laser Scanning Microscope" ;
NIFRID:synonym "Olympus IV-100 Imaging System" ;
definition: "Intravital laser scanning microscope for small animal imaging with up to four lasers 488nm, 561nm, 633nm, and 748nm. Able to image multiple fluorescence probes simultaneously. Scan head has tilting capability to image objective orientation in three dimensions.Three magnifications of MicroProbe lenses enable to capture either large field of view or high resolution images on living animal. Certain conventional microscope objectives can also be used on IV100 as well." .
SCR:018608 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_34700",
"SCR_020392" ;
rdfs:label "SelectScience | PELCO BioWave 34700 laboratory microwave system" ;
definition: "Laboratory microwave system that includes True Variable Wattage, water recirculation system, temperature restrictive temperature probe, RS232 Port, Cable and Software, Programmable times, Four intermittent power settings, Magnetron prewarming, Air Bubbler, and Vacuum Cycling. System has precision temperature control and monitoring for microwave assisted processing of tissue. Can be used for formalin fixation, decalcification, special stains, immunocytochemistry and complete processing of tissue into paraffin." .
SCR:018609 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Packard_Cobra_5000",
"SCR_020391" ;
rdfs:label "Packard | Cobra 5000 Gamma Counter" ;
definition: "Gamma counter available in single, five, or ten detector configurations. Can count RIA tubes, 16x100mm and variety of smaller micro tubes using available adapter.This instrument has dot Matrix Printer, tube racks, and protocol ID tags.Single detector model is available in 2 inch or 3 inch crystal configurations for research grade capabilities." .
SCR:018610 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2900TR",
"SCR_020389" ;
rdfs:label "Perkin Elmer | Packard Tri-Carb 2900TR Liquid Scintillation Analyzer" ;
NIFRID:synonym "Packard 2900TR Liquid Scintillation Analyzer" ;
definition: "Benchtop liquid scintillation analyzer that detects small amounts of alpha, beta, and gamma radioactivity. Time resolved liquid scintillation counting is used for low background counting of LS samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:018611 a owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MPS_16" ;
rdfs:label "Perkin Elmer | Titan MPS 16 Position Microwave Sample Preparation Device" ;
definition: "Microwave sample preparation device system designed to count and size particles individually. It can used for in service oil samples with only 4 mL of 10 times diluted samples." .
SCR:018612 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MVX10",
"SCR_020347" ;
rdfs:label "Olympus | MVX10 Macroview Stereo Fluorescence Microscope" ;
definition: "Microscope employs single zoom optical path with large diameter, which is optimized to collect light with efficiency and resolution at all magnifications. From fluorescent observation of whole organisms, such as zebrafish, at low magnification to detailed observation of gene expression at cellular level at high magnification, features pupil division mechanism in light path to mimic effect of stereo microscope." .
SCR:018613 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_20/20",
"SCR_019972" ;
rdfs:label "Promega | GloMax 20/20 Luminometer" ;
NIFRID:synonym "GloMax 20/20 Luminometer" ;
definition: "Luminometer combines instrumentation and software for uses includinh bioluminescent assays, protocols and support. You can measure flash or glow-type luminescence, have two fluorescent modules available, and it accommodates 1.5ml microcentrifuge tubes and 35mm petri dishes, with optional 12mm × 50mm test tube adapter. Measure light output from liquid and solid samples; no minimum volume requirements. The GloMax 20/20 blends user-friendly operation and a small footprint.This Instrument Was Retired September 1, 2023. Accessories and service available until September 1, 2028." .
SCR:018614 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GloMax_96",
"SCR_019964" ;
rdfs:label "Promega | GloMax 96 Microplate Luminometer" ;
NIFRID:synonym "GloMax 96 Microplate Luminometer" ;
definition: "Microplate luminometer that features two optional injectors and reads both glow- and flash-luminescent reactions in 96-well plates. The sensitivity and range enable a wide range of luminescent assays, including Promega bioluminescent reporter, cell-based and biochemical assays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:018615 a owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TBS_380" ;
rdfs:label "Promega | TBS-380 Fluorimeter" ;
definition: "Dual channel fluorimeter for fluorescence measurements when calibrated with known concentration to measure compounds at low concentration with low assay volume." .
SCR:018616 a owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_G3" ;
rdfs:label "Perkin Elmer | Zephy G3 NGS liquid handler" ;
definition: "Benchtop liquid handler designed to automate construction of 48 to 96 next generation sequencing libraries per day." .
SCR:018617 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Q96",
"SCR_020413" ;
rdfs:label "Qiagen | PyroMark Q96 System" ;
definition: "Sequencing and quantification platform for epigenetics, mutation gene expression analysis, and microbial identification and resistance typing. With its 96-well format, automatic base-calling function, and dedicated software solutions for methylation analysis and assay design." .
SCR:018618 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QIACube",
"SCR_020414" ;
rdfs:label "Qiagen | QIAcube Classic" ;
definition: "Purification system that performs fully automated purification of nucleic acids and proteins in molecular biology applications." .
SCR:018620 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Q24",
"SCR_020421" ;
rdfs:label "Qiagen | Pyromark Q24 Sequencer" ;
definition: "Sequencer that uses pyrosequencing technology for real time, sequence based detection, quantification of sequence variants, and epigenetic methylation. Used for analysis of CpG methylation, SNPs, insertion deletions, STRs, variable gene copy number, and for microbial identification and resistance typing." .
SCR:018621 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IVIS",
"SCR_020397" ;
rdfs:label "Perkin Elmer | IVIS Spectrum In Vivo Imaging System" ;
definition: "In vivo imaging system that combines two dimensional and three dimensional optical tomography in one platform.The system uses leading optical technology for preclinical imaging research and development best for non-invasive longitudinal monitoring of disease progression, cell trafficking and gene expression patterns in living animals." .
SCR:018622 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QIAgility",
"SCR_020417" ;
rdfs:label "Qiagen | QIAgility" ;
NIFRID:synonym "Qiagen QIAgility PCR Setup Robot" ;
definition: "PCR Setup Robot. Compact benchtop instrument for setup of PCR experiments with setup and automatic calculation of all mixes, eliminating the need to program pipetting steps." .
SCR:018623 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Tissue_Lyser_II",
"SCR_020420" ;
rdfs:label "Qiagen | Tissue Lyser II" ;
NIFRID:synonym "Qiagen Tissue Lyser II RNA/DNA Purification",
"TissueLyser II" ;
definition: "RNA and DNA purification analyzer that disrupts biological samples through high speed shaking in plastic tubes with stainless steel, tungsten carbide, or glass beads.Can analyze up to 48 or 192 samples at the same time." .
SCR:018624 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QIAxcel",
"SCR_020418" ;
rdfs:label "Qiagen | QIAxcel Genetic Analyzer" ;
NIFRID:synonym "Qiagen QIAxcel Advanced",
"QIAxcel Advanced" ;
definition: "Genetic analyzer that automates electrophoresis analysis of your DNA and RNA samples." .
SCR:018625 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Alchemist_II",
"SCR_019564" ;
rdfs:label "Rigaku | Alchemist II Liquid Handler" ;
definition: "Liquid handling system for production of complex liquid formulations produced from individual stock solutions of various chemical and liquid properties. With a CV of less than 2%." .
SCR:018626 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LightCycler_480",
"SCR_020502" ;
rdfs:label "Roche | LightCycler 480 Real Time PCR System" ;
NIFRID:synonym "LightCycler 480 Real-Time PCR System",
"Roche LightCycler 480 II Real Time PCR System" ;
definition: "System includes: LightCycler 480 instrument which is real-time PCR device, allowing the use of additional thermal block cycler units (96-well and 384-well format) with the system; LightCycler 480 Software which provides intuitive, easy-to-navigate user interface for real-time PCR programming, data capture, and data analysis to study gene expression and genetic variation. LightCycler 480 II represents newer generation of the same real-time PCR system, with improved features like enhanced optics for more uniform plate analysis across all wells, potentially leading to increased accuracy and consistency in data collection compared to original LightCycler 480." .
SCR:018627 a owl:NamedIndividual ;
rdfs:label "SCIEX | QStar XL Mass Spectrometer" ;
definition: "Hybrid quadrupole time of flight mass spectrometer with MS mass range 6,000 and 40,000 m z designed proteomics, drug discovery, metabolomics, and drug development. Instrument used with Analyst QS software." .
SCR:018628 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cytospin 3",
"SCR_020507" ;
rdfs:label "Thermo Fisher | Shandon Cytospin 3 Centrifuge" ;
definition: "Thermo Shandon Cytospin 3 is low speed centrifuge used to separate and deposit monolayer of cells on slides while maintaining cellular integrity.Centrifuge has speed range between 200 and 2000 RPM, and has holding capacity of up to 24 samples in 12 chambers." .
SCR:018629 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Integra_400_Plus",
"SCR_020504" ;
rdfs:label "Roche | Cobas Integra 400 Plus Chemistry Analyzer" ;
definition: "COBAS INTEGRA 400 plus analyzer is a chemistry analyzer with a broad test menu comprises over 120 assays and applications that consolidate clinical chemistry with specific proteins, therapeutic drug monitoring and drug abuse testing.The Cobas 400 analyzer is best for laboratories running up to 400 samples per day. This compact tabletop analyzer offers maximum versatility to improve efficiency and reduce costs. It uses the convenient cobas c pack reagent format, which standardizes patient results across integrated laboratory networks." .
SCR:018630 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sciex_4000_QTRAP",
"SCR_020508" ;
rdfs:label "SCIEX | 4000 QTRAP Mass Spectrometer" ;
definition: "Hybrid triple quadrupole linear ion trap mass spectrometer for drug discovery and development, metabolite identification, contaminant testing, proteomic applications, post translationally modified proteins discovery, protein identification, and biomarker validation." .
SCR:018631 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1800",
"SCR_020532" ;
rdfs:label "Stratagene | 1800 UV Crosslinker" ;
definition: "UV crosslinker designed to crosslink DNA or RNA to nylon, nitrocellulose, or nylon reinforced nitrocellulose membranes in 25 to 50 seconds. It is equipped with internal photodetector to compensate for aging ultraviolet bulbs." .
SCR:018632 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_325",
"SCR_020512" ;
rdfs:label "Thermo Fisher | Shandon 325 Manual Microtome" ;
NIFRID:synonym "Thermo Scientific Shandon Finesse 325 Manual Microtome" ;
definition: "Manual microtome with flywheel for routine paraffin sectioning. Can cut 1 to 30 um speciment thickness, and specimen tilt or orientation is plus or minus 5 degrees using X Y micro adjustment.Has quick release cassette clamp and x-y orientation head supplied as standard, disposable blades or standard microtome knives." .
SCR:018633 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_X-Stream_2000" ;
rdfs:label "Rigaku | X-Stream 2000 Cryo-Freezing System" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 11,2024. Self contained cryo freezing system designed cooling crystals with range of negative 80C to 4C. It produces nitrogen, which is then cooled to negative 196C, and then rewarmed to desired temperature." .
SCR:018634 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BNII",
"SCR_019838" ;
rdfs:label "Siemens | Dade Behring BNII Nephelometer System" ;
NIFRID:synonym "Dade Behring BN II Nephelometer",
"Siemens Dade Behring BNII Nephelometer" ;
definition: "Siemens Dade Behring BN II Nephelometer is leading fully automated system for plasma protein determinations. BN II systems offer advanced nephelometric technology that provides performance in plasma protein analysis. This instrument's menu covers assays, which support various clinical tests including cardiac risk assessment, kidney diseases and nutritional assessment. markers such as Cystatin C and Carbohydrate-Deficient Transferrin (CDT) are also supported. Other features of the Dade Behring BN II Nephelometer include rapid processing, easy operation and random-access mode. The nephelometer also permits users to put up to 100 samples on board, making it best for mid to high-volume processing." .
SCR:018635 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SH800Z",
"SCR_020521" ;
rdfs:label "Sony biotechnology | SH800Z Cell Sorter" ;
definition: "Automated cell sorter that has microfluidics sorting chip integrated with six fluorescence detectors and up to four collinear excitation lasers of 488 nm, 405 nm, 561 nm and 638 nm." .
SCR:018636 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_P97",
"SCR_020540" ;
rdfs:label "Sutter | P-97/PC Pipette Puller" ;
definition: "Pipette puller that fabricates pipettes for use in intracellular recording, patch clamping, transferring ICSI, ES Cells , microinjection, aspiration, and microperfusion. P-97 puller can indirectly sense viscosity of glass, giving the ability to pull pipettes from all glasses except quartz. Even difficult to pull formulations, such as aluminosilicate glasses, are handled with relative ease." .
SCR:018637 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_3200",
"SCR_019752" ;
rdfs:label "TA Instruments | Electroforce 3200 Mechanical Testing Apparatus" ;
NIFRID:synonym "TA Instruments Electroforce 3200 Series Mechanical Testing Apparatus" ;
definition: "Mechanical testing apparatus with 225 N or 450 N maximum force and range of static to 300 Hz frequency response. Tests include torsion testing, creep under dynamic loading, special environment hot cold chambers, biomedical research, and engineered materials test applications.." .
SCR:018638 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Hydra_II",
"SCR_020557" ;
rdfs:label "Thermo Fisher | Hydra II Microdispenser" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22,2024. Bench top 96 or 384 channel liquid handler capable of automating pipetting tasks, including low volume and viscous sample transfers. It utilizes syringe based technology to dispense solutions." .
SCR:018639 a owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TissueCyte_1000",
"SCR_020870" ;
rdfs:label "TissueVision | TissueCyte 1000 Photon Imaging System" ;
NIFRID:synonym "TissueCyte 1000" ;
definition: "Whole organ serial two photon tomography imaging platform that allows imaging of whole fixed organs based on high speed two photon microscopy TPM and integrated tissue sectioning. TissueCyte 1000 is a specialized Serial Two-Photon (STP) tomography system manufactured by TissueVision, Inc.. It is not available off-the-shelf. To acquire the TissueCyte 1000 or inquire about their newer platforms, you must contact TissueVision directly to request a hardware consultation, quote, or system setup." .
SCR:018640 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_P2000",
"SCR_020213",
"SCR_020537" ;
rdfs:label "Sutter | P-2000 Laser Micropipette Puller" ;
definition: "Microprocessor controlled, CO2 laser based micropipette puller.Default configuration allows fabrication of micropipettes for intracellular recording, patch clamping, microinjection and microperfusion.Can store up to 100 separate programs, each consisting of up to 8 command lines. The five parameters set in each command line allow exquisite control of the micropipette taper geometry. Allows the use of wide range of glass diameters from 0.125 to 1.2 mm." .
SCR:018641 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XT",
"SCR_019580" ;
rdfs:label "Thermo Fisher | Arcturus Cellect Laser Capture Microdissection System" ;
definition: "Laser capture microdissection system that includes infrared lasers. It can be used for laser capture microdissection LCM, ultraviolet UV laser cutting, sanger sequencing, next generation sequencing, and quantitative PCR." .
SCR:018642 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_815B",
"SCR_019587" ;
rdfs:label "Tousimis | Autosamdri 815B Critical Point Dryer" ;
definition: "Critical point dryer with wafer holders that allow automatic anti stiction processing up to 5 pieces of either 100mm, 75mm, 50mm wafers or 10mm square die per process run. All internal surfaces are inert to CO2 and ultra pure alcohols." .
SCR:018643 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ventana_Discovery_XT" ;
rdfs:label "Roche | Ventana Discovery XT Immunohistochemistry Processor" ;
definition: "Immunohistochemistry processor that can be used for immunohistochemistry and in situ hybridization slide preparation and processing." .
SCR:018644 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_K_MINC_1000",
"SCR_020879" ;
rdfs:label "Cook Medical | WilliamA Cook Australia K-MINC-1000 Benchtop Incubator" ;
definition: "Benchtop incubator microprocessor controlled, gassed, humidified, incubator intended for use in cell culture. It is designed to maintain temperature between 35 and 40 degrees celsius and gas flow within range of 15 to 25 ml min." .
SCR:018645 a owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_922_TEM",
"SCR_020912" ;
rdfs:label "Zeiss | 922 Transmission Electron Microscope" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12, 2024. Transmission electron research microscope with accelerating voltages of 120 and 200kV and has magnification from 80X to 1,000,000X with resolution line of 0.12nm." .
SCR:018646 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cytomat 6001",
"SCR_020541" ;
rdfs:label "Thermo Fisher | Cytomat 6001 Automated Wide Range Incubator" ;
definition: "Automated wide range incubator used to minimize plate movement, receive samples, store plates, and track plates.Temperature range is from 10 to 50 degrees Celsius with humidity level of up to 95 rH." .
SCR:018647 a owl:NamedIndividual ;
rdfs:label "Zeiss | PALM MicroTweezers" ;
definition: "Optical tweezers system for contact free cell manipulation as well as to trap, move, and sort microscopic particles, sort live cells, organelles, and other large biomolecules." .
SCR:018648 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Dynapro II",
"SCR_020886" ;
rdfs:label "Wyatt | Dynapro II Plate Reader" ;
definition: "Plate reader that automates dynamic light scattering measurements on macromolecular and nanoparticle samples in situ in 96, 384, or 1536 well microplates. It screens for particle size, thermal stability, aggregation temperature tonset, colloidal stability via diffusion interaction parameter kD or D1, and viscosity of protein solutions." .
SCR:018649 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2695",
"SCR_020877" ;
rdfs:label "Waters | 2695 HPLC System" ;
NIFRID:synonym "Waters Alliance 2695 Separations Module" ;
definition: "High performance liquid chromatographic system with quaternary, low pressure mixing pump and inline vacuum degassing. It has wavelengths of 190 to 800 nm and flow rates from 50 uL per min to 5 mL per min with 2.1 mm ID columns and larger. Autosampler has maximum capacity of 120 vials (12x32, 2 mL) with programmable temperature control from 4 to 40C. Heated column compartment provides temperatures from 5 degrees above ambient to 65C." .
SCR:018650 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TSQ Quantiva",
"SCR_020568" ;
rdfs:label "Thermo Fisher | TSQ Quantiva Triple-Stage Quadrupole Mass Spectrometer" ;
definition: "Triple stage quadrupole mass spectrometer for low level quantitation and has mass range of mass per charge 10 to 1800 mass per charge. Laboratory room temperature must be maintained between 18 to 27 C and cannot change by more than 5 C." .
SCR:018651 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:datanator",
"r3d100013339" ;
rdfs:label "Datanator" ;
definition: "Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition." .
SCR:018652 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:objtables" ;
rdfs:label "ObjTables" ;
definition: "Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort." .
SCR:018653 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bpforms" ;
rdfs:label "BpForms" ;
definition: "Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts." .
SCR:018654 a owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bcforms" ;
rdfs:label "BcForms" ;
definition: "Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models." .
SCR:018655 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LSRFortessa",
"SCR_01960",
"SCR_019600",
"SCR_019602",
"SCR_019605" ;
rdfs:label "BD Biosciences | LSRFortessa Cell Analyzer" ;
NIFRID:synonym "BD LSRFortessa" ;
definition: "BD LSRFortessa system can be configured with up to 7 lasers, blue, red, violet, UV and yellow-green. The instrument can accommodate the detection of up to 18 colors simultaneously with defined set of optical filters that meet or exceed the majority of today's assay requirements. BD FACSDiva software controls the efficient setup, acquisition, and analysis of flow cytometry data from the BD LSRFortessa workstation. The software is common across BD FACS instrument families, including the BD FACSCanto cell analyzer and BD FACSAria cell sorter systems." .
SCR:018656 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "McKinley | Cellometer Auto 2000 Cell Viability Counter" ;
definition: "Cell viability counter. Touchscreen fluorescent automated cell counter for primary samples by Nexcelom Bioscience." .
SCR:018657 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MSTools" ;
definition: "Web based application for visualization and presentation of HXMS data. Comprises tools helping in preparation of H/D experiments as well as tools for turning simple tables with data on H/D exchange into different ways of representation." .
SCR:018658 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "trend" ;
NIFRID:synonym "Non-Parametric Trend Tests and Change-Point Detection" ;
definition: "Software package includes tests for trends and change points detection. Used in analysis of environmental data." .
SCR:018659 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:precrec" ;
rdfs:label "precrec" ;
definition: "Software R package for fast and accurate precision recall and ROC curve calculations. Calculates accurate precision recall and Receiver Operator Characteristics curves." .
SCR:018660 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:mygene.info",
"biotools:mygene.info" ;
rdfs:label "MyGene.info" ;
definition: "Web service for querying or retrieving gene annotation data." .
SCR:018661 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:minet" ;
rdfs:label "minet" ;
NIFRID:synonym "Mutual Information NETworks" ;
definition: "Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data." .
SCR:018662 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Discrete Morse" ;
NIFRID:synonym "DiscreteMorse" ;
NIFRID:abbrev "DM" ;
definition: "Discrete Morse based pipeline for neuron tracing on tracer injection and single neuron data sets. Automatically generates set of trees summarization of given neuron imaging data. Used to extract tree skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections." .
SCR:018663 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ehrtemporalvariability" ;
rdfs:label "EHRtemporalVariability" ;
NIFRID:synonym "Electronic Health Records temporal variability" ;
definition: "Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users." .
SCR:018664 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:preseq" ;
rdfs:label "Preseq" ;
definition: "Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries." .
SCR:018665 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QoRTs" ;
definition: "Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R." .
SCR:018666 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UniProt Proteomes" ;
definition: "Protein sets from fully sequenced genomes. Proteomes portal offers protein sequence sets obtained from translation of completely sequenced genomes. Published genomes from NCBI Genome are brought into UniProt if genome is annotated and set of coding sequences is available. Number of predicted coding sequences falls within statistically significant range of published proteomes from neighbouring species." .
SCR:018667 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_44" ;
rdfs:label "Vermont University Proteomics Core Facility" ;
NIFRID:synonym "University of Vermont Proteomics Facility",
"UVM-Proteomics Facility" ;
definition: "Provides central resource of mass spectrometry based proteomics technologies to identify, characterize and quantify target proteins in various biological and biomedical samples. Provides mass spectrometry expertise for analyzing proteins and peptides for proteomics studies, support for data analysis from proteomics measurements, training in proteomics methods, and experimental design." .
SCR:018668 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_226" ;
rdfs:label "Stanford University School of Medicine Protein and Nucleic Acid Core Facility" ;
NIFRID:synonym "Protein and Nucleic Acid Facility (PAN)",
"Stanford School of Medicine Protein and Nucleic Acid Facility",
"Stanford University Protein and Nucleic Acid Facility (PAN)" ;
NIFRID:abbrev "PAN" ;
definition: "Offers instrumentation and technical capabilities and plays significant consultative role in application of these technologies to basic science projects.Genomic Services include Oligo Synthesis,Gene Expression,Real-Time PCR,PyroSequencing,Next-Generation Sequencing (NGS),DNA Sequencing (Sanger)/Fragment AnalysisSingle Cell Genomics,RNA-DNA QC - Bioanalyzer and Fragment Analyzer QC.Protein Services include Peptide Synthesis,Mass Spectrometry,Protein Analytics - Mass Mapping/Edman Sequencing,Surface Plasmon Resonance (Biacore)." .
SCR:018669 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_344" ;
rdfs:label "Johns Hopkins University School of Medicine Genetic Resources Core Facility" ;
NIFRID:synonym "Genetic Resources Core Facility",
"Genetic Resources Core Facility (GRCF) BioRepository and Cell Center",
"GRCF Biorepository and Cell Center",
"GRCF Cell Center",
"GRCF DNA Services",
"JHU BioBank",
"JHU Nucleic Acid Technologies",
"JHU-NAT" ;
NIFRID:abbrev "GRCF" ;
definition: "Established to produce immortalized cell lines from human blood (EBV transformations). Offers genomics applications for single cells, including RNA-seq, gene expression profiling by qPCR and DNA amplification for whole-genome or targeted (exome or PCR-based analysis) through 10x Genomics Chromium platform (similar to Drop Seq). Offers custom genotyping to analyze short tandem repeats, variable number tandem repeats and single nucleotide polymorphisms." .
SCR:018670 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_104" ;
rdfs:label "Rochester University Human Immunology Center Core Facility" ;
NIFRID:synonym "RHIC Core lab",
"Rochester Human Immunology Center",
"Rochester Human Immunology Center Core Laboratory" ;
NIFRID:abbrev "RHIC" ;
definition: "Designed to enhance multi-disciplinary research initiatives catalyzing key clinical and basic immunology research in vaccines, HIV/AIDS, autoimmunity, allergy/asthma, transplantation as well as cancer immunology.Provides expertise in multichromatic flow cytometry (immunophenotyping, antigen-specific intracellular cytokine staining and cell sorting), T and B cell Elispot, Fluorispot, T regulatory cell assays, magnetic bead selection of cell populations, and Luminex multiplexed bead array assays.Provides specialized clinical specimen analysis services for clinical studies or contracts." .
SCR:018671 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_251" ;
rdfs:label "Kansas University Lawrence Biomolecular NMR Laboratory Core Facility" ;
NIFRID:synonym "Bio-NMR Laboratory",
"Biomolecular NMR Laboratory",
"COBRE Biomolecular NMR Laboratory",
"Kansas University Lawrence Bio-NMR Laboratory" ;
definition: "NMR Laboratory maintains two high field NMR spectrometers in support of structural and dynamics studies of biomolecules. Its capabilities include determining high resolution structures, biological macromolecules, elucidation and structural mapping of protein-protein, protein-nucleic acid, protein-peptide, protein-drug interactions, and studies of dynamics of proteins and their complexes in solution. Laboratory staff provide advice,consultation, training,assistance and complete structure elucidation services.Staff is responsible for maintenance, upgrades, implementation of new NMR pulse sequences, and assisting local and remote users with technical problems.Equipped with Bruker Avance 800 MHz NMR instrument fitted with TCI cryoprobe and Bruker Avance III 600 MHz with variety of probes." .
SCR:018672 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_390",
"SCR_015366" ;
rdfs:label "University of Massachusetts Medical School Metabolic Disease Research Center Core Facility" ;
NIFRID:synonym "Massachusetts University Medical School Mouse Phenotyping Center Core Facility",
"Massachusetts University Medical School National Mouse Metabolic Phenotyping Center",
"National Mouse Metabolic Phenotyping Center",
"UMass Medical School Metabolic Disease Research Center",
"University of Massachusetts Medical School Mouse Phenotyping Center Core Facility" ;
NIFRID:abbrev "MDRC",
"MMPC",
"UMass MMPC" ;
definition: "UMass Metabolic Disease Research Center (MDRC), formerly the National Mouse Metabolic Phenotyping Center, is a core facility that performs standardized experiments using state-of-the-art equipment for the purpose of investigating transgenic mouse models of diabetes, obesity, and metabolic liver disease. Provides metabolic and functional characterization of mouse models of human diseases that are developed by academic and industry researchers in joint efforts to understand metabolic diseases and to identify new therapies." .
SCR:018673 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_981" ;
rdfs:label "Harvard Center for Biological Imaging Core Facility" ;
NIFRID:synonym "Harvard Center for Biological Imaging",
"Harvard Center for Biological Imaging (HCBI)" ;
NIFRID:abbrev "HCBI" ;
definition: "Microscopy facility. Contains microscopes including confocal, super-resolution, multi-photon, light sheet, live cell imaging, high-content screening, slide scanning, laser dissection and macroscopy stations. Features wet lab space, eukaryotic and prokaryotic incubation, and access to nearby animal care facilities for wide range of species.Services include Cell Imaging,Confocal Microscopy,Consultations,Data Analysis,Data Processing And Interpretation,High Content Screening,Laser Capture Microdissection,Microscopy,Multiphoton Microscopy,Optical Imaging,Slide Scanning,Whole Slide Imaging." .
SCR:018674 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_767" ;
rdfs:label "Massachusetts Institute of Technology Swanson Biotechnology Center Nanotechnology Materials Core Facility" ;
NIFRID:synonym "Bio and CryoEM in the Nanotechnology Materials Core" ;
definition: "Provides instruments for materials and nanomaterials research and full service TEM and cryoTEM sample preparation and imaging. Conducts CLEM and cryoCLEM workflows utilizing cryoFluorescence, cryoSEM and cryoFIB with focus on bio samples.Provides equipment and expertise to work with nanomaterials for characterization and imaging purpose. Core imaging capabilities include high performance field emission transmission electron microscope equipped with STEM, EELS, EDS and cryo-imaging, high performance field emission scanning electron microscope and focused ion beam equipped with STEM and cryo-imaging, cryo-fluorescent confocal microscope for CLEM workflows, and atomic force microscope equipped with liquid cell. Instrumentation for material characterization includes high throughputdynamic light scattering, nanoparticle sizing and counting, and rheometry." .
SCR:018675 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_434" ;
rdfs:label "Louisiana State University Pennington Biomedical Research Center Genomics Core Facility" ;
NIFRID:synonym "Pennington Biomedical Research Center Genomics Core",
"Pennington Genomics Core" ;
NIFRID:abbrev "GCF" ;
definition: """Provides services which include Sanger and next-generation DNA sequencing,DNA fragment analysis,qualitative and quantitative analysis of DNA, protein, and RNA samples, quantitative PCR, microarray RNA labeling, hybridization, and scanning
robotics,bioinformatics.Individual and small group training and consultation services are offered for sequence analysis, real-time PCR, next-generation sequencing and microarray analysis.""" .
SCR:018676 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1002" ;
rdfs:label "Rutgers Waksman Institute of Microbiology Cell and Cell Products Fermentation Core Facility" ;
NIFRID:synonym "Cell and Cell Products Fermentation Facility",
"Waksman Institute of Microbiology (Busch Campus)" ;
definition: """Provides fermentation services. Produces range of bulk biologics including antimicrobials, cosmetic substrates, flavors/fragrances, biopesticides/bioherbicides and plasmid derived proteins, enzymes, growth factors and diagnostics. Exceptions for pathogenic or opportunistic organisms and mammalian and insect cell lines. Includes Material Preparation Laboratory,Fermentation In-Process/Computer Control,Product Recovery and Analytical Services.
""" .
SCR:018677 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_689" ;
rdfs:label "University of Tennessee JIAM Diffraction Core Facility" ;
NIFRID:synonym "JIAM Diffraction Facility",
"JIAM X-Ray Diffraction Core",
"JIAM X-ray Diffraction Core Facility",
"University of Tennessee JIAM X-Ray Diffraction Core" ;
definition: "Provides users with access to Panalytical XPert3 MRD and Panalytical Empyrean XRD platforms to perform variety of X-ray diffraction experiments including phase identification, phase quantification, crystallite size and microstrain determination, pole figures, residual stress, high-temperature in situ measurements. These instruments are available for both assisted and unassisted use with prior approval." .
SCR:018678 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_835" ;
rdfs:label "Certified Genetool, Inc." ;
NIFRID:synonym "Certified Genetool" ;
definition: """Provides services for USED lab instrument repairs.Recertified laboratory equipment commercially available. Comes fully re-certified to manufacturers standards with 90 day warranty.
""" .
SCR:018681 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProteinPilot Software" ;
NIFRID:synonym "Protein Pilot",
"Protein Pilot Software" ;
definition: "Software tool for protein identification and relative protein expression analysis. Used in protein research to identify proteins and search large numbers of post translational modifications. Compatible with all proteomics MS/MS systems." .
SCR:018683 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StructuralVariantAnnotation" ;
definition: "Software R package for structural variant analysis. Contains helper functions for dealing with structural variants in VCF format. Contains functions for parsing VCFs from number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects." .
SCR:018684 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012862" ;
rdfs:label "Carbohydrate Structure Database" ;
NIFRID:synonym "CSDB version 1" ;
NIFRID:abbrev "CSDB" ;
definition: "Database contains manually curated natural carbohydrate structures, taxonomy, bibliography, NMR data. Bacterial and Plant and Fungal databases were merged to improve quality of content-dependent services, such as taxon clustering or NMR simulation. These separate databases will be supported in parallel until 2020." .
SCR:018685 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Monocle3" ;
NIFRID:synonym "Monocle",
"Monocle 3" ;
definition: "Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points." .
SCR:018686 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford Medicine Research Data Repository" ;
NIFRID:synonym "STAnford medicine Research data Repository",
"STRIDE-web" ;
NIFRID:abbrev "STARR" ;
definition: "Platform developed and operated by Stanford Medicine Research IT team for working with clinical data for research purposes. Permits collection and aggregation of all clinical data generated at Stanford for care purposes, and articulates formal approval process each research project must follow in order to obtain and work with this data for research purpose. Home of stride/web tools for Cohort Discovery and Chart Review." .
SCR:018687 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rapid Response Viral Data Collection Portal" ;
definition: "Community portal to crowd source viral data collection and viral resources." .
SCR:018688 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pandora White Matter Atlas" ;
definition: "Population based collection of white matter atlases represented in both volumetric and surface coordinates in standard space. These atlases include white matter fascicles derived from different tractography techniques including Automated Fiber-tract Quantification, Automated Fiber-tract Quantification clipped, Recobundles, Tracula, TractSeg, and Xtract." .
SCR:018690 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CATlas" ;
NIFRID:synonym "Cis-element Atlas",
"Ren lab web portal for chromatin accessibility data" ;
definition: "Atlas of gene regulatory elements in adult mouse cerebrum. Atlas of CIS elements, providing information on accessible chromatin in individual cells from regions of adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei. Uses resulting data to define candidate cis-regulatory DNA elements in distinct cell groups. Many are linked to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Used for analysis of gene regulatory programs of mammalian brain and interpretation of non-coding risk variants associated with various neurological disease and traits in humans." .
SCR:018692 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Islet eQTL Explorer" ;
definition: "Web tool for exploring variants in islet expression quantitative trait loci. Data is result of collaboration between Michigan University Parker lab, Department of Biostatistics and Center for Statistical Genetics at University of Michigan, National Human Genome Research Institute, Jackson Laboratory for Genomic Medicine, Department of Genetics at University of North Carolina, European Bioinformatics Institute, Department of Preventive Medicine at University of Southern California, and Department of Physiology and Biophysics at University of Southern California." .
SCR:018693 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "piNET" ;
definition: "Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values." .
SCR:018694 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | LTQ-Orbitrap Elite nano LC/MS system" ;
NIFRID:synonym "LTQ-Orbitrap Elite nano LC/MS",
"Orbitrap Elite",
"Thermo LTQ-Orbitrap Elite nano LC/MS" ;
definition: "LTQ-Orbitrap Elite mass spectrometer with Waters nanoAcquity system. Used for proteomic applications." .
SCR:018695 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | 7890/5975 GC/MS system" ;
NIFRID:synonym "Agilent 7890/5975 GC/MS" ;
definition: "Agilent GC/MS is single quadrupole instrument with electron ionization. GC/MS runs under ChemStation open access software, and trained open access users select from menu of standard methods to analyze their samples." .
SCR:018696 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_019779" ;
rdfs:label "Bruker | Microflex MALDI TOF mass spectrometer" ;
NIFRID:synonym "Bruker Microflex MALDI-TOF",
"Bruker Microflex MALDI-TOF mass spectrometer" ;
definition: "Microflex LRF mass spectrometer is specialized for protein, peptide, and polymer analysis. This MALDI-TOF instrument can be operated in linear mode for high mass accuracy characterization, or in reflector mode to achieve enhanced resolution." .
SCR:018697 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker | micrOTOF-Q II LC/MS system" ;
NIFRID:synonym "Bruker micrOTOF-Q II LC/MS" ;
definition: "Bruker micrOTOF-Q II is benchtop Q-Tof mass spectrometer, applied to applications such as small molecule accurate mass determination, intact protein analysis including antibodies, peptide mapping, and other custom projects. This system is operated with Agilent 1260 UPLC and includes inline diode array detector and ESI source." .
SCR:018698 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker | Scion TQ GC/MS mass spectrometer" ;
NIFRID:synonym "Bruker Scion TQ GC/MS" ;
definition: "Scion GC triple quad is applied to targeted trace level analysis of metabolites and other small molecules. Electron ionization combines with MS/MS capability for outstanding selectivity. Samples are often derivatized for compatibility with GC/MS." .
SCR:018699 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8030_triple_quadrupole" ;
rdfs:label "Stanford Shimadzu 8030 LC/MS mass spectrometer" ;
NIFRID:synonym "Shimadzu 8030 LC/MS" ;
definition: "Shimadzu 8030 triple quadrupole mass spectrometer used for targeted quantitation applications. Listed by Stanford University Mass Spectrometry Vincent Coates Foundation Instruments." .
SCR:018700 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Exactive Orbitrap LC/MS system" ;
NIFRID:synonym "Thermo Exactive Orbitrap LC/MS" ;
definition: "Thermo Exactive benchtop Orbitrap operates with Waters Acquity UPLC and generates high resolution, high mass accuracy full MS data. Available to advanced open access users for reversed phase and HILIC LC/MS applications." .
SCR:018701 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | LTQ XL LC/MS system" ;
NIFRID:synonym "Thermo LTQ XL LC/MS" ;
definition: "LTQ XL ion trap mass spectrometer with Agilent 1100 HPLC system for metabolite identification, stability testing, degradation products, and high abundance quantitation." .
SCR:018702 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Orbitrap Fusion nanoLC/MS system" ;
NIFRID:synonym "Orbitrap Fusion nanoLC/MS",
"Thermo Orbitrap Fusion nanoLC/MS" ;
definition: "System includes Thermo Orbitrap Fusion Tribrid mass spectrometer and Waters M-Class Acquity nanoUPLC. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments." .
SCR:018703 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | QE-HFX mass spectrometer" ;
NIFRID:synonym "Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer",
"Thermo QE-HFX" ;
definition: "HFX offers scanning rate to improve proteomic depth for discovery applications. Integrates well with targeted applications such as parallel reaction monitoring. Mass Spectrometer to identify and quantify proteins, peptides, lipids, glycans and small molecules accurately." .
SCR:018704 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Vantage LC/MS mass spectrometer" ;
NIFRID:synonym "Thermo Vantage LC/MS" ;
definition: "Triple quad mass spectrometer for quantitative work and selective assays of targeted analytes. Can analyze metabolites, peptides from matrices such as serum, tissue, cell culture, and other biological sources." .
SCR:018705 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Waters | Quattro Premier LC/MS system" ;
NIFRID:synonym "Micromass Quattro Premier LC/MS system",
"Waters Quattro Premier LC/MS" ;
definition: "Micromass (now Waters) Quattro Premier triple quadrupole operates with Agilent 1100 HPLC and specializes in quantitative work and selective of targeted analytes including metabolites and other small molecules, and peptides from complex matrices such as serum, tissue, cell culture, and other biological sources." .
SCR:018706 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Cellinsight CX7 High-Content Screening Platform" ;
NIFRID:synonym "Thermo Scientific CellInsight CX7 High-Content Screening Platform" ;
definition: "Integrated software and instrument system for performance in cell-based screening and analysis." .
SCR:018707 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:rvista" ;
rdfs:label "rVista" ;
NIFRID:synonym "rVista 2.0" ;
definition: """Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences.
rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites.""" .
SCR:018708 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Quantitative Analysis of Spatial distributions in Images using Mosaic segmentation and Dual parameter Optimization in Histograms" ;
NIFRID:abbrev "QuASIMoDOH" .
SCR:018709 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "SPARC Anatomy Working Group" ;
NIFRID:synonym "Stimulating Peripheral Activity to Relieve Conditions Anatomy Working Group" ;
NIFRID:abbrev "SAWG" ;
definition: """Group of anatomical experts tasked with enhancing structured vocabularies around nerve to organ connections. Responsible for integrity of anatomical knowledge in SPARC. Provides relevant guidance and expertise about defining and naming anatomical terms,
maintaining ontologies and anatomical knowledge, compliling and curating computable knowledge about multiscale route pathways.
Provides access to data generated by SAWG which includes links to documentation about vocabulary services, term request and connectivity. Page will be continuously updated.""" .
SCR:018710 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:CRISPR-ERA" ;
rdfs:label "CRISPR-ERA" ;
NIFRID:synonym "CRISP-Editing",
"Repression and Activation" ;
definition: "Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design." .
SCR:018711 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FunCoup" ;
definition: "Database of genome wide functional coupling networks. Provides tools to explore predicted networks and to retrieve detailed information about data underlying each prediction. Web service for functional coupling search." .
SCR:018712 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_020238" ;
rdfs:label "Thermo Fisher | QuantStudio 3 Real Time PCR System" ;
NIFRID:synonym "ABI QuantStudio3 Flex instrument",
"Applied Biosystems QuantStudio 3 Real-Time PCR System",
"Life Technologies QuantStudio 3 Real Time PCR System",
"QuantStudio 3 RT PCR System",
"QuantStudio TM 3 Real-Time PCR System" ;
definition: "System designed for users who need easy-to-use real-time PCR system. QuantStudio 3 Real Time PCR System supports 96-well (0.2ml or 0.1ml) or 384-well (QS5 only) consumables. Can detect extremely small changes in gene expression, as little as 1.5-fold. Its dynamic range of up to 10 logs allows for tracking wide range of expression changes across various sample types and conditions. When connected to Thermo Fisher Cloud, QuantStudio 3 system provides access to your data wherever and whenever you want." .
SCR:018713 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Leica_DMI6000_B",
"SCR_020216",
"SCR_020220",
"SCR_020228" ;
rdfs:label "Leica | DMI6000 B inverted microscope" ;
NIFRID:synonym "Leica DMI6000 B",
"Leica DMI6000 B Fully Automated Inverted Research Microscope" ;
definition: "Inverted microscope for biomedical research. Offers Differential Interference Contrast for relief imaging of specimens with varying indices of refraction. Used for fluorescence, live cell, time-lapse imaging, high-speed multi-fluorescence optical sectioning, and micromanipulation. Features automated contrast and illumination manager, motorized Z focus, parfocality function, automatic brightness and diaphragm adjustment, and many other automated functions that provide convenience and reproducible results. Archived Product. Replaced by DMi8 S." .
SCR:018714 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Leica_TCS_SP5_II" ;
rdfs:label "Leica | TCS SP5 II microscope" ;
NIFRID:synonym "Leica TCS SP5 II" ;
definition: "Confocal microscope covers broad range of requirements in confocal and multiphoton imaging with array of scan speeds at highest resolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:018715 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher |GeneAtlas System" ;
NIFRID:synonym "Affymetrix GeneAtlas System",
"GeneAtlas System" ;
definition: "System for processing Affymetrix microarrays. Microarray analysis system. Includes array strip and hybridization assembly, Fluidics station, Imaging station." .
SCR:018716 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NGScloud2" ;
NIFRID:synonym "NGScloud" ;
definition: "Software tool for RNA-seq analysis of non model species using cloud computing. Provides user friendly front end to operate Amazon hardware resources and to control workflows of bioinformatic analysis of de novo RNA-seq, reference-based RNA-seq and functional annotation specifically oriented to plant species." .
SCR:018718 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Affymetrix Transcriptome Analysis Console Software" ;
NIFRID:abbrev "Affymetrix TAC" ;
definition: "Software to generate differential expression analysis and visualization for easy interpretation. Takes normalized and summarized data from Affymetrix Expression Console software to next level, providing differential expression analysis and visualization for easy interpretation." .
SCR:018719 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ARRIVE" ;
NIFRID:synonym "Animal Research: Reporting of In Vivo Experiments" ;
definition: "Guidelines to improve reporting of research using animals by maximizing information published and minimizing unnecessary studies. Guidelines, originally published in PLOS Biology, were developed in consultation with scientific community as part of NC3Rs initiative to improve standard of reporting of research using animals. Can be applied to any area of bioscience research using laboratory animals." .
SCR:018720 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CONSORT" ;
NIFRID:synonym "Consolidated Standards of Reporting Trials" ;
definition: "Standards for transparent trials reporting. Encompasses various initiatives developed by CONSORT Group to alleviate problems arising from inadequate reporting of randomized controlled trials. Main product of CONSORT is CONSORT Statement, which is evidence based, minimum set of recommendations for reporting randomized trials. CONSORT Statement is endorsed by medical journals and leading editorial organizations." .
SCR:018721 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRISMA" ;
NIFRID:synonym "Preferred Reporting Items for Systematic Reviews and Meta-Analyses" ;
definition: "Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions." .
SCR:018722 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCLA Diffraction Anisotropy Server" ;
definition: "Web server to indicate severity of anisotropy in data set. Degree of anisotropy is indicated by anisotropic delta B statistic." .
SCR:018723 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Chinese National Compound Library" ;
NIFRID:abbrev "CNCL" ;
definition: "Library with storage capacity of over million compounds possessing diversified structures. Coupled with this library will be advanced sample handling, information management and quality control systems. As important material and information resource, CNCL will work with both domestic and international stakeholders to promote sustained development of Chinese pharmaceutical industry." .
SCR:018724 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MicroFilePlus" ;
NIFRID:synonym "MicroFile+",
"microfileplus" ;
definition: "Software tool as microscopy image file format converter by MBF Bioscience. Converts common microscopy image files to JPEG2000 and OME-TIFF. Used to view, analyze, and share big image data from many sources." .
SCR:018725 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:MiXCR",
"biotools:MiXCR" ;
rdfs:label "MiXCR" ;
definition: "Software tool to processes big immunome data from raw sequences to quantitated clonotypes by MiLaboratory LLC. Universal software for analysis of T- and B-cell receptor repertoire high throughput sequencing data. Software for comprehensive adaptive immunity profiling." .
SCR:018726 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:graph2go",
"SCR_018727" ;
rdfs:label "Graph2GO" ;
definition: "Software tool as graph based representation learning method for protein function prediction. Multi modal graph based representation learning model that can integrate heterogeneous information including multiple types of interaction networks including sequence similarity network and protein-protein interaction network, and protein features including amino acid sequence, sub cellular location and protein domains, to predict protein functions on Gene Ontology." .
SCR:018728 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TheCellMap" ;
NIFRID:synonym "TheCellMap.org" ;
definition: "Web accessible database for visualizing and mining global yeast genetic interaction network. Allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize sub networks, using data driven network layouts in intuitive and interactive manner. Used for storing and visualizing genetic interactions in S. cerevisiae." .
SCR:018729 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Conserved Domains Search" ;
NIFRID:synonym "CD-search" ;
definition: "Web tool for conserved domains searching within protein or coding nucleotide sequence." .
SCR:018730 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:betavaeimputation" ;
rdfs:label "betaVAEImputation" ;
definition: "Software tool as deep learning framework based on variational autoencoder to impute missing values in transcriptome and methylome data analysis." .
SCR:018731 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:seq-annot" ;
rdfs:label "seq-annot" ;
definition: "Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes." .
SCR:018732 a "software",
owl:NamedIndividual ;
rdfs:label "EEGsynth" ;
definition: "Open source Python codebase that provides real-time interface between open-hardware devices for electrophysiological recordings like EEG, EMG, and ECG, and analog and digital devices like MIDI, OSC, and analog synthesizers. This allows one to use electrical brain/body activity to flexibly control devices in real-time." .
SCR:018733 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:biosimulations" ;
rdfs:label "BioSimulations" ;
definition: "Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell." .
SCR:018734 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "emmeans" ;
NIFRID:synonym "Estimated Marginal Means",
"Least Squares Means" ;
definition: "Software R package to obtain estimated marginal means for linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays." .
SCR:018735 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iMol" ;
definition: "Software molecular visualization application for Mac OS X operating system. Tool for chemists and molecular biologists used for handling small and large molecules, loading multiple molecules, moving and rotating them independently, or displaying molecular dynamics trajectory. Allows loading molecules using file formats: PDB, XYZ, MOL2, HIN, CAR, ALC, BIO." .
SCR:018736 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1018",
"SCR_018744" ;
rdfs:label "Virginia University School of Medicine Advanced Microscopy Core Facility" ;
NIFRID:synonym "University of Virginia UVA Advanced Microscopy Facility",
"UVA Advanced Microscopy Facility" ;
NIFRID:abbrev "AMF" ;
definition: "Advanced Microscopy Facility is microscopy service and shared instrumentation facility in University of Virginia biomedical research community. Pprovides expertise and instrument access for electron and light microscopy imaging technologies as well as image analysis tools and services for basic scientists and clinical researchers within University of Virginia and across Commonwealth." .
SCR:018737 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TIMER" ;
NIFRID:synonym "Tumor IMmune Estimation Resource" ;
definition: "Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features." .
SCR:018738 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FEI MAPS" ;
NIFRID:synonym "FEI MAPS 2.0" ;
definition: "Software tool for automated acquisition of high resolution images from large areas." .
SCR:018739 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:phaseme" ;
rdfs:label "PhaseME" ;
definition: "Software tool set to assess quality of per read phasing information and help to reduce errors during this process." .
SCR:018740 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:prognoscan",
"SCR_018741" ;
rdfs:label "PrognoScan" ;
definition: "Database for meta analysis of prognostic value of genes from server at Kyushu Institute of Technology. Collection of publicly available cancer microarray datasets with clinical annotation, as well as tool for assessing biological relationship between gene expression and prognosis. Provides platform for evaluating potential tumor markers and therapeutic targets." .
SCR:018742 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bioptechs | CFCS2 Instrument" ;
NIFRID:synonym "CFS2",
"Cooled FCS2",
"Cooled Focht Chamber System 2" ;
definition: "Cooled Focht Chamber System 2 designed for live cell imaging. Has same optical and specimen accommodations as standard FCS2 but is modified to include fluid ports in base to accommodate circulation of external refrigerant." .
SCR:018745 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:EVcouplings" ;
rdfs:label "Evolutionary Couplings Server" ;
NIFRID:synonym "EVcouplings" ;
definition: "Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs." .
SCR:018747 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018748" ;
rdfs:label "Limitation-Recognizer" ;
NIFRID:synonym "limitation recognizer",
"limitation-recognizer",
"limitationrecognizer" ;
definition: "Software tool to recognize self acknowledged limitation sentences in biomedical articles. Automatic recognition of self acknowledged limitations in clinical research literature to support efforts in improving research transparency." .
SCR:018749 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FunGene" ;
NIFRID:synonym "FunGene Pipeline" ;
definition: "Functional gene pipeline and repository. Functional gene repository provides collections of genes in interactive platform, while functional gene pipeline offers suite of tools for functional gene amplicon processing and analysis. Together they enable key steps in functional gene based microbial community analysis, from target selection and primer analysis to amplicon processing and ecological discovery." .
SCR:018753 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kaplan Meier Plotter" ;
NIFRID:synonym "Kaplan-Meier Plotter",
"KM plotter" ;
definition: "Web tool for meta analysis based discovery and validation of survival biomarkers. Assesses effect of genes on survival using cancer samples including breast, ovarian, lung, and gastric cancer. Sources for databases include GEO, EGA, and TCGA." .
SCR:018754 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hierarchical Unsupervised Generative Embedding toolbox" ;
NIFRID:synonym "Hierarchical Unsupervised Generative Embedding",
"Hierarchical Unsupervised Generative Embedding (HUGE) toolbox",
"Hierarchical Unsupervised Generative Embedding Toolbox" ;
NIFRID:abbrev "HUGE" ;
definition: "Software toolbox to implement hierarchical extension to dynamic causal models for analyzing task based fMRI data." .
SCR:018755 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "robvis" ;
NIFRID:synonym "Risk Of Bias VISualization" ;
definition: "Software R package and web app, which facilitates rapid production of publication quality risk of bias assessment figures. Used to produce high quality figures that summarize the risk-of-bias assessments performed as part of systematic review or research synthesis project." .
SCR:018756 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:cd-search" ;
rdfs:label "Batch Web CD-Search Tool" ;
NIFRID:synonym "Batch conserved domain search",
"CD-search",
"Conserved Domain Search service",
"NCBI Batch CD Search Tool" ;
definition: "Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence." .
SCR:018757 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013422" ;
rdfs:label "National COVID Cohort Collaborative" ;
NIFRID:abbrev "N3C" ;
definition: "Portal for centralized national data to study COVID-19 and identify potential treatments.Centralized, secure analytics platform where patient privacy is protected. Enables collection and analysis of clinical, laboratory and diagnostic data from hospitals and health care plans. Data are provided after executing data transfer agreement with National Center for Advancing Translational Sciences. N3C is partnership among NCATS supported Clinical and Translational Science Awards Program hubs and National Center for Data to Health with overall stewardship by NCATS." .
SCR:018759 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation" ;
definition: "Portal for quantitative models using virus sequence variation to predict mutation effects for SARS-CoV-2 proteins, alignments to homologs in other viruses, 3D structures, evolutionarily coupled residues and structure predictions." .
SCR:018763 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BALBES " ;
definition: "Software system for solving protein structures using x-ray crystallographic data. Automatic molecular replacement pipeline for molecular replacement in CCP4. Integrates into one system all components necessary for solving crystal structure by Molecular Replacement. System is automated so that it needs no user intervention when running combination of jobs such as model searching, molecular replacement and refinement." .
SCR:018764 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ROSIE" ;
NIFRID:synonym "Rosetta Online Server that Includes Everyone" ;
definition: "Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community." .
SCR:018765 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " XRNA" ;
definition: "Software Java based suite of tools for creation, annotation and display of RNA secondary structure diagrams.Provides editing tools for easy modification of publication quality secondary diagrams that can be either drawn manually, or through automatic generation. Other features include grouping, numbering and structure annotation. Secondary structures may be saved in native format, or exported as postscript for printing and further manipulation in programs such as Adobe Illustrator." .
SCR:018766 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MNE-BIDS" ;
NIFRID:synonym "Minimum Norm current Estimates - Brain Imaging Data Structure" ;
definition: "Software Python package to link Brain Imaging Data Structure and MNE-Python software for analyzing neurophysiology data with goal to make analyses faster to code, more robust to errors, and easily shareable with colleagues. Provides programmable interface for BIDS datasets in electrophysiology with MNE-Python. Used for organizing electrophysiological data into BIDS format and facilitating their analysis." .
SCR:018768 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Random DNA Sequence Generator" ;
definition: "Web application to generate random DNA sequences." .
SCR:018769 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fetal calf serum free database" ;
NIFRID:synonym "FCS-free Database" ;
definition: "Database, part of 3Rs Database Programme, provides overview of FCS free media for cell culture. Forum function for each record allows researchers to discuss applicability of each product. Database is offered by 3Rs-Centre ULS in collaboration with Animal Free Research UK." .
SCR:018770 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DE-Sim" ;
NIFRID:synonym "Discrete Event Simulation",
"object oriented Discrete Event-Simulation tool" ;
definition: "Software object oriented discrete event simulation tool for complex, data driven modeling. Open source, Python based object oriented discrete event simulation tool that makes it easy to use large, heterogeneous datasets and high level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models." .
SCR:018771 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DoubletFinder" ;
definition: "Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data." .
SCR:018772 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PSORT II" ;
NIFRID:synonym "prediction of protein sorting signals and localization sites in amino acid sequencies",
"psort2",
"psort II" ;
definition: "Web tool for prediction of protein sorting signals and localization sites in amino acid sequencies. Recommended for animal/yeast sequences. Analyzes input sequence by applying stored rules for various sequence features of known protein sorting signals to report possiblity for input protein to be localized at each candidate site with additional information." .
SCR:018773 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Science Chain" ;
NIFRID:abbrev "OSC" ;
definition: "Provides data integrity using blockchain. Used for protecting integrity and provenance of research data.Open science chain utilizes distributed ledger technology (consortium blockchain) to securely store information about scientific data including its provenance to enable independent verification of its authenticity to establish trust in the research community." .
SCR:018774 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:ODAM",
"biotools:ODAM" ;
rdfs:label "ODAM" ;
NIFRID:synonym "Open Data for Access and Mining" ;
definition: "Software experimental data table management system to make research data accessible and available for reuse with minimal effort on part of data provider. Allows any scientist or data researcher to be able to explore dataset and then extract some or all of data according to their needs. Designed to manage experimental data tables in quick and easy way for users." .
SCR:018775 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "C-IMMSIM" ;
definition: "Web prediction tool for molecular binding in simulation of immune system. Agent based simulator of immune response that represents pathogens, as well as lymphocytes receptors, by means of their amino acid sequences and makes use of bioinformatics methods for T and B cell epitope prediction.Calculates immune response to generic pathogenic secondary structure. Allows users to submit antigen protein sequence and specify schedule of its injection as well as host haplotype." .
SCR:018776 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Minimum-Hypergeometric Test" ;
NIFRID:abbrev "mHG" ;
definition: "Software R package to run minimum hypergeometric test." .
SCR:018777 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QUARK" ;
definition: "Computer algorithm for ab initio protein structure prediction and protein peptide folding, which aims to construct correct protein 3D model from amino acid sequence only. Server is suitable for proteins that do not have homologous templates in PDB library." .
SCR:018778 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PHD SECONDARY STRUCTURE" ;
definition: "Web tool for secondary structure prediction. Used for network protein sequence analysis." .
SCR:018779 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ANTIGENpro" ;
definition: "Web tool as sequence-based, alignment-free and pathogen-independent predictor of protein antigenicity.Predicts likelihood that protein is protective antigen. Integrated in SCRATCH suite of predictors." .
SCR:018780 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:algpred" ;
rdfs:label "AlgPred" ;
definition: "Web tool for prediction of allergens based on similarity of known epitope with any region of protein. Used for prediction of allergenic proteins and mapping of IgE epitopes." .
SCR:018781 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NetSurfP" ;
NIFRID:synonym "NetSurfP-2.0" ;
definition: "Web tool for prediction of surface accessibility, secondary structure, disorder, and phi/psi dihedral angles of amino acids in amino acid sequence. Used to predict solvent accessibility, secondary structure, structural disorder, and backbone dihedral angles for each residue of input sequences." .
SCR:018782 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Trec | Thomas Motorized Electrode Manipulator" ;
NIFRID:synonym "Thomas Motorized Electrode Manipulator (MEM)",
"Thomas recording - Motorized electrode manipulator" ;
definition: "Driver system for electrode wires or linear electrode arrays. Microdrive system for extracellular recordings by Thomas RECORDING GmbH. Can be used with different conventional extracellular recording electrodes and preamplifier systems. MEM System is adapted to special requirements e.g. MEM holder is customized so that it fits to your stereotaxic instrument." .
SCR:018783 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Plexon | 16-channel digital headstage" ;
NIFRID:synonym "Plexon 16-channel digital headstage (Generation 2)" ;
definition: "Headstage that attaches to 16-channel linear electrode arrays by Plexon Inc. Digitizes analog voltage signals and outputs them to data acquisition systems." .
SCR:018784 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Plexon | 16 channel V-Probe" ;
definition: "Linear electrode array used for intracranial electrophysiological recordings. V-Probe is multi-use, multi-site, linear electrode with recording sites positioned on side of sharpened, symmetric cone by Plexon Inc. Minimizes trauma to brain tissue upon insertion. Durable, highly customizable, and often used in acute research with medium to large animals." .
SCR:018785 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1020" ;
rdfs:label "Indiana University School of Medicine Chemical Genomics Core Facility" ;
NIFRID:synonym "Indiana University at Purdue University Indianapolis IUSM-Chemical Genomics Core Facility",
"IUSM-Chemical Genomics Core Facility" ;
NIFRID:abbrev "CGCF" ;
definition: "Core provides collection of diversity-oriented, drug-like, and natural small molecules in non-redundant libraries, variety of automated liquid handling and assay detection systems such as EnVision Multiplate reader and ArrayScan HCA System, modern equipment for medicinal and analytical chemistry including NMR, LC-QTOF MS, HPLC, Peptide Synthesizer, and sophisticated chemoinformatics tools. Besides traditional high-throughput screening and hit compound optimization services, newly adapted technologies include arrayed CRISPR screening, phage display, and SAR by NMR." .
SCR:018786 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ALOGPS" ;
NIFRID:synonym "ALOGPS 2.1" ;
definition: "Software tool to predict lipophilicity and aqueous solubility of molecules. ALOGPS 2.1 can increase its prediction for molecules up to 5 times LIBRARY mode. You can create and use your own LIBRARY." .
SCR:018787 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PREPARE" ;
NIFRID:synonym "Planning Research and Experimental Procedures on Animals: Recommendations for Excellence",
"PREPARE guidelines" ;
definition: "Guidelines to improve planning of animal experiments. Covers areas which determine quality of preparation for animal studies including formulation, dialogue between scientists and animal facility, and quality control of various components in study.Includes harm–benefit assessment, health risks, waste disposal and decontamination, quarantine and health monitoring,use of humane endpoints, fate of animals like humane killing, release, re-use or re-homing, and necropsy." .
SCR:018788 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Strengthening the Reporting of Observational Studies in Epidemiology (STROBE)",
"STROBE statement" ;
definition: "Guidelines for strengthening reporting of observational studies in epidemiology. International, collaborative initiative of epidemiologists, methodologists, statisticians, researchers and journal editors involved in developing recommendations on what should be included in accurate and complete report of observational study. Recommendations to cover study designs in cohort, case-control, and cross-sectional studies." .
SCR:018789 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AsPredicted" ;
definition: "Website for study pre-registration. Defines minimum required criteria for pre-registration and allows authors to pre-register their study. It is standardized pre-registration that requires only what is necessary to separate exploratory from confirmatory analyses." .
SCR:018790 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018791" ;
rdfs:label "Subcellular App" ;
NIFRID:synonym "Subcellular app",
"Subcellular Application",
"subcellular application" ;
definition: "Web interface for simulation of biological molecular networks. Web based environment for creation and simulation of reaction-diffusion models integrated with molecular repository. Allows to import, combine and simulate existing models expressed with BNGL and SBML languages. Application is integrated with number of solvers for reaction-diffusion systems of equations." .
SCR:018793 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Viral Integrated Structural Evolution Dynamic Database" ;
NIFRID:synonym "SARS-CoV-2 dynamicome database" ;
NIFRID:abbrev "VIStEDD" ;
definition: "Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein." .
SCR:018794 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IST Online" ;
definition: "Database by Medisapiens Ltd. as fully integrated and annotated human gene expression data source. All genes are comparable across all samples. Provides data analysis options using database of human transcriptome." .
SCR:018795 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EVmiRNA" ;
NIFRID:synonym "Extracellular Vesicles miRNA Database" ;
definition: "Collection of comprehensive miRNA expression profiles in extracellular vesicles from tissues. Includes miRNA expression profiles, miRNA regulated pathways, miRNA function, miRNA related drugs and publications to support miRNA biomarker discovery." .
SCR:018796 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:StoatyDive",
"SCR_018800" ;
rdfs:label "StoatyDive" ;
definition: "Software tool to evaluate and classify predicted peak profiles to assess binding specificity of protein to its targets. Can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data." .
SCR:018797 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Simple Assignment of Spots to Surfaces" ;
NIFRID:abbrev "SASS" ;
definition: "Software tool as custom analysis code combining single-cell traces and spot detection from live imaging movies and using Imaris output." .
SCR:018798 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ASSRUnit" ;
NIFRID:synonym "Auditory Steady State Response Unit" ;
definition: "Software tool as module for automated validation and comparison of models of auditory steady state response deficits in psychiatric disorders. Module that integrates databases of experimental studies on ASSR deficits in psychiatric with repository of computational models of these deficits using SciUnit framework." .
SCR:018799 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LE8700TS" ;
rdfs:label "BIOSEB | Treadmill" ;
NIFRID:synonym "Bioseb Treadmill",
"Bioseb Treadmill Model LE8700TS" ;
definition: "Behavioral apparatus to study locomotion. Small animal treadmill used for forced exercise training and accurate testing of fatigue in rodents. Apparatus consists of rolling belt with adjustable speed and slope, and control Unit, enabling forced exercise training and accurate testing of fatigue in rodents." .
SCR:018801 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:tricolor" ;
rdfs:label "TRiCoLOR" ;
definition: "Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments." .
SCR:018802 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chinese Glioma Genome Atlas" ;
NIFRID:abbrev "CGGA" ;
definition: "Web application for data storage and analysis to explore brain tumors datasets from Chinese cohorts. Data portal for storage and interactive exploration of multi-dimensional functional genomic data that includes primary and recurrent glioma samples from Chinese cohorts. Allows users to browse DNA mutation profile, mRNA/microRNA expression profile and methylation profile, and to do correlation and survival analysis in specific glioma subtype." .
SCR:018804 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FALCON" ;
NIFRID:synonym "FALCON@home" ;
definition: "Web tool as high throughput protein structure prediction service. High throughput server for protein structure prediction." .
SCR:018805 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:robetta" ;
rdfs:label "Robetta" ;
definition: "Web tool as protein structure prediction service. Provides automated structure prediction and analysis tools that can be used to infer protein structural information from genomic data. Produces model for entire protein sequence in presence or absence of sequence homology to protein of known structure." .
SCR:018806 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mutation and Patient Database" ;
NIFRID:synonym "NCL Mutation and Patient Database",
"NCL Mutation Database" ;
definition: "Collection of published mutations and sequence variations in genes that cause Neuronal Ceroid Lipofuscinoses together with unpublished data included with permission. There are two tables for each human NCL disease gene - Patient Datasheets list all published or reported patients and families, and Mutation Datasheets list all published or reported mutations, cross-referenced to patient table. Datasheets are available to view or download as excel files for off-site use to aid local needs or interests. Database follows mutation nomenclature recommendations of Human Genome Variation Society." .
SCR:018807 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WEBMAXC EXTENDED" ;
NIFRID:synonym "WEBMAXC Extended" ;
definition: "Web tool for computing metal ion concentrations in physiological solutions. Used for determining free metal concentration in presence of chelators or total metal given desired free concentration." .
SCR:018808 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Revvity | Celigo Imaging Cytometer" ;
definition: "Bench-top microwell plate based image cytometer for adherent and suspension cells." .
SCR:018809 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harmony" ;
NIFRID:synonym "Harmony 4.8" ;
definition: "Harmony high content imaging and analysis software. Used to quantify complex cellular phenotypes. Designed for PerkinElmer high content screening systems." .
SCR:018810 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Perkin Elmer | Operetta CLS" ;
NIFRID:synonym "Operetta CLS system" ;
definition: "High content image acquisition instrument. Automatic cell imaging system designed for quantitative cellular analysis of fixed or live cells. Contains sCMOS camera that provides large field of view and high resolution image capture." .
SCR:018811 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Muscle X" ;
NIFRID:synonym "Muscle X 1.14.12",
"MuscleX" ;
definition: "Software suite as collection of programs intended to assist with analyzing diffraction X-ray images. MuscleX diffraction X-ray image analyzing toolkit. Data reduction software for X-ray fiber diffraction data." .
SCR:018812 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scalable Analytics for Brain Exploration Research" ;
NIFRID:abbrev "SABER",
"saber" ;
definition: "Library of containerized tools and workflow deployment system for enabling processing of large neuroimaging datasets. Provides canonical neuroimaging workflows specified in standard workflow language (CWL), integration with workflow execution engine (Airflow), imaging database (bossDB), and parameter database (Datajoint) to deploy workflows at scale, and tools to automate deployment and optimization of neuroimaging pipelines." .
SCR:018813 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "morphologica" ;
definition: "Software tool as library of supporting code for numerical modelling (JSON config, HDF5 data, Modern OpenGL visualization). This code builds shared library called libmorphologica which contains simulation support facilities for our simulations of dynamical systems." .
SCR:018814 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mousecovid.org" ;
NIFRID:synonym "Global Mouse Models for COVID-19 Consortium" ;
NIFRID:abbrev "GMMCC" ;
definition: "Portal for Global Mouse Models for COVID-19 consortium. Presents consortium, its statement and membership, and URLs for mouse COVID-19 resources worldwide." .
SCR:018815 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AMBER parameter database" ;
NIFRID:synonym "Assisted Model Building with Energy Refinement parameter database" ;
definition: "Assisted model building with energy refinement parameter database. Family of force fields for molecular dynamics of biomolecules. Collection of equations and associated constants designed to reproduce molecular geometry and selected properties of tested structures." .
SCR:018819 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ScienceDynamics" ;
definition: "Software package to support parsing and extracting data from bibliometric datasets." .
SCR:018820 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:clustlasso" ;
rdfs:label "clustLasso" ;
definition: "Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach." .
SCR:018821 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_22" ;
rdfs:label "Vermont University Larner College of Medicine Microscopy Imaging Center Core Facility" ;
NIFRID:synonym "University of Vermont Larner College of Medicine Microscopy Imaging Center",
"UVM - Microscopy Imaging Center",
"Vermont University Larner College of Medicine Microscopy Imaging Center" ;
NIFRID:abbrev "MIC" ;
definition: "Core provides imaging equipment including JEOL 1400 transmission electron microscope with AMT 11 megapixel digital camera,JEOL JSM 6060 scanning electron microscope with attached Oxford INCA energy dispersive spectroscopy detector for element analysis,Nikon Air HD confocal scanning laser microscope, Nikon C2 confocal scanning laser microscope, Andor Spinning Disk confocal microscope, Zeiss LSM 7 Multiphoton confocal microscope, Nikon STORM super-resolution light microscope, Olympus BX50 research microscope for transmitted light, phase contrast, and epi-fluorescence microscopy, Asylum Research MFP-3D BIO atomic force microscope, Asylum Research Cypher Environmental atomic force microscope,Arcturus XT-Ti Laser Capture Microdissector system, Olympus IX70 inverted microscope with associated Applied BioPhysics Electri Cell-Substrate Impedance Sensing (ECIS Ztheta) system, Leica VERSA 8 whole slide imager, Dell workstations containing Molecular Devices MetaMorph image analysis software for complex quantitative image analysis, Indica Labs HALO software, Improvision Volocity, MBR StereoInvestigator." .
SCR:018822 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_67" ;
rdfs:label "Harvard Medical School PCMM Microscopy Core Facility" ;
NIFRID:synonym "BCH/PCMM Microscopy Core",
"Harvard Medical School PCMM Microscopy Core",
"PCMM Microscopy Core" ;
definition: "Core with advanced instrumentation in Light and Electron Microscopy.Core provides confocal, multiphoton microscopy,electron microscopy,image analysis." .
SCR:018823 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_781" ;
rdfs:label "University of Michigan ULAM Pathology Core Facility" ;
NIFRID:synonym "In Vivo Animal Core (IVAC)",
"ULAM In Vivo Animal Core (IVAC)",
"ULAM Pathology Core",
"University of Michigan In Vivo Animal Core Facility" ;
definition: """Our core is affiliated with the Unit for Laboratory Animal Medicine (ULAM) at the University of Michigan-Ann Arbor. We provide animal pathology services in support of non-GLP preclinical, translational, or basic science studies. Services include histology preparation, immunohistochemistry, animal hematology and serum chemistry assays, digital slide scanning/image analysis, and pathology interpretation by board-certified veterinary pathologists. Our core mission is to reduce bias and increase rigor within non-GLP animal research by providing high quality, documented, pathology support that may not be otherwise accessible within individual laboratories. Our laboratory maintains internal SOPs, documented quality control practices, and accountability/chain-of-custody records for all submissions. Additionally, we participate in an external quality control program
through the Veterinary Laboratory Association.""" .
SCR:018824 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_258" ;
rdfs:label "University of Kentucky College of Medicine, Lexington, Pathology Research Core Facility" ;
NIFRID:synonym "Lexington",
"Pathology Research Core",
"UK COCVD Pathology Core",
"University of Kentucky College of Medicine" ;
definition: "Core facilitates COCVD projects by providing equipment and technical expertise to paraffin-embed and section tissue specimens and perform chemical staining of tissue sections to be examined, photographed and analyzed chromogenically by light microscopy.Training in immunohistochemical staining is available." .
SCR:018825 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_260" ;
rdfs:label "Kentucky University, Lexington, Energy Balance and Body Composition Core Facility" ;
NIFRID:synonym "Lexington UK COCVD Energy Balance Core",
"UK COCVD Energy Balance Core",
"University of Kentucky" ;
definition: "Core primary focus is to identify mechanisms linking obesity to cardiovascular disease. Provides equipment and technical expertise for measurement of lean/fat mass and whole body metabolism in mice. Provides equipment for computerized quantitative measurement of oxygen consumption, food intake, water intake, and physical activity in mice.Echo MRI is utilized for non invasive quantitative assessment of lean and fat mass." .
SCR:018826 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_773" ;
rdfs:label "Vanderbilt University Genome Editing Resource Core Facility" ;
NIFRID:synonym "Transgenic Mouse ESC Shared Resource",
"Vanderbilt Genome Editing Resource",
"Vanderbilt University Genome Editing Resource" ;
NIFRID:abbrev "VGER" ;
definition: "Provides services, consultation, and collaborations to enable generation, storage and regeneration of genetically altered mice.Services include CRISPR-Cas9 Mouse Editing, Pronuclear Microinjection of DNAs,Sperm or Embryo Cryopreservation,In vitro Fertilization and Rederivation,Genome-Editing Design and Analysis Services." .
SCR:018827 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_762" ;
rdfs:label "New York University School of Medicine Langone Cytometry and Cell Sorting Core Facility" ;
NIFRID:synonym "Cytometry and Cell Sorting Laboratory",
"New York University Cytometry and Cell Sorting Laboratory" ;
definition: "Facility provides cytometry and cell sorting services. Services include immunophenotyping, cell cycle analysis, and intracellular fluorophore detection. Services can be tailored to research needs, certified cytometrists are available to help plan experiments. Offers online and hands-on training in use of cell analyzers and analysis software." .
SCR:018828 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_274" ;
rdfs:label "University of Nebraska Medical Center Nanoimaging Core Facility" ;
NIFRID:synonym "Nanoimaging Core Facility" ;
definition: "Provides service and expert advice to researches in their projects related to nanoimaging studies of molecular systems at single molecule and single cell levels utilizing Atomic Force Microscope, combination of Atomic Force Microscope with Fluorescence Optical Microscope, combination of Atomic Force Microscope with Raman Spectroscopy." .
SCR:018829 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_421" ;
rdfs:label "Iowa State University Hybridoma Core Facility" ;
NIFRID:synonym "Hybridoma Facility",
"Iowa State University Hybridoma Facility" ;
NIFRID:abbrev "HS" ;
definition: "Core provides services for monoclonal or polyclonal antibodies production,animal immunization, cell fusion and hybridoma culture maintenance, cell culture and maintenance of other cell lines used in biotechnology and virology labs, large scale mammalian cell culture (bioreactor), blood sera collection, antibody purification and isotyping, cryopreservation and cryostorage of cell lines, and ELISA tests." .
SCR:018830 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1021" ;
rdfs:label "University of Nebraska Medical Center Animal Behavior Core Facility" ;
NIFRID:synonym "Animal Behavior Core",
"University of Nebraska Medical Center UNMC Animal Behavior Core",
"UNMC Animal Behavior Core" ;
definition: "Provides investigators with expertise, equipment, and space that is required to conduct innovative acoustic, behavioral, and cognitive research with focus on rigor, reproducibility, and maintaining the highest standards of animal welfare." .
SCR:018831 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:tracespipe" ;
rdfs:label "TRACESPipe" ;
definition: "Software tool as hybrid pipeline for reconstruction and analysis of viral and host genomes at multi-organ level. Pipeline for identification, assembly, and analysis of viral genomes, that combine DNA sequence data from multiple organs. Cooperation between compression based prediction, sequence alignment, and de-novo assembly. Provides transmission and storage of data." .
SCR:018832 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_998" ;
rdfs:label "Virginia Commonwealth University School of Pharmacy Institute for Structural Biology, Drug Discovery and Development Core Facility" ;
NIFRID:synonym "Biophysical Analysis and HT Screening and Imaging facility",
"Drug Discovery and Development Resources",
"""VCU School of Pharmacy
Institute for Structural Biology""" ;
definition: "Core provides services for Molecular Modeling, Biophysical Techniques, X-ray Crystallography, Protein Production,High Throughput Screening. Provided instruments to use after reservation include Clariostar Multimode Plate Reader, Echo 550 Acoustic Liquid Handler, X-Ray Diffractometer." .
SCR:018833 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ADInstruments | PowerLab/4SP acquisition system" ;
NIFRID:synonym "PowerLab/4SP" ;
definition: "Integrated system of hardware and software designed to record, display, and analyse experimental data. Consists of PowerLab recording unit and possible ancillary devices, software that run on computer to which PowerLab is connected. PowerLab/4SP has four inputs for recording external signals." .
SCR:018834 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harvard Apparatus | Inspira Advanced Safety Ventilator, Volume Controlled" ;
NIFRID:synonym "Inspira Advanced Safety Ventilator",
"Volume Controlled" ;
definition: "Volume Controlled Ventilator delivers desired tidal volume to animal by precisely controlling stroke of piston. Since actual stroke length may be modified for given stroke, sigh breaths are supported." .
SCR:018835 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_845" ;
rdfs:label "Maryland University School of Medicine Flow Cytometry and Mass Cytometry Core Facility" ;
NIFRID:synonym "CVD Flow Cytometry and Mass Cytometry Core",
"Maryland University School of Medicine Flow Cytometry and Mass Cytometry Core" ;
definition: "Core provides researchers with flow cytometry and mass cytometry services and equipment and help from highly trained and experienced staff." .
SCR:018836 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_799" ;
rdfs:label "Claflin University Molecular Science Research Center Core Facility" ;
NIFRID:synonym "MOLECULAR SCIENCES RESEARCH LABORATORY" ;
definition: "Core facility is equipped with instrumentation to support proteomic and metabolomic research, as well as equipment for materials characterization. Key instruments include a Bruker 700MHz NMR, two Bruker XRDs (Powder and Crystal), and Bruker Micro ToF mass spectrometer." .
SCR:018838 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus | BX50 microscope" ;
NIFRID:synonym "BX50 fluorescence microscope",
"Olympus BX50 Fluorescence Microscope" ;
definition: "BX50 fluorescence microscope comes with 4 position mercury fluorescence lamphouse and power supply. Filters can be added as needed. Trinocular viewing head allows you to add camera to this system." .
SCR:018840 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018892" ;
rdfs:label "Millar | PCU-2000 Pressure Control Unit with Patient Isolation" ;
NIFRID:synonym "PCU-2000 Dual Channel Pressure Control Unit",
"PCU-2000 Pressure Control Unit" ;
definition: "Pressure Control Unit is two channel, patient isolated, line powered bridge amplifier for connecting one or two single sensor Millar Mikro-Tip catheters to clinical patient monitor or standalone data acquisition system. Provides built in ridge excitation eliminating need for separate bridge amplifier. Analog output signal level of 1V/100 mmHg is compatible with most pressure monitors and data acquisition systems. In line power supply adapts automatically to line voltages from 100 to 240 volts AC." .
SCR:018841 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Molecular Devices | Axoprobe 1A microelectrode amplifier" ;
NIFRID:synonym "AX0PR0BE-1A" ;
definition: "Multipurpose microelectrode amplifier contains two microelectrode amplifiers ME1 and ME2. These amplifiers may be independently used for intracellular and extracellular voltage recording with simultaneous current passing, or for recording with ion sensitive electrodes." .
SCR:018846 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CED | Micro1401-4 data acquisition unit" ;
NIFRID:synonym "Cost effective Data Acquisition Unit (CED)" ;
definition: "Unit records waveform data, digital event and marker information and can simultaneously generate waveform and digital outputs in real time for multi tasking experimental control." .
SCR:018852 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | SP8 DIVE multi photon microscope" ;
NIFRID:synonym "SP8 Deep In Vivo Explorer" ;
NIFRID:abbrev "SP8 DIVE" ;
definition: "Multiphoton confocal microscope with spectrally tunable detection. Equipped with 4Tune, tunable, non descanned detection unit." .
SCR:018857 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nikon | microscope camera DS-Fi3" ;
NIFRID:abbrev "DS-Fi3" ;
definition: "High definition color microscope camera equipped with 5.9 megapixel CMOS image sensor which enables capture of high definition images of up to 2880 x 2048 pixels. Enables various observations such as brightfield, DIC, phase contrast and fluorescence." .
SCR:018860 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sutter | Movable Objective Microscope" ;
NIFRID:synonym "Movable Objective Microscope (MOM)",
"Sutter MOM" ;
NIFRID:abbrev "MOM" ;
definition: "Two photon microscope capable of imaging deep within living specimens when combined with Ti:Sapphire Laser. Provides 3D objective movement and rotation allowing specimen to remain stationary." .
SCR:018863 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Imspector" ;
definition: "Software tool for real time analysis and data visualization. Software system for experimental control and quantitative data analysis in microscopy and spectroscopy.Integration of data processing and acquisition allows real time analysis and visualization of experimental results." .
SCR:018866 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Molecular Devices | Axopatch 200B Patch Clamp Amplifier" ;
NIFRID:synonym "Axon Instruments Patch Clamp Amplifier",
"Axopatch 200B Capacitor Feedback Patch Clamp Amplifier" ;
definition: "Patch clamp amplifiers to minimize signal to noise ratio." .
SCR:018870 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenSCAD" ;
NIFRID:synonym "Solid 3D CAD Modeller" ;
definition: "Software tool for creating solid 3D CAD objects. Used for creating 3D models focusing on CAD aspects of 3D modeling of machine parts. Reads in script file that describes object and renders 3D model from this script file." .
SCR:018875 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Attofluor cell chamber" ;
definition: "Cell chamber with coverslip holder designed for viewing live cell specimens on upright or inverted microscopes. Surgical stainless steel chamber is autoclavable so cells can be grown directly on coverslips within unit. O-ring seal is designed to prevent samples from being contaminated by oil or leakage of media from coverslips. Chamber accepts 25 mm round coverslips and mounts in standard 35 mm diameter stage holder." .
SCR:018876 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_018856" ;
rdfs:label "Zeiss | Axio Imager 2" ;
NIFRID:synonym "Axio Imager 2" ;
definition: "Axio Imager 2 resolves samples from tissue sections in pathology to brain specimens in neuroscience to multi dyed FISH specimens. Works with ZEN imaging software." .
SCR:018877 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:geco3" ;
rdfs:label "GeCo3" ;
definition: "Software tool as DNA compressor that uses neural network to do mixing of experts." .
SCR:018878 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:dicomtypetranslation" ;
rdfs:label "DicomTypeTranslator" ;
definition: "Open source software tool to extract metadata from DICOM files for indexing and storage in SQL database." .
SCR:018879 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:badmedicine" ;
rdfs:label "BadMedicine" ;
definition: "Software library and command line tool for generating realistic looking synthetic Electronic Health Records data for testing purposes." .
SCR:018880 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ribotaper" ;
rdfs:label "RiboTaper" ;
definition: "Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data." .
SCR:018881 a owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:smi_services" ;
rdfs:label "SMI Services" ;
NIFRID:synonym "Scottish Medical Imaging Services" ;
definition: "Software suite of tools for cataloguing and anonymising DICOM files, as used for Scottish Medical Imaging project. Software suite of microservices for loading, anonymising, linking and extracting large volumnes of dicom medical images to support medical research. Platform allows dicom tags extracted from clinical images to be loaded into MongoDB and relational database tables for purposes of generating anonymous linked research extracts including image anonymisation." .
SCR:018882 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Guidelines in cardiovascular research" ;
definition: "Collection of guidelines to encourage rigorous and reproducible research practices for cardiovascular physiology." .
SCR:018883 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1024" ;
rdfs:label "Virginia University School of Medicine Genome Analysis and Technology Core Facility" ;
NIFRID:synonym "Genome Analysis and Technology Core",
"University of Virginia School of Medicine Genome Analysis and Technology Core Facility",
"University of Virginia UVA Genome Analysis and Technology Core",
"UVA Genome Analysis and Technology Core" ;
NIFRID:abbrev "GATC" ;
definition: "Core offers instrumentation and expertise in all areas of bulk and single cell NGS genomics and transcriptomics, as well as training to access core shared instrumentations. Services include RNA Seq, CHIP Seq, ATAC Seq, Amplicon DNA Seq, 16S ribosomal gene sequencing, shot gun sequencing for small genomes and whole exome sequencing.10X Genomics resources include single cell CNV, VDJ, and 3 or 5 RNA seq as well as linked reads.Core provides real time and droplet digital PCR services most suitable for targeted gene expression, SNP genotyping and CNV discovery." .
SCR:018884 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_889" ;
rdfs:label "Medical University of South Carolina College of Dental Medicine Gnotobiotic Animal Core Facility" ;
NIFRID:synonym "Medical University of South Carolina MUSC Gnotobiotic Animal Core",
"MUSC Gnotobiotic Animal Core" ;
NIFRID:abbrev "G-COHR" ;
definition: "Core offers investigators opportunity to address research questions that require use of gnotobiotic animals. Standard services provide germ free mice (e.g. BALB/c, C57BL/6), deriving new strains of mice into germ free state by caesarean section, tissue collection and/or fluid from mice that have not received treatment or manipulations, exporting germ free mice in sterile transporters to other institutions. Non-Standard Services include maintaining and breeding newly derived germ free mice, administration of specialized diets, administration of compounds as therapeutic or disease-inducing agents, tissue collection and/or fluid from mice that have received treatment or manipulations." .
SCR:018885 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_163" ;
rdfs:label "Marshall University School of Medicine Genomics Core Facility" ;
NIFRID:synonym "Marshall University Genomics and Bioinformatics Core Facilities",
"Marshall University Genomics Core Facility",
"MU Genomics Core Facility" ;
definition: "Core provides services including high throughput next generation sequencing (NGS) to support whole genome, whole exome, RNA-Seq, single cell RNA-Seq, microbiome and global chromatin and methylation studies, biostatistical and bioinformatic support for NGS projects, access to DNA/RNA sequence analysis software, automated Sanger DNA sequencing, genotyping and RNA/DNA quality assessment, access to shared instrumentation such as plate readers, real time thermal cyclers, Agilent Bioanalyzers, fluorimeters, and spectrophotometers." .
SCR:018886 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ScanItD" ;
rdfs:label "ScanITD" ;
NIFRID:synonym "Scan Internal Tandem Duplications" ;
definition: "Open source software Python tool for detecting internal tandem duplication with variant allele frequency estimation." .
SCR:018887 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:stamp-metagenomic" ;
rdfs:label "STAMP" ;
NIFRID:synonym "STAMP v2.1.3",
"statistical analysis of taxonomic and functional profiles" ;
definition: "Open source software package for analyzing taxonomic or metabolic profiles that promotes best practices in choosing appropriate statistical techniques and reporting results. Graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. Supports tests for comparing pairs of samples or samples organized into two or more treatment groups." .
SCR:018888 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5666" ;
rdfs:label "University of Melbourne Biological Optical Microscopy Platform (BOMP) Core Facility" ;
NIFRID:synonym "Biological Optical Microscopy Platform" ;
NIFRID:abbrev "BOMP" ;
definition: "Core provides access to fluorescence microscopy equipment including Deltavision OMX Blaze Super Resolution (3D-SIM/SMLM), Leica SP8 inverted confocal, La Vision Ultramicroscope II Lightsheet Microscope,Nikon Andor WD spinning disk, Nikon A1R inverted confocal x2, Olympus FV-MPERS Multi Photon,Olympus FV3000 inverted confocal (live cell) ISS Fast-FLIM, Perkin Elmer Operetta High Content Imaging, Zeiss LSM800 upright Airyscan, Zeiss LSM880 upright Airyscan fast, Zeiss Elyra/LSM880 inverted (live cell), super resolution (Airyscan/SMLM). Staff can help with image analysis, super resolution microscopy, fluorescence lifetime imaging microscopy, high content imaging and light sheet microscopy techniques." .
SCR:018889 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "A.M.P.I. | Master 8 stimulator" ;
NIFRID:synonym "Master-8 EIGHT CHANNEL PROGRAMMABLE PULSE GENERATOR",
"Master-8 Eight Channel Programmable Pulse Generator" ;
definition: "Pulse generator that can hold 8 different pre-programmed paradigms all of which can use up to all 8 channels." .
SCR:018890 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Plexon | PlexStim Electrical Stimulator System" ;
NIFRID:synonym "PLEXON PlexStim Electrical Stimulator System",
"PlexStim Electrical Stimulator System" ;
definition: "Programmable constant current stimulator system with 16 channels." .
SCR:018891 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "A-M SYSTEMS | model 2200 analog stimulus isolator" ;
NIFRID:synonym "A‐M SYSTEMS MODEL 2200 ANALOG STIMULUS ISOLATOR" ;
definition: "Stimulus isolator which does opto-electrical isolation, signal scaling, and signal conversion." .
SCR:018893 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Beckman Coulter | Life Sciences MoFlo Astrios EQ Cell Sorter" ;
NIFRID:synonym "MoFlo Astrios Cell Sorter" ;
definition: "High speed flow cytometry sorter." .
SCR:018894 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Millar | MPVS Ultra Pressure Volume Loop System" ;
NIFRID:synonym "Pressure Volume Loop System" ;
definition: "Pressure volume loop system with seven available volume segments, range of gain settings, integrated internal ECG circuit and dual pressure amplifiers. System can be used in either large or small animal subjects, depending on which size catheter is used." .
SCR:018895 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | DM4000 B Microscope" ;
definition: "Fluorescent microscope which supports fluorescence contrast techniques. This product is archived and has been replaced by the Leica DM4000 B LED." .
SCR:018896 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DM5500_B",
"SCR_020219" ;
rdfs:label "Leica | DM5500 B Automated Upright Microscope System" ;
NIFRID:synonym "Leica DM5500 B Microscope" ;
definition: "Fluorescence microscope capable of contrast microscopy and has ability for fully automated Differential Interference Contrast techniques. This product has been archived and replaced with the Leica DM4 B and DM6 B microscopes." .
SCR:018897 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ripple Neuro | Grapevine Neural Interface Processor" ;
definition: "Interface processor as 512 channel stimulation and recording electrophysiology tool. Designed to be safe for human subjects." .
SCR:018898 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ultimaker Cura" ;
NIFRID:synonym "Ultimaker Cura 3D Printing Software" ;
definition: "Software used for 3D printing, can integrate with CAD software and has variety of custom settings." .
SCR:018900 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Perma Pure | Nafion Fuel Cell Humidifier" ;
NIFRID:synonym "Perma Pure Fuel Cell Humidifier" ;
definition: "FC Series humidifier. Nafion tubing provides consistent, repeatable humidification of air and hydrogen across specified flow range, for portable, stationary, automotive and aerospace applications. Perma Pure Fuel Cell Humidifier features low pressure drop and do not require power to operate." .
SCR:018901 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Repetier Host" ;
NIFRID:synonym "Repetier-Host" ;
definition: "Open source 3D printing software which supports multi part printing and has slicers." .
SCR:018902 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "syngo DynaCT" ;
NIFRID:synonym "Siemens Healthineers syngo DynaCT" ;
definition: "Software tool to construct 3D models of soft tissue using CT-like cross sectional imaging." .
SCR:018903 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IronClust" ;
definition: "Spike sorting software for multi day recordings from high channel count probes during electrophysiology experiments." .
SCR:018904 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:gemb" ;
rdfs:label "GEMB" ;
NIFRID:synonym "Gene Set Enrichment for Mathematical Biology" ;
definition: "Software tool to introduce gene set enrichment for mathematical biology. Measures association between disease of interest and set of genes related to biological pathway. Used for defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict effects of genetic perturbations on particular downstream function." .
SCR:018905 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RatsPub" ;
NIFRID:synonym "Rats.pub",
"rats.pub",
"Relationship with Addiction Through Searches of PubMed" ;
definition: "Web service that conducts comprehensive literature mining to identify roles of genes in addiction. Searches PubMed to find abstracts containing genes of interest and list of curated addiction related keywords." .
SCR:018906 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "The Turing Way" ;
definition: "Open source community driven guide to reproducible, ethical, inclusive and collaborative data science. Provides information that data scientists in academia, industry and government need at start of their projects to ensure that they are easy to reproduce and reuse at the end. Expanded to series of books covering reproducible research, project design, communication, collaboration, and ethical research." .
SCR:018907 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Systematic Review Facility" ;
NIFRID:synonym "CAMARADES Preclinical Systematic Review and Meta analysis Facility",
"Collaborative Approach to Meta-Analysis and Review of Animal Data from Experimental Studies Preclinical Systematic Review" ;
NIFRID:abbrev "SyRF" ;
definition: "Software tool as fully integrated online platform for performing systematic reviews of preclinical studies." .
SCR:018908 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Optimus Pipeline" ;
NIFRID:synonym "Optimus" ;
definition: "Optimus is a pipeline developed by the Data Coordination Platform (DCP) of the Human Cell Atlas (HCA) Project that supports processing of any 3' single-cell and single-nuclei expression data generated with the 10x Genomic v2 or v3 assay. It is an alignment and transcriptome quantification pipeline that corrects cell barcodes, aligns reads to the genome, corrects Unique Molecular Identifiers (UMIs), generates an expression matrix in a UMI-aware manner, calculates summary metrics for genes and cells, detects empty droplets, returns read outputs in BAM format, and returns gene counts in NumPy matrix and Loom matrix formats." .
SCR:018909 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:copydetective" ;
rdfs:label "CopyDetective" ;
definition: "Software tool for detection threshold aware CNV calling in matched whole exome sequencing data." .
SCR:018910 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PAXdb" ;
NIFRID:synonym "PaxDb version 4.0" ;
definition: "Database of protein abundance averages across all three domains of life. Protein abundance database, which contains whole genome protein abundance information across organisms and tissues. Publicly available experimental data are imported and mapped onto common name space and, in case of tandem mass spectrometry data, re-processed using in-house standardized spectral counting pipeline. All datasets in are scored and ranked by importing protein network information. Orthology relations at various hierarchy levels are pre-computed for each protein." .
SCR:018911 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ABCD-ReproNim Course" ;
NIFRID:synonym "Adolescent Brain Cognitive Development ReproNim Course" ;
definition: "Course provides training for reproducible analyses of Adolescent Brain Cognitive Development Study data. Designed to provide comprehensive background to ABCD study while delivering hands on instruction on reproducible ReproNim workflows and outcomes." .
SCR:018912 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:nanogalaxy" ;
rdfs:label "NanoGalaxy" ;
definition: "Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance." .
SCR:018913 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "T2DSystems" ;
NIFRID:synonym "Type 2 Diabetes Systems" ;
definition: "Project to bridge gap between in vitro human islet studies and clinical studies in human subjects. Used to integrate cellular and medical research data, collected by partners, with computational modelling to identify pathophysiological mechanisms and markers of spectrum of biological and cellular processes involved in pancreatic beta cell failure leading to impaired glucose tolerance and T2D." .
SCR:018914 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Diabetic Foot Consortium" ;
NIFRID:abbrev "DFC" ;
definition: "Group of academic institutions committed to studying diabetic foot conditions, such as foot ulcers and wound healing, to develop predictive biomarkers which can be later used to create better treatment plans and improve health and quality of life for people living with diabetes." .
SCR:018915 a owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:spottool",
"DOI:10.5281/zenodo.3873219" ;
rdfs:label "Spot" ;
NIFRID:synonym "Spot: File-based localization of numerical perturbations in data analysis pipelines" ;
definition: "Open source software tool for file based localization of numerical perturbations in data analysis pipelines. Identifies components in pipeline, at resolution level of system process, that produce different results in different execution conditions." .
SCR:018916 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | ASP300S Fully Enclosed Tissue Processor" ;
definition: "Processor that automatically washes tissue sample which needs to be usable in downstream processes. Designed for routine and research histopathology of up to 300 cassettes." .
SCR:018918 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scTHI" ;
definition: "Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment." .
SCR:018919 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scATAC Pipeline" ;
NIFRID:synonym "scATAC",
"single cell ATAC" ;
definition: "Pipeline developed in collaboration with Bing Ren lab and supports processing of BICCN single-cell/nucleus ATAC-seq datasets. Pipeline uses python module SnapTools to align and process paired reads in form of FASTQ files. Produces hdf5-structured Snap file that includes cell-by-bin count matrix. Final outputs also include GA4GH compliant aligned BAM and QC metrics." .
SCR:018920 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Smart-seq2 Multi-Sample Pipeline" ;
definition: "The Smart-seq2 Single Nucleus Multi-Sample (Multi-snSS2) pipeline was developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) to process single-nucleus RNAseq (snRNAseq) data generated by Smart-seq2 assays." .
SCR:018921 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mcule" ;
definition: "Software drug discovery platform to integrate purchasable chemical space with molecular modeling tools. Chemical marketplace for drug discovery with services based around small molecule compound sourcing. Integrated molecular modeling tools, compound database, IT infrastructure and compound procurement service with web interface. Virtual screens can be run to identify new hits and modeling applications can be used to improve their affinity and other properties." .
SCR:018922 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hetindel" ;
definition: "Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels." .
SCR:018923 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Progenesis QI" ;
definition: "Software tool as next generation in LC-MS proteomics data analysis software by Nonlinear Dynamics." .
SCR:018924 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Computational Analysis of gene Family Evolution" ;
NIFRID:synonym "CAFE v2.0",
"CAFE v3.0",
"CAFE v4.0",
"CAFE v5.0" ;
NIFRID:abbrev "CAFE" ;
definition: "Software tool for computational analysis of gene family evolution. Used for statistical analysis of evolution gene family sizes. Models evolution of gene family sizes over phylogeny." .
SCR:018925 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Long Ranger" ;
definition: "Software tool as set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants by 10x Genomics." .
SCR:018926 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SeqKit" ;
definition: "Software tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation." .
SCR:018927 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:seqtk",
"OMICS_09736" ;
rdfs:label "Seqtk" ;
NIFRID:synonym "SEQTK" ;
definition: "Software fast and lightweight tool for processing sequences in FASTA or FASTQ format." .
SCR:018928 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fgenesh plus plus" ;
NIFRID:synonym "FGENESH Plus Plus",
"FGENESH plus plus",
"Fgenesh Plus Plus" ;
definition: "Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software." .
SCR:018929 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mosdepth",
"OMICS_20873" ;
rdfs:label "mosdepth" ;
definition: "Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes." .
SCR:018930 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Trinotate" ;
NIFRID:synonym "Transcriptome Functional Annotation and Analysis" ;
definition: "Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms." .
SCR:018931 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EnhancedVolcano" ;
definition: "Software R package to produce publication ready volcano plots with enhanced colouring and labeling. Used to visualise results of differential expression analyses." .
SCR:018932 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Molecular Devices | SpectraMax 190 microplate reader" ;
NIFRID:synonym "SpectraMax 190 Microplate Reader" ;
definition: """Microplate Reader from Molecular Devices is ideal for UV-Vis life science applications, especially DNA analysis. Multi channel design mimics dual beam spectrophotometer. Each sample has discrete sample beam and reference beam so that each well is
measured directly, eliminating error due to variations in light output between optic fibers. System consists of eight sample
beams and detectors and eight reference beams and detectors to deliver both precision and speed of reading across microplate through 4.0 OD. Detects 16 ng per well of DNA and quantitates 50 ng of DNA.""" .
SCR:018933 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ELDA" ;
NIFRID:synonym "Extreme Limiting Dilution Analysis" ;
definition: "Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly." .
SCR:018934 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FACSAria II",
"SCR_018091" ;
rdfs:label "BD Biosciences | FACSAria II Cell Sorter" ;
NIFRID:synonym "BD Biosciences FACS Aria II Cell Sorter",
"BD FACS Aria II Cell Sorter" ;
definition: "Cell sorter features hardware and software enhancements that improve overall ease of use, flexibility,and aseptic capability. Offers new options in lasers and nozzles to support more advanced multicolor applications. Built on fixed alignment technology. FACSAria II cell sorter is first generation of BD FACSAria system where flow cell is in true fixed alignment with laser, to reduce startup time and improve reproducibility." .
SCR:018935 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RAPIDO" ;
NIFRID:synonym "Rapid Alignment of Proteins in terms of Domains",
"Rapid alignment of proteins in terms of domains" ;
definition: "Web server for alignment of protein structures in presence of conformational changes. Used for 3D alignment of crystal structures of different protein molecules in presence of conformational change. Can identify structurally equivalent regions also when distant in terms of sequence and separated by other movable domains." .
SCR:018936 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PDB-REDO" ;
NIFRID:synonym "PDB_REDO" ;
definition: "Web server for macromolecular structure model optimisation and databank of optimised structure models. Focuses on automating final steps of crystallographic process: optimisation of structure model through refinement, rebuilding, and validation. Can automatically optimise most of crystallographic structure models based on input model and diffraction data. Web server works on user provided data, databank has updated versions of Protein Data Bank entries based on original experimental data that were deposited with atomic coordinates in PDB." .
SCR:018937 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FGENESH Plus" ;
NIFRID:synonym "Fgenesh plus" ;
definition: "Web tool as HMM plus similar protein based gene prediction. Used for multiple gene prediction in genomic DNA with using information from similar protein. Used if you know protein sequence similar with protein which is encoded by gene in your sequence." .
SCR:018938 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCSC Xena" ;
NIFRID:synonym "UCSC Xena Browser",
"Xena Browser" ;
definition: "Web tool where one component is front end Xena Browser and another component is back end Xena Hubs. Web based Xena Browser empowers biologists to explore data across multiple Xena Hubs with variety of visualizations and analyses. Xena Hubs host genomics data from laptops, public servers, behind firewall, or in cloud, and can be public or private. Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into single coherent visualization within browser. Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables." .
SCR:018939 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scPancMeta App" ;
definition: "Portal for islet research community. Data for eight scRNA-seq datasets are combined to give consensus overview of islet cell type defining genes. Tools are provided for interacting with and comparing novel genesets generated." .
SCR:018940 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica QWin" ;
definition: "Software tool as image analysis and processing solution for quantitative microscopy which provides control of Leica microscopes and Leica digital cameras. Capability ranges from simple interactive image measurements to automatic, multi-parameter measurements. Available in editions including QWin Runner, QWin Lite, QWin Plus, QWin Standard and QWin Professional." .
SCR:018941 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DEGreport" ;
definition: "Software R package for creation of HTML report of differential expression analyses of count data. Integrates some of code mentioned in DESeq2 and edgeR vignettes, and reports ranked list of genes according to fold changes mean and variability for each selected gene." .
SCR:018942 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Computational Psychiatry Research Map" ;
NIFRID:synonym "Computational Psychiatry Research Map Database",
"CPSYMAP database" ;
NIFRID:abbrev "CPSYMAP" ;
definition: "Software tool for visualizing research papers from computational psychiatry as two dimensional map. Shows distribution of papers along neuroscientific, psychiatric, and computational dimensions to enable anyone to find niche research and deepen their understanding of the field. Database for visualizing research papers." .
SCR:018943 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automate Scientific | Brain Slice Keeper 4" ;
NIFRID:abbrev "BSK-4" ;
definition: "Slice keeper holds four sets of brain slices and features container with lid and integrated air stone for bubbling carbogen into ACSF, needle valve for adjusting gas flow included, and curved bottom designed to keep bubbles away from slices while promoting fresh solution flow over slices." .
SCR:018944 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FHC | Platinum-Iridium Cluster Bipolar Electrode CE2C55" ;
definition: "Cluster microelectrode for recording or stimulation in chronic applications. Custom Microelectrode Code CE2C55 with Inner Pole Diameter 25 um and Length 50mm." .
SCR:018945 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "A.M.P.I. | ISO-Flex isolator" ;
NIFRID:synonym "ISO-Flex",
"ISO-Flex- The Flexible Stimulus Isolator" ;
definition: "Flexible stimulus isolator since it is optically isolated. Unit can be switched to constant current or constant voltage. You can get bipolar pulses by connecting two isolators." .
SCR:018946 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "A-M SYSTEMS | Model 1800 2-Channel Microelectrode AC Amplifier" ;
definition: "Two channel, differential amplifier by A-M Systems, intended for extracellular recording and/or stimulating with high impedance metal microelectrodes. Used for single cell spike recordings, applications requiring extracellular neurophysiological recording from excitable tissue such as nerve, muscle EMG, EEG, EKG, and ERG recordings. Each channel contains high gain, low noise differential amplifier stage followed by low pass, high pass, and notch filters. Three operating modes are available to accomodate recording, stimulating, and verification of electrode impedance." .
SCR:018947 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NI | PCIe-6321 Multifunction I/O Device" ;
definition: "Digitizer offers analog I/O, digital I/O, and four 32‑bit counters/timers for PWM, encoder, frequency, event counting, and more. Delivers functionality leveraging high throughput PCI Express bus and multicore optimized driver and application software. Suited for broad range of applications, from basic data logging to control and test automation." .
SCR:018949 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus | BX51 Fluorescence Microscope" ;
definition: "Microscope with differential interference contrast ,bright field, dark field components. TR30-2 Trinocular observation head with WH10X 22 eyepieces. 0.5X parfocal C mount camera adapter. Universal reflected and transmitted light stage. Capable of both transmitted and reflected light observations." .
SCR:018950 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus | Compact Stereo Microscope SZ61" ;
NIFRID:synonym "Olympus SZ61",
"Olympus SZ61 Zoom Stereomicroscope" ;
definition: "Standard model SZ61 Zoom Stereomicroscope with magnification range from 6.7x to 45x (using 10x eyepieces), with wide zoom ratio of 6.7:1, enabling macro to micro zooming that speeds routine workflows. Inward angle allows combination of high level flatness and depth of focus for 3D viewing." .
SCR:018951 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1026" ;
rdfs:label "Donald Danforth Plant Science Center Advanced Bioimaging Laboratory Core Facility" ;
NIFRID:synonym "Advanced Bioimaging Laboratory",
"Donald Danforth Plant Science Center Integrated Microscopy Facility" ;
definition: "Core provides instruments for live cell imaging including Leica SP8-X confocal microscope and other fluorescence microscopes. Facility provides workstation for confocal image processing, ancillary equipment required for transmission electron microscopy. Services are provided as self services after user training by IMF staff or as full services done by core facility staff." .
SCR:018952 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1031" ;
rdfs:label "PostGIS" ;
definition: "Software tool as spatial database extender for PostgreSQL object relational database. It adds support for geographic objects." .
SCR:018954 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Culture Collection of Pathogenic Fungi Core Facility" ;
NIFRID:synonym "National Culture Collection of Pathogenic Fungi" ;
NIFRID:abbrev "NCCPF" ;
definition: "National core facility for deposition, maintenance, identification and supply of all pathogenic fungi. Services include depositing cultures, retrieval of same and identification of isolates and more. Facility of international standard for preservation and to handle deposits of medically important fungi and to supply authentic strains to investigators in India. Scientists have access to database of preserved medically important fungi. Will initiate fungal taxonomy research and impart training on taxonomy." .
SCR:018955 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gilson | Minipuls Evolution peristaltic pump" ;
NIFRID:synonym "Perfusion Pump",
"Peristaltic Pump" ;
definition: "Multi channel peristaltic pump for applications with different viscous or abrasive fluids. Allows for channel cartridges, from one to sixteen, to be changed while pump is running." .
SCR:018956 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harvard Apparatus | Single Animal Tabletop Isoflurane Anesthesia System with Small Induction Box" ;
NIFRID:synonym "Anesthesia Chamber",
"Tabletop Anesthesia System" ;
definition: "Tabletop anesthesia system suitable for mice, rats and other small animals under 10 lb. Passive scavenging systems. Funnel fill isoflurane vaporizers." .
SCR:018957 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PPA-Pred2" ;
NIFRID:synonym "Protein-Protein Affinity Predictor 2" ;
definition: "Web server for protein protein affinity prediction. Used for predicting binding affinity of protein protein complexes." .
SCR:018958 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "repro4everyone" ;
NIFRID:synonym "repro4everyone website",
"Reproducibility for Everyone",
"reproducibility for everyone" ;
NIFRID:abbrev "R4E" ;
definition: "Community project portal by team consisting of members of eLife Early Career Advisory Group, Protocols.io, Addgene and Code Ocean, developing resources and teaching workshops to enable researchers to do reproducible research. Collaboration between volunteers in research, industry, and startups in area of reproducibility to make researchers aware of tools that they can use to improve reproducibility of their work." .
SCR:018959 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CPRDLooksups.R" ;
definition: "Software R tool used to identify and retrieve CPRD clinical additional record information such as, smoking, weight/BMI, and medical tests." .
SCR:018960 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CGN Server" ;
NIFRID:synonym "Common Ga Numbering Server" ;
definition: "Web server allows comparing different Ga protein sequences and structures by mapping them to Common Ga Numbering system. Used as superscript for individual positions of specific G protein." .
SCR:018961 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Robot Reviewer" ;
definition: "Software tool as machine learning system that automatically assesses bias in clinical trials. From PDF formatted trial report determines risks of bias for domains defined by Cochrane Risk of Bias (RoB) tool, and extracts supporting text for these judgments." .
SCR:018962 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:corrdrugtumormsi" ;
rdfs:label "CorrDrugTumorMSI" ;
definition: "Software R pipeline to correlate drug distribution with tumor tissue types in mass spectrometry imaging data." .
SCR:018963 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:IMGt_StatClonotype" ;
rdfs:label "IMGT/StatClonotype" ;
NIFRID:synonym "IMGTStatClonotype",
"ImMunoGeneTics/StatClonotype" ;
definition: "Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences." .
SCR:018964 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_10582" ;
rdfs:label "BRAKER" ;
NIFRID:synonym "BRAKER1",
"BRAKER2" ;
definition: "Software tool as pipeline for accurate and automated gene prediction in novel eukaryotic genomes. Automated gene prediction training and gene prediction pipeline.BRAKER1 is eukaryotic genome annotation pipeline. BRAKER2 is extension of BRAKER1 which allows for fully automated training of gene prediction tools GeneMark EX R14, R15, R17, F1 and AUGUSTUS from RNA Seq and/or protein homology information, and that integrates extrinsic evidence from RNA-Seq and protein homology information into prediction." .
SCR:018965 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_28050" ;
rdfs:label "gffread " ;
NIFRID:synonym "General Feature Format Read",
"GFF Read" ;
definition: "Open source software tool to manipulate files in GFF format. Used to convert, sort, filter, transform, or cluster genomic features." .
SCR:018966 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pychopper" ;
NIFRID:synonym "Pychopper v2" ;
definition: "Software tool to identify, orient and trim full length Nanopore cDNA reads. Able to rescue fused reads." .
SCR:018967 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:d-genies" ;
rdfs:label "D-GENIES" ;
NIFRID:synonym "Dot plot large GENomes in an Interactive",
"Efficient and Simple way" ;
definition: "Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file." .
SCR:018968 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:vmatch",
"OMICS_19963" ;
rdfs:label "Vmatch" ;
definition: "Software tool for efficiently solving large scale sequence matching tasks." .
SCR:018969 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:LTR_FINDER_parallel" ;
rdfs:label "LTR_FINDER_parallel" ;
definition: "Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons." .
SCR:018970 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LTRharvest" ;
definition: "Software tool for de novo detection of full length LTR retrotransposons in large sequence sets. Delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs." .
SCR:018971 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GCBI database" ;
NIFRID:synonym "Gene radar" ;
definition: "Database provides information on research status of gene related diseases, gene expression in different tissues, regulatory relationship among genes, information of diseases, mRNA, Transcription Fctor, miRNA and other information shared among genes." .
SCR:018972 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MethylDetectR - Calculate Your Scores" ;
definition: "Web tool for calculating DNA methylation based predictors of human traits and health." .
SCR:018973 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MethylDetectR" ;
definition: "Web translational and research tool for DNA methylation based health profiling." .
SCR:018974 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FastGap" ;
NIFRID:synonym "FastGap 1.2" ;
definition: """Software tool for assembly of DNA sequence alignment files in BioEdit fasta format into NEXUS format ready for analysis in programs such as PAUP or MrBayes. Used to calibrate
gap in sequence after alignment.""" .
SCR:018975 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CaspBase" ;
NIFRID:synonym "Caspase Sequence Database" ;
definition: "Database for evolutionary biochemical studies of caspase functional divergence and ancestral sequence inference. Tool to rapidly disseminate organized caspase sequence data. Includes all animal species with currently available annotated genomes in NCBI genome database. Manually curated and not curated sequences are available to download." .
SCR:018976 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Qiagen | Rotor-Gene Q" ;
NIFRID:synonym "Qiagen Rotor Gene Q",
"Rotor-Gene Q" ;
definition: "Qiagen RT PCR cycler for performance in Real Time PCR. Enables streamlined analysis for wide range of applications." .
SCR:018977 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:GOnet" ;
rdfs:label "GOnet" ;
definition: "Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists." .
SCR:018978 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DirectOverlay" ;
definition: "Software package for display of light microscopy images together with atomic force microscopy images." .
SCR:018979 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:tral" ;
rdfs:label "TRAL" ;
NIFRID:synonym "Tandem Repeat Annotation Library" ;
definition: "Software tool to make annotation of tandem repeats in amino acid and nucleic data simple. Includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs. Used for statistical significance analysis of putative tandem repeats, and filtering of redundant predictions." .
SCR:018980 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Annotree" ;
rdfs:label "Annotree" ;
NIFRID:synonym "AnnoTree 1.2" ;
definition: "Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes." .
SCR:018981 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fitness Browser" ;
definition: "Web tool for browsing genome wide fitness experiments for diverse bacteria from Deutschbauer lab, the Arkin lab, and collaborators. Collection of mutant phenotypes for bacterial genes of unknown function." .
SCR:018982 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Guide Design Resources" ;
definition: "Laboratory portal about research including new approaches for precision gene editing, delivery of molecular and genetic cargo, discovery of novel programmable systems, and engineering of immune system to develop next generation of therapeutics. Provides collection of tools for guide design.CRISPR.MIT.EDU of Guide Design Tools is no longer available, documented on August 28,2020." .
SCR:018983 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "reshape" ;
NIFRID:synonym "reshape 0.8" ;
definition: "Software R package for flexibly restructuring and aggregating data." .
SCR:018984 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1036" ;
rdfs:label "Colorado University at Boulder JILA Keck Lab and Fabrication Core Facility" ;
NIFRID:synonym "JILA Keck Lab and Fabrication Facility",
"""W. M. Keck Optical Measurement Lab
JILA Micro and Nanofabrication Facility""" ;
NIFRID:abbrev "JILA Keck Lab",
"Keck Lab" ;
definition: "Core provides number of specialized measuring tools for optical and surface characterization, as well as expertise in fiber optics.Fabrication facility is clean room for fabrication at micron and nanometer scale. Training and consultation is provided." .
SCR:018985 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1037" ;
rdfs:label "Colorado University at Boulder Shared Instrumentation in Nanofabrication and Characterization Core Facility" ;
NIFRID:synonym "Colorado Shared Instrumentation in Nanofabrication and Characterization" ;
NIFRID:abbrev "COSINC" ;
definition: "Multidisciplinary core research facility and service center, within College of Engineering and Applied Science, that provides access to equipment in areas of micro and nanofabrication, nanomaterials characterization and metrology and offers expertise and advanced hands-on training. Offers common platform for convergence of multiple scientific and engineering disciplines and facilitates collaborative research with strategic partners and information exchange." .
SCR:018986 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1038" ;
rdfs:label "Colorado University at Boulder Biochemistry Shared Instruments Pool Core Facility" ;
NIFRID:synonym "Biochemistry and Shared Instrumentation",
"Biochemistry Shared Instruments Pool" ;
definition: "Provides access to multitude of instruments and techniques, including EPR, CD and fluorescence spectroscopy, DLS, Sec-MALS, ITC, MST, stopped-flow spectroscopy, chemical quench-flow, imaging systems, centrifuges, scintillation counters, sonicators and more." .
SCR:018987 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1039" ;
rdfs:label "Colorado University at Boulder Center for Infrastructure, Energy, and Space Testing Core Facility" ;
NIFRID:synonym "and Space Testing",
"Center for Infrastructure",
"Energy" ;
NIFRID:abbrev "CIEST" ;
definition: "Provides centrally managed experimental testing facility offering geotechnical centrifuge, structural dynamics and materials testing. Facility boasts unique large-scale, fast loading rate, gravitational and environmental control capabilities." .
SCR:018988 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1040" ;
rdfs:label "Colorado University at Boulder Biochemistry Cell Culture Core Facility" ;
NIFRID:synonym "Biochemistry Cell Culture Facility" ;
definition: """Provides investigators within the Department a user-friendly, shared environment where researchers can advance discovery in diverse areas such as cancer biology, drug discovery, nanomaterial analysis and basic life science. Provides Biosafety Cabinets, CO2 Incubators including viral and variable oxygen (tri-gas)
Insect cell incubator and shaker, Large-scale mammalian incubator, Routine mycoplasma testing,FBS testing,Training, In-house media preparation.""" .
SCR:018989 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1043",
"SCR_019027" ;
rdfs:label "Colorado University at Boulder Green Labs Core Facility" ;
NIFRID:synonym "CU Green Labs",
"CU Green Labs Shared Ultra-Low Temperature (ULT) Freezers",
"CU- Boulder Green Labs",
"University of Colorado – Boulder Green Labs" ;
definition: "Core provides help to efficiently use of resources by involving individual laboratory members in identifying opportunities for efficiency in their laboratory and promoting efficient behaviors, upgrading inefficient laboratory equipment and techniques, compelling labs to use lab space, fume hoods, and lab equipment resources efficiently and in collaborative manner, developing means to reduce large flow of lab materials into waste stream, promoting green chemistry and chemical re-use where feasible.Core provides instruments including Shared Stirling Ultracold Ultra Low Temperature Freezer and Shared Thermo Scientific Ultracold Ultra Low Temperature Freezer." .
SCR:018990 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1045" ;
rdfs:label "Colorado University at Boulder Intermountain Neuroimaging Consortium Core Facility" ;
NIFRID:synonym "Intermountain Neuroimaging Consortium" ;
definition: "Magnetic resonance imaging research facility. Provides Tesla Siemens MAGNETOM Prismafit MRI scanner, located at Center for Innovation and Creativity (CINC) on CU Boulder campus." .
SCR:018992 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1044" ;
rdfs:label "Colorado University at Boulder Central Analytical Mass Spectrometry Core Facility" ;
NIFRID:synonym "Central Analytical Mass Spectrometry Laboratory" ;
definition: "Offers analytical and instructional expertise in mass spectrometry with practical training and access to instrumentation.Located in room C1B90 of Jennie Smoly Caruthers Biotechnology Building houses six mass spectrometry systems.Instruments are interfaced with chromatographic system in order to separate complex mixture samples. Offers training for open access to some instruments including Thermo ISO LT GCMS, Synapt G2 HDMS, Agilent 6120 LCMS, and 4000 Q-trap QQQ instruments." .
SCR:018993 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1041" ;
rdfs:label "Colorado University at Boulder Light Microscopy Core Facility" ;
NIFRID:synonym "Light Microscopy Core Facility" ;
definition: "Provides access to instruments and training. Instruments including Dell Precision 7910 Analysis PC,Leica DMRXA Upright Widefield Microscope, Nikon E600 Upright Widefield Microscope, Nikon N-SIM structured illumination super-resolution and A1 laser scanning confocal microscope, Nikon Inverted Spinning Disk Confocal Microscope, Zeiss 510 Laser Scanning Confocal Microscope." .
SCR:018994 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1046" ;
rdfs:label "Colorado University at Boulder Stem Cell Research and Technology Resource Center Core Facility" ;
NIFRID:synonym "CU Boulder Stem Cell Research and Technology Resource Center",
"Stem Cell Research and Technology Resource Center" ;
definition: "Shared facility provides space for culturing human induced plurupotent stem cells on second floor of Porter Biosciences. Provides biosafety cabinets,CO2 and variable oxygen control incubators, inverted phase contrast microscopes, and sterile dissection hood equipped with dissecting microscope and heated stage,inverted fluorescence microscopes with live-cell time-lapse capabilities, centrifuges, liquid nitrogen cryostorage space, refrigerators, freezers, water baths, dedicated bioengineering space, and viral expression core. Routine mycoplasma testing is performed in-house and karyotyping services are carried out via contract." .
SCR:018995 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ULTRA-DD" ;
NIFRID:synonym "Unrestricted Leveraging of Targets for Research Advancement and Drug Discovery" ;
definition: "Project aim is to identify and validate novel targets in auto immune and inflammatory diseases. Used to create and profile target directed chemical and antibody probes in patient cell derived assays, provide biomarker and phenotypic read outs in more disease relevant context." .
SCR:018996 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_019004" ;
rdfs:label "SODA" ;
NIFRID:synonym "Software for Organizing Data Automatically" ;
definition: "Software application intended to simplify dataset curation and submission process for SPARC investigators by providing one stop tool to accomplish all required steps. Desktop software to facilitate data organization and submission process for Stimulating Peripheral Activity to Relieve Conditions (SPARC) investigators and thus promote FAIR Data Principles. Git repository tool for SODA data deposition for SPARC researchers." .
SCR:018997 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "o²S²PARC" ;
NIFRID:synonym "open online Simulation platform for Stimulating Peripheral Activity to Relieve Conditions" ;
NIFRID:abbrev "osparc" ;
definition: "Simulation platform that enables users to create, access, tune, and run models or computational algorithms through web based interface. Web interactive simulation platform that hosts SPARC computational models and solvers. Allows collaborative development and sharing, model coupling and cloud based execution, data visualization and analysis, and ensures sustainability of computational models developed within SPARC. Enables users to create predictive, multiscale, multi-physics models spanning from modulation sources acting on peripheral nervous system (PNS) to resulting modulation of organ functional response." .
SCR:018998 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ApiNATOMY" ;
definition: "Software toolkit for visualizing multiscale anatomy schematics with phenotype related information. Used for visualisation of multiscale physiology circuitboards and to support clinical and scientific graphical user interfaces and dashboards for biomedical resource management and data analytics. Creates FAIR models of vascular and neural connectivity information for molecular, subcellular, cellular and tissue conduits across multiple scales. Provides interface between physiology knowledge and data relevant to physiology through intuitive graphical interface for managing semantic metadata and ontologies relevant to physiology. Brings together expertise in computer science, image processing, bioengineering and medicine to manage knowledge in physiology and pathology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:018999 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pennsieve Data Management Platform" ;
NIFRID:synonym "Blackfynn Data Management Platform" ;
definition: "Open platform that accepts data from peripheral nervous system data. It was previously the Blackfynn data platform. Pennsieve provides advanced functionality to organize files and complex metadata describing datasets and allows users to interact, search, and analyze these data through web application or programmatically using Python client. Provides end-to-end solution for publishing datasets through Pennsieve Discover, assigning DOIs and ensuring that published data becomes available to larger academic community in sustainable and FAIR manner." .
SCR:019001 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenCOR" ;
definition: "Open source cross platform modeling environment for reproducible science. Used to organise, edit, simulate and analyse models described in CellML format, using SED-ML and COMBINE archives." .
SCR:019002 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ScaffoldFitter" ;
definition: "3D scaffold fitting software designed for making connection between 3D scaffold and data in dataset." .
SCR:019003 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ScaffoldMaker" ;
definition: "3D scaffold creation software designed for capturing anatomical features using image data." .
SCR:019007 a NLX:63400,
owl:NamedIndividual ;
NIFRID:abbrev "VMAS" ;
definition: "Software tool to generate whole connected 3D brain ventricular shape model and encode ventricular surface deformation information that is inaccessible by ventricle volume measure. Contains automated segmentation approach and surface based multivariate morphometry statistics." .
SCR:019008 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Real-Time Experimental Control with Graphical User Interface" ;
NIFRID:abbrev "REC-GUI" ;
definition: "Software tool as open source network based parallel processing solution for performing behavioral control, high precision stimulus presentation, and high density neurophysiological measurements. Framework uses network based parallel processing to implement experimental control and synchronize devices." .
SCR:019009 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dandi-cli" ;
NIFRID:synonym "DANDI client",
"Distributed Archives for Neurophysiology Data Integration client" ;
definition: "Command line client to facilitate common operations." .
SCR:019010 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TwoSampleMR" ;
definition: "Software R package for performing Mendelian randomization using genome wide association study summary data." .
SCR:019011 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vesiclepedia" ;
NIFRID:synonym "Vesiclepedia 2019" ;
definition: "Web based database of proteins, RNA, lipids and metabolites that are identified in extracellular vesicles. Compendium for extracellular vesicles with continuous community annotation and with manually curated data from published literature." .
SCR:019012 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GNPS" ;
NIFRID:synonym "Global Natural Products Social Molecular Networking" ;
definition: "Web based mass spectrometry ecosystem that aims to be open access knowledge base for community wide organization and sharing of raw, processed or identified tandem mass spectrometry data. Database of mass spectrometry datasets." .
SCR:019013 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allen Institute Mouse Whole Cortex and Hippocampus SMART-seq" ;
NIFRID:synonym "Mouse Whole Cortex and Hippocampus SMART-seq" ;
definition: "Collection of data set including single cell transcriptomes from multiple cortical areas and hippocampal formation. Samples were collected from dissections of brain regions from 8 week old male and female mice, primarily from pan GABAergic, pan glutamatergic, and pan neuronal transgenic lines, with addition of more specific transgenic lines and some retrogradely labeled cells in VISp and ALM." .
SCR:019014 a NLX:63400,
owl:NamedIndividual .
SCR:019015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hiroshima University Amphibian Research Center" ;
NIFRID:synonym "Amphibian Research Center",
"Institute for Amphibian Biology" ;
NIFRID:abbrev "ARC",
"HUARC" ;
definition: "Stock center that provides amphibian organisms, frogs and newts, primarily to Japanese investigators. The center runs the National BioResource Project (NBRP) Clawed frogs / Newts, which is financially supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, to distribute these resources. Contributes to maintenance of biologically important strains of frogs and study biological characteristics of amphibian focusing genetics, developmental regulation, speciation, phylogeny, phenotype expression, and environment-induced mutagenesis." .
SCR:019017 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "electronic Data Archive Library" ;
NIFRID:synonym "e!DAL" ;
definition: """Software tool as Java based framework to store, share and publish research data. Free software infrastructure to FAIRly maintain and publish in-house stored research data.
Used for version tracking, metadata management, information retrieval, journal and founding agency proven registration of persistent identifiers (DOI), embedded HTTP(S) server for public data access, access as network file system, and scalable storage backend.""" .
SCR:019018 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:clintrajan" ;
rdfs:label "ClinTrajAn" ;
definition: "Software Python package for analysis of trajectories in clinical datasets." .
SCR:019019 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:Enterobase" ;
rdfs:label "EnteroBase" ;
definition: "Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella." .
SCR:019020 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:GigaSOM.jl" ;
rdfs:label "GigaSOM.jl" ;
definition: "Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets." .
SCR:019021 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_468" ;
rdfs:label "Case Western Reserve University Genomics Core Facility" ;
NIFRID:synonym "Case Western Reserve University CWRU Genomics Core",
"CWRU Genomics Core" ;
definition: "Core provides centralized resource working to take difficulty out of Next Generation Sequencing projects for both novice and experienced users alike. Provides assistance in all facets of experimentation from design to data analysis including grant and manuscript preparations.Offers NGS, Sanger, Informatics and Genotyping services based off of Illumina platform." .
SCR:019022 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TargetP" ;
NIFRID:synonym "TargetP-2.0 Server" ;
definition: "Web server predicts presence of N-terminal presequences: signal peptide (SP), mitochondrial transit peptide (mTP), chloroplast transit peptide (cTP) or thylakoid luminal transit peptide (luTP). Predicts potential cleavage site for sequences predicted to contain N-terminal presequence." .
SCR:019023 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mitoprot" ;
definition: "Web server for prediction of mitochondrial targeting sequences." .
SCR:019024 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TCoffee" ;
NIFRID:synonym "T-Coffee" ;
definition: "Web server for simple multiple sequence alignment. Can align protein, DNA and RNA sequences." .
SCR:019025 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:metaxplor" ;
rdfs:label "metaXplor" ;
definition: "Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures." .
SCR:019026 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pyro Oxygen Logger" ;
definition: "Software tool used for setting up PyroScience FireStingO2 (FSO2-4) oxygen meter and calibrating sensors. Measured values are displayed numerically and graphically and can be logged in respective data files for further data processing." .
SCR:019028 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cole-Parmer | Masterflex L/S Variable Speed Digital Drive with Remote I/O peristaltic pump" ;
NIFRID:synonym "6 to 600 rpm; 90 to 260 VAC",
"Masterflex L/S Variable-Speed Digital Drive with Remote I/O" ;
definition: "Peristaltic pump with flow rate 0.06 to 3400 mL/min, three digit LED display, reversible motor, LED indicators to confirm motor direction and speed range from 6 to 600 rpm." .
SCR:019029 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Toolbox for Representational Similarity Analysis" ;
NIFRID:synonym "RSA toolbox" ;
definition: "Software Matlab toolbox to perform representational similarity analysis for neural data." .
SCR:019030 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pyntacle" ;
rdfs:label "Pyntacle" ;
definition: "Software Python package and command line tool for graphs analysis. Used to search for important components of graphs. Implements and provides ancillary methods for community finding, set operations between graphs, and quick data type conversion tools." .
SCR:019031 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1048" ;
rdfs:label "University of Virginia School of Medicine Molecular Electron Microscopy Core Facility" ;
NIFRID:synonym "Molecular Electron Microscopy Core",
"University of Virginia Molecular Electron Microscopy Core",
"UVa-Molecular Electron Microscopy Core" ;
NIFRID:abbrev "MEMC" ;
definition: "Facility dedicated to high resolution electron cryomicroscopy and electron cryotomography. It houses three electron microscopes,120kV Spirit, 200kV F20, and 300kV Titan Krios. These microscopes are available to researchers either for direct use, or aided by MEMC personnel, to collect data aimed at high resolution structural biology projects." .
SCR:019032 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1049" ;
rdfs:label "Sainte-Justine University Hospital Research Center Platform for Imaging by Microscopy Core Facility" ;
NIFRID:synonym "Centre Hospitalier Universitaire Sainte-Justine CHUSJ - PIM Platform for Imaging by Microscopy",
"CHUSJ - PIM Platform for Imaging by Microscopy" ;
NIFRID:abbrev "PIM" ;
definition: "Core offers light microscopy instruments, image analysis tools, consultations and training. Platform for imaging by microscopy." .
SCR:019033 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Infinite_M200_Pro" ;
rdfs:label "Tecan | Infinite M200 Pro Multimode Microplate Reader" ;
NIFRID:synonym "Infinite M200 Pro",
"Tecan Infinite M200 Pro" ;
definition: "Tecan Infinite M200 Pro is multi-detection microplate reader used for biological applications including protein quantification, ELISA, binding studies, DNA quantification, gene expression, immunoassays, toxicity, cell viability, RNA quantification, cell-based and enzyme assays.This modular Tecan plate reader is monochromator based system, with no need for filters, giving range from 230-1000 nm Abs or 300-600nm FI in 1 nm steps. With spectrally enhanced, red-sensitive PMT, the FI range extends to 330-850nm for NIR readings. Modules featured can be Monochromator absorbance, fluorescence top, fluorescence bottom, Luminescence, Incubation, injection, and enhanced photomultiplier tube (PMT) for red sensitivity that brings the detection limit to 45 pM. Please see individual SKU numbers for a list of installed modules. Heating module that’s installed on the microplate reader, allows for the chamber to keep at 37°C for those temperature sensitive samples. Can read microplates from 6 up to 384 well plates, along with PCR plates. Tecan M200 Microplate Reader is driven by Magellan software, which allows you to easily navigate run from start to finish. The user can choose from predetermined assays or build their own from scratch." .
SCR:019034 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CLIP Tool Kit" ;
NIFRID:abbrev "CTK" ;
definition: "Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer." .
SCR:019036 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Rad | Trans-Blot SD Semi-Dry Transfer Cell" ;
NIFRID:synonym "Trans-Blot SD Semi-Dry Transfer Cell" ;
definition: "Transfer cell allows fast, efficient, economical blotting without a buffer tank or gel cassettes." .
SCR:019037 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Rad | ChemiDoc MP Imaging System" ;
NIFRID:synonym "ChemiDoc MP Imaging System",
"Wester Blot Imaging" ;
definition: "Instrument for imaging and analyzing gels and western blots by Bio Rad. Designed to address multiplex fluorescent western blotting, chemiluminescence detection, general gel documentation applications, and stain-free technology imaging needs." .
SCR:019038 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IDseq" ;
NIFRID:synonym "IDseq Portal",
"Infectious Disease Sequencing Platform" ;
definition: "Open source cloud based pipeline and analysis service for metagenomic pathogen detection and monitoring. Hypothesis free global software platform that helps scientists identify pathogens in metagenomic sequencing data. IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes assembly based alignment pipeline which results in assignment of reads and contigs to taxonomic categories." .
SCR:019039 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:vicmpred" ;
rdfs:label "VICMpred" ;
NIFRID:synonym "Cellular process and Metabolism molecule in the bacterial proteins.",
"Information molecule",
"Prediction of Virulence factors" ;
definition: "Software tool as SVM based method for prediction of functional proteins of gram negative bacteria using amino acid patterns and composition. Webserver for functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule." .
SCR:019040 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RAVE" ;
NIFRID:synonym "R Analysis and Visualization of intracranial EEG" ;
definition: "Open source software tool for reproducible analysis and visualization of intracranial EEG data. Used for analysis of intracranial electroencephalogram data, including data collected using strips and grids (electrocorticography, ECoG) and depth electrodes (stereotactic EEG)." .
SCR:019041 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CCP4mg" ;
definition: "Software tool as molecular graphics program designed to give straightforward and complex static and dynamic representations of macromolecular structures. Used to create publication quality images and movies and to superpose and analyse structures." .
SCR:019042 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cello2Go" ;
NIFRID:synonym "subCELlular LOcalization prediction with functional Gene Ontology annotation" ;
definition: "Web server for protein subcellular localization prediction with functional gene ontology annotation. Web based system for screening various properties of targeted protein and its subcellular localization." .
SCR:019043 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PROCHECK" ;
definition: "Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR." .
SCR:019044 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Protein.Plus" ;
definition: "Web server is focused on protein ligand interactions. Provides support for initial steps when dealing with protein structures, namely structure search, quality assessment, and preprocessing. Furthermore, advanced options, such as protein pocket detection, ensemble generation or prediction of metal coordinations are supported." .
SCR:019045 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:fracridge" ;
rdfs:label "fracridge" ;
NIFRID:synonym "fractional ridge regression" ;
definition: "Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python." .
SCR:019046 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Qsonica | Ultrasound Sonicator Q125" ;
NIFRID:synonym "Qsonica Q125",
"Ultrasound Sonicator" ;
definition: "Microprocessor based, programmable ultrasonic processor. Features include pulse mode and digital display of both wattage and joules.Used for standard cell disruption, DNA/RNA shearing, homogenization and many other applications." .
SCR:019047 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | MicroCL 21R microcentrifuge" ;
NIFRID:synonym "MicroCL 21R microcentrifuge" ;
definition: "Refrigerated benchtop microcentrifuge with rotor designed to provide acceleration up to 21,100xg." .
SCR:019048 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1050" ;
rdfs:label "Oregon Health and Science University Medicinal Chemistry Core Facility" ;
NIFRID:synonym "OHSU Medicinal Chemistry Core",
"Oregon Health and Science University OHSU Medicinal Chemistry Core" ;
definition: "Core helps researchers investigate interactions between small molecules and biological systems by providing medicinal chemistry and chemical biology expertise and organic synthesis support." .
SCR:019049 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1051" ;
rdfs:label "Donald Danforth Plant Science Center Phenotyping Core Facility" ;
NIFRID:synonym "DDPSC-Bellwether Phenotyping Facility",
"Donald Danforth Plant Science Center DDPSC-Bellwether Phenotyping Facility" ;
definition: "Core provides instruments including Scanalyzer 3D platform which consists of multiple digital imaging chambers connected to controlled environment Conviron growth house by conveyor belt system, resulting in continuous imaging loop and enables repeatedly image plants at multiple points throughout time.RGB imaging allows visualization and quantification of plant color and structural morphology. Near-infrared (NIR) enables visualization and quantification of plant water-use efficiency.Watering and weighing stations are customizable to deliver water and nutrients on specified schedule by volume or weight. Standard phenotyping services include operation and maintenance of LemnaTec Scanalyzer system, as well as technical support and troubleshooting." .
SCR:019050 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nephroseq" ;
NIFRID:synonym "Nephroseq v5" ;
definition: "Web based gene expression database and analysis platform. Used for integrative data mining of genotype and phenotype data, with optimized workflows." .
SCR:019052 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ,
;
rdfs:label "CueMol" ;
NIFRID:synonym "Que" ;
definition: "Software tool for macromolecular structure visualization. Molecular visualization framework to visualize crystallographic models of macromolecules. Used to visualize and create publication quality images of macromolecular structures with user friendly interfaces." .
SCR:019053 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sklearn" ;
NIFRID:synonym "Scikit-learn",
"scikits.learn" ;
definition: "Software Python package part of nonnegative matrix factorization NMF. Features various classification, regression and clustering algorithms including support vector machines, random forests, gradient boosting, k-means and DBSCAN, and is designed to interoperate with Python numerical and scientific libraries NumPy and SciPy." .
SCR:019054 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dmetar" ;
NIFRID:synonym "Doing Meta Analysis in R",
"Doing Meta-Analysis in R",
"Doing_Meta_Analysis_in_R" ;
definition: "Software package serves as companion R package for online guide Doing Meta-Analysis in R - A Hands-on Guide written by Mathias Harrer, Pim Cuijpers, Toshi Furukawa and David Ebert. Guide shows how to perform meta-analyses in R from scratch with no prior R knowledge required." .
SCR:019055 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "meta" ;
NIFRID:synonym "meta in R" ;
definition: "Software general R package providing standard methods for meta analysis." .
SCR:019056 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ;
rdfs:label "Engauge Digitizer" ;
definition: "Software tool accepts image files (like PNG, JPEG and TIFF) containing graphs, and recovers the data points from those graphs. Used to convert graphs to data points. Imports image file and then digitizes it by placing points along axes and curves." .
SCR:019057 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colorado University at Boulder BioChemistry Krios Electron Microscopy Core Facility" ;
NIFRID:synonym "BioChemistry Krios Electron Microscopy",
"BioChemistry Krios Electron Microscopy facility" ;
NIFRID:abbrev "BioKEM" ;
definition: "Provides single particle cryo EM and cryo tomography of plunge frozen samples. Using Titan Krios G3i for high resolution data collection on Gatan K3 Direct Detection Camera facility is able to offer data collection at atomic level resolution.Facility uses Serial EM for SPA and cryo-ET data acquisition." .
SCR:019058 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:d-ee" ;
rdfs:label "D-EE" ;
definition: "Software tool for distributed dimensionality reduction and visualization. Distributed software for visualizing intrinsic structure of large scale single cell data written in C language. Its distributed storage and distributed computation technique allows efficiently analyze large scale single cell data at cost of constant time speedup." .
SCR:019059 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Urinary Stone Disease Research Network" ;
NIFRID:abbrev "USDRN" ;
definition: "Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies." .
SCR:019060 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1052" ;
rdfs:label "University of North Carolina at Chapel Hill School of Medicine Neuroscience Microscopy Core Facility" ;
NIFRID:synonym "UNC Neuroscience Microscopy Core",
"UNC School of Medicine Neuroscience Microscopy Core Facility",
"University of North Carolina at Chapel Hill UNC Neuroscience Microscopy Core" ;
NIFRID:abbrev "NMC" ;
definition: "Microscopy Core for high resolution imaging and aims to make this technology accessible to neuroscientists and other scientific researchers.Provides advanced systems for cellular and molecular imaging of in vitro and in vivo samples, implements new imaging technologies, particularly related to real time and tissue clearing based imaging of neurodevelopment and neural functions, offers training, consultation, data analysis, image processing, and centralized technical expertise." .
SCR:019061 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PROSPERO" ;
definition: "International database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is health related outcome. Key features from review protocol are recorded and maintained as permanent record. Aims to provide comprehensive listing of systematic reviews registered at inception to help avoid duplication and reduce opportunity for reporting bias by enabling comparison of completed review with what was planned in protocol." .
SCR:019062 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of York, York, England" ;
definition: "Collegiate research university, located in the city of York, England. Established in 1963, the university has expanded to more than thirty departments and centres, covering a wide range of subjects. " .
SCR:019063 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1054" ;
rdfs:label "UMass Amherst Mass Spectrometry Core Facility" ;
NIFRID:synonym "UMass Amherst Mass Spectrometry Core" ;
definition: "Core offers instrumentation for characterizing elements and compounds across the entire mass range. Specialized mass spectrometers encompass variety of ionization techniques and separation devices to cover wide range of analytical capabilities.Facility accepts samples and will perform requested analysis.Offers training to conduct experimentation. Instruments include Bruker SolariX FT-ICR,Bruker MicroTOF II ESI,Bruker MicroFLEX MALDI,JEOL MStation sector with EI and FAB sources." .
SCR:019064 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scayle" ;
NIFRID:synonym "open.scayle.es" ;
definition: "Open source data platform and multidisciplinary online repository where research groups and different organizations store and make public their datasets, managed by Scayle. Collection of public datasets are available through open.scayle.es and can be reused. NetFlow is network protocol developed by Cisco for collection and monitoring of network traffic flow data generated. Netflow datasets have been used to train machine learning models." .
SCR:019071 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Leon, Spain" ;
definition: "Spanish public university with campus in Leon and Ponferrada." .
SCR:019072 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BRO_annotation" ;
definition: "Software tool as tutorial for genome annotation using Augustus and PASA pipelines. Annotation of Hapalochlanea maculosa genome. Contains all scripts and code required to reproduce annotation of Blue Ringed Octopus genome." .
SCR:019073 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ONPRC18 Multimodal MRI Atlas" ;
definition: "Atlas includes co-registered templates constructed from MR images frequently used to characterize macroscopic brain structure T2/SPACE and T1/MP-RAGE, and diffusion tensor imaging template." .
SCR:019074 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012603" ;
rdfs:label "SwissLipids" ;
definition: "Expert curated resource that provides framework for integration of lipid and lipidomic data with biological knowledge and models. Provides curated knowledge of lipid structures and metabolism which is used to generate in silico library of feasible lipid structures. These are arranged in hierarchical classification that links mass spectrometry analytical outputs to all possible lipid structures, metabolic reactions and enzymes. Provides reference namespace for lipidomic data publication, data exploration and hypothesis generation." .
SCR:019075 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LipidLynxX" ;
definition: "Open access tool to convert, cross-match, and link various lipid annotations to tools supporting lipid ontology, pathway, and network analysis aiming systems wide integration and functional annotation of lipidome dynamics in health and disease.Data transfer hub to support integration of large scale lipidomics datasets." .
SCR:019076 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:drivaer" ;
rdfs:label "DrivAER" ;
NIFRID:synonym "Driving transcriptional programs using AutoEncoder based Relevance scores" ;
definition: "Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data." .
SCR:019078 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CFTR2" ;
NIFRID:synonym "cftr2",
"Clinical and Functional TRanslation 2",
"Clinical and Functional TRanslation of CFTR" ;
definition: "International initiative led by team of researchers and clinicians and supported by the US Cystic Fibrosis Foundation that seeks to provide complete, advanced and expert reviewed functional and clinical information on CFTR mutations. Provides information for patients, researchers, and general public about specific variants. For each variant or variant combination included in database, website will provide information about whether variant or variant combination is CF-causing, and information about sweat chloride, lung function, pancreatic status, and Pseudomonas infection rate in patients in CFTR2 database with this variant or variant combination." .
SCR:019079 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lncRNAKB" ;
NIFRID:synonym "long non coding RNA Knowledgebase" ;
definition: "Integrated long non coding RNA knowledgebase to explore lncRNA biology in context of tissue of interest, disease of interest, or simply browse by names. Knowledgebase of tissue specific functional annotation and trait association of long noncoding RNA." .
SCR:019080 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bisulfite Bolt" ;
NIFRID:abbrev "BSBolt" ;
definition: "Software tool as bisulfite sequencing analysis platform. Offers support for bisulfite sequencing read simulation, alignment, methylation calling, data aggregation, and data imputation. Works with array of bisulfite sequencing data,including whole genome bisulfite sequencing, reduced representative bisulfite sequencing data, and targeted methylation sequencing data." .
SCR:019081 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent MassHunter Qualitative Analysis" ;
NIFRID:synonym "MassHunter Qualitative Analysis" ;
definition: "Mass spectrometry screening software for confirmation of target or suspect compounds, and for identification of unknown analytes. Advanced data mining and processing options let find all detectable compounds and confirm targets or identify unknowns. Results can be displayed using data reporting with either preconfigured reports that simplify basic analyses, or completely customized PDF reports." .
SCR:019082 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QuickFigures" ;
definition: "Software package to quickly transform microscope images into quality figures. User friendly tool for creating and formatting scientific figures, can export files into popular softwares like Adobe Illustrator, Microsoft Powerpoint, and Inkscape." .
SCR:019084 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "DataTags Language Tools",
"DataTags toolset" ;
definition: "Software tool to help humans interactively assess artifacts or situations against set of rules. Model consists of n-dimensional space and decision graph that guides users through that space using questions. Open source software tool for DataTags Decision Graph language, used to create questionnaires and tag spaces. Can be used to perform interactive interviews which yield concrete treatment that is both human readable and machine actionable. Models can also be visualized, and can be analyzed to find caveats or loopholes." .
SCR:019085 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_787" ;
rdfs:label "University of Hawaii at Manoa Cancer Center Genomics and Bioinformatics Shared Resource Core Facility" ;
NIFRID:synonym "UHCC Genomics and Bioinformatics Shared Resource",
"University of Hawaii at Manoa UHCC Genomics and Bioinformatics Shared Resource" ;
NIFRID:abbrev "GBSR" ;
definition: "Core offers central service that uses genomic technologies combined with expert data analysis.Provides genomic analyses and bioinformatics as well as technical and scientific consultation,collaboration and initial data interpretation to all UH faculty with priority given to Cancer Center members with federal funding for cancer related projects. Offers expertise in molecular biology, genetics, genomics and bioinformatics, and can provide project planning, advice, and troubleshooting at all phases of the project.Genomic analysis services include DNA/RNA isolation, plating, and quality analysis, custom genotyping, Real-Time qPCR-based gene expression, copy number and methylation assays, pyrosequencing, Affymetrix and Illumina microarray based assays,Next Generation Sequencing on NextSeq500, iSeq100, NanoString nCounter analysis." .
SCR:019086 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1057" ;
rdfs:label "University of British Columbia NeuroImaging and NeuroComputation Centre Core Facility" ;
NIFRID:synonym "UBC NeuroImaging-NeuroComputation Centre",
"University of British Columbia UBC NeuroImaging-NeuroComputation Centre" ;
NIFRID:abbrev "NINC" ;
definition: "Core facility at Djavad Mowafaghian Centre for Brain Health located at University of British Columbia Hospital on Point Grey campus in Vancouver, BC. NINC offers access to advanced imaging systems and computational resources including confocal and two photon microscopes,live cell imaging, optical coherence tomography, training students and researchers in neuroscience research techniques." .
SCR:019087 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "git-annex" ;
definition: "Software tool to allow managing files with git, without checking file contents into git. While that may seem paradoxical, it is useful when dealing with files larger than git can currently easily handle, whether due to limitations in memory, time, or disk space." .
SCR:019088 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:e-crisp" ;
rdfs:label "E-CRISP" ;
definition: "Web application to design gRNA sequences. Uses algorithms to identify sgRNA target sequences in any nucleotide sequence for use in CRISPR/Cas mediated genome editing. Used for fast CRISPR target site identification. Enables designing of multiple libraries and creates genome scale libraries for several organisms in few hours." .
SCR:019089 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "datasets.datalad.org" ;
definition: "DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data." .
SCR:019091 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HADDOCK" ;
NIFRID:synonym "HADDOCK2.2",
"HADDOCK2.4",
"High Ambiguity Driven protein-protein DOCKing" ;
definition: """Software tool as information driven flexible docking approach for modeling of biomolecular complexes.User friendly integrative modeling of biomolecular complexes.HADDOCK v 2.2
offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in user friendly interface.""" .
SCR:019092 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "T2DiACoD" ;
NIFRID:synonym "Type 2 Diabetes Mellitus Associated Complex Disorders" ;
definition: "Gene atlas of Type 2 Diabetes Mellitus associated complex disorders. Provides curated and integrated information about genes involved in development and progression of Type 2 Diabetes Mellitus, genes and pathways with evidence for role in diabetes under risk factors including obesity, diet, inflammation, stress and complex disorders that are associated with Type 2 Diabetes Mellitus including atherosclerosis, diabetic retinopathy, diabetic nephropathy, diabetic neuropathy, cardiovascular disease." .
SCR:019093 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SC2diseases" ;
definition: "Manually curated database of single cell transcriptome for human diseases. scRNA-seq database derived from numerous human studies. Provides researchers with encyclopedia of biomarkers at level of genes, cells, and diseases." .
SCR:019094 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BiostaTGV" ;
definition: "Portal provides table of statistical hypothesis tests accessible to anyone wishing to do statistical calculations. All calculations available on this site are carried out using R statistics software." .
SCR:019095 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DinoCapture" ;
NIFRID:synonym "DinoCapture 2.0" ;
definition: "Video capture software for Dino-Lite USB camera/microscopes. Works with Dino-Lite USB products." .
SCR:019097 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COVID-19 Data Discovery from Clinical Records" ;
NIFRID:synonym "Covid-19 Clinical Data Consult" ;
definition: "Resource for questions and answers about COVID-19.Electronic health record data from leading medical centers to answer clinical questions related to COVID-19 while maintaining patient and institutional privacy. Data never leaves medical centers, only aggregate statistics are exchanged." .
SCR:019099 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Power Analysis and Sample Size software" ;
NIFRID:synonym "PASS 2020",
"Power Analysis and Sample Size" ;
NIFRID:abbrev "PASS" ;
definition: "Sample size software for clinical trial, pharmaceutical, and other medical research where sample size calculation or evaluation is needed. Provides sample size tools for statistical test and confidence interval scenarios. Each tool has been validated with published articles and texts." .
SCR:019100 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " NEMAR" ;
NIFRID:synonym "NEuroelectroMagnetic data Archive and tools Resource" ;
definition: "Portal for human electrophysiological data, supports, sharing and in depth analysis of identified human neuroelectromagnetic brain data including scalp EEG, its magnetic counterpart, MEG, and, intracranial iEEG and ECoG. Open access EEG and MEG data archives, analysis, and visualization. Neuroelectromagnetic data, tools, and compute resource." .
SCR:019101 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CAIRN" ;
NIFRID:synonym "Copy Alterations Intuitive Rendering Navigator" ;
definition: "Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions." .
SCR:019102 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FairSubset" ;
definition: "Web tool to choose representative subsets of data for use with replicates or groups of different sample sizes. Used to retain distribution information at single datum level and may be considered for standardized use in fair publishing practices." .
SCR:019103 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ensembldb" ;
rdfs:label "ensembldb" ;
NIFRID:synonym "ensembldb v2.6.8" ;
definition: "Software R package to create and use Ensembl based annotation resources." .
SCR:019104 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:riborex" ;
rdfs:label "riborex" ;
NIFRID:synonym "riborex v2.3.4" ;
definition: "Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency." .
SCR:019105 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COVID-19 Data Repository" ;
definition: "Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings." .
SCR:019106 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012693" ;
rdfs:label "OpenICPSR" ;
NIFRID:synonym "Inter-university Consortium for Political and Social Research" ;
definition: "Web service of Inter-university Consortium for Political and Social Research. Self-publishing repository for social, behavioral, and health sciences research data. Used for deposit of replication data sets for researchers who need to publish their raw data associated with journal article so that other researchers can replicate their findings." .
SCR:019107 a NLX:63400,
owl:NamedIndividual .
SCR:019108 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FluorTools" ;
NIFRID:synonym "FluorTools.com" ;
definition: "Provides data analysis software for spectroscopy and imaging. Includes FRETmatrix software, a|e software, DecayFit software and AniFit software." .
SCR:019109 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Proteome Software" ;
definition: "Company provides analytics software tools for mass spectrometry. Proteomics and metabolomics software tools for mass spectrometry analysis." .
SCR:019110 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:runbiosimulations" ;
rdfs:label "runBioSimulations" ;
definition: "Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource." .
SCR:019111 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:biosimulators" ;
rdfs:label "BioSimulators" ;
definition: "Web tool as collection of containerized biosimulation tools that provide consistent interfaces and guide to choosing simulator. Helps to find simulation tools that have capabilities, including supported modeling frameworks, simulation algorithms, and modeling formats, needed for specific modeling projects." .
SCR:019112 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:amplicontagger",
"SCR_019113" ;
rdfs:label "AmpliconTagger" ;
definition: "Software tool as rRNA marker gene amplicon pipeline coded in python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. Designed to work within HPC environment, supporting complex network of job dependencies with smart restart mechanism in case of job failure or parameter modifications." .
SCR:019114 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Network-Based R-Statistics" ;
NIFRID:abbrev "NBR" ;
definition: "Software tool as implementation of network based statistics toolbox in R. Includes mixed effects models." .
SCR:019115 a "Research",
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1063" ;
rdfs:label "University of Zurich Center for Microscopy and Image Analysis Core Facility" ;
NIFRID:synonym "Center for Microscopy and Image Analysis",
"University of Zurich Center for Microscopy and Image Analysis" ;
NIFRID:abbrev "ZMB" ;
definition: "Advanced imaging facility providing various imaging techniques in microscopy. Focus is on techniques, instrumentation and know-how in electron and light microscopy including preparation." .
SCR:019116 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:long-read-tools" ;
rdfs:label "long-read-tools" ;
NIFRID:synonym "Long-Read-Tools",
"long-read-tools.org" ;
definition: "Interactive database of software tools for analysis of long read sequencing data.Catalogue of long-read sequencing data analysis tools. Catalogue of downstream analysis tools of real and synthetic long-read technologies." .
SCR:019118 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Warsaw International Institute of Molecular and Cell Biology Core Facility" ;
NIFRID:synonym "International Institute of Molecular and Cell Biology in Warsaw" ;
definition: "Core provides services in bioimaging and high throughput screening, structural biology, mass spectrometry, biomolecular analytics, cell biology and genomics." .
SCR:019119 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_646" ;
rdfs:label "University of Florida ICBR Cytometry Core Facility" ;
NIFRID:synonym "UF ICBR Cytometry",
"University of Florida UF ICBR Cytometry" ;
NIFRID:abbrev "ICBR Cytometry" ;
definition: "Cytometry core offers project consulting, experimental design and optimization as well as data analysis services. Provides tools and staff expertise for both live and fixed cell analysis. Provides FACS ARIA and SONY SH800 sorters to help users sort cells of interest. Offers microscopes for self service users. Microscope brands include Leica SP5 Confocal, Nikon Multiphoton Confocal system, Nikon Live cell Imaging platform, Olympus spinning Disk Confocal instruments, Keyence BZX800." .
SCR:019120 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_645" ;
rdfs:label "University of Florida ICBR Bioinformatics Core Facility" ;
NIFRID:synonym "UF ICBR Bioinformatics",
"University of Florida UF ICBR Bioinformatics" ;
definition: """Core offers bioinformatics consulting and data analysis services to help researchers analyze and understand large data sets acquired from next generation sequencing and array based technologies.Bioinformatics staff members have extensive experience in bioinformatics, genomics, transcriptomics and translational informatics in plant, animal and microbial systems. Expertise includes big data analysis, statistical analysis, software development and high performance computing.
""" .
SCR:019121 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tracer" ;
NIFRID:synonym "Tracer v1.6",
"Tracer v1.7.1" ;
definition: "Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more." .
SCR:019122 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tree analysis using New Technology" ;
NIFRID:synonym "TNT version 1.5" ;
NIFRID:abbrev "TNT" ;
definition: "Software tool for phylogenetic analysis under parsimony as well as extensive tree handling and diagnosis capabilities." .
SCR:019123 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pavo" ;
NIFRID:synonym "PAVO",
"PAVO 2",
"pavo 2",
"Perceptual Analysis",
"Visualization and Organization of Spectral Colour Data" ;
definition: "Software R package for perceptual analysis, visualization and organization of spectral colour data. Software framework for parsing, analyzing and organizing colour from spectral data. Used for spectral and spatial analysis of color patterns." .
SCR:019124 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cvequality" ;
definition: "Software R package contains functions to test for significant differences in coefficients of variation among multiple groups of observations." .
SCR:019125 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Modern Applied Statistics with S" ;
NIFRID:abbrev "MASS" ;
definition: """Software R package to support functions and datasets for Venables and Ripley MASS.
Used for statistical and graphical analysis of data.""" .
SCR:019126 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "PRIMER-e" ;
definition: "Commercial organization provides software PRIMER and PERMANOVA for multivariate analysis. PRIMER v7 used for range of univariate, graphical and multivariate routines for analysing arrays of species by samples data from community ecology." .
SCR:019127 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100014074" ;
rdfs:label "NCI Imaging Data Commons" ;
NIFRID:synonym "National Cancer Institute Imaging Data Commons" ;
NIFRID:abbrev "NCI IDC" ;
definition: "Portal for finding and analyzing cancer imaging data. Part of Cancer Research Data Commons to support cancer imaging research. Provides cloud based access to medical imaging data and library of analytical tools and workflows to share, analyze, and visualize multi modal imaging data from both clinical and basic cancer research studies." .
SCR:019128 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cancer Research Data Commons" ;
NIFRID:synonym "NCI Cancer Research Data Commons",
"NCI CRDC" ;
NIFRID:abbrev "CRDC" ;
definition: "Cloud based data science infrastructure that provides secure access to cancer research data from NCI programs and key external cancer programs. Serves as coordinated resource for public data sharing of NCI funded programs. Users can explore and use analytical and visualization tools for data analysis. Enables to search and aggregate data across repositories including Cancer Data Service, Clinical Trial Data Commons, Genomic Data Commons, Imaging Data Commons, Integrated Canine Data Commons, Proteomic Data Commons." .
SCR:019129 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PAST" ;
NIFRID:synonym "PAleontological STatistics",
"PAST 4.03" ;
definition: "Software package for education and data analysis. Used for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy." .
SCR:019130 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:big_slice" ;
rdfs:label "BiG-SLiCE" ;
NIFRID:synonym "Biosynthetic Gene clusters - Super Linear Clustering Engine" ;
definition: "Software tool to perform large scale clustering analysis of Biosynthetic Gene Cluster data." .
SCR:019131 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenTaR" ;
definition: "System that consists of Application Programming Interface which controls access to information stored in database, and web interface that provides way of interacting with data stored in GenTaR database. Users can track production and phenotyping of different types of mutant allele. Allows consortia to follow progress made in characterising set of genes that they are interested in. To create new project or plan, or to view consortium gene list in GenTaR credentials to log into GenTaR are required. Project search box enables to look for projects working on specific gene by entering gene symbol or gene MGI accession identifier. Search results without logging in will only include public data. Otherwise application search results also include data for Protected and Restricted projects." .
SCR:019132 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:gmove" ;
rdfs:label "Gmove" ;
NIFRID:synonym "Gene MOdeling using Various Evidence" ;
definition: "Software tool for genome annotation. Eukaryotic gene prediction tool focused on evidence supported by expressed sequences like transcripts and conserved proteins alignments. Can be used to reannotate genomes, to do comparative gene prediction and improve existing genome annotation. Can predict gene models with canonical and non-canonical splice sites." .
SCR:019133 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LAMA" ;
NIFRID:synonym "Lightweight Analysis of Morphological Abnormalities" ;
definition: "Open source pipeline to automatically identify embryo dysmorphology from 3D volumetric images. Automated image analysis for developmental phenotyping of mouse embryos." .
SCR:019134 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaBAT" ;
NIFRID:synonym "MetaBAT2" ;
definition: "Software statistical framework for reconstructing genomes from metagenome data. Open source software tool for accurately reconstructing single genomes from complex microbial communities." .
SCR:019135 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_10468" ;
rdfs:label "Mash" ;
definition: "Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated." .
SCR:019136 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:GtDb-tk" ;
rdfs:label "GTDB-Tk" ;
NIFRID:synonym "Genome Database Taxonomy-Tk",
"GTDB-Tk v1.3.0" ;
definition: "Open source software tool for assigning objective taxonomic classifications to bacterial and archaeal genomes based on Genome Database Taxonomy. Designed to work with recent advances that allow metagenome assembled genomes to be obtained directly from environmental samples. Can also be applied to isolate and single cell genomes." .
SCR:019137 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "elNemo" ;
NIFRID:synonym "elastic Network model",
"elNémo" ;
definition: "Web interface to Elastic Network Model that provides tool for computing, visualizing and analysing low frequency normal modes of macromolecule. Normal mode web server for protein movement analysis and generation of templates for molecular replacement with no upper limit to protein size that can be treated. Input of protein structure is in Protein Data Bank format." .
SCR:019138 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RIKEN BDR Laboratory for Animal Resources and Genetic Engineering Core Facility" ;
NIFRID:synonym "Laboratory for Animal Resources and Genetic Engineering",
"LARGE",
"RIKEN BDR LARGE",
"Riken Center for Biosystems Research Laboratory for Animal Resources and Genetic Engineering" ;
definition: "Integrates advanced reproductive and developmental biology technologies. Environment for animal research experiments through innovative research in development of novel experimental animal models and related technical support activities. Manages SPF rodent facility at RIKEN Kobe Campus and accommodates variety of animal research needs, including animal material and resource support, technical training, and education for proper conduct of animal research. Provides established colonies of Soricomorpha species, suncus (Suncus murinus), metatherian species, gray short-tail opossum (Monodelphis domestica), and reptilian species, gecko (Paroedura picta) for prospective distribution services of these new resources to research community. Generates and distributes novel genetically engineered mice with domestic and international biomedical research community, as well as conducting original research projects in live imaging and analyses of early mouse development." .
SCR:019139 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhyloPic" ;
definition: "Silhouette images of animals, plants, and other life forms, available for reuse. Database stores reusable silhouette images and phylogenetic taxonomy of all organisms. Each image is associated with one or more taxonomic names and indicates roughly what ancestral member of each taxon looked like." .
SCR:019140 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neutron Scattering Length and Cross Sections" ;
definition: """Web tool for thermal neutron cross sections. Data of scattering lengths and corresponding scattering and absorption cross sections of elements. Data go through element number
96Cm. Used for study of condensed matter structure and dynamics.""" .
SCR:019141 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1070" ;
rdfs:label "Cardiff University Central Biotechnology Services Core Facility" ;
NIFRID:synonym "Central Biotechnology Services",
"CU-Central Biotechnology Services" ;
definition: "Core provides facilities including cell analysis and imaging, genomics and bioinformatics, proteins and diagnostics. Services include experimental design advice, sample preparation,data generation,data analysis." .
SCR:019142 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iGenomics" ;
definition: "Mobile genome analysis application, with capabilities to align reads, call variants, and visualize results entirely on iOS device. Optimized to run in mobile environment and has performance comparable to popular desktop genomics software." .
SCR:019143 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Prescription Drug Monitoring Programs" ;
NIFRID:synonym "PDMPs",
"Prescription Drug Monitoring Program" ;
NIFRID:abbrev "PDMP" ;
definition: "Electronic database that tracks controlled substance prescriptions in state. PDMPs can provide health authorities timely information about prescribing and patient behaviors that contribute to epidemic and facilitate nimble and targeted response. This public tool is used for drug overdose monitoring from Centers for Disease Control and Prevention." .
SCR:019144 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nurses Health Study" ;
NIFRID:synonym "Nurses study" ;
definition: "Portal about prospective investigations into risk factors for major chronic diseases in women. Nurses were selected as study population because of their knowledge about health and their ability to provide complete and accurate information regarding various diseases, due to their nursing education.The largest longitudinal study of women. Started in 1976, involving 275000 participants." .
SCR:019145 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_647" ;
rdfs:label "University of Florida ICBR Gene Expression and Genotyping Core Facility" ;
NIFRID:synonym "UF ICBR Gene Expression & Genotyping",
"University of Florida ICBR Gene Expression and Genotyping" ;
definition: "Core provides services and consultation on Single Cell RNA-Seq, RNA-Seq, 16s metagenomics and Affymetrix gene expression arrays. High-throughput RNA-seq libraries, 16s libraries and sequencing capture libraries can be done by using Agilent Bravo robot. QuantiGene RNA Assays measure up to 80 gene targets directly with degraded and cross-linked RNA in FFPE tissues and blood, with no RNA purification required.BioRad QX200 AutoDG Droplet Digital PCR System provides absolute quantification of target DNA or RNA molecules with greater precision and sensitivity than qPCR, sensitivity off ddPCR System can facilitate expanded analysis of single cells. Genotyping services include fragment analysis using AB3730, 96 capillary technology, development of microsatellite libraries using Illumina sequence data, and genotyping using mouse tails or ear punches." .
SCR:019146 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_648" ;
rdfs:label "University of Florida ICBR Electron Microscopy Core Facility" ;
NIFRID:synonym "UF ICBR Electron Microscopy",
"University of Florida UF ICBR Electron Microscopy" ;
definition: "ICBR Electron Microscopy supports researchers in visualizing microscopic structures through imaging projects and user training. Provided serives include room temperature and cryo transmission and scanning electron microscopy, confocal laser scanning microscopy, sample preparation and user training." .
SCR:019147 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_649" ;
rdfs:label "University of Florida ICBR Monoclonal Antibody Core Facility" ;
NIFRID:synonym "UF ICBR Monoclonal Antibody",
"University of Florida UF ICBR Monoclonal Antibody" ;
definition: "Core develops new mouse monoclonal antibodies for investigators to use in basic and applied research.Provided services include immunization of mice, cell fusion, cell cloning, screening by ELISA and Western blot, monoclonal antibody production, purification and labeling, monoclonal antibody analyses such as antibody/antigen affinity measurements, epitope binning and identification of matched antibody pairs. Customer training on select self-service instruments is also offered." .
SCR:019148 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Differential Methylation Analysis Package" ;
NIFRID:abbrev "DMAP" ;
definition: "Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity." .
SCR:019149 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dadasnake" ;
definition: "Software tool as snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology." .
SCR:019150 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Collaborative on Childhood Obesity Research" ;
NIFRID:abbrev "NCCOR" ;
definition: "Brings together Centers for Disease Control and Prevention, National Institutes of Health, Robert Wood Johnson Foundation, and U.S. Department of Agriculture to accelerate progress in reducing childhood obesity in America, to manage projects and reach common goals, to coordinate funding to make the most of available resources, to share insights and expertise to strengthen research. NCCOR focuses on efforts that have to benefit children, teens, and their families, and communities in which they live." .
SCR:019151 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_651" ;
rdfs:label "University of Florida ICBR Proteomics and Mass Spectrometry Core Facility" ;
NIFRID:synonym "ICBR Proteomics and Mass Spectrometry Facility",
"ICBR-Proteomics",
"UF ICBR Proteomics and Mass Spectrometry" ;
definition: "Provides service and training in proteomics and mass spectrometry. Services in proteomics, differential proteomics, two dimensional difference gel electrophoresis, isobaric tags for relative and absolute quantitation, tandem mass tags, iodoTMT, stable isotope labeling with amino acids in cell culture, quantification of proteins by label-free LC-MS/MS, and analysis of protein post translational modifications and molecular weight determination. Core offers education, consultation, data processing and reporting, and support of grant application." .
SCR:019152 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_650" ;
rdfs:label "University of Florida ICBR NextGen DNA Sequencing Core Facility" ;
NIFRID:synonym "UF ICBR NextGen DNA Sequencing",
"University of Florida UF ICBR NextGen DNA Sequencing" ;
NIFRID:abbrev "ICBR-NGS" ;
definition: "Core provides platforms including Illumina NextSeq500 and MiSeq, HiSeq3000 and Pacific Biosciences SEQUEL system. Offers free consultation in sequencing technologies including read length, error rate, predominant type of error, data output/run, speed, cost. Services include de novo sequencing of whole genomes, targeted sequencing, transcriptome sequencing, chromatin immunoprecipitation sequencing, methylation analysis and metagenomics." .
SCR:019153 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1073" ;
rdfs:label "University of Heidelberg Interdisciplinary Neurobehavioral Core Facility" ;
NIFRID:synonym "Interdisciplinary Neurobehavioral Core",
"Interdisciplinary Neurobehavioral Core INBC" ;
NIFRID:abbrev "INBC" ;
definition: "Multidisciplinary in vivo core facility equipped with equipment for detailed behavioral analyses and surgical procedures in context of mouse and rat models of neurological, cognitive and psychiatric disorders.Services include Behavioral analyses, Cognitive function,learning and memory, Sensory motor function, Emotional function and social interactions,Pain sensitivity tests, Disease models, Viral gene delivery, stereotactic and surgical manipulations, Optogenetics, In vivo electrophysiology." .
SCR:019155 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_019161" ;
rdfs:label "Akoya inForm Tissue Analysis Software" ;
NIFRID:synonym "inForm",
"inForm 2",
"inForm 2.4.10",
"inForm Tissue Analysis Software" ;
definition: "Automated image analysis software package for accurately visualizing and quantifying biomarkers in tissue sections. Designed to meet workflow and throughput needs of research pathology, oncology, immunology. Used for tissue analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:019156 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_019160" ;
rdfs:label "Phenochart" ;
NIFRID:synonym "Phenochart 1.0.12" ;
definition: "Software tool as whole slide viewer for slides scanned with Vectra Polaris and Vectra 3 ., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:019157 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SoftWoRx software" ;
NIFRID:synonym "softWoRx 6.5.2",
"softWoRx 7.0" ;
definition: "Software for acquisition, deconvolution, processing, analysis, and display of DeltaVision images. Used in DeltaVision OMX SR imaging system., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:019158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fragon" ;
definition: "Software tool for rapid high resolution structure determination from ideal protein fragments. Pipeline to determine crystal structures using molecular replacement with small fragments followed by density modification. It is available through CCP4." .
SCR:019159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Australian Government Data Portal" ;
definition: "Portal as central source of Australian open government data. Used to find, explore and reuse Australia public data. Anyone can access the anonymised public data published by federal, state and local government agencies, publicly funded research data and datasets from private institutions that are in public interest." .
SCR:019162 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NSW BioNet" ;
NIFRID:synonym "New South Wales BioNet" ;
definition: "Repository for biodiversity data products managed by Department of Planning, Industry and Environment, New South Wales, Australia. It stores species sightings, systematic surveys, threatened biodiversity records and species names." .
SCR:019163 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ICEDIG Digital Specimen Repository" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 14, 2023. Repository of specimen in European Union associated with DISScO project." .
SCR:019164 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pm4ngs" ;
rdfs:label "PM4NGS" ;
NIFRID:synonym "Project Manager for Next Generation Sequencing" ;
definition: "Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution." .
SCR:019165 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dartmouth Geisel School of Medicine Immunoassay and Flow Cytometry Core Facility" ;
NIFRID:synonym "DartLab Immune Monitoring and Flow Cytometry Shared Resource",
"Dartmouth College Geisel School of Medicine DartLab",
"Dartmouth DartLab",
"Geisel School of Medicine at Dartmouth DartLab Immune Monitoring and Flow Cytometry Shared Resource" .
SCR:019166 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_172" ;
rdfs:label "Mount Desert Island Biological Laboratory Light Microscopy Core Facility" ;
NIFRID:synonym "Light Microscopy Facility MDIBL",
"MDIBL Light Microscopy Facility" ;
NIFRID:abbrev "LMF MDIBL" ;
definition: "Core provides professional scientific expertise in light microscopy. Offers access to hardware and software as well as expert guidance at any step of imaging project, from experimental design to image analysis.Comprises eight microscope systems including two laser scanning confocal microscopes including one Olympus inverted confocal microscope system (FV1000) and one Zeiss inverted confocal microscope system (LSM-980) equipped with Airy scan 2 for super resolution and 2-photon technology for in-vivo deep imaging with temperature controlled chamber. One spinning disk confocal including Nikon inverted spinning disk microscope system with incubation chamber (Eclipse Ti with Yokogawa disk CSU-W1), two Zeiss widefield microscopes for brightfield and epifluorescence illumination (Zeiss Apotome and Zeiss Colibri), three macroscopes systems to observe large samples or complete model organisms in brightfield and epifluorescence including one Olympus stereomicroscope system (MVX10) and two Zeiss stereomicroscope systems (SteREO Discovery V12), fully automated and one AxioZoom V16 , fully automated with ApoTome attachment." .
SCR:019167 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_393" ;
rdfs:label "UMass Medical School Media Prep Core Facility" ;
NIFRID:synonym "UMass Media Prep Core" ;
definition: "Provides custom made microbiological media for bacteria,yeast,C.elegans,Chlamydamonas research in liquid and agar forms. Common lab buffers and solutions are also available." .
SCR:019168 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_522" ;
rdfs:label "University of Michigan Medical School Bioinformatics Core" ;
NIFRID:synonym "Bioinformatics Core",
"UMMS Bioinformatics Core" ;
definition: "Core helps researchers identify and interpret patterns in RNA and DNA by placing sequencing data into biologically meaningful context. Services include experimental design, developing reproducible workflows, analyzing next-generation sequencing data, and supporting manuscript development/publication." .
SCR:019169 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_539" ;
rdfs:label "Rutgers New Jersey Medical School Molecular Resource Core Facility" ;
NIFRID:synonym "Molecular Resource Facility",
"Rutgers University at Newark Molecular Resource Facility" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2022. Provides services in molecular biology with DNA sequencing, capillary and high throughput services, single cell sequencing services using 10X genomics and Drop-Seq platforms, Luminex, oligonucleotide synthesis (IDT), HPLC analysis and purification, real time PCR and others." .
SCR:019170 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_606",
"SCR_010999" ;
rdfs:label "University of North Carolina at Chapel Hill Flow Cytometry Core Facility" ;
NIFRID:synonym "UNC Flow Cytometry Core Facility",
"UNC School of Medicine Flow Cytometry Core Facility" ;
NIFRID:abbrev "FlowCore" ;
definition: "Core provides flow cytometry services to UNCCH research community as well as to others in Research Triangle Park area.Provides help with experimental design, sample acquisition, data analysis, and sorting, training to run analyzers independently at reduced cost, guidance about rigor and reproducibility in all aspects of experimental design, data acquisition, analysis and reporting." .
SCR:019171 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_679" ;
rdfs:label "University of Chicago Transgenic and ES Cell Technology Mouse Core Facility" ;
NIFRID:synonym "Transgenic and ES Cell Technology Core (Mouse)",
"Transgenic Mouse and Embryonic Stem Cell Facility" ;
definition: "Provides investigators with genetically manipulated mice through transgenic technology or embryonic stem cell manipulation. Provides fully operational construction and gene targeting service. Offers annual course in Mouse Handling and Breeding. Provides transgenic plasmid and BAC, CRISPR and TARGATT injections, ES Cell targeting, screening, culture and blastocyst injections, rederivation, breeding and mouse services and consultation on project development." .
SCR:019172 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_750" ;
rdfs:label "University of Kentucky College of Medicine Protein Core Facility" ;
NIFRID:synonym "UK Protein Core",
"University of Kentucky Lexington UK Protein Core" ;
definition: "Core provides nanobodies production for research as well as protein production, purification, and macromolecular characterization. Offers training on all instruments and equipment, as well as higher level of assistance when projects warrant." .
SCR:019173 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_591" ;
rdfs:label "University of Miami Center for Advanced Microscopy Core Facility" ;
NIFRID:synonym "University of Miami Center for Advanced Microscopy (UMCAM)" ;
NIFRID:abbrev "UMCAM" ;
definition: "Provides scanning electron microscopy services including biological tissues and cells,and particulate characterization." .
SCR:019174 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_664" ;
rdfs:label "Boise State University Biomolecular Research Center Core Facility" ;
NIFRID:synonym "The Biomolecular Research Center" ;
NIFRID:abbrev "BRC" ;
definition: "Designed to provide supportive environment for interdisciplinary research and education with opportunities for students and faculty members alike with focus on biomolecules study with emphasis on proteins and protein interactions. Provides instrumentation and facilities for characterization of biomolecules and their role in variety of biomedical and environmental processes. Partnerships between Center and Idaho-BRIN/INBRE, UI, ISU, Boise VA Medical Center, College of Idaho, and Northwest Nazarene University. BRC provides seminars, training workshops, and other networking opportunities." .
SCR:019175 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1075" ;
rdfs:label "University of Alberta Faculty of Medicine and Dentistry Transgenic Core Facility" ;
NIFRID:synonym "Faculty of Medicine and Dentistry Transgenic Core" ;
definition: "Core provides mouse transgenic and cryopreservation services including Sperm cryopreservation, Mouse in vitro fertilization, Mouse Rederivation, Transgenic Mouse Generation,DNA microinjection,CRISPR/Cas9-Mediated Genetically Engineered Mouse Production. Core equipment includes Hamilton Thorne Computer-Aided Sperm Analysis System,Sutter Xenoworks Micromanipulator,Sutter Xenoworks Digital Microinjector,Nikon TE2000 inverted microscope,MINC benchtop incubator,Leica M165 dissecting microscope." .
SCR:019176 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1076" ;
rdfs:label "University of Alberta Faculty of Medicine and Dentistry Lipidomics Core Facility" ;
NIFRID:synonym "Faculty of Medicine and Dentistry Lipidomics Core",
"University of Alberta Lipidomics Core Facility" ;
definition: "Core assists researchers in isolating and quantifying lipids and lipid related molecules in experimental samples.Core uses high performance liquid chromatography, gas chromatography, and fast protein liquid chromatography for both qualitative and quantitative analysis of lipids and lipoproteins, as well as other compounds by special request.Not-for-profit, pay-per-use facility, with graduated fee schedule based on client affiliation." .
SCR:019177 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_770" ;
rdfs:label "Massachusetts Institute of Technology Koch Institute Histology Core Facility" ;
NIFRID:synonym "Histology Core at KI-MIT",
"Koch Institute at MIT Histology Facility",
"Massachusetts Institute of Technology Koch Institute at MIT Histology Core Facility",
"MIT Koch Institute Histology Core Facility" ;
definition: "Core assists in producing quality histological slides.Provides equipment and expertise to produce sections from frozen, paraffin-embedded, and resin-embedded tissues,routine hematoxylin and eosin stained slides, immunohistochemical and special stains.Registration to iLab required." .
SCR:019178 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_819" ;
rdfs:label "New York University Grossman School of Medicine Applied Bioinformatics Laboratories Facility" ;
NIFRID:synonym "Applied Bioinformatics Laboratories" ;
definition: "Core provides computational analysis for high throughput genomic data, including but not limited to, next generation sequencing data. Our mission is to accelerate scientific discoveries by guiding experimental design, performing robust data quality assessment, and carrying out comprehensive computational analyses. Registration to iLab required." .
SCR:019179 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_821" ;
rdfs:label "New York University Grossman School of Medicine Langone Health Cytometry and Cell Sorting Laboratory Core Facility" ;
NIFRID:synonym "Cytometry and Cell Sorting Laboratory" ;
definition: "Provides access to flow cytometry and cell sorting technologies and instruments. If your research requires cytometric analysis, instruments acquire optical measurements using different lasers to detect fluorophores with high level of precision." .
SCR:019180 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1058" ;
rdfs:label "University of Alberta Faculty of Medicine and Dentistry Autoclave Repair Core Facility" ;
NIFRID:synonym "Faculty of Medicine and Dentistry Autoclave Repair Core" ;
definition: "Core provides on-site repair and maintenance services for autoclaves and laboratory washers.Core is also responsible, in collaboration with Environment, Health and Safety, for temperature probe calibrations of autoclaves located in FoMD enhanced biocontainment facilities." .
SCR:019181 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1074" ;
rdfs:label "University of Alberta Faculty of Medicine and Dentistry Workshop Core Facility" ;
NIFRID:synonym "Faculty of Medicine and Dentistry Workshop" ;
definition: "Core provides services, including repair of lab equipment and biosafety cabinets, metal and acrylic fabrication, woodworking, welding, machining, and calibration of pipets." .
SCR:019182 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1078" ;
rdfs:label "University of Alberta Faculty of Medicine and Dentistry High Content Analysis Core Facility" ;
NIFRID:synonym "Faculty of Medicine and Dentistry High Content Analysis Core" ;
NIFRID:abbrev "FoMD HCA" ;
definition: "Core houses equipment to manage and automate large-scale experiments in areas such as drug discovery and single cell analysis. From sample processing and liquid handling to quantitative analysis of sequencing, imaging, and fluorescent data, core offers high throughput methods for screening needs." .
SCR:019183 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Chimpanzee Brain Resource" ;
NIFRID:abbrev "NCBR" ;
definition: "Collection and distribution of chimpanzee neuroimaging data and postmortem brain tissue. Portal to access chimpanzee brain atlas tools, data repository, bibliography of publications, educational information, and links to other chimpanzee brain resources and datasets on the Internet. Serves as repository for in vivo structural MRI scans of chimpanzee brains, in vivo and postmortem diffusion tensor images (DTI), as well as postmortem fixed and frozen brain specimens." .
SCR:019184 a owl:NamedIndividual ;
rdfs:label "Computational Anatomy Toolbox for SPM" ;
NIFRID:synonym "CAT12" ;
NIFRID:abbrev "CAT" ;
definition: "Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry." .
SCR:019185 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openxlsx" ;
NIFRID:synonym "openxlsx 4.2.3" ;
definition: "Software R package to simplify creation of .xlsx files by providing high level interface to writing, styling and editing worksheets." .
SCR:019186 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tidyverse" ;
NIFRID:synonym "tidyverse 1.3.0" ;
definition: "Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses." .
SCR:019187 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:parliament2" ;
rdfs:label "Parliament2" ;
definition: """Software tool to identify structural variants in given sample relative to reference genome.
Runs combination of tools to generate structural variant calls on whole genome sequencing data.""" .
SCR:019188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPHERE" ;
NIFRID:synonym "Server Program for Hydrogen Exchange Rate Estimation" ;
definition: "Web service for Hydrogen exchange rate estimation. Predicts peptide amide hydrogen exchange rates using correction factors and empirical rates." .
SCR:019189 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Poulsen IDP/IUP random coil chemical shifts" ;
definition: "Web tool to calculate random coil chemical shifts for any protein sequence." .
SCR:019190 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ObjectJ" ;
definition: "Software tool used for non destructive marking and linked results in ImageJ. Integrates image analysis across many images or stacks into single project file." .
SCR:019191 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Research Diets | BioDAQ E3 food intake monitoring system" ;
NIFRID:synonym "Research Diets BioDAQ (E3) food intake monitoring system" ;
NIFRID:abbrev "BioDAQ E3" ;
definition: "BioDAQ E3 by Research Diets Inc., features automated gate controller to program gate to open or close at specified time when specified amount of food or liquid is consumed." .
SCR:019192 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DISCOVERY WORKBENCH" ;
NIFRID:synonym "DISCOVERY WORKBENCH v 4.0" ;
definition: "Software tool for acquiring and analyzing assay data using MSD instruments. Version 4.0 includes features designed to increase efficiency and improve data quality. Tools for plate layout and experimental design simplify workflows. Enhanced functions for data analysis and visualization make generating reports and presentations easy." .
SCR:019193 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:soupx" ;
rdfs:label "SoupX" ;
definition: "Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data." .
SCR:019194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Shiny Volcano Plot" ;
definition: "Software R tool that allows user to upload data and visualize it in user friendly interface." .
SCR:019195 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1080" ;
rdfs:label "University of Alberta Faculty of Medicine and Dentistry Flow Cytometry Core Facility" ;
NIFRID:synonym "Faculty of Medicine and Dentistry Flow Cytometry Facility" ;
definition: "Flow Cytometry Facility offers analytical flow cytometry, cell sorting and data analysis.Instruments include FACSArias, FACSCanto II, LSR-Fortessas, Attune NxT, and Amnis ImageStream mkII." .
SCR:019196 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1082" ;
rdfs:label "University of Chicago Functional Genomics Core Facility" ;
NIFRID:synonym "Functional Genomics" ;
definition: "Facility offers Next-Gen Illumina and Pacific Biosciences Sequencing and Library prep services, Micro-array Illumina genotyping and EPIC arrays services, Sanger DNA Sequencing, and Bioanalyzer/Fragment analyzer sample QC services. For Single Cell sequencing project Facility operates DROP-SEQ and 10X Genomics instrument., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:019197 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1083" ;
rdfs:label "University of Chicago Integrated Light Microscopy Core Facility" ;
NIFRID:synonym "Integrated Light Microscopy" ;
definition: "Offers microscopy imaging, including bright field color and DIC, fluorescence multi-dimension,TIRFM including bleaching, ablation, FLIM and high resolution, highspeed, high sensitivity, confocal, and physiologic techniques, STED, GSD3D, lightsheet selective plane illumination and lattice lightsheet structured illumination super resolution microscopy." .
SCR:019198 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1084" ;
rdfs:label "University of Chicago Advanced Electron Microscopy Core Facility" ;
NIFRID:synonym "Advanced Electron Microscopy" ;
definition: "Offers instruments including Titan Krios with Gatan K3 detector, Aquilos Cryo-DualBeam system, Apreo Volume Scope Serial Blockface SEM, FEI Talos Cryo-EM." .
SCR:019199 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1085" ;
rdfs:label "University of Chicago Human Tissue Resource Center Core Facility" ;
NIFRID:synonym "Human Tissue Resource Center" ;
definition: "Coordinated, centralized, and dedicated program for procuring, processing, dispersing and assessing all types of biospecimens together with downstream histology services. CAP Accredited." .
SCR:019200 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1081" ;
rdfs:label "University of Alberta Faculty of Medicine and Dentistry Cell Imaging Centre Core Facility" ;
NIFRID:synonym "Faculty of Medicine and Dentistry Cell Imaging Centre" ;
NIFRID:abbrev "FoMD" ;
definition: "Cell Imaging Centre provides services and training for imaging and analysis of live or fixed cells and tissues.Image acquisition equipment and expert consultation for experimental design related to light and electron microscopy are offered, with full technical assistance, from sample processing through image analysis." .
SCR:019201 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1088" ;
rdfs:label "University of Chicago Cellular and Tissue Based Processing cGMP Core Facility" ;
NIFRID:synonym "Cellular & Tissue Based Processing cGMP Facility" ;
definition: "Facility to manufacture cell based products and clinical grade reagents for treatment of patients on Phase I, II and III clinical trials. Cleanroom environment for manufacturing and preparing human cells, tissues and tissue based products. CAP Accredited." .
SCR:019202 a "Open",
owl:NamedIndividual ;
rdfs:label "New York University School of Medicine Langone Health Cryo-Electron Microscopy Laboratory Core Facility" ;
NIFRID:synonym "New York University School of Medicine Langone Health Cryo-Electron Microscopy Laboratory" ;
definition: "Shared resource hosting advanced cryo–electron microscopes fitted with direct detectors as well as equipment for sample preparation." .
SCR:019203 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ATCC STR database" ;
NIFRID:synonym "Short Tandem Repeat database",
"STR database" ;
definition: "Comprehensive database of Short Tandem Repeat DNA profiles for all of ATCC human cell lines. ATCC data collection as part of continuing efforts to characterize and authenticate cell lines in Cell Biology collection." .
SCR:019204 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:variancepartition" ;
rdfs:label "variancePartition" ;
definition: "Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays." .
SCR:019205 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Flywire.ai" ;
NIFRID:synonym "FlyWire" ;
definition: "Online community for whole brain connectomics.Game like platform open to all to help crowdsource first complete wiring diagram of centralized brain. In fruit fly brain sliced and imaged by electron microscopy, we identified pieces of neurons by artificial intelligence. Players search for right pieces and put together 3D neurons that advance understanding of brain circuits. Enables circuit analysis by reconstructing and analysing connectome of mechanosensory neurons." .
SCR:019206 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MSQuant" ;
definition: "Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine." .
SCR:019207 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Numbat" ;
NIFRID:synonym "Numbat Systematic Review Manager" ;
definition: "Software tool for managing extraction of large volumes of data from primary sources among multiple users, and then reconciling differences between them. Designed for use in systematic review projects in academic context." .
SCR:019208 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Galactic" ;
NIFRID:synonym "Galactic AI" ;
definition: "Platform of Biorelate to all auto curated data captured from millions of textual articles. Galactic lets you build intuitive queries and explore results through different views that best suit your research needs.Used by pharmaceutical and biotech companies to explore auto curated knowledge from millions of text sources, revealing hidden insights that might otherwise be lost." .
SCR:019209 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Editage" ;
definition: "Web service for all stages of manuscript writing and publication. Offers Translation services where manuscript will be converted to English by translators ,Publication Support services to assist with journal selection and journal submission, manuscript editing." .
SCR:019210 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1092" ;
rdfs:label "University of California at Los Angeles Lipidomics Lab Core Facility" ;
NIFRID:synonym "Los Angeles UCLA Lipidomics Lab",
"UCLA Lipidomics Lab",
"University of California" ;
definition: "Offers automated sample preparation and two distinct mass spectrometry platforms with services, ranging from shotgun lipidomics to isotope labeling and mathematical modeling of lipid flux parameters.Offers data analysis and consultation services to provide users with accurate analysis of lipid metabolic parameters." .
SCR:019211 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Trial Registration Number screener" ;
NIFRID:synonym "Trial registration number screener" ;
NIFRID:abbrev "TRNscreener" ;
definition: "Software tool as R script to provide function that takes two arguments: path to folder of plain text files named by their DOI, and output filename. For each file in folder, it searches for trial identifiers based on regex matching and writes CSV that contains all trial registration numbers and in case of ClinicalTrials.gov entries, whether they correspond to registry entry on ClinicalTrials.gov." .
SCR:019212 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:genomic_annotation_in_livestock_for_positional_candidate_loci_gallo" ;
rdfs:label "Genomic Annotation in Livestock for positional candidate LOci" ;
NIFRID:abbrev "GALLO" ;
definition: "Software R package developed for accurate annotation of genes and quantitative trait loci located in regions identified in common genomic analyses performed in livestock, such as Genome Wide Association Studies and transcriptomics using RNA-Sequencing. Allows graphical visualization of gene and QTL annotation results, data comparison among different grouping factors like methods, breeds, tissues, statistical models, studies and QTL enrichment in different livestock species including cattle, pigs, sheep, and chickens." .
SCR:019213 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ShinyGO" ;
rdfs:label "ShinyGO" ;
NIFRID:synonym "Shiny Gene Ontology",
"ShinyGO 0.77",
"ShinyGO 0.80",
"ShinyGO v0.61" ;
definition: "Software graphical gene set enrichment tool for animals and plants. Graphical web application to gain insights from gene sets. Features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for retrieval of pathway diagrams and protein-protein interaction networks." .
SCR:019214 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:biomart" ;
rdfs:label "biomaRt" ;
NIFRID:synonym "biomaRt v 2.42.1" ;
definition: "Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis." .
SCR:019215 a NIFSTD:NEMO_0569000,
owl:NamedIndividual ;
rdfs:label "South Dakota State University; South Dakota; USA" ;
NIFRID:abbrev "SDSU" ;
definition: "Public land grant research university in Brookings, South Dakota. Founded in 1881, it is the largest and most comprehensive university and the oldest continually operating university in South Dakota." .
SCR:019216 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ConPlot" ;
definition: "Web application for visualisation of information derived from residue contact predictions in combination with other sources of information, such as secondary structure predictions, transmembrane helical topology, sequence conservation.Provides interactive interface for researchers in field of protein bioinformatics that are interested in analysing data on given protein." .
SCR:019217 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COPDESS" ;
NIFRID:synonym "Coalition for Publishing Data in the Earth and Space Sciences" ;
definition: "Project to connect Earth and space science publishers and data facilities to help translate aspirations of open, available, and useful data from policy into practice. Community driven project to implement common policies and standards to accelerate scientific discovery by promoting open and FAIR data." .
SCR:019218 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Federated Research Data Repository" ;
NIFRID:abbrev "FRDR" ;
definition: "Canadian data repositories project. Data submitted to FRDR is housed on Compute Canada managed infrastructure at University of Victoria, BC or at University of Waterloo, ON. Research data submitted to FRDR does not leave Canada.Most of metadata is shared with Globus, running on Amazon Web Services in the USA, to be indexed and made available for discovering datasets. Certain metadata fields, for example, submitter contact information, are not shared with Globus.Larger uploads are made using Globus, only public metadata is stored there." .
SCR:019219 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:chira" ;
rdfs:label "ChiRA" ;
NIFRID:synonym "Chimeric Read Analyzer" ;
definition: "Software tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc." .
SCR:019220 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012820" ;
rdfs:label "Progenetix" ;
definition: "Collection of mutation data in cancer, with focus on copy number abnormalities for all types of human malignancies." .
SCR:019221 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:epitopepredict" ;
rdfs:label "epitopepredict" ;
definition: "Open source software tool as programmatic framework and command line tool designed to aid process of MHC binding prediction. Provides access to multiple binding prediction algorithms under single interface and scales for whole genomes using multiple target MHC alleles.Software should be run on Linux operating system. Ubuntu is recommended but most major distributions will be fine. Windows is not supported." .
SCR:019222 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_019224" ;
rdfs:label "ABF Utility" ;
definition: "Software tool to convert data files from Mac program such as Igor and Pulse or John Dempster CDR, WinTida, to ABF formats and analyze them with Mini Analysis Program." .
SCR:019223 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenClinica" ;
definition: "Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system." .
SCR:019225 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "igraph" ;
NIFRID:synonym "igraph 0.8.4",
"igraph 1.2.6" ;
definition: "Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus." .
SCR:019226 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Authentication Reports" ;
definition: "dkNET service that assists researchers in preparing authentication plans for cell lines or antibodies to comply with NIH Submission Policy when submitting proposal or publication. Automated tool to enable researchers to create customized report based on key biological resources they plan to use. These customized reports provide additional information such as known problems with particular cell line or antibody." .
SCR:019227 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Resource Reports" ;
definition: "dkNET service that provides detailed overview of individual research resources along with citation metrics from biomedical literature, community feedback and alerts, information about who used resource, and information about what resources have been used together. The only integrated data set and analytics platform combining Research Resource Identifiers (RRIDs), text mining and data aggregation. Users can identify key resources while also tracking resource use and performance." .
SCR:019228 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BIDS Manager" ;
NIFRID:synonym "BIDS Manager v0.2.7",
"BIDS Manager v5",
"Brain Imaging Data Structure Manager" ;
definition: "Software Python package to collect, organise and manage neuroscience data in Brain Imaging Data Structure format.Software package for Windows 10 to collect, organise and manage neuroscience data in BIDS format." .
SCR:019229 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cthist" ;
definition: "Software tool for mass downloading of historical clinical trial data from ClinicalTrials.gov." .
SCR:019230 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clinical Trials Viewer" ;
definition: "Software tool to download and parse information from ClinicalTrials.gov at the time of search to populate the graph of clinical trials. FDA information is updated weekly from Drugs at FDA dataset and FDA postmarketing commitment data set." .
SCR:019231 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phase Holographic Imaging | HoloMonitor live cell imaging and analysis system" ;
NIFRID:synonym "HoloMonitor live cell imaging and analysis system",
"HoloMonitor M3",
"HoloMonitor microscope",
"HoloMonitor® M4" ;
definition: """HoloMonitor live cell imaging and analysis system by Phase Holographic Imaging PHI AB.
Contains small, digital live cell, quantitative phase imaging microscope HoloMonitor M4 designed to operate constantly inside incubator and HoloMonitor cell imaging software App Suite or Hstudio to continuously monitor and quantitatively analyze both individual cells and cell populations over time without any cellular labels or stains. Microscope can operate in cell incubator, hypoxia chamber or on lab bench.""" .
SCR:019232 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Perkin Elmer | VICTOR3 multilabel plate reader" ;
NIFRID:synonym "VICTOR3" ;
definition: "Versatile plate reader that can be used to measure fluorescence intensity from both top and bottom of plate, colorimetric absorbance and luminescence." .
SCR:019233 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:RADAR-base" ;
rdfs:label "RADAR-base" ;
NIFRID:synonym "Radar-base",
"Remote Assessment of Disease And Relapses" ;
definition: "Open source mobile health platform for collecting, monitoring, and analyzing data using sensors, wearables, and mobile devices. Enables study design and set up, active and passive remote data collection, secure data transmission via Wifi and/or Bluetooth and scalable solutions for data storage, management and access. Allows study participants to share their health data with clinicians and researchers in secure way." .
SCR:019234 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Elektra Academy" ;
definition: "Free curriculum, resources, and research for those considering incorporation of remote health monitoring." .
SCR:019235 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FAIR Data Informatics Laboratory" ;
NIFRID:abbrev "FAIR Data Informatics Lab",
"FDI Lab",
"FDI Laboratory",
"FDIL" ;
definition: "UCSD based bioinformatics lab composed of several projects in different biomedical disciplines. Established in 2008 as Neuroscience Information Framework and has since expanded to include broader field of biomedical research. Leader in developing and providing novel informatics infrastructure and tools for making data FAIR: Findable, Accessible, Interoperable and Reusable. FAIR Data informatics laboratory develops SciCrunch.org platform." .
SCR:019236 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DatA Tag Suite" ;
NIFRID:abbrev "DATS" ;
definition: "Software suite to enable discoverability of datasets. Enables submission of metadata on datasets to DataMed. Has core set of elements, which are generic and applicable to any type of dataset, and extended set that can accommodate more specialized data types. Platform independent model developed by NIH BD2K bioCADDIE project for DataMed Data Discovery Index prototype being developed. Also available as annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex." .
SCR:019237 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Electron Microscopy Public Image Archive " ;
NIFRID:abbrev "EMPIAR" ;
definition: "Public archive for raw electron microscopy image data. Resource for raw 2D electron microscopy images. Used to browse, upload and download raw images to build 3D structure. Provides access to raw data to facilitate methods development and validation. Complements Electron Microscopy Data Bank where 3D volumes are stored, and uses Aspera platform for data transfers." .
SCR:019238 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:tradeseq" ;
rdfs:label "tradeSeq" ;
NIFRID:synonym "TRAjectory-based Differential Expression analysis for SEQuencing data" ;
definition: "Software tool as suite of tests for identifying dynamic temporal gene regulation using single cell RNA-seq data.Trajectory based differential expression analysis for sequencing data." .
SCR:019239 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:https:cite-seq-count" ;
rdfs:label "CITE-seq-Count" ;
NIFRID:synonym "Cellular Indexing of Transcriptomes and Epitopes by Sequencing Count",
"CITE-seq-Count v1.4.0" ;
definition: "Software python package that allows to count antibody TAGS from CITE-seq and/or cell hashing experiment. Software tool that allows to get UMI counts from single cell protein assay. Used to count (UMI counts) antibody-derived-tags (ADTs) or Cell Hashing tags (HTOs) in raw sequencing reads and build count matrix." .
SCR:019240 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IKMB GWAS Association Testing Pipeline" ;
definition: "Software tool as scalable GWAS Association Testing pipeline for biobank scale datasets." .
SCR:019241 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GWAS Quality Control Pipeline" ;
NIFRID:synonym "BIGwas QC" ;
definition: "Software tool as scalable GWAS Quality Control pipeline for biobank scale datasets." .
SCR:019243 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeePhage" ;
definition: "Software tool to distinguish virulent and temperate phage derived sequences in metavirome data with deep learning approach. Used to identify virome sequences as temperate phage derived or virulent phage derived fragments." .
SCR:019244 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fruit Fly Brain Observatory" ;
NIFRID:abbrev "FFBO" ;
definition: "Open source software platform for studying fruit fly brain function, and for investigating fruit fly brain disease models that are highly relevant to mechanisms of human neurological and psychiatric disorders. Collaborative ecosystem for accelerating discovery of functional logic of fruit fly brain. Includes FlyBrainLab and BrainMapsViz. Stores and integrates fruit fly brain research data. Repository of tools and methods to build, emulate and compare fruit fly brain models in health and disease. Open framework for fruit fly brain data processing and model execution." .
SCR:019246 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1115" ;
rdfs:label "University of Queensland School of Biomedical Sciences Imaging and Analytics Core Facility" ;
NIFRID:synonym "UQ SBMS Imaging and Analytics Facility" ;
definition: "Provides microscopes for life science research, including number of confocals, widefield systems, slide scanners, and analysis packages. Provides analytic instruments such as flow cytometers, imaging systems, and PCR equipment among others. Our team consists of experienced biologists and are available to help you with experiment building, troubleshooting, and data analysis." .
SCR:019247 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRI Compatible and Customizable Microdrive Design for Neuroscience Research" ;
definition: "Open source designs for customizable, MRI compatible microdrive capable of positioning probes including stimulating electrodes, recording electrodes, drug cannulae, or optogenetic fibers within brain. Design integrates cranial implant, penetration grid for guiding probes, and microdrive body assembly with actuators. Used by neuroscience community related to electrical microstimulation, neuronal recording, and local drug delivery." .
SCR:019249 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "PhosphoSolutions" ;
definition: "An antibody manufacturer based in Aurora, Colorado." .
SCR:019250 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "SouthernBiotech" ;
definition: "Commercial antibody company that focuses on the development, production, purification, conjugation, and commercialization of antibodies." .
SCR:019251 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Aeonian Biotech" ;
definition: "Commercial antibody company that uses proprietary selection criteria and selects antibodies to be sold under their name." .
SCR:019252 a NLX:152342,
owl:NamedIndividual ;
rdfs:label "Leinco Technologies" ;
definition: "A manufacturer of early discovery research products including antibodies, recombinant proteins, ELISA kits, second step reagents and other life sciences products." .
SCR:019253 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ScanNeo" ;
definition: "Open software pipeline for analyzing RNA-seq to predict neoepitopes derived from small to large sized indels. Used for identifying indel derived neoantigens using RNA-Seq data." .
SCR:019254 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Interact" ;
definition: "Software platform for synchronized viewing and analysis of video footage and audio files in observational research by Mangold International GmbH. Qualitative and quantitative video coding software." .
SCR:019255 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lung Genome Browser" ;
definition: "Project to provide data on genome and epigenome of human lung to facilitate research efforts of investigators studying diseases of lung including COVID-19.Collaboration among multiple groups at University of California including Center for Epigenomics, Gaulton lab and Sun lab at UCSD Department of Pediatrics. This work is conducted as part of LungMAP consortitum." .
SCR:019258 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Deep Collaborative Learning" ;
NIFRID:synonym "dcl_model" ;
NIFRID:abbrev "DCL" ;
definition: "Software tool as deep collaborative learning with application to study of multimodal brain development. Uses deep network to represent original data and then seeks their correlations, while also linking data representation with phenotypical information." .
SCR:019259 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:rna-stability" ;
rdfs:label "rna-stability" ;
definition: "Software tool as parallel processing framework for large scale generation of secondary RNA structures and folding statistics for transcriptome of any species." .
SCR:019260 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013325" ;
rdfs:label "EBRAINS" ;
NIFRID:synonym "Ebrains",
"ebrains" ;
definition: "Research infrastructure for the EU Human Brain Project. Provides digital tools and services which can be used to address challenges in brain research and brain inspired technology development. Digital research infrastructure, created by EU-funded Human Brain Project, that gathers extensive range of data and tools for brain-related research. EBRAINS will capitalize on the work performed by the Human Brain Project teams in digital neuroscience, brain medicine, and brain-inspired technology.You can share your neuroscience data, models and software." .
SCR:019261 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpikeForrest" ;
definition: "Software reproducible, continuously updating platform which benchmarks performance of spike sorting codes across large curated database of electrophysiological recordings with ground truth. Website and open source computing framework for evaluating and comparing spike sorting algorithms for neurophysiology data analysis. Project of Center for Computational Mathematics at Flatiron Institute." .
SCR:019262 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EIDORS:Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software" ;
NIFRID:abbrev "EIDORS" ;
definition: "Free software algorithms for forward and inverse modelling for Electrical Impedance Tomography (EIT) and Diffusion based Optical Tomography, in medical and industrial settings, and to share data and promote collaboration between groups working these fields." .
SCR:019263 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HistoloZee" ;
definition: "Software tool that integrates histology reconstruction, MRI co-registration, and manual segmentation tools in easy-to-use and intuitive interface. Permits real-time interaction with complex and large histology datasets during co-registration steps of histology reconstruction. Software tool for interactively mapping 2D and 3D molecular and anatomical histology into Common Coordinate Frameworks. Has simple, interactive registration workflows that connect user images with CCFs." .
SCR:019264 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_022792" ;
rdfs:label "CellLocator" ;
NIFRID:synonym "BICCN Cell Locator",
"cell-locator",
"CellLocator by Allen Institute" ;
definition: "Open source and multi-platform pinning software tool to facilitate mapping samples into common 3D spaces. Desktop application based on 3D Slicer that displays Allen Institute for Brain Science CCF or MNI atlas, color segmented by structure of brain, and allows user to create planar polyline annotation to facilitate mapping samples into corresponding atlas." .
SCR:019265 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Semi-Manual Alignment to Reference Templates" ;
NIFRID:abbrev "SMART" ;
definition: "Software tool that extends WholeBrain framework in R for segmenting and registering experimental images to Allen Mouse Common Coordinate Framework (CCF). Streamlines processing of large volumetric LSFM datasets and solves issues with non-uniform morphing across anterior-posterior axis with interactive “choice game.” Accounts for duplicate cell counts in adjacent z images and presents new ways to easily parse apart and interactively visualize final mapped datasets." .
SCR:019266 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Blue Brain Cell Atlas" ;
NIFRID:synonym "The Blue Brain Cell Atlas" ;
definition: "Describes number, types, and positions of cells in all areas of mouse brain. Provides densities and positions of all excitatory, inhibitory and neuromodulatory neurons, as well as astrocytes, oligodendrocytes and microglia in each of brain regions defined in Allen Mouse Brain Atlas. Users can download cell numbers for statistical analysis, cell positions and types for modeling and visualizing brain areas. Underlying workflow uses imaging data from Allen Institute Common Coordinate Framework to generate cell positions and assign their type using API for data access." .
SCR:019267 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas" ;
definition: "Website to visualize and share anatomical labels. Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). Cell type specific transgenic mice and MRI atlas were used to adjust and further segment labels. New segmentations were created in dorsal striatum using cortico-striatal connectivity data. Anatomical labels were digitized based on Allen ontology, and web-interface was created for easy visualization. These labels provide resource to isolate and identify mouse brain anatomical structures. Open source data sharing will facilitate further refinement of anatomical labels and integration of data interpretation within single anatomical platform." .
SCR:019268 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cloud-transcriptome-annotation" ;
NIFRID:synonym "Cloud comparison for Transcript-Annotation data analysis pipeline" ;
definition: "Cloud comparison for transcript annotation data analysis pipeline. Workflow for comparing transcriptome annotation pipelines." .
SCR:019269 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FASTQuick" ;
definition: "Software tool for rapid and comprehensive quality assessment of raw sequence reads. It generates comprehensive list of QC statistics, including ancestry and contamination estimation." .
SCR:019270 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neural Module" ;
NIFRID:synonym "Neural Software Module",
"NeuralMetricTool" ;
definition: "Neural Module by Axion BioSystems Inc, provides simplified approach to set up, execution and analysis of neural experiments. Enables Maestro Pro and Edge to record and analyze key parameters of neural network function, including activity, synchrony, and network oscillations." .
SCR:019271 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CMGUI" ;
NIFRID:synonym "Cmgui",
"Cmgui v3.0" ;
definition: "Standalone application for 3D visualisation and manipulation of mathematical field models. Cmgui is part of Continuum Mechanics, Imaging, Signal processing, System identification mathematical modelling environment. Generic open source modelling and visualisation package used to enable researchers to visualise biomedical images alongside dynamic geometry fields from computer models of cells, tissues and organs." .
SCR:019272 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ACD/ChemSketch" ;
NIFRID:synonym "ChemSketch" ;
definition: "Software tool as molecular structure drawing application by ACD Labs. Allows user to Draw chemical structures, reactions, and schema, and access variety of graphical tools and templates, Generate names from molecular structure and vice versa, Calculate molecular properties from chemical structure, Create professional reports, presentations, and publication ready figures, Communicate scientific information with clarity and ease." .
SCR:019276 a owl:NamedIndividual ;
rdfs:label "rtransparent" ;
definition: "An R package that automatically identifies and extracts indicators of transparency (data availability, code availability, statements of conflicts of interest, statements of funding, statements of protocol registration) from TXT and PMC XML versions of published research articles in biomedicine." .
SCR:019277 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:gedit" ;
rdfs:label "GEDIT" ;
NIFRID:synonym "Gene Expression Deconvolution Interactive Tool" ;
definition: "Software tool for accurate cell type quantification from gene expression data. Uses gene expression data to estimate cell type abundances. Allows user to supply custom reference matrices." .
SCR:019278 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RHD USB Interface Board Software" ;
definition: "Electrophysiological recording software for use with RHD USB Interface Board by Intan Technologies." .
SCR:019279 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sandwich Estimator Toolbox" ;
NIFRID:abbrev "SwE" ;
definition: "Software tool as SPM extension for longitudinal and repeated measures data. Modelling of longitudinal and repeated measures neuroimaging data.Implemented as Matlab toolbox for SPM8 or SPM12." .
SCR:019280 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VORTEX" ;
definition: "Software tool to model population dynamics as discrete, sequential events that occur according to probabilities that are random variables following user-specified distributions.Simulation of deterministic forces as well as demographic, environmental and genetic stochastic events on wildlife populations.Can model many of extinction vortices that can threaten persistence of small populations." .
SCR:019281 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Program MARK" ;
definition: "Software tool to provide parameter estimates from marked animals when they are re-encountered at later time, to create population size estimates. Used for analysis of data from marked individuals." .
SCR:019282 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mp3" ;
rdfs:label "MP3 tool" ;
NIFRID:synonym "MP3" ;
definition: "Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:019283 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "1KA" ;
definition: "Open source software application that enables services for online surveys. Provides advanced support for all steps of web survey process. Conduct research and analysis from beginning to end." .
SCR:019284 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1119",
"nlx_56885",
"SCR_004576" ;
rdfs:label "University of Nottingham NASC Nottingham Arabidopsis Stock Centre" ;
NIFRID:synonym "European Arabidopsis Stock Centre",
"NASC code",
"NASC-Nottingham Arabidopsis Stock Centre",
"Nottingham Arabidopsis Stock Centre",
"uNASC",
"University of Nottingham NASC-Nottingham Arabidopsis Stock Centre" ;
NIFRID:abbrev "NASC" ;
definition: """National and international arabidopsis germplasm resource.Stores over million genotypes in physical stocks servicing worldwide Arabidopsis community in more than 50 countries.
Stocks are provided under identical cost recovery conditions to academic and commercial researchers. Non-transgenic stocks are sent gratis to K-17 institutions and in special cases.
Provides seed and information resources to International Arabidopsis Genome Programme and research community. Maintains accessions of Arabidopsis thaliana (and small number of other related species), including Characterized lines, Mapping populations, and Insertion lines. You may browse or search catalog.""" .
SCR:019285 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Expyfun" ;
definition: "Auditory and visual stimulus delivery library for psychoacoustics in Python." .
SCR:019286 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BrainVision PyCorder" ;
NIFRID:synonym "PyCorder" ;
definition: "Open source acquisition program, based on Python programming language, for setting up BrainVision actiCHamp amplifier and storing data." .
SCR:019287 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SIMR" ;
NIFRID:synonym "simR",
"simr" ;
definition: """Software R package for power analysis of generalized linear mixed models by simulation.
Used to calculate power for generalised linear mixed models.""" .
SCR:019288 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ARTS biomarker" ;
NIFRID:synonym "ARTS" ;
definition: "Software tool as automated biomarker that outputs score linked to likelihood person sufferring from arteriolosclerosis based on brain MRI data and basic demographic information. MRI data processing pipeline and classifier are packaged into software container.Users do not need to perform any image processing, and are only required to install Singularity to run ARTS." .
SCR:019289 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mb-gan" ;
rdfs:label "MB-GAN" ;
NIFRID:synonym "Microbiome Simulation via Generative Adversarial Network" ;
definition: "Software tool as deep learning simulation framework for simulating realistic microbiome data. Can automatically learn from given microbial abundances and compute simulated abundances that are indistinguishable from it." .
SCR:019290 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gbs2ploidy" ;
definition: "Software R package as functions for inference of ploidy from Genotyping By Sequencing data, including function to infer allelic ratios and allelic proportions in Bayesian framework." .
SCR:019291 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bayesepimodels" ;
rdfs:label "BayesEpiModels" ;
definition: "Software tool for accessing performance of different epidemiological models, including both growth and compartmental models, in Bayesian framework." .
SCR:019292 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BayesEpiModels Web App" ;
definition: "Web app to help assess both short- and long-term forecasts of COVID-19 across the United States at multiple levels. Done by implementing one time-series model (ARIMA), one compartmental models (basic SIR), and six classical growth models, which all yield satisfactory prediction results in the past and current pandemics at early stage." .
SCR:019293 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "vioplot" ;
definition: "Software R package for extensive customization of violin plots. Violin plot is combination of box plot and kernel density plot." .
SCR:019294 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "spdep" ;
NIFRID:synonym "spatial dependence",
"Spatial Dependence: Weighting Schemes and Statistics" ;
definition: "Software R package as collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree." .
SCR:019295 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scales" ;
definition: "Software R package as scale functions for visualization. Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends." .
SCR:019296 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "maps" ;
definition: "Software R package to draw geographical maps." .
SCR:019297 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1121" ;
rdfs:label "Baylor College of Medicine Optical Imaging and Vital Microscopy Core Facility" ;
NIFRID:synonym "Optical Imaging & Vital Microscopy (OiVM)" ;
NIFRID:abbrev "OiVM" ;
definition: "Core provides instrumentation, imaging and image analysis tools.Ddicated to vital and intravital imaging of cellular processes within cells, intact tissue explants, developing embryos and functioning organs within the live animal. Our users are focused on a variety of applications such as understanding cell migration, optimizing angiogenic therapies, how blood flow influences development and cancer, immune cell recruitment, stem cell-niche interactions and cancer metastasis." .
SCR:019298 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1095" ;
rdfs:label "University of Colorado Boulder Chemical and Bio. Engineering instrument and electronics Core Facility" ;
NIFRID:synonym "Chemical and Bio. Engineering instrument and electronics",
"Colorado University at Boulder Chemical and Bio. Engineering instrument and electronics Core Facility" ;
definition: "Provides mechanical and electrical design and fabrication services at CU Boulder.Provides solutions for instructional and research needs for any department or college. Collectively comprised of machine shop and electronics shop, both of which are located in basement level of Jennie Smoly Caruthers Biotechnology Building." .
SCR:019299 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1097" ;
rdfs:label "University of Colorado Boulder High Performance Computing PetaLibrary Core Facility" ;
NIFRID:synonym "Colorado University at Boulder High Performance Computing PetaLibrary Core Facility",
"High Performance Computing - CU PetaLibrary",
"University of Colorado at Boulder High Performance Computing PetaLibrary Core Facility" ;
NIFRID:abbrev "PetaLibrary" ;
definition: "Provides service to support storage, archival, and sharing of research data. Available at subsidized cost to any researcher affiliated with University of Colorado Boulder." .
SCR:019300 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1099" ;
rdfs:label "University of Colorado Boulder Earth Systems Stable Isotope Lab Core Facility" ;
NIFRID:synonym "Colorado University at Boulder Earth Systems Stable Isotope Lab Core Facility",
"Earth Systems Stable Isotope Lab (CUBES-SIL)",
"University of Colorado at Boulder Earth Systems Stable Isotope Lab Core Facility" ;
NIFRID:abbrev "CUBES-SIL" ;
definition: "Designed to measure relative abundance of stable isotopes of light elements and molecules." .
SCR:019301 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1096" ;
rdfs:label "University of Colorado Boulder Organic Geochemistry Laboratory Core Facility" ;
NIFRID:synonym "Colorado University at Boulder Organic Geochemistry Laboratory Core Facility",
"Organic Geochemistry Laboratory (OGL)",
"University of Colorado at Boulder Organic Geochemistry Laboratory Core Facility" ;
NIFRID:abbrev "OG Lab",
"OGL" ;
definition: "Shared analytical facility for multidisciplinary and collaborative research in fields as diverse as biogeochemistry, geobiology, astrobiology, environmental microbiology, paleoceanography, paleoclimatology, and energy, among others.Focuses on extraction, purification, separation, and chemical and isotopic characterization of organic molecules extracted from environmental and culture samples." .
SCR:019302 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1098" ;
rdfs:label "University of Colorado Boulder BioCore Core Facility" ;
NIFRID:synonym "BioCore",
"Colorado University at Boulder BioCore Core Facility",
"University of Colorado at Boulder BioCore Core Facility" ;
definition: "Purpose is to connect MCDB, EBIO, and IPHY researchers to campus research resources." .
SCR:019303 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1100" ;
rdfs:label "University of Colorado Boulder CU Thermochronology Research and Instrumentation Lab Core Facility" ;
NIFRID:synonym "Colorado University at Boulder CU Thermochronology Research and Instrumentation Lab Core Facility",
"CU Thermochronology Research and Instrumentation Lab (CU-TRaIL)",
"University of Colorado at Boulder CU Thermochronology Research and Instrumentation Lab Core Facility" ;
NIFRID:abbrev "CU TRaIL" ;
definition: "Fully equipped (U-Th)/He thermochronology facility." .
SCR:019304 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1103" ;
rdfs:label "Colorado University at Boulder Soft Materials Research Center X-Ray Diffraction Facility Core Facility" ;
NIFRID:synonym "Soft Materials Research Center X-Ray Diffraction Facility" ;
NIFRID:abbrev "SAXS" ;
definition: "Provides cutting edge capabilities for probing large lengthscale structures such as polymers, biological macromolecules, meso- and nano-porous materials, and molecular self-assemblies.Techniques that can be applied to study materials include SAXS, GISAXS, WAXS, and GIWAXS. The 30W Xenocs Genix 3D x-ray source and state-of-the-art Dectris Eiger R 1M detector provide an excellent way to probe almost any material of interest. In-situ x-ray studies may be carried out using temperature controlled sample holders in both SAXS and GISAXS modes.." .
SCR:019305 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1102" ;
rdfs:label "University of Colorado Boulder Raman Microspectroscopy Lab Core Facility" ;
NIFRID:synonym "Colorado University at Boulder Raman Microspectroscopy Lab Core Facility",
"Raman Microspectroscopy Lab",
"University of Colorado at Boulder Raman Microspectroscopy Lab Core Facility" ;
definition: "Core research facility housed in Department of Geological Sciences for fast, non-destructive characterization and chemical imaging of diverse materials spanning minerals (thin sections and powders), biological samples, fluids, dissolved gases, and much more." .
SCR:019306 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1101" ;
rdfs:label "Colorado University at Boulder Facility for Electron Microscopy of Materials Core Facility" ;
NIFRID:synonym "Facility for Electron Microscopy of Materials CU FEMM" ;
NIFRID:abbrev "CU FEMM" ;
definition: "Facility features electron microscopes housed in vibration, static-free, and temperature-controlled environment." .
SCR:019307 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1106" ;
rdfs:label "Colorado University at Boulder Materials Instrumentation and Multimodal Imaging Core Facility" ;
NIFRID:synonym "Materials Instrumentation and Multimodal Imaging Core (MIMIC) Facility" ;
NIFRID:abbrev "MIMIC" ;
definition: "Facility provides specialized services for assessment of material properties, chemistry and structure across multiple length scales with emphasis on assessment of biological tissues, biomaterials, and biologically inspired systems." .
SCR:019308 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1105" ;
rdfs:label "Colorado University at Boulder BioFrontiers Next-Gen Sequencing Facility Core Facility" ;
NIFRID:synonym "BioFrontiers Next-Gen Sequencing Facility" ;
definition: "Core instruments include Agilent Bioanalyzer 2100 system provides sizing, quantitation and quality control of DNA, RNA and proteins, Illumina MiSeq sequencer, able to sequence prepared Illumina DNA or RNA libraries at low- to mid- output (0.75 to 13 Gbp per run), Illumina NextSeq sequencer capable of sequencing Illumina DNA or RNA libraries, QuantStudio 6 Real-Time PCR uses fluorescence detection method for quantitative and qualitative analysis of nucleic acid sequences including gene expression, regulation and variation, Qubit Fluorimeter 3.0 capable of measuring DNA or RNA concentrations with high accuracy." .
SCR:019309 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1110" ;
rdfs:label "Colorado University at Boulder Flow Cytometry Shared Core Facility" ;
NIFRID:synonym "Flow Cytometry Shared Core" ;
definition: "Provides instruments including BD Accuri C6 Cytometer with Automated, multisampler/Flow Cytometer,BDFACSCelesta Flow Cytometer Analyzer,BD FACSAria Fusion Cell Sorter." .
SCR:019310 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1122" ;
rdfs:label "Colorado University at Boulder Macromolecular X-ray Crystallography Core Facility" ;
NIFRID:synonym "Macromolecular X-ray Crystallography Core" ;
definition: "Provides resources for crystallization and structure determination of biological macromolecules and complexes. Supports research in the Department of Biochemistry. We are happy to extend our help to researchers from the broader CU community and to researchers outside the university, if time and availability allow us too." .
SCR:019311 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1109" ;
rdfs:label "Colorado University at Boulder Nuclear Magnetic Resonance Spectroscopy Core Facility" ;
NIFRID:synonym "Nuclear Magnetic Resonance Spectroscopy Facility" ;
definition: "Core serves research needs of entire campus community as well as outside research entities. Facility maintains a variety of NMR spectrometers at variety of magnetic fields to support research needs." .
SCR:019312 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "syndRomics" ;
definition: "Software R package implements functions for helping in process of disease patterns analysis by means of principal components. These include component visualization, interpretation and stability analysis." .
SCR:019316 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:reactomepa" ;
rdfs:label "ReactomePA" ;
NIFRID:synonym "Reactome Pathway Analysis" ;
definition: "Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization." .
SCR:019317 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MSnbase" ;
definition: "Software R package provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. Used for isobaric tagged mass spectrometry data visualization, processing and quantitation." .
SCR:019318 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:synergyfinder" ;
rdfs:label "SynergyFinder" ;
NIFRID:synonym "synergyfinder" ;
definition: "Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations." .
SCR:019319 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ciliquant" ;
rdfs:label "CiLiQuant" ;
definition: "Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance." .
SCR:019320 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "alpha helix coordinate frame simulation" ;
NIFRID:synonym "alpha-helix coordinate frame simulation framework",
"alpha-helix-coordinate-frame-simulation" ;
definition: "Source code for alpha-helix simulation framework written in Matlab. Specifically tested on Talin-1 Rod Domain." .
SCR:019321 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:citefuse" ;
rdfs:label "CiteFuse" ;
NIFRID:synonym "Cellular Indexing of Transcriptomes and Epitopes Fuse",
"Cellular indexing of transcriptomes and epitopes Fuse" ;
definition: "Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data." .
SCR:019322 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FluCalc" ;
NIFRID:synonym "flucalc",
"fluctuation calculation" ;
definition: "Software tool as MSS-MLE calculator for Luria–Delbrück fluctuation analysis." .
SCR:019323 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "smoove" ;
definition: "Software tool to simplify and to speed calling and genotyping structural variants for short reads. Improves specificity by removing many spurious alignment signals that are indicative of low level noise and often contribute to spurious calls." .
SCR:019324 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "M2aia" ;
NIFRID:synonym "MSI applications for interactive analysis in MITK",
"M²aia" ;
definition: "Software tool enabling interactive signal processing and visualisation of mass spectrometry imaging datasets. Extends open source Medical Imaging and Interaction Toolkit. Designed to enable multi modal 2D registration and 3D MSI reconstruction." .
SCR:019326 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "10x Genomics | Chromium Controller Genetic Analyzer" ;
definition: "Genetic analyzer, referred to as Chromium Controller for combining large partition numbers with a diverse barcode library to generate >100,000 barcode-containing partitions. Chromium Controller runs low- and standard-throughput assays. It does not run high-throughput assays.Chromium Controller uses advanced microfluidics to perform single cell partitioning and barcoding in a matter of minutes. Powered by Next GEM technology, the Chromium Controller enables integrated analysis of single cells at massive scale." .
SCR:019327 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MZ6" ;
rdfs:label "Leica | MZ6 Dissecting Microscope" ;
definition: "Modular stereomicroscope with 6.3:1 zoom with 7-position ratchet stop enables repetitive inspection and measurements at a specific zoom position." .
SCR:019329 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Multidrop" ;
rdfs:label "Thermo Fisher | 384-well formats Thermo MultiDrop Combi with 50 plate feeders" ;
definition: "Reagent dispenser that handles a wide selection of plates and volume range and provides fast dispensing and high-throughput operation. It dispenses over a 0.5 to 2500�L range, ensuring reproducible assay data and accommodates microplates from 6 to 1536 wells and plate heights of 5 to 50mm." .
SCR:019330 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2700" ;
rdfs:label "Thermo Fisher: Applied Biosystems | ABI 2700 GeneAmp PCR System" ;
definition: "PCR bechtop thermal cycler measuring at only 36 x 21 x 22 cm and several machines can be stored and operated side-by-side." .
SCR:019331 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5500xl" ;
rdfs:label "Thermo Fisher: Applied Biosystems | ABI 5500xl 5500xl" ;
definition: "Genetic Analyzer with two FlowChips, embedded quality controls, user workflows, and project scalability. It can be used for whole exome sequencing or targeted resequencing with up to 96 barcodes." .
SCR:019332 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5800",
"SCR_019336" ;
rdfs:label "Thermo Fisher: Applied Biosystems | ABI 5800 Mass Spectrometer" ;
NIFRID:synonym "AB Sciex 5800 MALDI TOF/TOF Mass Spectrometer" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8th, 2023. Mass spectrometer for biomarker discovery, MALDI mass spectrometry imaging, and protein identification." .
SCR:019333 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5300" ;
rdfs:label "Thermo Fisher: Applied Biosystems | ABI 5300 Genetic Analyzer" ;
definition: "Genetic Analyzer used for human identification applications." .
SCR:019334 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7500FAST" ;
rdfs:label "Thermo Fisher: Applied Biosystems | ABI 7500 Real Time PCR System 7500FAST" ;
NIFRID:synonym "ABI 7500 Fast Real Time PCR System" ;
definition: "This Real-Time PCR System offers you high performance, multicolor real-time PCR." .
SCR:019335 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7300" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 7300 Real-Time Instrument" ;
definition: "Fast Real-Time PCR System uses fluorescent based PCR chemistries to provide quantitative detection of nucleic acid sequences using real-time analysis and qualitative detection of nucleic acid sequences using end-point and dissociation-curve analysis." .
SCR:019337 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2120" ;
rdfs:label "Advia 2120 Hematology Analyzer" ;
definition: "Hematology System is a bench-top analyzer designed for medium- to large-volume laboratories. This flow cytometry-based system uses light scatter, differential white blood cell (WBC) lysis, and myeloperoxidase and oxazine 750 staining to provide a complete blood cell count, a WBC differential, and a reticulocyte count. A cyanide-free method is used to measure hemoglobin colorimetrically." .
SCR:019338 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_3000 7G" ;
rdfs:label "Thermo Fisher: Affymetrix | 3000 7G Microarray Scanner" ;
definition: "Microarray scanner that is an extension of the GeneChip Scanner 3000 (GCS 3000) series that allows you to scan next-generation higher-density arrays, including SNP arrays with up to 900,000 SNPs, tiling arrays for transcription and all-exon arrays for whole-genome analysis." .
SCR:019339 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_428" ;
rdfs:label "Thermo Fisher: Affymetrix | 428 Array Scanner" ;
definition: "428 array scanner can analyze any microarray on a glass slide (25x75x1mm) that has been probed with DNA labeled with Cy3, or Cy5 as well as other common fluorescent dyes." .
SCR:019340 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Voyager" ;
rdfs:label "Thermo Fisher: Applied Biosystems | ABI Voyager DE Pro MALDI-Mass Spectrometer" ;
definition: "This mass spectrometer can be used for structural analysis of organic and inorganic compounds, protein identification studies, synthetic peptide validation experiments, small molecule and polymer analysis, and post source decay experiments." .
SCR:019341 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GCS_3000_7G" ;
rdfs:label "Thermo Fisher | GeneChip 3000 7G Microarray Scanner" ;
definition: "Microarray scanner that is an extension of the GeneChip Scanner 3000 (GCS 3000) series that allows you to scan next-generation higher-density arrays, including SNP arrays with up to 900,000 SNPs, tiling arrays for transcription and all-exon arrays for whole-genome analysis." .
SCR:019342 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5500" ;
rdfs:label "Thermo Fisher: Applied Biosystems | ABI 5500 Genetic Analyzer" ;
definition: "Genetic Analyzer that provides a robust, next-generation sequencing platform and gives you the choice to optimize for turnaround time or throughput." .
SCR:019343 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GeneAtlas" ;
rdfs:label "Thermo Fisher: Affymetrix | GeneAtlas Microarray Scanner" ;
definition: "GeneAtlas System utilizes the array strip format to provide simplified hybridization, robustness that protects precious samples, and array processing with common microwell-based labware." .
SCR:019344 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GeneTitan" ;
rdfs:label "Thermo Fisher: Affymetrix | GeneTitan Microarray Scanner" ;
definition: "GeneTitan Microarray Scanner integrates hybridization, washing, and imaging to provide automated array processing." .
SCR:019345 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GeneChip Hybridization Oven 645" ;
rdfs:label "Thermo Fisher: Affymetrix | GeneChip Hybridization Oven 645 RNA Analyzer" ;
definition: "Hybridization Oven with temperature and rotation control for hybridization of as many as 64 GeneChip cartridges at one time. The oven can be configured for 110 or 220V operation." .
SCR:019346 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GeneChip Hybridization Oven 640" ;
rdfs:label "Thermo Fisher: Affymetrix | GeneChip Hybridization Oven 640 RNA Analyzer" ;
definition: "GeneChip Hybridization Oven 640 automates your hybridization process for GeneChip brand probe arrays." .
SCR:019347 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | 100 Automated Disintegration Apparatus" ;
definition: "Automated Disintegration Apparatus provides compliant approach to disintegration testing. Used for drug dose disintegration testing. Reciprocating drive system, water bath, and heater/circulator are incorporated into single instrument. Apparatus is available in three basket model and comes complete with accessories required to perform standard United States Pharmacopeia disintegration test." .
SCR:019348 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_1100_HPLC" ;
rdfs:label "Agilent | 1100 High Performance Liquid Chromatography System" ;
definition: "1100 HPLC system is an efficient mixing and pulse-free pump action liquid chromatography system and advanced diagnostics and data analysis software." .
SCR:019349 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1220 Infinity II Analytical-Scale LC" ;
rdfs:label "Agilent | 1220 Infinity II Analytical-Scale LC Purification System" ;
definition: "Analytical-Scale LC Purification System provides sample purification for applications from routine analysis to specialized workflow solutions." .
SCR:019350 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II" ;
rdfs:label "Agilent | 1260 Infinity II Amino Acid Analysis System" ;
definition: "Amino Acid Analysis System provides complete solution for automated HPLC amino acid analysis." .
SCR:019351 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II Analytical-Scale" ;
rdfs:label "Agilent | 1260 Infinity II Analytical-Scale LC Purification System" ;
definition: "This system purifies multi milligram quantities of materials, handling flow rates between 0.1 and 10 mL min with 2.1 and 10.0 mm id columns." .
SCR:019352 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1220 Infinity II" ;
rdfs:label "Agilent | 1220 Infinity II LC System" ;
definition: "This LC System performs routine HPLC analysis in analytical and QA QC labs." .
SCR:019353 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RS1000" ;
rdfs:label "Agena | RS1000 Nanodispenser robot" ;
definition: "RS1000 Nanodispenser robot" .
SCR:019354 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II Bio-Inert" ;
rdfs:label "Agilent | 1260 Infinity II Bio-Inert LC System" ;
definition: "Bio-Inert LC System analyzes large biomolecules in biological samples." .
SCR:019355 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II LC" ;
rdfs:label "Agilent | 1260 Infinity II LC System" ;
definition: "This HPLC offers choice of modules for analytical HPLC and entry level UHPLC, delivering performance, reliability, and robustness." .
SCR:019356 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II GPC/SEC" ;
rdfs:label "Agilent | 1260 Infinity II GPC/SEC System" ;
definition: "Bechtop thermal cycler. The small foot-print means that this device makes good use of available bench space, allowing this device to fit into any laboratory it will even fit easily on the researcher's personal work bench. The desktop footprint measures only 36 x 21 cm and it stands 22 cm above the desk. Because the air-flow for the cooling system is located at the back of the unit, several machines can be stored and operated side-by-side, with no space between, for efficient space usage." .
SCR:019357 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II Manual Preparative" ;
rdfs:label "Agilent | 1260 Infinity II Manual Preparative LC System" ;
definition: "This binary gradient system delivers dynamic flow rates up to 50 mL min at 420 bar, equipped with manual injection valve." .
SCR:019358 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II Multi-Method" ;
rdfs:label "Agilent | 1260 Infinity II Multi-Method System" ;
definition: "This Multi-Method System offers maximum system utilization with minimum manual interaction." .
SCR:019359 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II Multidetector Bio-SEC" ;
rdfs:label "Agilent | 1260 Infinity II Bio-SEC Multi-Detector System" ;
definition: "Bio-SEC Multi-Detector System can be used to determine protein shape and size." .
SCR:019360 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II Method Development" ;
rdfs:label "Agilent | 1260 Infinity II Method Development System" ;
definition: "Method Development System provides robust and technology for everyday automated HPLC method development challenges." .
SCR:019361 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II Prime LC" ;
rdfs:label "Agilent | 1260 Infinity II Prime LC System" ;
definition: "Prime LC System provides sample purification for applications from routine analysis to specialized workflow solutions." .
SCR:019362 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II High-Temperature GPC" ;
rdfs:label "Agilent | 1260 Infinity II High-Temperature GPC System" ;
definition: "High-Temperature GPC System provides information about engineering polymers." .
SCR:019363 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II Preparative LC/MSD" ;
rdfs:label "Agilent | 1260 Infinity II Preparative LC/MSD System" ;
definition: "Preparative LC/MSD System increases daily sample throughput, maximizes purity and minimizes re analysis." .
SCR:019364 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II Preparative LC" ;
rdfs:label "Agilent | 1260 Infinity II Preparative LC System" ;
definition: "Preparative LC System is used for automated sample injection." .
SCR:019365 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II SFC/UHPLC Hybrid" ;
rdfs:label "Agilent | 1260 Infinity II SFC/UHPLC Hybrid System" ;
definition: "This hybrid system performs supercritical fluid chromatography SFC and ultrahigh performance liquid chromatography UHPLC." .
SCR:019366 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II 2D-LC" ;
rdfs:label "Agilent | 1290 Infinity II 2D-LC System" ;
definition: "2D-LC System separates co eluting compounds, achieves highest peak capacity and makes buffer separations compatible to MS detection." .
SCR:019367 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II Analytical-Scale LC" ;
rdfs:label "Agilent | 1290 Infinity II Analytical-Scale LC Purification System" ;
definition: "This purification system detects UV or MS and clusters of multiple fraction collectors." .
SCR:019368 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II SFC" ;
rdfs:label "Agilent | 1260 Infinity II SFC System" ;
definition: "SFC System provides sample purification for applications from routine analysis to specialized workflow solutions." .
SCR:019369 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II Autoscale Preparative LC/MSD" ;
rdfs:label "Agilent 1290 Infinity II Autoscale Preparative LC/MSD System" ;
definition: "Agilent Autoscale Preparative LC/MSD System enables automated transfer of purification methodologies from analytical to preparative scale purification." .
SCR:019370 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260 Infinity II Multi-Detector GPC/SEC" ;
rdfs:label "Agilent | 1260 Infinity II Multi-Detector GPC/SEC System" ;
definition: "The Multi-Detector GPC/SEC System delivers accurate, absolute molecular weights and sizes, and can be used to analyze polymers." .
SCR:019371 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II Autoscale Preparative LC" ;
rdfs:label "Agilent | 1290 Infinity II Autoscale Preparative LC System" ;
definition: "Agilent Autoscale Preparative LC System enables automated transfer of purification methodologies from analytical to preparative scale purification." .
SCR:019372 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II High-Throughput" ;
rdfs:label "Agilent | 1290 Infinity II High-Throughput System" ;
definition: "This high-throughput system utilizes autosampler capacity of up to 16 cooled microplates to achieve highest analysis speeds." .
SCR:019373 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II GPC/SEC" ;
rdfs:label "Agilent | 1290 Infinity II GPC/SEC System" ;
definition: "GPC SEC analysis solution that is capable of both analytical or microscale operation." .
SCR:019374 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II HDR-DAD Impurity Analyzer" ;
rdfs:label "Agilent | 1290 Infinity II HDR-DAD Impurity Analyzer System" ;
definition: "HDR-DAD Impurity Analyzer System detects and quantifies every component in your sample." .
SCR:019375 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II LC" ;
rdfs:label "Agilent | 1290 Infinity II LC System" ;
definition: "This LC System provides sample purification for applications from routine analysis to specialized workflow solutions." .
SCR:019376 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II Method Development" ;
rdfs:label "Agilent | 1290 Infinity II Method Development System" ;
definition: "UHPLC method development instrument provides maximum flexibility and performance to solve complex method development challenges." .
SCR:019377 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II Method Transfer" ;
rdfs:label "Agilent | 1290 Infinity II Method Transfer System" ;
definition: "Method Transfer System delivers similar retention times and peak resolution for methods that were developed on legacy HPLCs or UHPLCs from other vendors." .
SCR:019378 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II Multi-Method" ;
rdfs:label "Agilent | 1290 Infinity II Multi-Method System" ;
definition: "Multi-Method System is used for system utilization and automation with multiple method UHPLC capabilities for different users at same system." .
SCR:019379 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II Preparative LC" ;
rdfs:label "Agilent | 1290 Infinity II Preparative LC System" ;
definition: "Preparataive LC System offers automated sample injection and fraction collection, smooth control of LC valves, and access to analytical and preparative columns." .
SCR:019380 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1290 Infinity II Online SPE" ;
rdfs:label "Agilent | 1290 Infinity II Online SPE System" ;
definition: "Online SPE System automates solid phase extraction to enrich analytes, remove matrix components or lower detection limits." .
SCR:019381 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Infinity_II" ;
rdfs:label "Agilent | 1290 Infinity II Preparative LC/MSD System" ;
definition: "Preparative LC/MSD System enables high throughput purification and delivers high quality compounds." .
SCR:019382 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | 2100 Bioanalyzer Laptop" ;
definition: "This Bioanalyzer Laptop is used with Agilent Bioanalyzer to ensure processes are optimized." .
SCR:019383 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_240" ;
rdfs:label "Agilent | 240 AA Atomic Absorption System" ;
definition: "Combines rugged and hardware with easy to use software, making it best for low throughput laboratories." .
SCR:019385 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_240Z_AA" ;
rdfs:label "Agilent | 240Z AA Atomic Absorption System" ;
definition: "Atomic Absorption System is used for detection limits and analyzes difficult matrices." .
SCR:019386 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_280_DS" ;
rdfs:label "Agilent | 280-DS Mechanical Qualification System" ;
definition: "Mechanical Qualification System measures physical parameters of dissolution apparatus and enables the physical qualification of any dissolution apparatus." .
SCR:019387 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_280FS" ;
rdfs:label "Agilent | 280FS AA Atomic Absorption System" ;
definition: "Atomic Absorption System determines the concentration of all elements from a single aspiration." .
SCR:019390 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4100" ;
rdfs:label "Agilent | 4100 MP-AES" ;
definition: "Discontinued Superseded by 4210 MP AES System." .
SCR:019391 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_28OZ" ;
rdfs:label "Agilent | 280Z AA Atomic Absorption System" ;
definition: "Atomic Absorption System is used for detection limits and analyzes difficult matrices." .
SCR:019392 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_400_DS" ;
rdfs:label "Agilent | 400-DS Dissolution Apparatus 7" ;
definition: "Dissolution apparatus 7 is used for small volume dissolution testing of combination drug products." .
SCR:019393 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_019394" ;
rdfs:label "Agilent | 4150 TapeStation System" ;
NIFRID:synonym "Agilent 4150 Tapestation Genetic Analyzer" ;
definition: "System is automated electrophoresis platform for nucleic acid sample quality control. Allows analysis of DNA and RNA samples for up to 16 samples per run. Used for quality control of RNA and DNA samples in next-generation sequencing, biobank, or vaccine development workflows." .
SCR:019396 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4200_MP-AES" ;
rdfs:label "Agilent | 4200 MP-AES" ;
definition: "High sensitivity atomic emission spectrometer. MP-AES Instrument utilizes microwave plasma and as it runs on air instead of combustible gases, it can be installed in either centralized laboratory or remote location. Detection limits down to ppb levels and no sample pretreatment necessary." .
SCR:019397 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_240FS" ;
rdfs:label "Agilent | 240FS AA Atomic Absorption System" ;
definition: "Atomic Absorption System determines the concentration of all elements from a single aspiration." .
SCR:019399 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4210" ;
rdfs:label "Agilent | 4210 MP-AES" ;
definition: "MP-AES provides detection limits and large linear dynamic range." .
SCR:019400 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4300" ;
rdfs:label "Agilent | 4300 Handheld FTIR" ;
definition: "Handheld FTIR is used for mobile nondestructive testing and analysis of polymers, coatings, composites, bulk material, cleaning verification, and historical artifacts and artwork." .
SCR:019401 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4500 Portable FTIR",
"SCR_019403" ;
rdfs:label "Agilent | 4500 Portable FTIR Spectrometer" ;
definition: "Portable FTIR spectrometer supports efforts associated with on spot analysis of incoming materials and outgoing finished products in chemical, food and polymer industries." .
SCR:019402 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4500a" ;
rdfs:label "Agilent | 4500a Forensics FTIR Analyzer Package" ;
definition: "FTIR Analyzer Package identifies liquid or solid substances with little or no sample preparation." .
SCR:019404 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_490_Micro GC" ;
rdfs:label "Agilent | 490 Micro GC System" ;
definition: "Micro GC System is used for gas analysis and offers comprehensive system control, data acquisition and report generation.." .
SCR:019405 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_490_ Micro GC_Biogas" ;
rdfs:label "Agilent | 490 Micro GC Biogas Analyzer" ;
definition: "Micro GC Biogas Analyzer is used to analyze biogas and related sample streams and provide results." .
SCR:019406 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5100",
"SCR_019408" ;
rdfs:label "Agilent | 5100 Inductively-Coupled Plasma-Optical Emission Spectrometer" ;
NIFRID:synonym "Agilent 5110 ICP-OES Instrument" ;
definition: "Agilent 5110 ICP-OES Instrument enables synchronous radial and axial measurements and runs samples up to 55% faster using 50% less argon." .
SCR:019407 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_490-Mobile" ;
rdfs:label "Agilent | 490-Mobile Micro GC System" ;
definition: "490-Mobile Micro GC System allows analysis results to be viewed in full or reported in true/false." .
SCR:019409 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_490-PRO" ;
rdfs:label "Agilent | 490-PRO Micro GC System" ;
definition: "This gas chromatograph delivers information with modular design and MEMS technology based components." .
SCR:019410 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5400" ;
rdfs:label "Agilent | 5400 Fragment Analyzer System" ;
definition: "Fragment Analyzer System uses automated parallel capillary electrophoresis to redefine bounds of nucleic acid QC analysis" .
SCR:019411 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5300_Fragment" ;
rdfs:label "Agilent | 5300 Fragment Analyzer System" ;
definition: "Capillary electrophoresis instrument that can separate up to 48 or 96 samples in parallel. Enables DNA quality control for NGS libraries, gDNA, cfDNA, and large DNA fragments. RNA quality can be checked by this system where small RNA, total RNA, and mRNA vaccines are applicable for RNA integrity, sizing, and quantification analysis." .
SCR:019412 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_5500_Compact_FTIR" ;
rdfs:label "Agilent | 5500 Series Compact FTIR" ;
definition: "Portable FTIR analyzer from Agilent 5500 Series with compact dimentions are small-sized, mid-infrared region spectrometers designed to provide capabilities of larger, traditional FTIR systems." .
SCR:019413 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_55B" ;
rdfs:label "Agilent | 55B AA Atomic Absorption System" ;
definition: "55B AA Atomic Absorption System is used for flame atomization" .
SCR:019414 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5800_ICP-OES" ;
rdfs:label "Agilent | 5800 ICP-OES" ;
NIFRID:synonym "Agilent 5800 Inductively Coupled Plasma - Optical Emission Spectrometer" ;
definition: "Spectrometer to identify spectral interferences that can affect accuracy, providing recommendations allowing to quickly select the best wavelength and preventing unnecessary remeasurement.Uses embedded sensors, algorithms and diagnostics to identify problems, maximize uptime and minimize the number of samples you need to remeasure." .
SCR:019415 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5975C",
"SCR_019419" ;
rdfs:label "Agilent | 5975C Gas Chromatography Mass Spectrometer" ;
definition: "Agilent 5975C inert Mass Selective Detector delivers better MS resolution and the lowest mass deviation available and offers superior sensitivity and spectral integrity.The 5977 is the new Agilent GC/MSD platform and replaces the 5975C." .
SCR:019416 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5900" ;
rdfs:label "Agilent | 5900 ICP-OES Instrument" ;
definition: "ICP-OES Instrument is used to run samples with Synchronous Vertical Dual View (SVDV) and captures both the axial and radial views of the plasma in one reading." .
SCR:019417 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5200 Fragment Analyzer" ;
rdfs:label "Agilent | 5200 Fragment Analyzer System" ;
definition: "Fragment Analyzer System allows you to separate 12 samples in parallel in as little as 15 minutes." .
SCR:019418 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6230B" ;
rdfs:label "Agilent | 6230B Time of Flight (TOF) LC/MS" ;
definition: "Time of Flight LC/MS gives you full spectrum data for screening, profiling and identification of small molecules, large biologic compounds, and everything in between." .
SCR:019420 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5977B" ;
rdfs:label "Agilent | 5977B GC/MSD" ;
definition: "GC/MSD is used for environmental, chemical, petrochemical, food, forensic, pharmaceutical, and material testing." .
SCR:019421 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6470" ;
rdfs:label "Agilent | 6470 Triple Quadrupole Liquid Chromatography Mass Spectrometer System" ;
definition: "Triple quadrupole LC/MS system for commercial, regulatory, life sciences, and research applications. It has Agilent Jet Stream ion source and curved geometry collision cell. It detects target compounds at low levels in diverse matrices, while achieving wide linear dynamic range." .
SCR:019422 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6470A" ;
rdfs:label "Agilent | 6470A Triple Quadrupole LC/MS" ;
definition: "Triple Quadrupole LC/MS detects target compounds at low levels in diverse matrices, while achieving wide linear dynamic range." .
SCR:019423 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6530" ;
rdfs:label "Agilent | 6530 Q-TOF LC/MS" ;
definition: "Q-TOF LC/MS is used for analysis for applications in the pharmaceutical industry as well as life sciences and governmental agencies." .
SCR:019424 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6495C" ;
rdfs:label "Agilent | 6495C Triple Quadrupole LC/MS" ;
definition: "6495C triple quadrupole LC/MS system is used for peptide quantitation and applications that require ppt sensitivity." .
SCR:019425 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6530BA" ;
rdfs:label "Agilent | 6530BA Quadrupole Time of Flight Liquid Chromatography Mass Spectrometer" ;
definition: "Agilent 6530A Quadrupole Time of Flight LC/MS system analyzes low molecular weight compounds and delivers accurate mass quantitation." .
SCR:019426 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_5500_AFM" ;
rdfs:label "Agilent | 5500 Atomic Force Microscope" ;
definition: "Atomic force microscope with top-down scanning, environmental and temperature control, and modularity. The universal microscope base permits easy integration with an environmental chamber or an inverted optical microscope." .
SCR:019427 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6538" ;
rdfs:label "Agilent | 6538 Quadrupole Time of Flight Mass Spectrometer" ;
definition: "Quadrupole time of flight mass spectrometer suitable for applications in the pharmaceutical industry as well as life sciences and governmental agencies." .
SCR:019428 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6545",
"SCR_019429" ;
rdfs:label "Agilent | 6545 Liquid Chromatography" ;
NIFRID:synonym "Agilent 6545 LC/Q-TOF" ;
definition: "THIS RESOURCE IS NO LONGER AVAILABLE. Documented on August 4th, 2023. Mid-range Quadrupole Time-of-Flight liquid chromatography mass spectrometer designed for untargeted sample analysis, it enables broad screening, comprehensive profiling, identification of unknowns, mass accuracy, and isotopic fidelity." .
SCR:019430 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6545XT" ;
rdfs:label "Agilent | 6545XT AdvanceBio LC/Q-TOF" ;
definition: "AdvanceBio LC/Q-TOF is used to access information at intact protein level, automatically confirm sequence through peptide mapping, and understand PTMs." .
SCR:019431 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6560",
"SCR_019434" ;
rdfs:label "Agilent | 6560 Ion Mobility LC/Q-TOF" ;
NIFRID:synonym "Agilent 6560 Ion Mobility Quadrupole Time-of-Flight Liquid Chromatography Mass Spectrometer" ;
definition: "Ion Mobility LC/Q-TOF delivers unrivaled separation and selectivity by combining chromatography, ion mobility, and mass spectrometry.Quadrupole Time-of-Flight liquid chromatography mass spectrometer that combines chromatography, ion mobility, and mass spectrometry. The system has electrodynamic ion funnel technology and an attractive low field drift tube design." .
SCR:019432 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6546" ;
rdfs:label "Agilent | 6546 LC/Q-TOF" ;
definition: "LC/Q-TOF enables comprehensive workflows in metabolomics research, food safety, food authenticity, and environmental screening." .
SCR:019433 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6550" ;
rdfs:label "Agilent | 6550 iFunnel Q-TOF LC/MS" ;
definition: "This iFunnel Q-TOF LC/MS used for proteomics research allows you to acquire fragment data faster and reduces duty cycle substantially." .
SCR:019435 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7000D" ;
rdfs:label "Agilent | 7000D Triple Quadrupole GC/MS" ;
definition: "7000D GC TQ is used to create and validate many now standard GC MS MS methods." .
SCR:019436 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7010B" ;
rdfs:label "Agilent | 7010B Triple Quadrupole GC/MS" ;
definition: "Agilent 7010B Triple Quadrupole GC MS can produce at least 20 times as many ions as previous generation." .
SCR:019437 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7100" ;
rdfs:label "Agilent | 7100 Capillary Electrophoresis System" ;
definition: "Capillary Electrophoresis System offers fast separations with efficiency and resolution for analytical challenges." .
SCR:019438 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7650A" ;
rdfs:label "Agilent | 7650A Automatic Liquid Sampler" ;
definition: "Automataic Liquid Sampler provides fast and precise injections for Agilent GC and GC MS systems." .
SCR:019439 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7693A" ;
rdfs:label "Agilent | 7693A Automatic Liquid Sampler" ;
definition: "Automataic Liquid Sampler provides fast and precise injections for Agilent GC and GC MS systems." .
SCR:019440 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7697A" ;
rdfs:label "Agilent | 7697A Headspace Sampler" ;
definition: "Headspace Sampler includes Automatic Leak Check, which ensures each vial is leak free prior to analysis." .
SCR:019441 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7250" ;
rdfs:label "Agilent | 7250 GC/Q-TOF" ;
definition: "GC/Q-TOF delivers full spectrum, resolution, and mass data with wide range for identifying and quantifying GC amenable compounds." .
SCR:019442 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7700e" ;
rdfs:label "Agilent | 7700e ICP-MS" ;
definition: "Discontinued. ICP-MS Instruments offer matrix tolerance and unmatched interference removal and deliver fast, accurate, and consistently reproducible results." .
SCR:019443 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7700s" ;
rdfs:label "Agilent | 7700s ICP-MS" ;
definition: "Discontinued. Has interference removal utilizing ORS3 cell that removes spectral interferences using He mode, reaction mode using hydrogen cell gas and 3rd cell gas line for other reaction gases, cool plasma capability also delivers ionized elements in high-purity materials in matrices, built-in tuning and method templates for common semiconductor applications, including collision and reaction mode and cool plasma, lower heat output and reduced exhaust vent flow with cooling air flow management system, uses ICP-MS MassHunter software platform, and compact benchtop design." .
SCR:019444 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_708_DS" ;
rdfs:label "Agilent | 708-DS Dissolution Apparatus" ;
definition: "Modular system is used for manual or automated dissolution testing." .
SCR:019445 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7820A" ;
rdfs:label "Agilent | 7820A GC System" ;
definition: "System provides capabilities for wide range of application areas, meeting regulatory and SOP needs for small to medium sized labs." .
SCR:019446 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7696A" ;
rdfs:label "Agilent | 7696A Sample Prep Workbench" ;
definition: "Sample Prep Workbench provides consistent precision and eliminates manual errors in procedures such as dilutions, internal standard additions, and derivatization." .
SCR:019447 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7890/5975" ;
rdfs:label "Agilent | 7890/5975 GC/MS (open access)" ;
definition: "Single quadrupole instrument is used for fragment spectra for volatile compounds. It uses ChemStation open access software." .
SCR:019448 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7700x" ;
rdfs:label "Agilent | 7700x ICP-MS" ;
definition: "Discontinued. ICP-MS Instruments offer matrix tolerance and unmatched interference removal and deliver fast, accurate, and consistently reproducible results." .
SCR:019449 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_7890B_GC" ;
rdfs:label "Agilent | 7890B GC System" ;
definition: "7890 GC System features accurate temperature controls, precise injection systems, and high performance Electronic Pneumatic Control (EPC) modules for good retention time and area count repeatability." .
SCR:019450 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7890_5975" ;
rdfs:label "Agilent | 78905975 Gas Chromatograph Mass Spectrometer" ;
definition: "Single quadrupole mass spectrometer is used for fragment spectra for volatile compounds. It uses ChemStation open access software." .
SCR:019451 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7900" ;
rdfs:label "Agilent | 7900 ICP-MS" ;
definition: "Quadrupole mass spectrometry system provides low detection limits, dynamic range, and helium collision mode." .
SCR:019452 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7800" ;
rdfs:label "Agilent | 7800 ICP Mass Spectometer" ;
definition: "Quadrupole ICP mass spectrometer simplifies routine ICP MS analysis and provides matrix tolerance, range, and control of polyatomic interferences." .
SCR:019453 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8255" ;
rdfs:label "Agilent | 8255 Nitrogen Chemiluminescence Detector" ;
definition: "Nitrogen Chemiluminescence Detector produces linear and equimolar response to nitrogen compounds." .
SCR:019454 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8453" ;
rdfs:label "Agilent | 8453 UV-Vis spectrophotometer" ;
definition: "UV-visible spectrophotometer with diode-array technology, small footprint, prealigned deuterium and tungsten lamp light sources." .
SCR:019455 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8700" ;
rdfs:label "Agilent | 8700 LDIR Chemical Imaging System" ;
definition: "Chemical Imaging System provides highly automated approach for obtaining high definition chemical images of constituents on surface." .
SCR:019456 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8355" ;
rdfs:label "Agilent | 8355 Sulfur Chemiluminescence Detector" ;
definition: "Chemiluminescence Detector is used to simplify operation of centrifuge while maximizing productivity." .
SCR:019457 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_8800_ ICP-QQQ" ;
rdfs:label "Agilent | 8800 Triple Quadrupole ICP-MS" ;
definition: "Triple Quadrupole ICP-MS enables MS MS operation, providing control of reaction processes in the ORS3 collision and reaction cell." .
SCR:019458 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_850_DS" ;
rdfs:label "Agilent | 850-DS Dissolution Sampling Station System" ;
definition: "Sampling Station System offers latest capabilities for centralizing laboratory workflow of sample transfer, filtration and collection." .
SCR:019459 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_8890_GC" ;
rdfs:label "Agilent | 8890 GC System" ;
NIFRID:synonym "Agilent 8890 Gas Chromatograph" ;
definition: "Gas Chromatography System to deliver fast and accurate results with flexible configuration capabilities to address specific analysis demands.Gas chromatograph uses advanced electronic pneumatic control modules and high performance GC oven temperature control, which lead to extremely precise retention time reproducibility, the basis for all chromatographic measurement." .
SCR:019460 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8900" ;
rdfs:label "Agilent | 8900 Triple Quadrupole ICP-MS" ;
definition: "Triple Quadrupole ICP-MS offers range of configurations to cover applications from routine contract analysis to advanced research and high performance materials analysis." .
SCR:019461 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AA Duo" ;
rdfs:label "Agilent | AA Duo Atomic Absorption System" ;
definition: "AA Duo atomic absorption spectrometer is used for simultaneous operation of flame and graphite furnace." .
SCR:019462 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_990" ;
rdfs:label "Agilent | 990 Micro GC System" ;
definition: "Micro GC System is used to analyze gas samples." .
SCR:019463 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ADM" ;
rdfs:label "Agilent | ADM Flow Meter" ;
definition: "ADM Flow Meter measures gas streams with composite gas composition." .
SCR:019464 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8860" ;
rdfs:label "Agilent | 8860 GC System" ;
definition: "GC System is used for routine GC analysis and addresses wide range of routine GC application areas." .
SCR:019465 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BenchCel" ;
rdfs:label "Agilent | BenchCel Microplate Handler" ;
definition: "Microplate Handler is a storage and handling system used for integration with variety of laboratory devices." .
SCR:019466 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | Blood Alcohol Analyzer" ;
definition: "Dual channel blood alcohol analyzer delivers reproducible and court defendable data. Analyzer combines power of 8890 GC with either Agilent 8697 headspace sampler or Agilent 7697A headspace sampler, offering rapid cycle time to maximize sample throughput with no carryover." .
SCR:019467 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Artisan_Link_Pro" ;
rdfs:label "Agilent | Artisan Link Pro Special Staining System" ;
definition: "In vitro diagnostic device automates slide based special stains on formalin fixed, paraffin embedded tissue sections." .
SCR:019468 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_Bravo_BenchCel" ;
rdfs:label "Agilent | Bravo BenchCel Workstation" ;
definition: "Automated Liquid Handling Platform facilitates processing of high numbers of microplates in small footprint." .
SCR:019469 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AriaMx" ;
rdfs:label "Agilent | AriaMx Real-time PCR System" ;
definition: "Real-time PCR System is used for amplification, detection, and data analysis." .
SCR:019470 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AGD-100" ;
rdfs:label "Agilent | AGD-100 Gauge Controller" ;
definition: "Gauge Controller automatically identifies active gauge connected and is compatible with FRG 7xx, PVG 5xx, PCG 75x and CDG 500 series of active gauges." .
SCR:019471 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary_300" ;
rdfs:label "Agilent | Cary 300 UV-Vis System" ;
definition: "Discontinued. UV-Vis System is used in a range of applications and provides exceptional resolution and unmatched linearity." .
SCR:019472 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XTI" ;
rdfs:label "Agilent | Array Scanner XTI Array Scanner" ;
definition: "XTI Array Scanner provides automated cellular imaging and analysis and facilitates automated, quantitative cellular and subcellular imaging and analysis." .
SCR:019473 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_Bravo_NGS",
"SCR_019475" ;
rdfs:label "Agilent | Bravo NGS" ;
NIFRID:synonym "Agilent Bravo NGS Workstation" ;
definition: "Workstation is built on Bravo automated liquid handling robot preconfigured for library prep and target enrichment using Next-Generation Sequencing protocols. Workstation modules add microplate handling. Intuitive Agilent VWorks software enables setup of preprogrammed protocols and allows users to create custom protocols., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:019474 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BIO_DS" ;
rdfs:label "Agilent | BIO-DIS Reciprocating Cylinder Dissolution Apparatus" ;
definition: "Dissolution Apparatus is used for imitating pH changes that occur in body." .
SCR:019476 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary_3500" ;
rdfs:label "Agilent | Cary 3500 UV-Vis System" ;
definition: "UV-Vis System offers photometric performance together with measurement capabilities and multizone multicell." .
SCR:019477 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary 4000" ;
rdfs:label "Agilent | Cary 4000 UV-Vis System" ;
definition: "UV-Vis System is used for analyzing biotechnology samples with minimal sample preparation." .
SCR:019478 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary 5000" ;
rdfs:label "Agilent Cary 5000 UV-Vis-NIR System" ;
definition: "UV-Vis NIR System is used for materials science research and performs powerful analysis." .
SCR:019479 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary_60_Fiber" ;
rdfs:label "Agilent | Cary 60 Fiber Optic UV Dissolution System" ;
definition: "Cary 60 UV Vis Spectrophotometer provides optical transmission and reproducibility capabilities and extended linear photometric range for fiber optic analysis." .
SCR:019480 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary_60_Multicell" ;
rdfs:label "Agilent | Cary 60 Multicell UV Dissolution System" ;
definition: "Multicell UV Dissolution System takes samples simultaneously and reads each one sequentially." .
SCR:019481 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary_100" ;
rdfs:label "Agilent | Cary 100 UV-Vis System" ;
definition: "Discontinued. UV-Vis System is used in a range of applications and provides exceptional resolution and unmatched linearity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:019482 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary 630" ;
rdfs:label "Agilent | Cary 630 FTIR Spectrometer Benchtop System" ;
definition: "FTIR Spectrometer Benchtop System provides quantitative and qualitative information for routine analysis of solids, liquids, and gases." .
SCR:019483 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary 6000i" ;
rdfs:label "Agilent | Cary 6000i UV-Vis-NIR System" ;
definition: "UV Visible NIR spectrophotometer is used for photometric performance and materials characterization spectroscopy." .
SCR:019484 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary 610/620" ;
rdfs:label "Agilent | Cary 610/620 FTIR Microscopes" ;
definition: "Discontinued Agilent line of Cary 600 series infrared microscopy Cary 610 FTIR and chemical imaging systems Cary 620 FTIR." .
SCR:019485 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary_7000" ;
rdfs:label "Agilent | Cary 7000 Universal Measurement Spectrophotometer (UMS)" ;
definition: "Cary 7000 UMS collects UV Vis NIR spectra, characterizes optical components and delivers solutions for research, development and QA QC in optics, thin films coatings, solar and glass." .
SCR:019486 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_Cary_8454_UV-VIS" ;
rdfs:label "Agilent | Cary 8454 UV-Vis Diode Array System" ;
NIFRID:synonym "Agilent Cary 8454 UV-Vis System" ;
definition: "Agilent Cary 8454 UV-Visible spectroscopy system includes UV-Visible instrument based on leading LC photodiode array detector technology. System measures full spectrum, in as little as 0.1 seconds, has high throughput, low photometric noise, excellent wavelength accuracy and reproducibility, and excellent photometric stability. Spectrophotometer optical system is dual lamp set up consisting of deuterium-discharge lamp for ultraviolet wavelength range, and tungsten lamp for visible and short wave near-infrared wavelength range, from 190 to 1100nm." .
SCR:019487 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Insight100" ;
rdfs:label "Agilent | Cobalt Insight100 Series Aviation Security" ;
definition: "Insight100M system screens all container types and provides detection with ultra low false alarm rate for non metallic containers." .
SCR:019488 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary_60" ;
rdfs:label "Agilent | Cary 60 UV-Vis Spectrometer" ;
definition: "UV-Vis Spectrometer is used to measure life-science samples without sample photodegradation." .
SCR:019489 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_8890_Gas Chromatography" ;
rdfs:label "Agilent | CO-CO2 Analyzers" ;
definition: "8890 Gas Chromatography based CO-CO2 analyzers for analysis of permanent gases. System can be selected from standard or custom analyzer configurations to addresses specific analytical requirements." .
SCR:019490 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Insight200M" ;
rdfs:label "Agilent | Cobalt Insight200M Aviation Security - Bottle Screener for Liquid, Aerosols & Gels" ;
definition: "Airport security liquid explosive detection system LEDS screens all common container types with low false alarm rate." .
SCR:019491 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary Eclipse" ;
rdfs:label "Agilent | Cary Eclipse Fluorescence Spectrophotometer" ;
definition: "Fluorescence spectrophotometer gives you superior sensitivity, renowned reliability and enhanced sampling capabilities." .
SCR:019492 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FPD Plus" ;
rdfs:label "Agilent | Flame Photometric Detector Plus (FPD Plus)" ;
definition: "Flame Photometric Detector Plus utilizes photomultipliers, proprietary deactivation treatments and other design enhancements to help its lower MDLs in sulfur or phosphorous modes." .
SCR:019493 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SureTarget" ;
rdfs:label "Agilent | GC/MS SureTarget Water Pollutants Screener" ;
definition: "SureTarget Water Pollutants Screener provides fast data review and reporting of water pollutants and screening for unknown compounds." .
SCR:019494 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cary_8454_UV_Dissolution" ;
rdfs:label "Agilent | Cary 8454 UV Dissolution System" ;
definition: "UV Dissolution System analyzes single and select multicomponent products using diode array technology." .
SCR:019495 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Omnis" ;
rdfs:label "Agilent | Dako Omnis Solution for IHC & ISH" ;
definition: "Omnis Solution for IHC & ISH enables you to run IHC, IF, FISH and CISH simultaneously, each with combination of reagents." .
SCR:019496 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Dako" ;
rdfs:label "Agilent | Dako CoverStainer Automated H&E Staining" ;
definition: "CoverStainer Automated H&E Staining automates H&E process from baking, dewaxing and staining through to dehydrated, coverslipped and dried slide." .
SCR:019497 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | Greenhouse Gas Analyzer" ;
definition: "Greenhouse Gas Analyzer helps industrial customers monitor GHG emissions." .
SCR:019499 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EPA_200_8" ;
rdfs:label "Agilent | EPA 200.8 ICP-MS Water Analyzer" ;
definition: "ICP-MS Water Analyzer streamlines steps taken to put ICP MS instrument in production and implements regulated water analysis." .
SCR:019500 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_G1888" ;
rdfs:label "Agilent | G1888 Headspace Sampler" ;
definition: "Headspace Sampler is used for chemical performance over wide range of analyses without analyte degradation or loss." .
SCR:019501 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BR15" ;
rdfs:label "Agilent | HLD BR15 Bench Helium Leak Detector" ;
definition: "Bench Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems." .
SCR:019502 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HGC-536" ;
rdfs:label "Agilent | HGC-536 Portable Gauge Controller" ;
definition: "HGC-536 gauge controller displays vacuum readings in either numbers or easy-to-read graphs and helps baseline pumps by providing pump down graphics." .
SCR:019503 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BD15" ;
rdfs:label "Agilent | HLD BD15 Bench Dry Helium Leak Detector" ;
definition: "Bench Dry Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems." .
SCR:019504 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MD15" ;
rdfs:label "Agilent | HLD MD15 Mobile Dry Helium Leak Detector" ;
definition: "Mobile Dry Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems." .
SCR:019505 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BR30" ;
rdfs:label "Agilent | HLD BR30 Bench Helium Leak Detector" ;
definition: "Bench Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems." .
SCR:019506 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MD30" ;
rdfs:label "Agilent | HLD MD30 Mobile Dry Helium Leak Detector" ;
definition: "Mobile Dry Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems." .
SCR:019507 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MR15" ;
rdfs:label "Agilent | HLD MR15 Mobile Helium Leak Detector" ;
definition: "Mobile Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems." .
SCR:019508 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BD30" ;
rdfs:label "Agilent | HLD BD30 Bench Dry Helium Leak Detector" ;
definition: "Bench Dry Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems." .
SCR:019509 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Dako_Hybridizer" ;
rdfs:label "Agilent | Hybridizer" ;
definition: "Hybridizer is used for slide based fluorescence FISH and chromogenic CISH in situ hybridization." .
SCR:019510 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MR30" ;
rdfs:label "Agilent | HLD MR30 Mobile Helium Leak Detector" ;
definition: "Mobile Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems." .
SCR:019511 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1260" ;
rdfs:label "Agilent | Infinity 1260 Liquid Chromatography System" ;
definition: "A liquid chromatography system is an HPLC and UHPLC system that is compatible with legacy LC instrumentation and modular." .
SCR:019512 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HP_640" ;
rdfs:label "Agilent | HP 640 Notebook PC" ;
definition: "Notebook PC ensures that all Aria processes can be easily integrated into existing facilities and workflows without disrupting existing computing resources." .
SCR:019513 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PR02" ;
rdfs:label "Agilent | HLD PR02 Portable Helium Leak Detector" ;
definition: "Portable Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems." .
SCR:019514 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PD03" ;
rdfs:label "Agilent | HLD PD03 Portable Dry Helium Leak Detector" ;
definition: "Portable Dry Helium Leak Detector uses mass spectrometer tuned to detect helium to locate and measure small leaks in enclosed devices or systems." .
SCR:019515 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_Intuvo_9000_GC",
"SCR_019516",
"SCR_019521" ;
rdfs:label "Agilent | Intuvo 9000 GC System" ;
definition: "Gas Chromatography System eliminates column maintenance and changes columns and ensures reproducible chromatography and allows for higher throughput in laboratory.Gas chromatographer delivers reproducible and court defendable data.Provides fast, accurate and reproducible analysis of Class 1 and Class 2A B solvent content in pharmaceutical products." .
SCR:019517 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Micro_ECD" ;
rdfs:label "Agilent | Micro-ECD GC Selective Detector" ;
definition: "DC detector provides trace level analysis of halogenated organic compounds and aromatic pollutants." .
SCR:019518 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_mRP-C18" ;
rdfs:label "Agilent | mRP-C18 High-Recovery Protein Column" ;
definition: "High-Recovery Protein Column reduces or eliminates strong adsorption of proteins." .
SCR:019519 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MLC400" ;
rdfs:label "Agilent | MLC400 Laser Based Illumination System" ;
definition: "Laser Based Illumination System is used for fluorescence and confocal microscopy research applications." .
SCR:019520 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ISO_17294" ;
rdfs:label "Agilent | ISO 17294 ICP-MS Water Analyzer" ;
definition: "ICP-MS Water Analyzer streamlines steps taken to put ICP MS instrument in production and implement regulated water analysis." .
SCR:019522 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NovoCyte" ;
rdfs:label "Agilent | NovoCyte Advanteon Flow Cytometer" ;
NIFRID:synonym "NovoCyte Advanteon Flow Cytometer" ;
definition: "Advanteon Flow Cytometer accommodates multicolor flow cytometry assays and provides flexibility of 1, 2, or 3 laser options." .
SCR:019523 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Mouse_3" ;
rdfs:label "Agilent | Multiple Affinity Removal Spin Cartridge Mouse 3" ;
definition: "Multiple Affinity Removal Spin Cartridge removes three interfering high abundance proteins from mouse plasma samples." .
SCR:019524 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PAL" ;
rdfs:label "Agilent | PAL Auto Sampler Systems" ;
definition: "Auto Sampler Systems provide high sample capacity and greater automated sample preparation capability to optimize lab productivity." .
SCR:019525 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PHD-4" ;
rdfs:label "Agilent | PHD-4 Sniffer" ;
definition: "PHD-4 Sniffer detects small leaks in objects that have slight helium air pressure inside." .
SCR:019526 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Mx3005P" ;
rdfs:label "Agilent | Mx3005P Real Time PCR Machine" ;
definition: "Agilent Mx3005P is used for gene expression analysis, microarray data validation, SNP genotyping, pathogen detection, DNA methylation analysis, and chromatin immuno-precipitation studies." .
SCR:019527 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PPM_48" ;
rdfs:label "Agilent | Positive Pressure Manifold 48 Processor (PPM-48)" ;
definition: "Pressure Manifold 96 Processor is used to create consistent gas flow through every channel and ensures reproducibility from cartridge to cartridge." .
SCR:019528 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PPM_96" ;
rdfs:label "Agilent | Positive Pressure Manifold 96 Processor (PPM-96)" ;
definition: "Positive Pressure Manifold 96 Processor provides consistent gas flow for up to 96 cartridges in applications such as SPE and SLE." .
SCR:019529 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Oligo_Pro_II" ;
rdfs:label "Agilent | Oligo Pro II System" ;
definition: "Oligo Pro II System delivers accurate purity assessments of ssDNA and ssRNA oligonucleotides without use of dyes." .
SCR:019530 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RapidFire 365" ;
rdfs:label "Agilent | RapidFire 365 High-Throughput Mass Spectrometry System" ;
definition: "Mass Spectrometry System replaces HPLC with automated solid phase extraction SPE to increase throughput of LC MS analyses." .
SCR:019531 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PlateLoc" ;
rdfs:label "Agilent | PlateLoc Thermal Microplate Sealer" ;
definition: "Pressure Manifold 48 Processor accommodates deep well, assay, PCR, and compound storage microplates with variety of seals for different applications." .
SCR:019532 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RapID" ;
rdfs:label "Agilent | RapID Raw Material ID Verification System" ;
definition: "Raw Material ID Verification System extends high throughput spectroscopic analysis through clear packaging to nontransparent and colored containers." .
SCR:019533 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Resolve" ;
rdfs:label "Agilent | Resolve Handheld Through-Barrier Identification System" ;
definition: "Resolve handheld Raman spectrometer enables rapid identification of explosives, narcotics, toxic industrial chemicals, chemical warfare agents and other materials through sealed, opaque containers." .
SCR:019534 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Apparatus_7" ;
rdfs:label "Agilent | Reciprocating Holder Dissolution Apparatus 7" ;
definition: "Dissolution Apparatus 7 is used for automatic dissolution testing of dosage forms requiring a change of media, smaller volume or more vigorous agitation." .
SCR:019535 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RPS_1401_301" ;
rdfs:label "Agilent | RPS-1401/301 Roots Pumping System" ;
definition: "Roots Pumping System is used for optimum system integration and enables continuous operation and monitoring of vacuum systems." .
SCR:019536 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RGC_100" ;
rdfs:label "Agilent | RGC-100 and RGC-150 Rough Gauge Controllers" ;
definition: "Rough Gauge Controllers are used for general vacuum measurement in rough vacuum range, monitoring forelines, chamber evacuation, and crossover to high vacuum pumps." .
SCR:019537 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RPS_751_301" ;
rdfs:label "Agilent | RPS-751/301 Roots Pumping System" ;
definition: "Roots Pumping System is used for optimum system integration and enables continuous operation and monitoring of vacuum systems." .
SCR:019539 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XFe24" ;
rdfs:label "Agilent | Seahorse XFe24 Cell Analyzer" ;
definition: "Seahorse XFe24 Analyzers measure OCR and ECAR of live cells in a 24-well plate format." .
SCR:019540 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XF_HS" ;
rdfs:label "Agilent | Seahorse XF HS Analyzer" ;
definition: "Seahorse XF HS Analyzer measures OCR and ECAR of live cells in 8 well miniplate format." .
SCR:019542 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RPS_1001_301" ;
rdfs:label "Agilent | RPS-1001/301 Roots Pumping System" ;
definition: "Roots Pumping System is used for optimum system integration and enables continuous operation and monitoring of vacuum systems." .
SCR:019543 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XF" ;
rdfs:label "Agilent | Seahorse XF Imaging and Normalization System" ;
definition: "Seahorse XF Imaging and Normalization System acquires brightfield and fluorescence images, calculates cell number in each well and transfers images and cell counts into Wave 2.6 software." .
SCR:019544 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Dx" ;
rdfs:label "Agilent | SureScan Dx Microarray Scanner" ;
definition: "SureScan Dx microarray scanner system analyzes many genomics and cytogenetics microarrays." .
SCR:019545 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Seahorse XFe96" ;
rdfs:label "Agilent | Seahorse XFe96 Analyzer" ;
NIFRID:synonym "Agilent Seahorse XFe96",
"Agilent Seahorse XFe96 Cell Analyzer" ;
definition: "Seahorse XFe96 Analyzer measures OCR and ECAR of live cells in 96 well plate format." .
SCR:019546 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TPS_compact" ;
rdfs:label "Agilent | TPS-compact Turbo Pumping System" ;
definition: "TPS-compact Turbo Pumping System is used for pump operation, control, and recording of system parameters." .
SCR:019547 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | TapeStation Laptop" ;
definition: "Standardize your data acquisition and analysis by using the Agilent validated TapeStation Laptop together with the TapeStation instrument. The laptop comes with the TapeStation Software and required drivers pre-installed and offers maximum convenience and security." .
SCR:019548 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | Sulfur and Nitrosamine Analyzers" ;
definition: "8890 Gas Chromatography system with Sulfur or Nitrosamine detectors for detection of trace level contaminants often found in refinery and petrochemical products. System can be selected from standard or custom analyzer configurations to addresses specific analytical requirements." .
SCR:019549 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TPS_mobile" ;
rdfs:label "Agilent | TPS-mobile Turbo Pumping System" ;
definition: "TPS-mobile Turbo Pumping System enables pump operation, control, and recording of system parameters." .
SCR:019550 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SureCycler_8800" ;
rdfs:label "Agilent | SureCycler 8800 PCR Thermal Cycler" ;
definition: "PCR Thermal Cycler runs thermal cycling techniques including time and temperature increments, touchdown PCR, and temperature gradients." .
SCR:019551 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TPS_flexy" ;
rdfs:label "Agilent | TPS-flexy Turbo Pumping System" ;
definition: "TPS-flexy Turbo Pumping System is used for pump operation, control, and recording of system parameters." .
SCR:019552 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_304_FS_AG" ;
rdfs:label "Agilent | TwisTorr 304 FS AG Rack Controller" ;
definition: "TwisTorr 304 FS Rack Controller drives the pump in real time and adapts speed and power as required by gas flow, gas type, pressures, and other factors such as cooling." .
SCR:019553 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TPS_mini" ;
rdfs:label "Agilent | TPS-mini Tubro Pumping System" ;
definition: "TPS-mini Tubro Pumping System is used for turbo pump operation, control, and recording of system parameters." .
SCR:019554 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_74_FS_AG" ;
rdfs:label "Agilent | TwisTorr 74 FS AG Rack Controller" ;
definition: "TwisTorr 74 FS AG Rack Controller adapts speed and power as required by gas flow, gas type, pressures, and other factors such as cooling." .
SCR:019555 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_74_FS" ;
rdfs:label "Agilent | TwisTorr 74 FS onboard controller" ;
definition: "TwisTorr 74 FS onboard controller to read pressure via active gauges." .
SCR:019556 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_304_FS" ;
rdfs:label "Agilent | TwisTorr 304 FS Onboard Controller" ;
definition: "TwisTorr 304 FS Onboard Controller is used in analytical instruments such as mass spectrometry and microscopy systems and can reach low base pressures in experiments." .
SCR:019557 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TRS100" ;
rdfs:label "Agilent | TRS100 Quantitative Pharmaceutical Analysis System" ;
definition: "Quantitative Pharmaceutical Analysis System enables whole tablet or capsule content uniformity and polymorph screening for pharmaceutical finished product testing and formulation development." .
SCR:019558 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_305_FS" ;
rdfs:label "Agilent | TwisTorr 305 FS Remote Controller" ;
definition: "Remote control unit drives pump in real time and adapts speed and power as required by gas flow, gas types, pressures, and other factors such as cooling." .
SCR:019559 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_84_FS" ;
rdfs:label "Agilent | TwisTorr 84 FS onboard controller" ;
definition: "TwisTorr 84 FS onboard controller is used to read pressure via active gauges." .
SCR:019560 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_84_FS_AG" ;
rdfs:label "Agilent | TwisTorr 84 FS-AG Rack Controller" ;
definition: "TwisTorr 84 FS drives the pump in real time and adapts speed and power as required by gas flow, gas type, pressures, and other factors such as cooling." .
SCR:019561 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Vaya" ;
rdfs:label "Agilent | Vaya Raman Raw Material Identity Verification System" ;
definition: "Handheld spectrometer increases raw material identity verification throughput and reduces need for sampling." .
SCR:019562 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SPS_24" ;
rdfs:label "Agilent | Vac Elut SPS 24 Manifold" ;
definition: "Vac Elut SPS 24 Manifold processes up to 24 SPE cartridges simultaneously." .
SCR:019563 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XGS-600" ;
rdfs:label "Agilent | XGS-600 Gauge Controller" ;
definition: "This Gauge Controller accepts any of three different kinds of gauge cards which operate Agilent vacuum gauges." .
SCR:019565 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VS_C15" ;
rdfs:label "Agilent | VS C15 Component Leak Detector" ;
definition: "Modular leak testing package is used for applications in which leak detector components are more or less permanently mounted to system." .
SCR:019566 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ISS Chronos" ;
rdfs:label "ISS | Alpha Science Corporation ChronosFD" ;
definition: "ChronosFD offers all the benefits of a complete time-resolved fluorometer." .
SCR:019567 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XL-A" ;
rdfs:label "Beckman Coulter | analytical ultracentrifuges (Beckman XL-I and XL-A) XL-A" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 5th,2023. Centrifuge with in-solution characterization of proteins, oligomers, aggregates, particles, colloids, and small structures. It allows for In-solution testing in native conditions. It measures the relative change in the distribution of molecular weights, providing an efficient way to measure heterogeneity, stoichiometry and self-associating systems." .
SCR:019568 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_ZAG_DNA" ;
rdfs:label "Agilent | ZAG DNA Analyzer System" ;
definition: "Automated DNA fragment analysis system for high-throughput workflows such as genotyping, PCR amplicons, restriction digests, and microsatellite analysis. Runs thousands of DNA fragment samples per 24 hours. Provides high resolution of separation and reliable sizing information for DNA fragment sizes between 35 and 20000 base pairs. Low sample volume and short run time abilities for rapid qualification analysis of DNA fragments." .
SCR:019571 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_eSight" ;
rdfs:label "Agilent | xCELLigence RTCA eSight Real-Time Cell Analyzer (RTCA)" ;
definition: "Real-Time Cell Analyzer enables comprehensive insight into cell health, cell behavior, cell function and cell biology processes." .
SCR:019572 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Triple_Quad_5500" ;
rdfs:label "SCIEX | Triple Quad 5500 LC-MS/MS System" ;
NIFRID:synonym "Triple Quad 5500",
"Triple Quad 5500 LC-MS/MS System" ;
definition: "Triple Quad 5500 LC-MS/MS system delivers high levels of sensitivity and robustness for matrices." .
SCR:019573 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4700",
"SCR_020409" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 4700 Proteomics Analyzer" ;
NIFRID:synonym "Applied Biosystems 4700 Mass Spectrometer" ;
definition: "MALDI tandem time-of-flight mass spectrometer that provides a new level of productivity in high-resolution proteome analysis and complex systems biology. It can be used for carbohydrate, lipid, proteins, peptides, and other biological component analysis." .
SCR:019576 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PixCell II" ;
rdfs:label "BridgePath | Arcturus PixCell II Laser Capture Microdissection Microscope" ;
definition: "Arcturus (PXL-200) PixCell II LCM, built around an Olympus IX50 inverted microscope, uses a near-infrared diode laser and a CapSure Macro/HS LCM Cap to capture target cells. When the laser is fired, dimples are created in the cap. These dimples wet a matrix which attaches to a targeted cell, which can be lifted off the glass slide without taking other cells around it. Once the cells are captured they can be used for various experiments such as amplification of DNA or RNA from the isolated cell(s) for analyses. During microdissection, the laser never touches or damages any of the cells. Laser capture microdissection (LCM) is a technique that provides a method to obtain targeted cells from a multi-cell population." .
SCR:019578 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_492" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 492 Protein Sequencer" ;
definition: "Protein Sequencing System that cleaves N-terminal amino acids from protein/peptide chains and analyzes the resulting phenylthiohydantoin (PTH)-amino acid residues. It is composed of four integrated modules: the Procise Protein Sequencer, the Model 140C Microgradient Delivery System, the variable-wavelength UV detector, and a computer." .
SCR:019579 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Crystal Gryphon" ;
rdfs:label "Art Robbins | Crystal Gryphon Liquid Crystal Polymer Setup System" ;
definition: "Gryphon LCP is a setup system for Lipidic Cubic Phase sandwich plates and bicelle assays as well as traditional protein crystallography plates. A dedicated syringe based LCP head dispenses the protein, and a 96 head dispenses the buffer solutions. A 96 well sandwich plate can be sealed in less than 2 minutes. An optional non-contact dispenser can be added at any time to set up vapor diffusion sitting drop and hanging drop plates. The Crystal Gryphon is a small, fast and option for setting up all of your crystal plates. The Crystal Gryphon fits into tight lab spaces and tight lab budgets. The 96-channel positive displacement head quickly fills screen reservoirs and protein wells. The head has no disposable tips, so the cost of operation and environmental waste is minimized. The 1-channel non-contact dispenser quickly aspirates and dispenses your proteins allowing your plate to be sealed without evaporation being a problem. This dispense head is designed specifically to handle proteins, features flow-through washing and positive displacement aspiration, to handle all of your proteins." .
SCR:019581 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MFP_3D",
"SCR_020365" ;
rdfs:label "Oxford | Asylum Research MFP 3D Atomic Force Microscopes" ;
definition: "Asylum Research MFP-3D family of AFM's extend beyond basic topography measurements with diverse set of available accessories designed to enhance capabilities of the AFM. These include accessories for making nano-electric measurements, for example conductivity and piezoelectric response, measurements under magnetic fields, measuring nanomechanical properties, and controlling the temperature and humidity." .
SCR:019582 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ViiA" ;
rdfs:label "Thermo Fisher: Applied Biosystems | ViiA" ;
definition: "ViiA 7 System provides enhanced fluorescence detection and enables more accurate and sensitive data analysis." .
SCR:019584 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | B-Pure Water Purification System" ;
NIFRID:synonym "Barnstead Pure Water Purification System" ;
definition: "Water purification system that is used for pretreatment or deionization. A design provides the ability to add additional single, double or half size holders when need arises." .
SCR:019585 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Hyb4" ;
rdfs:label "Ark Scientific | Hyb4 Microarray Hybridization System" ;
definition: "Ark Scientific Hyb4 Microarray Hybridization System automates hybridization temperature cycles with efficient agitation and post-hybridization washes of DNA, oligo or protein microarrays." .
SCR:019586 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VF" ;
rdfs:label "Baker | EdgeGARD VF Laminar Flow Workbench" ;
definition: "EdgeGARD VF provides protection for samples and work procedures where product protection and particulate control are required." .
SCR:019588 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HF" ;
rdfs:label "Baker | EdgeGARD HF" ;
definition: "Baker's EdgeGARD HF provides HEPA-filtered air and product protection and precise control of airflow volumes and velocities." .
SCR:019589 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RO" ;
rdfs:label "Thermo Fisher | Barnstead LabTower RO Water Purification System" ;
definition: "This water purification system converts tap water into reverse osmosis RO water with integrated 100L storage and allows user to read parameters with ultra modern controller." .
SCR:019590 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Nxt" ;
rdfs:label "Thermo Fisher | Attune Nxt Flow Cytometer" ;
definition: "2020 Attune NxT Flow Cytometer makes multiparametric flow cytometry available to both new and experienced researchers." .
SCR:019591 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_C6" ;
rdfs:label "BD Biosciences | Accuri C6 Plus Flow Cytometer" ;
NIFRID:synonym "BD Accuri C6 Plus" ;
definition: """Compact 11 x 14.75 x 16.5-inch footprint, light weight of 30 lb, and operational simplicity,
benchtop flow cytometer is equipped with blue and red laser, two light scatter detectors and four fluorescence detectors with optical filters optimized for detection of many popular fluorochromes, including FITC, PE, PerCP-Cy5.5 and APC. Data are digitally collected over wide dynamic range.""" .
SCR:019592 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Aria_IIu",
"SCR_019598" ;
rdfs:label "BD Biosciences | FACSAria IIu High Speed Cell Sorter" ;
definition: "High Speed Cell Sorter's primary function is to examine complex populations of cells and yield pure populations of cells." .
SCR:019593 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BD Biosciences | inFlux Cell Sorter" ;
definition: "Flexible flow cytometry platform that has up to ten lasers and a modular architecture and a combination of detection capabilities, hands-on controls, and high performance. This resource is discontinued." .
SCR:019594 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TII" ;
rdfs:label "Thermo Fisher | Barnstead LabTower TII Water Purification System" ;
definition: "This water purification system converts tap water into purity water with complete solution integrating purification and tank." .
SCR:019595 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Aria I" ;
rdfs:label "BD Biosciences | FACSAria Aria I Flow Cytometer" ;
definition: "BD FACSAria cell sorter incorporates a fixed-alignment cuvette flow cell that can detect up to 13 colors, for a total of 15parameters." .
SCR:019596 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FACS Scan" ;
rdfs:label "BD Biosciences | FACScan Scan" ;
definition: "FACScan system analyzes cells as they pass through a focused laser beam, can be used for routine research applications, immunophenotyping, and DNA cell-cycle analysis." .
SCR:019597 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Celesta" ;
rdfs:label "BD Biosciences | FACS Celesta Flow Cytometer" ;
definition: "BD FACSCelesta flow cytometer makes multicolor flow cytometry more accessible and enables insights in cell analysis." .
SCR:019599 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FACSJazz",
"SCR_019875" ;
rdfs:label "BD Biosciences | FACS Jazz Cell Sorter" ;
definition: "Cell sorter that uses principles of flow cytometry to collect only cells of interest from heterogenous suspension. Can be configured with up to three lasers and eight parameters." .
SCR:019603 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Biomek_3000" ;
rdfs:label "Beckman Coulter | Biomek 3000 Liquid Handler" ;
NIFRID:synonym "Biomek 3000 Laboratory Automation Workstation" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 28,2024. Biomek 3000 workstation is single head instrument with series of interchangeable tools. Different tools provide options for performing variety of functions, including liquid transfer and plate washing operations and moving labware around the deck. The modular design of the Biomek 3000 workstation allows expansion of the instrument capabilities to include additional operations such as filtration, plate shaking, photometric microplate measurement, and high-capacity operation." .
SCR:019604 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_680" ;
rdfs:label "Beckman Coulter | 680 Chemistry Analyzer" ;
definition: "AU680 clinical chemistry analyzer delivers field-proven reliability and efficiency to laboratories around the world." .
SCR:019606 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_22R" ;
rdfs:label "Beckman Coulter | 22R Microfuge" ;
definition: "Beckman Coulter Microfuge 22R Refrigerated Centrifuge offers you flexible high speed and rapid cooling in an easy to use package. This quiet operating benchtop centrifuge has a sound rating of less than 58 dBa, meaning you can keep it nearby without being a distraction. This refrigerated microfuge is an best choice for pelleting of DNA, RNA and proteins, as well as cell virus isolation thanks to its high g-force of 21,920 x g, spinning at up to 14000 rpm. Parameters for this refrigerated benchtop centrifuge are easy to program from the user-friendly control panel set at the front of the unit. This micro centrifuge also features a timed function, where users can set time up to 30 minutes, or choose a continuous run or pulse. The Beckman Coulter Microfuge 22R Refrigerated Centrifuge keeps precious samples at 4C even at maximum speeds, and has stand by cooling to minimize downtime. The temperature can be set in 2C increments through a range of between -10 to 40C. Rotors for the refrigerated microcentrifuge are interchange able to meet your needs, and come with an aerosol tight lid to help minimize cross contamination in the event of a broken tube. All rotors for the Beckman Coulter Microfuge 22R Refrigerated Centrifuge are autoclavable at 121C." .
SCR:019607 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Access_2" ;
rdfs:label "Beckman Coulter | Access 2 Immunoassay System" ;
definition: "Access 2 contains the robustness of a reference laboratory immunoassay analyzer and provides control over performance, reliability and speed." .
SCR:019608 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LH500" ;
rdfs:label "Beckman Coulter | 500 Cell Counter" ;
definition: "COULTER LH 500 helps increase productivity, enhances linearity, improves diff flagging and reduces false positive flagging in white cell differential analysis." .
SCR:019609 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AcT_5diff_CP" ;
rdfs:label "Beckman Coulter | AcT 5diff CP (Cap Pierce) Hematology Analyzer" ;
definition: "Hematology Analyzer reduces manual sample handling and enhances safety by eliminating operators exposure to biohazards." .
SCR:019610 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AcT_diff" ;
rdfs:label "Beckman Coulter | AcT diff Hematology Analyzer" ;
definition: "AcT diff Hematology Analyzer is used for whole blood analysis from both venous and capillary collections." .
SCR:019611 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AU4800" ;
rdfs:label "Beckman Coulter | AU480 Chemistry Analyzer" ;
definition: "Chemistry Analyzer delivers efficiency for laboratories around world." .
SCR:019612 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Allegra" ;
rdfs:label "Beckman Coulter | Allegra 6R Table top centrifuge" ;
definition: "Beckman Allegra 6R is a Refrigerated Centrifuge features smart balance technology and has a high capacity with the GH-3.8 swing bucket rotor. This benchtop centrifuge and its rotor can accommodate a wide range of vessels, from 1.5 ml tubes to 750 ml bottles and generally including tubes, bottles, microplates, specialty bottles, and blood bags. The Allegra 6 reaches maximum speeds up to 6,100 RPM with maximum RCF of 5,710 x g. Refrigerated temperature range from -5C to 25C. Features automatic rotor imbalance detection, auto door interlock, rugged drive, and fine-tuned suspension for performance, reliability, and safety in the lab. This rotor reaches a maximum speed of 3,750 RPM." .
SCR:019613 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AE-4022" ;
rdfs:label "Beckman Coulter | AUTION ELEVEN AE-4022 Semi-automated Urine Chemistry Analyzer" ;
definition: "Semi-automated Urine Chemistry Analyzer provides clinically significant reporting ranges for urine chemistry" .
SCR:019614 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PA 800" ;
rdfs:label "Beckman Coulter | PA 800 Plus system" ;
definition: "PA 800 Plus Pharmaceutical Analysis System runs multiple characterizations from a single system and produces qualitative and quantitative analyses." .
SCR:019615 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Astrios" ;
rdfs:label "Beckman Coulter | Astrios Cell Sorter" ;
definition: "MoFlo Astrios is the new standard for cell sorting with functionality, speed, and improved sensitivity. It is designed for researchers who desire high productivity with more analytical capability and with biosafety solutions. The ergonomic design of Astrios makes it faster and easier to operate. All components requiring operator control are within easy reach. Beyond the optic expansion, novel software components enhance the instruments capabilities. The Touch Screen Control Panel facilitates... Read more" .
SCR:019616 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AU5800" ;
rdfs:label "Beckman Coulter | AU5800 Series Clinical Chemistry Analyzers" ;
definition: "Clinical chemistry analyzers processes up to 2,000 tests per hour with full menu of assays, including Therapeutic Drug Monitoring and Drugs of Abuse." .
SCR:019617 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AX-4030" ;
rdfs:label "Beckman Coulter | AUTION MAX AX-4030 Fully Automated Urine Chemistry Analyzer" ;
definition: "AUTION MAX AX-4030 generates accurate and reliable urine chemistry results without interruption and offers high throughput and continuous loading." .
SCR:019618 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Biomek_4000" ;
rdfs:label "Beckman Coulter | Biomek 4000 Automated Liquid Handler" ;
definition: "Beckman Coulter Biomek 4000 Automated Liquid Handler helps standardize daily pipetting routines, maintain sample quality and generate repeatable results." .
SCR:019619 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MALDI" ;
rdfs:label "Beckman Coulter | Bruker MALDI Biotyper System" ;
definition: "This microbiology system is used for microbial identification and can provide solution for ID and AST testing." .
SCR:019620 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Beckman Coulter | CellaVision DM1200 and CellaVision DM9600 Solutions" ;
definition: "CellaVision digital morphology solutions increase efficiency of hematology workflow systems for mid to large volume laboratories." .
SCR:019621 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ACT10" ;
rdfs:label "Beckman Coulter | ACT10 Cell differential counter" ;
definition: "AcT 10 is an and hematology analyzer with whole blood and pre-dilute capabilities from Beckman/Coulter. Beckman/Coulter AcT 10 automated analyzer is intended for testing in any smaller lab facility and low-volume office labs. Ten parameters including WBC, RBC, Hgb, Hct, MCV, MCH, MCHC, Plt, Lymph # and Lymph % can be measured using this Beckman/Coulter AcT 10 analyzer. For abnormal samples, partial differential option is available. Sample volume required for the whole blood mode is 12 �L and 20 �L in pre-dilute mode." .
SCR:019622 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2500" ;
rdfs:label "Beckman Coulter | AutoMate 2500 Family Sample Processing System" ;
definition: "Automated sample processing systems streamlines pre and post analytical processes and eliminates steps between sample receipt and analysis." .
SCR:019623 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_WASP_DT" ;
rdfs:label "Beckman Coulter | Copan WASP DT: Walk-Away Specimen Processor" ;
definition: "Copan WASP DT automated specimen processor is used for preanalytical specimen management to standardize and improve quality of specimen culturing activities." .
SCR:019624 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AcT_5diff_AL" ;
rdfs:label "Beckman Coulter | Coulter AcT 5diff AL Hematology Analyzer" ;
NIFRID:synonym "Beckman Coulter Coulter AcT 5diff AL (Autoloader) Hematology Analyzer" ;
definition: "AL Hematology Analyzer improves sample handling by eliminating manual sample loading." .
SCR:019625 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Biomek_NXp",
"SCR_019720" ;
rdfs:label "Beckman Coulter | Biomek NXp Robotic Liquid Handler" ;
definition: "Beckman Coulter Biomek NXp Robotic Liquid Handler is and automated liquid handler designed to handle every aspect of liquid handling, pipetting, dilution, dispensing and integration in to one compact unit that will let you add laboratory automation where you need it. This efficient robotic liquid handler is set with a Span-8 pipette model, 4 fixed tip heads and 4 disposables, with rotating gripper and 8 channel liquid level sensing for an efficient and hands-free workflow. This automated workstation has up to 12 deck positions, automated labware positioners, and labware stacking for on deck storage. The open-ended flexibility of this robotic handler helps keep your lab agile and adaptable to your needs." .
SCR:019626 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AcT_diff2" ;
rdfs:label "Beckman Coulter | Coulter AcT diff2 Hematology Analyzer" ;
definition: "Hematology Analyzer delivers performance in open and closed analysis modes, wide operating range and multiple output formats." .
SCR:019627 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CytoFLEX" ;
rdfs:label "Beckman Coulter | CytoFLEX Flow Cytometer" ;
definition: "Flow Cytometer provides performance needed for sensitivity and resolution throughout all configurations." .
SCR:019628 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LH_750" ;
rdfs:label "Beckman Coulter | Coulter LH 750 Hematology Analyzer" ;
definition: "Hematology Analyzer is used for automated nucleated red blood cell NRBC enumeration." .
SCR:019629 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LH_780" ;
rdfs:label "Beckman Coulter | Coulter LH 780 Hematology Analyzer" ;
definition: "Hematology Analyzer is used for automated nucleated red blood cell NRBC enumeration." .
SCR:019630 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DiaSorin_LIAISON_XL" ;
rdfs:label "Beckman Coulter | DiaSorin LIAISON XL Chemiluminescence Immunoassay Analyzer" ;
definition: "Chemiluminescence Immunoassay Analyzer closes care gap and addresses challenges with blood viruses and infectious diseases." .
SCR:019631 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DU_530" ;
rdfs:label "Beckman Coulter | DU 530 Spectrophotometer" ;
definition: "This spectrophotometer functions with single cell module and supports alternative cell holders, like 16 mm test tube, 1 cm standard, 10cm rectangular turbidity, and 50uL microcell." .
SCR:019632 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DxA_5000" ;
rdfs:label "Beckman Coulter | DxA 5000 Total Laboratory Automation System" ;
definition: "This Automation System is used to provide consistent turnaround time for all samples and level of comprehensive pre analytical sample quality." .
SCR:019633 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DxC 700 AU" ;
rdfs:label "Beckman Coulter | DxC 700 AU Chemistry Analyzer" ;
definition: "This chemistry analyzer achieves maximal uptime, high reliability, and precise performance ." .
SCR:019634 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DxH 6000" ;
rdfs:label "Beckman Coulter | DxH 600 Hematology Analyzer" ;
definition: "Hematology Analyzer uses multi dimensional, high definition technology to characterize individual cells." .
SCR:019635 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DxH_800" ;
rdfs:label "Beckman Coulter | DxH 800 Hematology Analyzer" ;
definition: "DxH 800 hematology analyzer utilizes data about individual cell size, shape and structure to provide high quality results." .
SCR:019636 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DxH Slidemaker" ;
rdfs:label "Beckman Coulter | DxH Slidemaker Stainer II Cellular Analysis System" ;
definition: "Cellular Analysis System prepares slides automatically based on customizable rules." .
SCR:019637 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DxM_MicroScan" ;
rdfs:label "Beckman Coulter | DxM MicroScan WalkAway Microbiology System" ;
definition: "MicroScan WalkAway Microbiology System detects emerging and critical antimicrobial resistance." .
SCR:019638 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DxH_520" ;
rdfs:label "Beckman Coulter | DxH 520 Hematology Analyzer" ;
definition: "Hematology analyzer helps low volume laboratory enhance patient care." .
SCR:019639 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Gallios" ;
rdfs:label "Beckman Coulter | Gallios Flow Cytometer" ;
definition: "Flow Cytometer provides efficient acquisition of up to 12 parameters to achieve accurate size measurement and high resolution and processing." .
SCR:019640 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_iChemVELOCITY" ;
rdfs:label "Beckman Coulter | iChemVELOCITY Urinalysis Instrument" ;
definition: "Urinalysis Instrument used for automated urine chemistry analysis to identify possible ascorbic acid interference with key chemistry assays." .
SCR:019641 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DxH 900" ;
rdfs:label "Beckman Coulter | DxH 900 Hematology Analyzer" ;
definition: "900 Hematology Analyzer delivers reliable, reportable WBC differential results." .
SCR:019642 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IMMAGE_800" ;
rdfs:label "Beckman Coulter | IMMAGE 800 Protein Chemistry Analyzer" ;
definition: "Protein Chemistry Analyzer delivers Dual Detection Rate Nephelometric Technology and broad test menu including enhanced UDR capability." .
SCR:019644 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_iQ200" ;
rdfs:label "Beckman Coulter | iQ200 Series Urinalysis Microscopy Instrument" ;
definition: "iQ200 series automates sample microscopy and produces shortened TAT for low to high volume workloads." .
SCR:019645 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_autoSCAN_4" ;
rdfs:label "Beckman Coulter | MicroScan autoSCAN-4 System" ;
definition: "Provides simplified ID AST testing." .
SCR:019646 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_iQ" ;
rdfs:label "Beckman Coulter | iQ Series Urinalysis Workcell" ;
definition: "iQ Workcell series of automated walk away workcells analyzes urine chemistry and deliver standardized and accurate results." .
SCR:019647 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_iRICELL" ;
rdfs:label """Beckman Coulter | iRICELL Series
Urinalysis Workcell""" ;
definition: "Urinalysis Workcell combines urine chemistry and microscopy in fully automated, walk away workcell." .
SCR:019648 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Moflo XDP" ;
rdfs:label "Beckman Coulter | Moflo XDP" ;
definition: "Cell sorter that combines high-speed sorting capability with an open flexible design to enable a wide variety of sorting applications." .
SCR:019649 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_WalkAway_plus" ;
rdfs:label "Beckman Coulter | MicroScan WalkAway plus Microbiology System" ;
definition: "Microbiology system used for mid to high volume identification and antibiotic susceptibility testing." .
SCR:019650 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PK7400" ;
rdfs:label "Beckman Coulter | PK7400 Automated Microplate System" ;
definition: "Analyzer that uses agglutination technology and a comprehensive blood-typing menu to deliver the highest throughput of blood donor immunohematology testing." .
SCR:019651 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_L90K" ;
rdfs:label "Beckman Coulter | L-90K Ultracentrifuge" ;
definition: "Ultracentrifuge is used for centrifugation of subcellular particles, virus isolations, and high purity plasmid DNA." .
SCR:019652 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_L-90K",
"SCR_019673" ;
rdfs:label "Beckman Coulter | Optima L-90K Ultracentrifuge" ;
NIFRID:synonym "Beckman L-90K Ultracentrifuge" ;
definition: "Beckman Optima L-90K Ultracentrifuge has a performance capability of 694,000 x g at up to 90,000 rpm. This versatile floor model is compatible with a wide range of superior rotors including zonal and continuous flow for large-volume separations. The Optima L-90 K is for applications such as subcellular particles and virus isolations, and high-purity plasmid DNA. Featuring an imbalance-tolerant drive, the L-90 K provides unmatched reliability with its highly efficient vacuum-encased induction drive which allows smooth and quiet performance. Plus, this ultracentrifuge model is sized for efficient operation within laminar flow hoods. Equipped with easy-to-use, environment-friendly and microprocessor based control cooling systems, the Beckman L-90 K eliminated the use of CFCs and other dangerous liquid refrigerants. This Beckman centrifuge also has an overspeed system to ensure that rotors do not exceed maximum speed." .
SCR:019653 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PK7300" ;
rdfs:label "Beckman Coulter | PK7300 Automated Microplate System" ;
definition: "Analyzer used for pre-transfusion, automated blood donor testing that features 300 sample per hour throughput, full online system status updates, data transfer capabilities, and aspiration and dispense monitoring intelligence." .
SCR:019654 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CritSpin" ;
rdfs:label "Beckman Coulter | StatSpin CritSpin Digital Reader" ;
definition: "Digital reader with a large display used for hematocrit determinations." .
SCR:019655 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XL-I" ;
rdfs:label "Beckman Coulter | ProteomeLab XL-I AUC XL-I" ;
definition: """THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 5th,2023.
ProteomeLab XL-A/XL-I is a centrifuge with in-solution characterization of proteins, oligomers, aggregates, particles, colloids, and small structures delivers accurate results you can rely on time and again. In-solution characterization allows for testing in native conditions, meaning you determine the sample testing environment that best suits your needs. The column-free separating technique of the ProteomeLab XL-A/XL-I measures the relative change in the distribution of molecular weights, providing an efficient way to measure heterogeneity, stoichiometry and self-associating systems. And, because the measurements are based on the first principles of thermodynamics and hydrodynamics, no standards or calibrations are required. As a result, you spend less time on setup and more time on discovery. Our analytical ultracentrifuge platform offers a variety of customizable options, to meet your needs. Sensitive absorbance optics enable analysis of most samples, and interference optics can be used for low concentrations. Both systems can be implemented simultaneously, to maximize data acquisition in a single run. Additionally, we offer two different rotor configurations, and a variety of cell types, to enable multiple experimental designs. The wide range of rotational velocities also allow investigators to probe protein size, dimerization, and binding constants.""" .
SCR:019656 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cytofuge_2" ;
rdfs:label "Beckman Coulter | StatSpin Cytofuge 2 Cytocentrifuge" ;
definition: "Personal cytocentrifuge that provides high quality sample preparations with understandable controls and snap-seal filter concentrators." .
SCR:019657 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Express_3" ;
rdfs:label "Beckman Coulter | StatSpin Express 3 Centrifuge" ;
definition: "Primary tube centrifuge that can spin eight tubes up to 10mL and provides high quality plasma or serum in two to five minutes." .
SCR:019658 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Express_2" ;
rdfs:label "Beckman Coulter | StatSpin Express 2 Centrifuge" ;
definition: "Primary tube centrifuge that prepares high quality plasma or serum samples in two minutes." .
SCR:019659 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_B05033" ;
rdfs:label "Beckman Coulter | Power Link Workcell" ;
definition: "Workcell that combines a chemistry and immunoassay testing to streamline laboratory operations and provide a rapid TAT." .
SCR:019660 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MP" ;
rdfs:label "Beckman Coulter | StatSpin MP Centrifuge" ;
definition: "Centrifuge that is used for centrifuging microhematocrit tubes for packed cell volume determination, as well as rapid separation of whole blood and preparation of urine sediment for microscopic analysis." .
SCR:019661 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Express_4" ;
rdfs:label "Beckman Coulter | StatSpin Express 4 Centrifuge" ;
definition: "High-speed horizontal centrifuge that can produce high-quality serum or plasma separation in 3-, 5- or 10-minute cycles." .
SCR:019662 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_UniCel_DxH" ;
rdfs:label "Beckman Coulter | UniCel DxH Connected Workcell Solutions" ;
definition: "Series of connected hematology workcells used for multidimensional high-definition cellular analysis." .
SCR:019663 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Dxl_600" ;
rdfs:label "Beckman Coulter | UniCel DxI 600 Access Immunoassay System" ;
definition: "Immunoassay analyzer with a throughput of up to 200 tests per hour and up to 60 samples on board." .
SCR:019664 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Vicell XR",
"SCR_019672" ;
rdfs:label "Beckman Coulter | Vi-CELL XR Cell Viability Analyzer" ;
definition: "Cell counter that provides an automatic means to perform the Trypan Blue Dye Exclusion method, allowing users to load up to 9 samples at once for easy and automated cell analysis, and offers pre-programmed and customizable analysis options for consistent and accurate analysis." .
SCR:019665 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MoFlo XDP" ;
rdfs:label "Beckman Coulter | Moflo XDP Cell Sorter Flow Cytometer" ;
definition: "Cell sorter that can perform 70,000 sorts per second and offers a wide variety of sorting applications." .
SCR:019666 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CyAn ADP" ;
rdfs:label "Beckman Coulter | CyAn ADP High-Speed Analyzer" ;
definition: "Flow cytometer engineered for precision analysis of cells, bacteria, and other similarly sized particles. CyAn ADP utilizes three excitation lines with independent, alignment-free focusing optics, simultaneous nine color and two scatter parameters, analysis rates of 70,000 events per second, a full 9 × 9 inter-laser compensation matrix, and high sensitivity. The instrument is optimized for cell cycle, kinetics, fluorescent protein work, and multi-color immunophenotyping. Rare-event analysis, such as MHC Dextramer studies, and no-lyse whole blood applications are easily performed on the CyAn ADP. The instrument also provides simplified compensation before, during, and after acquisition in all fluorescent parameters." .
SCR:019667 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Aria IIu" ;
rdfs:label "BD Biosciences | Aria IIu Flow Cytometer" ;
definition: "Aria has four lasers, 405, 488, 561 and 633 nm, and can detect light in sixteen photomultiplier tubes. Its primary function is to examine complex populations of cells and yield pure populations of cells. The Aria can sort lymphocytes at a rate of approximately 15,000 events per second. For larger cells, the rate is much slower in order to optimize the passage of cells through the instrument. Cells from single populations can be sorted into 96-well plates. Alternatively, the Aria can sort into two 15-ml tubes or four 5-ml tubes. The Aria can purify samples that are simply positive and negative for a single fluorophore or as complex as nine-color samples with intricate gating schemes. The BD FACSAria IIu cell sorter is a high speed benchtop digital flow cytometer equipped with a sensitive, fixed-alignment cuvette flow cell. It has three spatially separated lasers - 405 nm, 488 nm and 633 nm. Its primary function is to analyze complex populations of cells and yield pure populations of cells meeting defined criteria. The sorter can purify samples that are simply positive and negative for a single fluorophore or as complex as multi-color samples with complex gating strategies. Sorting can be performed into two or four tubes with speeds up to 25,000 events/second. The system sorts by incorporating cells from the sample tube into a stream of sterile PBS. The stream is interrogated by the lasers at the flow cell and the system electronics keeps track of each cell as they pass through the laser and determines specific cells that meet the sort criteria. A transducer vibrates the stream and induces droplet formation, with cells in the stream being incorporated into the droplets. If a cell meets the sorting criteria and is in the last drop before the break off, the instrument will charge that drop. The charged droplet is then deflected into the proper collection tube by the charge plates. Different cell types can be sorted with the use of 70 �m, 85 �m and 100 �m nozzles. If you need a yellow-green (561 nm) laser, check the BD FACSAria III instead." .
SCR:019669 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_J2-21M/E" ;
rdfs:label "Beckman Coulter | J2-21M/E Centrifuge" ;
definition: "Beckman J2-21M is a high speed floor model centrifuge which features a brushless induction drive and maintenance-free system. Capable of performing at a speed of 21,000 rpm and forces up to 51,500 g, the J2-21M offers superior functionality, accuracy, and productivity. The system's microprocessor-controlled design provides quick and automatic operation. The J2-21M Centrifuge stores up to 10 programs and eliminates errors in repetitive runs. The system also offers a choice of ten dual-ramp acceleration and deceleration settings for gentle starts and quick running." .
SCR:019670 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Statspin" ;
rdfs:label "Beckman Coulter | StatSpin VT Centrifuge" ;
definition: "Centrifuge that is designed for veterinarians and used for centrifuging microhematocrit tubes for packed cell volume determination, as well as rapid separation of whole blood and preparation of urine sediment for microscopic analysis." .
SCR:019671 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Z1_Particle_Counter" ;
rdfs:label "Beckman Coulter | Z1 Particle Counter" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Cell counter that offers rapid cell sample analyses for a single cell type or diverse cell population" .
SCR:019674 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_L8_70M" ;
rdfs:label "Beckman Coulter | L8-70M Ultracentrifuge" ;
definition: "Ultracentrifuge that provides 9 slow acceleration profiles for greater protection of the gradient and sample-to-gradient interfaces and 10 slow deceleration profiles for integrity of separations. It has 3 modes of operation: manual, automatic and programmed" .
SCR:019675 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_166" ;
rdfs:label "Beckman Coulter | Model 166 UV detector" ;
definition: "Variable wavelength UV/Vis HPLC detector with low noise and drift over a wide wavelength range." .
SCR:019677 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ATA-27" ;
rdfs:label "Estigen | Beecher ATA-27 Automated Tissue Arrayer" ;
definition: "Automated Tissue Arrayer ATA-27 is designed for construction of high-density tissue microarray blocks fast, accurate and . Automated Tissue Arrayer ATA-27 is intended for laboratories requiring higher throughput in array production. It eliminates the tedious manual punching procedure from array construction workflow. After planning and designing the array layout using dedicated software, ATA-27 creates array blocks automatically using robotics to measure block heights, retrieve donor tissue cores, create holes in paraffin matrix and deposit tissue cores into holes." .
SCR:019678 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4000MP" ;
rdfs:label "Bio-Rad | 4000MP Versa Doc" ;
definition: "Imager for proteomic studies that has the ability to image colorimetric and fluorescently-stained gels and blots to detect chemiluminescent and other low-light. It features red, green, blue and white epi-illumination and UV and white transillumination." .
SCR:019679 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Biacore_T100" ;
rdfs:label "GE | Biacore T100 System" ;
definition: "System for analysis of biomolecular interactions, based on GE Healthcare surface plasmon resonance (SPR) technology. Control Software supplied with system offers easy-to-use wizards for assay development and common applications together with flexible facilities for designing custom analysis methods using graphical interface called Method Builder." .
SCR:019680 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MoFlo Legacy" ;
rdfs:label "Beckman Coulter | MoFlo Legacy" ;
definition: "MoFlo is a high speed cell sorter with three lasers, 9 colors, and two way sorting capability. It is equipped with a solid state 488nm laser, an I90 argon ion multiline UV laser, and an I70C spectrum tunable laser (providing wavelengths from 440nm to 568nm). A variety of collection devices may be used including: microscope slides, micro-tubes, 12 x 75ml test tubes, 15 or 50ml falcon tubes, as well as multi-well plates (6, 24, 96, or 384). This instrument is operated by staff on a fee for service basis." .
SCR:019681 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Biologic_LP",
"SCR_019682" ;
rdfs:label "Bio-Rad | Biologic Protein Purification System" ;
NIFRID:synonym "Bio-Rad BioLogic LP System" ;
definition: "Low-pressure chromatography system that is used for biomolecule purification with nucleic acid and protein detection. It has 254 and 280 nm filters, conductive cell, and a peristaltic pump with flow rate range of 0.05 to 40 ml per min." .
SCR:019683 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BR_2000" ;
rdfs:label "Bio-Rad | BR-2000 Vortexer" ;
definition: "Mixer that is designed for variety of mixing applications from gentle sample mixing to resuspending cell pellets." .
SCR:019684 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Chemidoc" ;
rdfs:label "Bio-Rad | Chemidoc Gel Imaging System" ;
definition: "Gel imaging system that enables visible light,RGB, far red, near infrared, FR, NIR, fluorescence and chemiluminescence detection. It visualizes proteins without gel staining." .
SCR:019685 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PDS 1000" ;
rdfs:label "Bio-Rad | 1000 1000" ;
definition: "PDS-1000/He is a Particle Delivery System that accelerates nucleic acid coated gold or tungsten microparticles (0.6 1.6 �m) to velocities necessary to transfect cells, tissues, or organelles. The system uses a burst of high-pressure helium gas to accelerate a plastic macrocarrier disk carrying microparticles toward target cells. The helium pressure used to propel the macrocarrier is determined by the choice of rupture disk, a plastic seal designed to burst at a specific pressure. A stopping screen retains the macrocarrier while allowing the microparticles to pass through and penetrate the target cells. To increase the efficiency of the process, the chamber may be evacuated to subatmospheric pressures, reducing the frictional drag on the microparticles as they travel toward the target cells" .
SCR:019686 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DuoFlow" ;
rdfs:label "Bio-Rad | BioLogic DuoFlow Medium-Pressure Chromatography Systems" ;
definition: "Series of chromatography systems that offer multiple system configurations, optional upgrades, and common software platform and are suitable for analytical and preparative chromatography." .
SCR:019687 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DCode" ;
rdfs:label "Bio-Rad | DCode Universal Mutation Detection System" ;
definition: "Universal mutation detection system that can scan for single-base changes by using a variety of electrophoretic techniques, including single-stranded conformation polymorphism, denaturing gradient gel electrophoresis, constant denaturing gel electrophoresis, and temporal temperature gradient gel electrophoresis." .
SCR:019688 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_C1000" ;
rdfs:label "Bio-Rad | C-1000 Thermal Cycler" ;
definition: "Thermal cycler with a touchscreen interface and dual 48 well reaction module that allows multiple independent protocols to be run simultaneously." .
SCR:019689 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ELx_808",
"SCR_019739" ;
rdfs:label "Agilent: BioTek | ELx808 Microplate Reader" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 31,2023. Microplate reader that offers performance for many applications, from endpoint to fast kinetic protocols. Offers 4 Zone temperature control, which optimizes conditions for temperature sensitive assays.Can be used for Kinetic ELISA, Protein quantification, ELISA, Endotoxin analysis, and Microbial growth assays. It is used with Gen5 software." .
SCR:019690 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Chemidoc_XRS" ;
rdfs:label "Bio-Rad | Chemidoc XRS Gel Imaging System" ;
definition: "Gel imaging system that is based on CCD detection technology and options for fluorescence, colorimetry, densitometry, chemiluminescence, and chemifluorescence." .
SCR:019691 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Experion" ;
rdfs:label "Bio-Rad | Experion Automated Electrophoresis System" ;
definition: "Electrophoresis system that automates nucleic acid and protein analysis and performs multiple electrophoresis steps in one platform." .
SCR:019692 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ddSEQ" ;
rdfs:label "Bio-Rad | ddSEQ Single-Cell Isolator" ;
definition: "Single-cell isolator that utilizes disposable microfluidic cartridges to coencapsulate single cells and barcodes into subnanoliter droplets, where cell lysis and barcoding occur." .
SCR:019693 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EP_1" ;
rdfs:label "Bio-Rad | Model EP-1 Econo Pump" ;
definition: "Peristaltic pump that is used for low pressure chromatography or for pumping liquids in general laboratory procedures." .
SCR:019694 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_16K" ;
rdfs:label "Bio-Rad | Model 16K Microcentrifuge" ;
definition: "Benchtop microcentrifuge with an 18-place rotor that can accommodate 1.5 and 2.0 ml tubes." .
SCR:019695 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Discover_100_Pro" ;
rdfs:label "Bio-Rad | NGC Discover 100 Pro Chromatography System" ;
definition: "Chromatography system that includes 100 ml/min pumps, multi-wavelength (UV/Vis) and conductivity detection, expanded scouting options, large-sample injection, outlet valve and column switching of up to 5 columns, for method development. It also performs fraction collection in combination with large-volume collection using a 12-port outlet valve." .
SCR:019696 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Discover_100" ;
rdfs:label "Bio-Rad | NGC Discover 100 Chromatography System" ;
definition: "Chromatography system that includes 100 ml/min pumps, multi-wavelength (UV/Vis) and conductivity detection, expanded scouting options, large-sample injection, outlet valve and column switching of up to 5 columns, for method development." .
SCR:019697 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Quest_100" ;
rdfs:label "Bio-Rad | NGC Quest 100 Chromatography System" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 31,2023. Chromatography system that is used for the all-purpose purification of biomolecules from samples in the mg to g range with accurate buffer gradients and high-resolution separations." .
SCR:019698 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Scout_10" ;
rdfs:label "Bio-Rad | NGC Scout 10 Chromatography System" ;
definition: "Chromatography system that includes 10 ml/min pumps, single-wavelength (UV) and conductivity detection, buffer blending options, for rapid pH scouting during sample purification." .
SCR:019699 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Quest_100_Plus" ;
rdfs:label "Bio-Rad | NGC Quest 100 Plus Chromatography System" ;
definition: "Chromatography system that is used for the all-purpose purification of biomolecules and simultaneous detection of proteins, peptides, nucleic acids, and chromogenic molecules at the mg to g scale with accurate buffer gradients and high-resolution separations." .
SCR:019700 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Scout_10_Plus" ;
rdfs:label "Bio-Rad | NGC Scout 10 Plus Chromatography System" ;
definition: "Chromatography system that includes 10 ml/min pumps, multi-wavelength (UV/Vis) and conductivity detection, buffer blending options, for rapid pH scouting during the purification of proteins, peptides, and nucleic acids." .
SCR:019701 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Scout_100" ;
rdfs:label "Bio-Rad | NGC Scout 100 Chromatography System" ;
definition: "Chromatography system that is used for the quick separation of proteins and peptides when rapidly scouting purification conditions with automated gradients and buffer preparation during purifications at the mg to g scale." .
SCR:019702 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Pharos_FX" ;
rdfs:label "Bio-Rad | Pharos FX Molecular Imager System" ;
definition: "Molecular imager system for fluorescence imaging that is used for analysis of DNA, RNA, or protein samples in gels, blots, or microplates." .
SCR:019703 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Scout_100_Plus" ;
rdfs:label "Bio-Rad | NGC Scout 100 Plus Chromatography System" ;
definition: "Chromatography system that is used for simultaneously detecting proteins, peptides, nucleic acids, and chromogenic molecules using expanded automated gradients, blending and scouting options during purifications at the mg to g scale." .
SCR:019704 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Profinia" ;
rdfs:label "Bio-Rad | Profinia Protein Purification Instrument" ;
definition: "Discontinued.Protein Purification Instrument." .
SCR:019705 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ProteOn_XPR36",
"SCR_018619" ;
rdfs:label "Bio-Rad | ProteOn XPR36 Protein Interaction Array System" ;
NIFRID:synonym "Bio-Rad ProteOn XPR36 Protein Interaction Array System",
"ProteOn XPR36 Surface Plasmon Resonance System" ;
definition: "ProteOn XPR36 protein interaction array system is surface plasmon resonance (SPR) biosensor platform that provides real-time label-free analysis of specificity, affinity and kinetics of biomolecular interactions." .
SCR:019706 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ProteomeWorks" ;
rdfs:label "Bio-Rad | ProteomeWorks Spot Cutter" ;
definition: "Spot cutter instrument that is used for location, excision and loading into microtiter plates of protein spots after separation on 2D electrophoresis gels or PVDF membranes." .
SCR:019707 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QX2000_Droplet" ;
rdfs:label "Bio-Rad | QX200 Droplet Digital PCR System" ;
definition: "Droplet generator and reader that provides absolute quantification of target DNA or RNA molecules for EvaGreen or probe-based digital PCR applications." .
SCR:019708 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QXDx" ;
rdfs:label "Bio-Rad | QXDx AutoDG ddPCR System" ;
definition: "Droplet generator and reader that is designed for high-throughput processing of samples in a 96-well format and provides precise and absolute quantification of target DNA and RNA molecules in a wide variety of research applications." .
SCR:019709 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Discover_10" ;
rdfs:label "Bio-Rad | NGC Discover 10 Chromatography System" ;
definition: "Chromatography system that includes 10 ml/min pumps, multi-wavelength (UV/Vis) and conductivity detection, expanded scouting options, large-sample injection, and column switching of up to 5 columns, for method development. This chromatography system may be used for method development, combining automated buffer blending with buffer inlets, a column switching valve, and a sample pump for expanded condition scouting options during the purification of proteins, peptides, and nucleic acids." .
SCR:019710 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_S3e" ;
rdfs:label "Bio-Rad | S3e Cell Sorter" ;
definition: "Cell sorter that allows performance of 1 to 4 color sorts and sorts large quantities of pure viable cells." .
SCR:019711 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VersaFluor" ;
rdfs:label "Bio-Rad | VersaFluor Fluorometer" ;
definition: "Fluorometer that provides fluorescent detection at high levels of sensitivity and selectivity for quantitating DNA, RNA, and proteins, detecting apoptosis, and performing reporter enzyme assays. This fluorometer has been discontinued." .
SCR:019712 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ZE5",
"SCR_019713",
"SCR_019717" ;
rdfs:label "Bio-Rad | ZE5 Cell Analyzer" ;
NIFRID:synonym "Bio-Rad ZE5 Cell Analyzer Flow Cytometer",
"Bio-Rad ZE5/Yeti Cell Analyzer Flow Cytometer",
"BioRad ZE5" ;
definition: "BioRad ZE5 was formerly known as the Propel Labs YETI Cytometer with configurations to meet broad range of experimental complexities and throughput needs. Accessible for novice flow cytometry users yet flexible enough for most experienced flow cytometry professionals." .
SCR:019714 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QX2000_AutoDG" ;
rdfs:label "Bio-Rad | QX200 AutoDG Droplet Digital PCR System" ;
definition: "Droplet generator that provides absolute quantification of target DNA or RNA molecules for EvaGreen and probe-based Droplet Digital PCR (ddPCR) applications." .
SCR:019715 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_2100" ;
rdfs:label "Agilent | BioAnalyzer 2100" ;
definition: "2100 Bioanalyzer system is an established automated electrophoresis tool for the sample quality control of biomolecules. The 2100 Bioanalyzer instrument, together with the 2100 Expert Software and Bioanalyzer assays, provide highly precise analytical evaluation of various samples types in many workflows, including next generation sequencing (NGS), gene expression, biopharmaceutical, and gene editing research. Digital data is provided in a timely manner and delivers objective assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for an accurate result, and the data may be exported in a many different formats for ease-of-use." .
SCR:019716 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Discover_10_Pro" ;
rdfs:label "Bio-Rad | NGC Discover 10 Pro Chromatography System" ;
definition: "Chromatography system that includes 10 ml/min pumps, multi-wavelength (UV/Vis) and conductivity detection, expanded scouting options, large-sample injection, outlet valve, and column switching of up to 5 columns, for method development. This chromatography system may be used for simultaneously detecting proteins, peptides, nucleic acids, and chromogenic molecules with expanded scouting options." .
SCR:019718 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_T200" ;
rdfs:label "GE | Bioacore T200 Protein Analysis System" ;
definition: "Biacore T200 software offers a range of tools for confident and kinetic analyses. These analyses can be performed using a multicycle approach (many samples against one ligand or when different ligands are immobilized), or alternatively, using singlecycle kinetics (fast runs without regeneration). Biacore T200 is a versatile system for high-quality characterization of molecular interactions, from ions to viruses. One platform for comprehensive characterization of molecular interactions in terms of kinetics, affinity, specificity, comparability, concentration, immunogenicity, and thermodynamics. ligand-binding assays, even for the most complex biologics Confident selection and characterization of the smallest organic compounds to large multidomain proteins Validated software meeting your regulatory expectations by supporting GxP procedures and 21 CFR Part 11 compliance" .
SCR:019719 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_192" ;
rdfs:label "BioAutomation | 192 Genetic Synthesizer" ;
definition: "Synthesizer that is designed to synthesize DNA, RNA & LNA oligonucleotides in a column format using standard or modified chemistries and can synthesize 192 oligos in less than 3 hours." .
SCR:019721 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IQ5" ;
rdfs:label "Bio-Rad | IQ5 5-channel Real time qPCR instrument" ;
definition: "Real Time PCR detection system that offers five-target analysis capabilities for multiplex PCR with a variety of detection chemistries." .
SCR:019722 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_405_LS" ;
rdfs:label "BioTek 405 LS Washer" ;
definition: "Microplate washer that has simple user interface for creation and execution of wash, dispense, aspirate and maintenance protocols within extensive onboard software." .
SCR:019723 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Helios_Gene_Gun" ;
rdfs:label "Bio-Rad | Helios Gene Gun System" ;
definition: "Handheld gene gun delivery system that provides direct transfection into range of targets in vivo. It uses adjustable low pressure helium pulse to sweep DNA, RNA, or biomaterial coated gold microcarriers from a plastic cartridge directly into target cells." .
SCR:019724 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BioSpec_TC-312" ;
rdfs:label "Bio-Techne | BioSpec TC-312 Thermal Cycler" ;
definition: "Laboratory instrument used to amplify segments of DNA or RNA through a process called Polymerase Chain Reaction (PCR). By rapidly heating and cooling samples, it forces DNA to replicate exponentially, allowing scientists to analyze or identify genetic material." .
SCR:019725 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_405_TS" ;
rdfs:label "Agilent: BioTek | 405 TS Washer" ;
definition: "Microplate washer that is designed to wash cell based assays, microsphere based assays and ELISA, for every application." .
SCR:019726 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_800_TS" ;
rdfs:label "Agilent: BioTek | 800 TS Absorbance Reader" ;
definition: "Microplate reader that measures absorbance in microplate-based assays. Applications extend from endpoint ELISA to temperature sensitive kinetic assays." .
SCR:019727 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_50_TS" ;
rdfs:label "Agilent: BioTek | 50 TS Washer" ;
definition: "Microplate washer that automates aspirate, dispense, shake, and soak steps required for assays including cell based assays, biomagnetic and polystyrene bead based assays." .
SCR:019728 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BioSpa_8",
"SCR_019729" ;
rdfs:label "Agilent | BioTek BioSpa 8 Automated Incubator" ;
NIFRID:synonym "Agilent BioTek BioSpa 8 Automated Incubator" ;
definition: "Incubator that links readers and imagers together with washers and dispensers for full workflow automation of up to 8 microplates or other labware. Temperature and CO2/O2 control, plus humidity monitoring and lid handling ensure an ideal environment for cell cultures during all experiment stages, with minimal manual intervention." .
SCR:019730 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cytation_1" ;
rdfs:label "BioTek Cytation 1 Cell Imaging Multi-Mode Reader" ;
definition: "Multi-mode plate reader that combines fluorescence and high contrast brightfield imaging with conventional multi-mode detection." .
SCR:019731 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cytation Hybrid" ;
rdfs:label "Agilent: BioTek | Cytation Hybrid Multi-Mode Microplate Reader" ;
definition: "Multi-mode plate reader offers UV-Vis absorbance, fluorescence and luminescence detection detection modes." .
SCR:019732 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cytation 5" ;
rdfs:label "Agilent: BioTek | Cytation 5 Cell Imaging Multi-Mode Reader" ;
definition: "Multi-mode plate reader that offers up to 60x magnification in fluorescence, brightfield, high contrast brightfield, color brightfield and phase contrast for maximum applications reach. The multi-mode detection modules include filter- and monochromator-based fluorescence detection, luminescence and UV-Vis absorbance detection." .
SCR:019733 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cytation_7" ;
rdfs:label "Agilent: BioTek | Cytation 7 Cell Imaging Multi-Mode Reader" ;
definition: "Multi-mode plate reader that combines automated digital upright and inverted widefield microscopy with conventional multi-mode microplate reading and provides sample visualization from 1.25x to 60x magnification in fluorescence, brightfield and color brightfield for a broad range of applications." .
SCR:019734 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BioStack" ;
rdfs:label "Agilent: BioTek | BioStack Microplate Stacker" ;
definition: "Microplate stacker compatible with BioTek's washers, dispensers, detectors and imaging systems and accommodates assay workflows for 96- and 384-well plates." .
SCR:019735 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EL406",
"SCR_019747" ;
rdfs:label "Agilent: BioTek | EL406 Washer Dispenser" ;
NIFRID:synonym "BioTek EL406 Microtiter Plate Washer" ;
definition: "Microplate washer that is equipped for full plate washing along with three reagent dispensers in one and includes washing and dispensing for standard assays, biomagnetic separation and vacuum filtration protocols." .
SCR:019736 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MyIQ" ;
rdfs:label "Biorad MyIQ single-channel QPCR instrument" ;
definition: "MyiQ Single Color Real Time PCR Detection System builds on the strengths of the iCycler Thermal Cycler, which provides the optimum performance for PCR. The MyiQ system features a tungsten halogen lamp as the light source. The filter-based optical design allows the use of optimal wavelengths of light for excitation and emission, resulting in excellent sensitivity and discrimination between multiple fluorophores. The CCD detector captures a simultaneous image of all 96 wells. This results in a comprehensive data set illustrating the kinetic behavior of the data during each cycle. Simultaneous image collection insures that well-to-well data may reliably be compared. The MyiQ system reports data on the PCR in progress in real time, allowing immediate feedback on reaction success. All of these features demonstrate that the MyiQ system hardware was built to promote reliability and flexibility. The MyiQ software includes features that make software easy and useful. The software is designed for offering speedy setup and analytical results. Many functions are presented graphically for ease of use. Tips on usage are available as your mouse rolls over the buttons. In addition, the Online Help Manual is available at all times simply by pressing the F1 key. The MyiQ software automatically analyzes the collected data at the touch of a button, yet leaves room for additional optimization of results based on your analysis preferences." .
SCR:019737 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ELx405" ;
rdfs:label "Agilent: BioTek | ELx405 Select Deep Well Washer" ;
definition: "Microplate washer that aspirates and dispenses into 96- and 384-well plates." .
SCR:019738 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ELX405U" ;
rdfs:label "Agilent: BioTek | ELX405U Microplate Washer" ;
definition: "Microplate washer that is designed to rapidly wash 96 or 384 well microplates. Keypad interface has independent control of plate position during dispense and aspiration cycles, as well as fully programmable fluid volumes and flow rates, shaking, and soaking." .
SCR:019740 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Epoch_2" ;
rdfs:label "Agilent: BioTek | Epoch 2 Microplate Spectrophotometer" ;
definition: "Spectrophotometer that is used for UV-Vis measurements in 6- to 384-well microplates, cuvettes and in micro-volume samples with the available Take3 Micro-Volume Plate. Endpoint, kinetic, spectral scanning and well area scanning modes, plus incubation and shaking enable wide-ranging applications." .
SCR:019741 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Epoch" ;
rdfs:label "Agilent: BioTek | Epoch Microplate Spectrophotometer" ;
definition: "Spectrophotometer that offers filter free, wide wavelength range for UV-Vis absorbance measurements in variety of microplate formats, and in 2 uL samples when available Take3 plate is used." .
SCR:019742 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VersArray_Chipwritter_Pro" ;
rdfs:label "Bio-Rad | VersArray Chipwritter Pro System" ;
definition: "Microarray that is used for printing DNA, proteins, or other biological samples. It has modular component design and software for microruns or unattended highthroughput prints." .
SCR:019743 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FLX_800" ;
rdfs:label "Agilent: BioTek | FLX800 Multi-Detection Microplate Reader" ;
definition: "Microplate reader that includes several models with options that meet specific needs of research and OEM users. Top and bottom reading are available to read anything from 6 well to 384 well microplates, and PCR plates. Optional external dispenser module allows running applications such as ion channel assays and flash luminescence assays." .
SCR:019744 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Lionheart FX" ;
rdfs:label "Agilent: BioTek | Lionheart FX Automated Microscope" ;
definition: "Microscope that offers up to 60x air; 60x and 100x oil immersion magnification, with fluorescence, brightfield, color brightfield, and phase contrast channels for maximum application reach." .
SCR:019745 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Lionheart_LX" ;
rdfs:label "Agilent: BioTek | Lionheart LX Automated Microscope" ;
definition: "Microscope that enables augmented microscopy, which fully automates image capture, processing and analysis." .
SCR:019746 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MultiFlo FX" ;
rdfs:label "Agilent: BioTek | MultiFlo FX Multi-Mode Dispenser" ;
definition: "Automated multi-mode reagent dispenser for 6- to 1536-well microplates." .
SCR:019748 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Synergy_H1" ;
rdfs:label "Agilent | BioTek Synergy H1 Multimode Reader" ;
NIFRID:synonym "Agilent BioTek Synergy H1",
"BioTek Synergy H1 Hybrid Multi-Mode Microplate Reader",
"BioTek Synergy H1 Multimode Reader" ;
definition: "Modular multimode microplate reader, with monochromator-based optics and filter-based optics for fluorescence and luminescence detection, plus filter-free UV-Vis absorbance. Hybrid is the term that Agilent BioTek uses to describe the unique optical systems available for Synergy H1 multimode readers. Each of these readers is configurable to include filter-based or monochromator-based optics for fluorescence and luminescence detection, or they can include both filter- and monochromator-based optics for maximum assay flexibility, sensitivity, and specificity. The bandwidth can be set between 9 and 50 nm, in 1 nm increments, to fully optimize reader settings for best sensitivity and specificity compared to fixed bandwidth systems. Comes with Gen5 Data Analysis Software." .
SCR:019749 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Synergy_HTX" ;
rdfs:label "Agilent | BioTek Synergy HTX Multi-Mode Microplate Reader" ;
NIFRID:synonym "BioTek Synergy HTX" ;
definition: """Compact multimode reader for 6- to 384-well microplates and Take3 microvolume plates. The unique dual optics design provides superior performance for UV-Vis absorbance, fluorescence, luminescence, and AlphaScreen/AlphaLISA workflows.
With incubation and shaking, plus a dual reagent injector module, the system will meet all your assay requirements now and in the future. Synergy HTX is controlled by the easy-to-use, yet powerful, Gen5 software for data collection, analysis, exporting, and reporting.""" .
SCR:019750 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Synergy H4" ;
rdfs:label "Agilent: BioTek | Synergy H4 Hybrid Plate Reader" ;
definition: "Synergy H4 combines the sensitivity of a filter-based system with the of monochromator-based optics to provide the broadest range of applications available on the market today. Detection modes: Fluorescence Intensity, Time-Resolved Fluorescence, Fluorescence Polarization, AlphaScreen/AlphaLISA, Luminescence, UV-Visible absorbance, FRET, TR-FRET, BRET, well area scanning and spectral scanning.Synergy H4 optics incorporates two double-grating monochromators. This quadruple design provides the best in spectral scanning performance and flexibility. Synergy H4's filter/dichroic combination provides the best possible performance in fluorescence, time resolved fluorescence and fluorescence polarization applications." .
SCR:019751 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SpectrostarNano" ;
rdfs:label "BMG Labtech Spectrostar Nano Microplate Reader" ;
definition: "BMG LABTECH's SPECTROstar NANO is the premiere absorbance microplate reader. The SPECTROstar NANO is a spectrometer-based absorbance reader that can capture a full UV-visible spectrum, 220nm to 1000nm, in less than 1 sec/well at 1nm resolution, offering you speed and precision that cannot be matched by older monochromator or filter absorbance reading technology. The SPECTROstar NANO has a built in cuvette port, 45C incubation, push button operation, is 1536 well capable, and has 2uL nano spot DNA quantitation capability allow the fastest measurements of DNA, RNA, ELISAs, and much more." .
SCR:019753 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_OpenArray NT Cycler",
"SCR_020349" ;
rdfs:label "Select Science | BioTrove OpenArray NT Cycler System" ;
definition: "Optical thermal cycler that is capable of cycling and imaging up to three OpenArray plates simultaneously. System includes: NT Cycler, computer, flat-panel monitor, OpenArray AutoLoader, and Case Sealing Station. Requires analysis software kit for operation." .
SCR:019754 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BI-200SM",
"SCR_019755" ;
rdfs:label "Brookhaven Instruments | BI-200SM Research Goniometer" ;
NIFRID:synonym "Brookhaven Instruments BI-200SM Goniometer" ;
definition: "Goniometer that is used for macro molecular studies and submicron particle sizing with static and dynamic light scattering. It can be used with neutral density filters, polarizer, analyzer, and reference detector." .
SCR:019756 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Carbplex" ;
rdfs:label "Bruker | Carbaplex IVD PCR" ;
definition: "PCR assay kit that detects the five most prevalent carbapenemase gene families. Detection of carbapenemase genes from rectal swabs supports timely deployment of infection control procedures and appropriate patient management." .
SCR:019757 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Autoflex_III",
"SCR_019758" ;
rdfs:label "Bruker | Autoflex III MALDI TOF Mass Spectrometer" ;
NIFRID:synonym "Bruker Autoflex III Smartbeam MALDI-TOF/TOF" ;
definition: "Mass spectrometer that is used for analysis of large biomolecules (such as proteins, polymers, sugar, etc.) to identify and characterize the structures. The instrument has a capability of TOF/TOF technology (LIFT) for tandem MS (MS/MS). It is worked either linear or reflectron configuration with both positive and negative modes. System includes computer pre-loaded with software." .
SCR:019759 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7T" ;
rdfs:label "Bruker | Clinscan 7T Magnetic Resonance Imager" ;
definition: "ClinScan is Bruker BioSpin's solution for an emerging market of research MRI systems that allows a direct and fast transfer of preclinical studies on animal models to clinical studies on humans. 7 T Bruker USR magnet (Ultra Shielded Refrigerated, bore size 20 cm or 30 cm) n Bruker gradient and shim coil (gradient strength of 290 mT/m or 630 mT/m, slew rate of 1160 T/m/s or 6300 T/m/s) n Bruker RF array coil technology in combination with numerous animal handling accessories n Siemens MAGNETOM Avanto technology with up to 32 receive channels n Clinical routine user interface syngo MR to enable efficient workflow and highly automated state-of-the-art MRI and MRS applications on small animals" .
SCR:019760 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2510" ;
rdfs:label "Emerson | Branson 2510 Ultrasonic Cleaner" ;
definition: "Ultrasonic bath that features heated cleaning with the ability to set temperatures from 20C/68F to 69C/156.2F and can also be used for cell separation, sample preparation and degassing of liquids." .
SCR:019761 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_D8" ;
rdfs:label "Bruker | D8 Advance XRD" ;
definition: "D8 ADVANCE is a real quick-change artist that can be configured to take on a single analytical task with great focus and dedicated components, or a fully featured, multi-purpose solution that is capable of dealing with very diverse analytical needs with highest competence. Our famous DAVINCI design ensures for all those solutions easy (re)configuration and extensibility to exactly satisfy your analytical needs, now and in the future. XRD data are typically collected in one direction, 2Theta. Simultaneously collecting data along a second dimension, the Gamma direction, can speed up data collection and provide additional information about the properties of crystalline samples, such as texture, residual stress, grain size and epitaxial relations." .
SCR:019762 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BRAVO" ;
rdfs:label "Bruker | BRAVO Handheld Raman Spectrometer" ;
definition: "Mass spectrometer that features SSE and fluorescence mitigation, duo LASER excitation, intelliTip and automated measuring tip recognition, automated batch scan reporting, inbuilt wavenumber calibration, and wireless data exchange." .
SCR:019763 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Synergy_LX" ;
rdfs:label "Agilent: BioTek | Synergy LX Multi-Mode Microplate Reader" ;
definition: "Microplate reader with an optic design that provides accurate data in absorbance, fluorescence and luminescence detection modes, enabling many common assays including nucleic acid and protein quantification, ELISA, BCA, Bradford and cell viability." .
SCR:019764 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EM27_SUN" ;
rdfs:label "Bruker | EM27/SUN Remote Sensor" ;
definition: "Spectrometer that quantifies gases such as carbon dioxide and methane in the atmosphere by analyzing the radiation of the sun utilizing the CAMTracker system." .
SCR:019765 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Synergy Neo2" ;
rdfs:label "Agilent: BioTek | Synergy Neo2 Hybrid Multi-Mode Microplate Reader" ;
definition: "Microplate reader that is designed for a screening laboratory and combines variable bandwidth quad monochromators, sensitive high transmission filter-based optics, laser TRF and up to 4 PMTs to provide fast measurements." .
SCR:019766 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EM27" ;
rdfs:label "Bruker | EM27 Remote Sensor" ;
definition: "Spectrometer that is used for remote sensing of chemical substances in atmosphere." .
SCR:019767 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GLOBULYSER" ;
rdfs:label "Bruker | GLOBULYSER Homogenizer Efficiency Analyzer" ;
definition: "Analyzer that is used for the determination of the mean fat globule size in milk and liquid milk products as well as in dissolved milk powders." .
SCR:019768 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_InVi" ;
rdfs:label "Bruker | InVi SPIM Light-Sheet Microscope" ;
definition: "Microscope that has been optimized for long term 3D fluorescence imaging of living specimens." .
SCR:019769 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HI_90" ;
rdfs:label "Bruker | HI 90 Remote Sensor" ;
definition: "Imaging remote sensing system that is based on combination of Michelson interferometer and focal plane array detector. Each pixel of array records interferogram from corresponding field of view. System allows identification, quantification and visualization of potentially hazardous gases from long distances." .
SCR:019770 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IRcube" ;
rdfs:label "Bruker | IRcube FTIR/FT-NIR Process Spectrometer" ;
definition: "Spectrometer with splash proof housing and aligned optics that allows OEMs to create integrations and applications.IRcube can be used as UHV chamber coupling module, reflectance module, or gas analyzer." .
SCR:019771 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MATRIX" ;
rdfs:label "Bruker MATRIX-MF FTIR/FT-NIR Process Spectrometer" ;
definition: "Spectrometer that can be fiber optically coupled to measure chemical reactions in laboratory and/or process environments." .
SCR:019772 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LCS" ;
rdfs:label "Bruker | LCS SPIM Light-Sheet Microscope" ;
definition: "Microscope with a cuvette-based sample mounting approach that provides fast 3D imaging of large cleared samples." .
SCR:019773 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MS FX Pro" ;
rdfs:label "Bruker | In-Vivo MS FX Pro In-Vivo Mass Spectrometer" ;
definition: "MS FX PRO In-Vivo Mass Spectrometer brings the broadest range of imaging applications with multispectral fluorescence, luminescence, radioisotopic and high resolution X-ray imaging in one system. Functions range from protein blots to complex, longitudinal studies of disease states in vivo - to your lab. Whether you need to develop fluorescent probes; track NIR fluorescent nanoparticles, peptides or proteins; quantify changes in localization and tumor burden; screen radioisotopic probes in multiple animals; study changes in bone density or perform ex vivo validation, the MS FX PRO drives your research to new levels of excellence." .
SCR:019774 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MATRIX_MG01" ;
rdfs:label "Bruker MATRIX-MG01 Gas Analyzer" ;
definition: "Gas analyzer that features a gas cell with 10 cm optical path length and is especially well suited for the quantification of gas compounds with very high concentration." .
SCR:019775 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_maXis" ;
rdfs:label "Bruker | maXis 4G Liquid Chromatography Time of Flight Mass Spectrometer" ;
definition: "Mass spectrometer that measures and identifies small molecules, proteins and intact large molecules in both MS and MS/MS modes." .
SCR:019776 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MATRIX_MG2" ;
rdfs:label "Bruker MATRIX-MG2 Gas Analyzer" ;
definition: "Gas analyzer that features a 2 m multi-reflection gas cell and is designed for the quantification of gas compounds in a very broad concentration range." .
SCR:019777 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MATRIX_MG5" ;
rdfs:label "Bruker | MATRIX-MG5 Gas Analyzer" ;
definition: "Gas analyzer that features a 5 m multi-reflection gas cell and is designed for the high-precision quantification of gas compounds from very low concentrations on the ppb level up to one hundred percent." .
SCR:019778 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_M4" ;
rdfs:label "Bruker | M4 Tornado Micro X-Ray Fluorescence Device" ;
definition: "M4 TORNADO is the tool of choice for sample characterization using small-spot Micro X-ray Fluorescence (Micro-XRF) for information on composition and element distribution. Optimized for analysis speed and without compromising accuracy it measures a wide range of samples. Whether small or large, even or irregularly shaped equipped with a large high-speed stage it supports 2D analysis of virtually any kind of inorganic, organic ,and even of liquid sample. Its large vacuum chamber enables light element detection." .
SCR:019780 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Microflex" ;
rdfs:label "Bruker | MicroFlex MALDI Microflex Mass Spectrometer" ;
definition: "Mass spectrometer that is designed for automated protein identification and characterization, biomarker detection, oligonucleotide quality control, and SNP genotyping." .
SCR:019781 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_micrOTOF-Q II",
"SCR_019784" ;
rdfs:label "Bruker | micrOTOF-Q II Liquid Chromatography Mass Spectrometer" ;
NIFRID:synonym "Bruker micrOTOF-Q II LC/MS" ;
definition: "Benchtop Q-Tof, applied to a variety of applications such as small molecule accurate mass determination (HRMS), intact protein analysis including antibodies, peptide mapping, and other custom projects. This system is operated with an Agilent 1260 UPLC and includes an inline diode array detector and ESI source." .
SCR:019782 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MIRA" ;
rdfs:label "Bruker | MIRA Infrared Milk Analyzer" ;
definition: "Dairy analyzer that can analyze parameters like fat, protein, total solids and lactose. High pressure homogenizer provides evenly homogenized samples for repeatability and accuracy. Can also determine freezing point." .
SCR:019783 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MultiMode" ;
rdfs:label "Bruker | Multimode 8 Atomic Force Microscope" ;
definition: "MultiMode 8-HR is an atomic force microscope which is well suited for imaging in both air and fluid. Heating to 250C, cooling to -35C with temperature control accessories. Nanothermal analysis for local polymer phase transition temperatures up to 350C.. Atomic resolution electrochemistry with AFM, STM, and SECPM. Invent your own mode by accessing and modifying any signal, high or low voltage. A large variety of standard operating modes and many capabilities enable the MultiMode 8-HR AFM system to characterize everything from mechanical to electrical properties" .
SCR:019785 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MultiRAM" ;
rdfs:label "Bruker | MultiRAM Raman Spectrometer" ;
definition: "Spectrometer with OPUS software that controls data collection and manipulation functions for MultiRAM. Real time spectrum display permits software control of analysis conditions, including optimization of laser power and sample position." .
SCR:019786 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_OMEGA_5" ;
rdfs:label "Bruker | OMEGA 5 Gas Analyzer" ;
definition: "Gas analyzer with a 19-inch rack mount box that is equipped with 5 m multi reflection gas cell, spectral resolution, TE cooled detector for sensitivity without need for liquid nitrogen, nickel plated gas cell and gold coated mirrors that enable measurement of corrosive gases, and accounts for variable pressure and temperature of gas by sensors included inside gas cell." .
SCR:019787 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PMA_50" ;
rdfs:label "Bruker | PMA 50 FT-IR Spectrometer" ;
definition: "External spectrometer accessory that was developed for Polarization Modulation measurements. Both linear dichroitic measurement techniques, like PM IRRAS, and circular dichroitic experiments, like VCD spectroscopy, can be realized using this system." .
SCR:019788 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QuVi" ;
rdfs:label "Bruker QuVi SPIM Light-Sheet Microscope" ;
definition: "Microscope that combines dual views with dual detection channels for large scale 3D imaging of life specimens and cleared samples. System enables transition between living and cleared tissue imaging." .
SCR:019789 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Opterra_II" ;
rdfs:label "Bruker | Opterra II 4D Fluorescence Confocal Microscopy" ;
definition: "Confocal microscope that utilizes proprietary one dimensional pinhole array technology to combine resolution and speed. It has short acquisition times and cell protecting minimization of photobleaching and phototoxicity for advanced live cell imaging." .
SCR:019790 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_S2_POLAR" ;
rdfs:label "Bruker | S2 POLAR EDXRF" ;
definition: "Energy-Dispersive X-ray Fluorescence spectrometer that features all requirements for S analysis from diesel to crude oils. This also includes continuous process control of higher sulfur levels in refineries as well as norm-compliant Ultra-Low Sulfur analysis of final products." .
SCR:019791 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MuVi" ;
rdfs:label "Bruker | MuVi SPIM Light-Sheet Microscope" ;
definition: "Microscope with a 4-axis concept and two-sided illumination that allows for four combinations of illumination and detection." .
SCR:019792 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_S6_JAGUAR" ;
rdfs:label "Bruker | S6 JAGUAR WDXRF" ;
definition: "WDXRF spectrometer that features compact WDXRF goniometer, closely coupled optics, and 400 W direct excitation power. It has linear range of more than two Million cps based on HighSense XE detector." .
SCR:019793 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_OPS" ;
rdfs:label "Bruker | OPS Remote Sensor" ;
definition: "Spectrometer that is based on method of Fourier transform infrared spectroscopy. Infrared radiation is modulated by interferometer and transmitted to array of retroreflectors positioned at distance of typically several hundred meters using telescope. Reflected radiation is received by same telescope and focused onto detector." .
SCR:019794 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Scion" ;
rdfs:label "Bruker | Scion TQ Gas Chromatograph Mass Spectrometer" ;
definition: "Triple quadrupole gas chromatograph that provides targeted trace-level analysis of metabolites and other small molecules. Samples are often derivatized for compatibility with GC-MS." .
SCR:019795 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RAM_II" ;
rdfs:label "Bruker | RAM II FT Raman Module" ;
definition: "Add-on module that can be coupled to a research spectrometer and allows automated switching between FT Raman and FT IR measurements." .
SCR:019796 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TruLive3D" ;
rdfs:label "Bruker | TruLive3D Imager Light-Sheet Microscope" ;
definition: "Dual sided illumination light-sheet microscope that is optimized for 3D multi-sample imaging of live specimens in their 3D environment. It is especially suited for multi position imaging of small embryos, 3D spheroids, oocytes and more, enabling time lapse, high throughput imaging experiments." .
SCR:019797 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SIGIS_2" ;
rdfs:label "Bruker | SIGIS 2 Remote Sensor" ;
definition: "Scanning imaging remote sensing system that allows identification, quantification, and visualization of potentially hazardous gas clouds from long distances. It is based on the combination of an infrared spectrometer with a single detector element and a scanner system." .
SCR:019798 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2Pplus" ;
rdfs:label "Bruker Ultima 2Pplus Multiphoton Microscope" ;
definition: "Multiphoton microscope that is designed for intravital imaging, with fully motorized control of objective X-Y-Z position, as well as two axes of rotation for precise imaging orientation. Second scan path enables simultaneous imaging and photoactivation." .
SCR:019799 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultraflex III_MALDI-TOF/TOF" ;
rdfs:label "Bruker | Ultraflex III MALDI TOF/TOF Mass Spectrometer" ;
NIFRID:synonym "MALDI-TOF/TOF Ultraflex III" ;
definition: "MALDI (Matrix Assisted Laser Desorption/Ionization) tandem mass spectrometer specially designed for automated MS and MS/MS high throughput identification of proteins and peptides. Tandem Mass Spectrometry is a technique that utilizes more than one mass selective stage in a mass spectrometer." .
SCR:019801 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultraflextreme" ;
rdfs:label "Bruker | ultraXtreme X-Ray Imaging System" ;
definition: "Smartbeam-II laser enables ultra-high data acquisition speed in both MS and MS/MS at full systems performance. The well-established proprietary smartbeam laser provides unprecedented analytical and matrix flexibility in workflows from protein tissue imaging, intact proteins analysis, Glycoproteomics, biologics or oligo QC, to LC-MALDI proteomics - all fully enabled at 1-2000 Hz repetition rates. Bruker's patented smartbeam technology is already widely accepted as the most viable MALDI imaging laser technology. The new ultrafleXtreme now enables low pixel sizes for high spatial resolution imaging. Importantly, outstanding spectral quality and signal intensity are maintained at even the smallest laser beam diameters." .
SCR:019802 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TG_FT_IR" ;
rdfs:label "Bruker TG-FT-IR Spectrometer" ;
definition: "Spectrometer that combines the quantitative capabilities of TG and the identification capabilities of FT-IR spectroscopy. Thermodynamic transitions, thermal stability, decomposition and chemical reactions can be detected and quantified with high accuracy over a broad temperature range." .
SCR:019803 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Samplmet 2" ;
rdfs:label "Buehler Samplmet 2 Abrasive Cutter" ;
definition: "95-C1700-160 SAMPLMET 2 Abrasive Cutter is a complete bench top unit with recirculating coolant system that includes totally enclosed cutter with 1 HP (735W) motor and 3400 RPM no load speed with a 1¼″ (32mm) diameter solid bar cutting capacity. The cutter has a 1½″ (38mm) vise capacity, light alloy base casting, molded glass-reinforced-plastichood, left-hand cam activated vise, operator controls, clean-out hose, recirculating system with 1�10 HP, 1 phase motor, baffled 7 gallon (27 liter) tank with flow control vavle, 1″ (25mm) coolant drain, interconnecting hoses and electrical cable. Includes samples of COOLMET and assorted 9″ (229mm) abrasice cut-off wheels." .
SCR:019804 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Vultara_352" ;
rdfs:label "Bruker | Vutara 352 Super Resolution Microscope" ;
definition: "Fluorescence microscope that enables quantitative imaging at nanoscale using fluorescence microscopy based on single molecule localization. Includes techniques such as PALM, STORM, dSTORM, DNA PAINT." .
SCR:019805 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CAS_4200" ;
rdfs:label "Corbett | CAS 4200 Automated PCR Setup Robot" ;
definition: "Pipetting robot for qPCR setup and compatible with any real-time instrument. All qPCR tube formats and plate types are supported, including capillaries. It easily interfaces with upstream sample-prep systems such Corbett X-tractor-Gene, Roche MagNA Pure, QIAGEN BioRobot M48 Workstation, and others. CAS-4200 is identical to the CAS-1200 quantitative PCR setup robot but with over twice the deck capacity." .
SCR:019806 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BI200SM" ;
rdfs:label "Thermo Fisher | Bulb Replacement Kits for Environmental Chambers" ;
definition: "Bulb replacement kit that contains 7 fluorescent bulbs for light module." .
SCR:019807 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Investigator" ;
rdfs:label "Bruker | Ultima Investigator Multiphoton Microscope" ;
definition: "Multiphoton microscope that features a base system specifically optimized for in vivo studies and is designed for add-on flexibility with a host of specialized options." .
SCR:019808 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_verTera" ;
rdfs:label "Bruker verTera Terahertz Spectroscopy" ;
definition: "Spectrometer extension that makes use of high precision semiconductor based photomixers, converting near infrared laser light into THz radiation. The extension provides access to the single digit wavenumber regime and highest resolution without the need of cryogenically cooled components." .
SCR:019809 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:omics-data-paper-shinyapp-golem" ;
rdfs:label "Omics Data Paper Generator" ;
NIFRID:synonym "omicsdatapaper" ;
definition: """Software package for streamlined import of omics metadata from European Nucleotide Archive into OMICS Data Paper manuscript. Omics Data Paper R Shiny app demonstrates workflow for automatic import of ENA genomic metadata into omics data paper manuscript.
Streamlined conversion of metadata into manuscript facilitates authoring of omics data papers, which allow omics dataset creators to receive credit for their work and to improve description and visibility of their datasets.""" .
SCR:019810 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ms-utils.org" ;
definition: "Open source software suite for mass spectrometry based proteomics. Software repository and collection of free software for analysis of mass spectrometry data. Software and code snippets for visualization and analysis of mass spectrometry data with emphasis on automated methods for proteomics and protein analysis." .
SCR:019811 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Orange Data Mining" ;
definition: "Open source machine learning and data visualization. Data Mining Toolbox in Python used to build data analysis workflows visually, with large, diverse toolbox." .
SCR:019812 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Autodesk Netfabb Premium" ;
NIFRID:synonym "Autodesk Netfabb Premium 2019" ;
definition: "Software tool to open and assess stereolithographic data. Software application tailored for additive manufacturing, rapid prototyping, and 3D printing." .
SCR:019813 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CB1000" ;
rdfs:label "McKinley | Cell Biosciences CB1000 Immunoassay" ;
definition: "Immunoassay system that enables rapid, quantitative analysis of specific proteins in as few as 25 cells per assay. Detailed information is generated on the post-translational modification status of critical signaling proteins. The system is fully automated and speeds samples from a standard 384-well microplate to final results, ensuring sample-to-sample consistency., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:019814 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CellASIC ONIX" ;
rdfs:label "Millipore | CellASIC CellASIC ONIX" ;
definition: "Set of microfluidic plates with pre-primed, disposable plates for live cell analysis." .
SCR:019815 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_COBOS" ;
rdfs:label "Thermo Fisher | Countess Cell Counting Chamber Slides" ;
definition: "Countess Cell Counting Chamber Slides are designed for use with Countess Automated Cell Counter. This set includes 100 boxes of slides 50 slides per box and 2 × 100 mL bottles of trypan blue 0.4 percent. Provides total cell count, percent viable cells, and average cell size in 30 seconds. Each slide has two separate, enclosed chambers that can be used to count one sample in duplicate or to count two different samples." .
SCR:019816 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | CO2 and LN2 Backup Systems Refrigerator and Freezer Accessories" ;
definition: "CO2 and LN2 backup system that ensures security for critical samples by using ultra low temperature freezers. Systems inject liquid CO2 or LN2 into cabinet when cabinet temperature warms to preset level." .
SCR:019817 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_E220_Evolution" ;
rdfs:label "Covaris | E220evolution Focused ultrasonicator" ;
definition: "Focused ultrasonicator that enables multi sample, batch preparation, capable of processing wide range of sample types and volumes." .
SCR:019818 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ME220" ;
rdfs:label "Covaris | ME220 Focused Ultrasonicator" ;
definition: "Focused ultrasonicator with compact, easy to use system, formatted for 1 to 8 sample batch processing with integrated chiller and automated water management." .
SCR:019819 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ML230" ;
rdfs:label "Covaris | ML230 Focused-Ultrasonicator" ;
definition: "Focused ultrasonicator that was developed for superior precision and accuracy, new and advanced engineering designs enables easier maintenance and user friendly experience." .
SCR:019820 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CL-1000" ;
rdfs:label "Spectrum Chemical | CL-1000 UV Crosslinker CL-1000" ;
definition: "Preset and manual controls for UV or time exposure settings. Internal microprocessor measures and controls UV output, ensuring maximum energy efficiency. Consistent crosslinking takes seconds with 8W shortwave UV tubes. Select shortwave for sterilization and bonding DNA; midrange for gel electrophoresis; or long wave for UV curing. Crosslinker has maximum energy setting of 999,900 �J/cm2. Uses five 8W UV tubes. Digital LED displays settings. Viewing window blocks UV while allowing visibility of chamber interior. An internal interlocking safety system is designed for automatic shutoff when the door is opened. 115V, 60Hz; ETL-/ETLc-certified. External dimensions (D x W x H) in. (cm): 13.7 x 15.6 x 8.75 (34.8 x 39.6 x 22.2)." .
SCR:019821 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_R230" ;
rdfs:label "Covaris | R230 Focused-Ultrasonicator" ;
definition: "Focused ultrasonicator that can be fully integrated on many liquid handler platforms with high throughput sample processing with AFA energetics and AFA TUBE TPX plates." .
SCR:019822 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_C4xx_LiN" ;
rdfs:label "Thermo Fisher | Cytomat 2 C4xx-LiN Series Automated Incubators" ;
definition: "Series of automated incubators that ensure reproducible process, temperature uniformity and stability for incubation storage of cell culture applications. Cytomat incubators available in various temperature ranges and gate positions for hand off to lab automation robot. Can be integrated with mean access time of 12 sec." .
SCR:019823 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CAS_1200" ;
rdfs:label "Corbett | CAS 1200 PCR" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 28,2024. RT PCR preparation liquid handler that features single channel dispense head capable of delivering volumes as low as 1 microliter. The single channel ensures precise dispensing for various tube types in addition to standard 96-well and 384-well microplates." .
SCR:019824 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_208 HR" ;
rdfs:label "Cressington | 208 HR Sputter Coater" ;
definition: "Cressington 208HR now offers real solutions to the problems encountered when coating difficult samples for FE-SEM. In order to minimize the effects of grain size the 208HR offers a full range of coating materials and gives unprecedented control over thickness and deposition conditions. To minimize charging effects the 208HR stage design and wide range of operating pressures allows precise control of the uniformity and conformity of the coating. The HIGH/LOW chamber configuration allows easy adjustment of working distance." .
SCR:019825 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SMZ-2B" ;
rdfs:label "Nikon | Defonbrune SMZ-2B Microforage Stereo Microscope" ;
definition: "Compact stereo microscope that is used for reflected light observation. Configurable with desk mount boom stand or base plate boom stands. Typical factory magnification comes 8 - 50X. It can accomodate a high intensity light source." .
SCR:019826 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Aurora" ;
rdfs:label "CyTekBio | Aurora Spectral Analyzer" ;
NIFRID:synonym "Cytek Aurora" ;
definition: "Analyzer with up to five lasers, three scattering channels, and 64 fluorescence channels, the Aurora suits every laboratory's needs, from to high complexity applications. A paradigm shifting optical design provides unprecedented flexibility, enabling the use of a wide array of new fluorochrome combinations without reconfiguring your system for each application. The state-of-the-art optics and low-noise electronics provide excellent sensitivity and resolution. Flat-top beam profiles, combined with a ly designed fluidics system, translate to outstanding performance at high sample flow rates." .
SCR:019827 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_150" ;
rdfs:label "Veeco | Dektak 150 Surface Profiler" ;
definition: "Stylus profiler that can be configured with 4-inch Y auto stage to enable 3D imaging or be equipped with a 6-inch X-Y auto stage that, in addition to 3D mapping, provides automation and programmability of over 200 sample sites." .
SCR:019828 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_M605" ;
rdfs:label "Dell | M605 Blade Servers" ;
definition: "Blade server that features up to six-core processors. The blades are designed to combat data center sprawl and IT complexity." .
SCR:019829 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_M820" ;
rdfs:label "Dell | M820 Server" ;
definition: "Blade server that is designed for high-end databases and dense data center environments." .
SCR:019830 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PE6950" ;
rdfs:label "Dell | PE6950" ;
definition: "PowerEdge 6950 rack-dense 4U is a server that delivers performance with impressive low power consumption helping organisations address increasing datacentre complexity. Featuring quad-socket, dual-core AMD Opteron processing power, it provides high performance scalability. The design of the system provides for seamless upgrades from dual-core to quadcore within the same thermal envelope. The PowerEdge 6950 server is built to handle demanding enterprise applications without stressing datacentre resources making it for large databases, server consolidation, virtualisation and migrations from costly RISC-based systems." .
SCR:019831 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_R730",
"SCR_019843" ;
rdfs:label "Dell | PowerEdge R730 Rack Server" ;
definition: "Server delivers outstanding functionality in just 2U of rack space. With the combination of processors, large memory, fast storage options and GPU accelerator support, the R730 performs exceptionally well in a number of demanding environments." .
SCR:019832 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_R815" ;
rdfs:label "Dell | PowerEdge R815 Rack Server" ;
definition: "Dell PowerEdge R815 is a 4-socket rack server offering the latest AMD Opteron processors with up to 48 processor cores and an excellent balance of advanced manageability, memory scalability, I/O, and redundancy in a space-saving 2U form factor." .
SCR:019833 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_T5500" ;
rdfs:label "Dell | T5500 Workstation" ;
definition: "Windows 7 Professional (32-Bit OS). Built for environments where space is at a premium, the Dell Precision T5500 delivers dual-socket workstation performance in a compact, quiet package. Incredibly fast and efficient despite its size, the Dell Precision T5500 features dual-socket Inte Xeon architecture with Intel QuickPath technology (in which each processor core features an integrated memory controller and high-speed interconnects), as well as support for up to 72GB* of DDR3 Registered ECC memory. For even more stunning levels of performance, the optional NVIDIA Tesla C2075 GPU card can be added, creating your own “personal supercomputer� for CUDA-enabled applications." .
SCR:019834 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_M905" ;
rdfs:label "Dell | M905 Server" ;
definition: "Server with large memory capacity, multiple redundant fabrics and massive total throughput. The server delivers 24 DIMM slots, up to 192GB total RAM, and highly available redundant throughput capacity." .
SCR:019835 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DV-502" ;
rdfs:label "Denton | DV-502 Vacuum Evaporator" ;
definition: "Thermal Evaporation system evaporates many of the metals and compounds involved in optical coatings, metallization, and electron microscope specimen preparation with no discernible contamination. This thin film deposition system also offers flexibility with a range of configurations available to meet your needs, including evaporation from a range of sources such as tungsten filaments, wire baskets, foil boats, baffle box heaters as well as carbon rod or yarn accessories., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:019836 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_T7500" ;
rdfs:label "Dell | T7500 Workstation Computer" ;
definition: "Our most workstation delivers the multi-core processing punch you,ve been waiting for with levels of performance you,ve only dreamed about. Developed in close collaboration with hardware and software partners, the nextgeneration Dell Precision T7500 workstation helps you create, design, render and analyze without compromise. Designed to deliver groundbreaking performance, blistering speed and scalability for compute and graphics-intensive environments, the Dell Precision T7500 helps you power through the most complex tasks and complete projects even faster with up to 50% more system memory than its predecessor." .
SCR:019837 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_V1500-AB" ;
rdfs:label "Custom Biogenic Systems | Dewer V1500-AB Isothermal Freezer" ;
definition: "Custom BioGenic Systems V1500-AB Isothermal Liquid Nitrogen Freezers offer liquid nitrogen storage temperatures without liquid nitrogen contact. Liquid nitrogen is stored in our patented jacketed space in the wall of the freezer. This technology offers safe dry storage for your samples. With no liquid nitrogen in the storage area the risk of cross contamination and the safety risks associated with the handling of liquid nitrogen are greatly reduced. This also means that the entire storage space can be used for inventory. Our wide lid opening provides easy, unrestricted access to samples and won't affect the temperature inside the freezer. All Isothermal freezers use our time tested and 2301 controller with a dual temperature display, autofill and many additional features. Custom BioGenic Isothermal Liquid Nitrogen Freezers have an industry best temperature gradient that averages -193C inside the storage area." .
SCR:019839 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ICS6000" ;
rdfs:label "Thermo Fisher | Dionex ICS-6000 Carbohydrate Removal Accessory Kit for ED Electrochemical Detection" ;
definition: "Accessory for ion chromatography instruments that provides amino acid quantification by removing carbohydrates from amino acid samples in line." .
SCR:019840 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Dionex_Ultimate_3000",
"SCR_020563" ;
rdfs:label "Dionex | Ultimate 3000 system" ;
definition: "Liquid Chromatography Mass Spectrometer system that has been designed to optimize low flow separations and facilitate easy coupling to mass spectrometry to provide the best resolution, sensitivity, and selectivity for nano LC and proteomics applications. Dionex has played a pioneering role in the field of nano HPLC, a technique that generally involves the application of columns with an internal diameter of 75,�m and low flow rates of around 300 nL/min. These configurations are best for analysis with limited sample starting amounts, due to the sensitivity enhancement of the smaller column i.d. Dionex offers several solutions to accommodate and robust nano LC as a front end to mass spectrometry and to fulfill three typical requirements:" .
SCR:019841 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Dionex_PC10" ;
rdfs:label "Thermo Fisher | Dionex PC10 Postcolumn Pneumatic Delivery" ;
NIFRID:synonym "PC10 Postcolumn Pneumatic Delivery System" ;
definition: "Reaction system that ensures consistent, pulse free reagent delivery for applications with high background absorbances, such as trace level transition metal analysis using post column reaction with 4 2 pyridylazoresorcinol PAR. Provides reagent with less pressure pulsation by applying constant pressure, eliminating need for pump. Assures optimal flow by applying constant pressure, eliminating need for pump." .
SCR:019842 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EpiSonic_1100" ;
rdfs:label "Epigentek | EpiSonic 1100 Sonicator" ;
NIFRID:synonym "EpiSonic Multi-Functional Bioprocessor 1100 system" ;
definition: "EpiSonic Multi-Functional Bioprocessor 1100 system is a multi-sample sonication instrument of the latest generation for use in a wide range of biological applications, in particular for DNA and chromatin shearing. This completely digital instrument allows for simultaneous optimized processing of 1 to 12 samples by tube, best for NGS applications, and can be easily integrated into existing lab workflows. Chiller is included at no additional charge. The EpiSonic 1100 sonicator was designed and built with the processing of biological samples specifically in mind, particularly NGS applications via Illumina or Ion Torrent workflows." .
SCR:019844 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_306" ;
rdfs:label "Edwards | Auto 306 e-beam Evaporator" ;
definition: "E-beam evaporator recommended for oxide and nitride materials. Designed to operate around the e-5 millibar vacuum range, EE-2 can also be used to deposit metals (non-toxic materials) if very low pressure is not a critical factor in your process. The water-cooled substrate holder can accommodate one wafer up to 3� diameter. EE-2 has a rotary-vane mechanical roughing pump and a turbo high-vacuum pump, and is a relatively low voltage (~3.8kV) electron beam evaporation deposition system with a 4-pocket, water-cooled rotating hearth." .
SCR:019845 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5075" ;
rdfs:label "Eppendorf | 5075 epMotion Automated Liquid Handling System" ;
definition: "System provides precise, accurate alternative to time-consuming manual pipetting and liquid handling tasks. The combination of accelerated operational speed, new software & hardware features and an increased number of worktable positions make the systems best for and flexible laboratory use across a wide range of liquid handling applications. To ensure easy and consistent use, epMotion 5075 employs both Eppendorf's established epBlue software and an new software assistant concept. This supports the programming of applications and ensures that all users can use the system with only initial training. In addition, novel features such as a new CleanCap option, including UV light decontamination and a HEPA filter for purified air, offer new standards of decontamination and sample safety. This is supported even further by an optical sensor that checks labware, liquid levels and tip counts and type at the start of each cycle, hugely decreasing any risk of error during the run." .
SCR:019846 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5414" ;
rdfs:label "Eppendorf | 5414 Microcentrifuge" ;
definition: "Benchtop centrifuge with maximum speed of 15,000 rpm. It features a 30-minute built-in timer, LED light that cycles at 1 second intervals, and a pushbutton switch for short momentary spins." .
SCR:019847 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5417R" ;
rdfs:label "Eppendorf 5417R Refrigerated Centrifuge" ;
definition: "Eppendorf 5417R is a refrigerated centrifuge with a brushless motor that spins up to 16,400 RPM with maximum RCF up to 25,000 x g. The Eppendorf 5417R comes equipped with an integrated cooling fan that helps remove residual heat build-up. Compact design and quiet operation (<60dB) makes the Eppendorf 5417R on a crowded lab bench or in a cold room. Automatic rotor detection system senses the rotor type and prevents the centrifuge from exceeding the rotor speed limit. Time (selectable in minutes or seconds; up to 99 minutes or hold) and speed (variable in rpm or rcf) are easily set using the keypad and are displayed on the LED read-out. All functions are microprocessor controlled. The Eppendorf 5417R conforms to International Safety Standard IEC1010 and features a steel plated rotor housing and double locking lid for maximum end user protection. RS 232 interface provides data output for computer control or data recording." .
SCR:019848 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5424" ;
rdfs:label "Eppendorf | 5424 Microcentrifuge" ;
definition: "Eppendorf centrifuge 5424 (Eppendorf microcentrifuge models 5424 and 5424R) are versatile 24-place centrifuges that set new standards for silence, speed, and simplicity in operation. The fixed-angle rotor is best for standard applications and centrifugation of biohazardous or radioactive samples. The miniprep spin column rotor features an extra-high rim to support open tube lids. The PCR tube rotor is best in \"knockdown\" spin applications for liquids after reaction setup. Certified aerosol-tight rotors have red screw-tops for easy identification. These are the direct replacements for the legendary models 5415D and 5415R." .
SCR:019849 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5430R" ;
rdfs:label "Eppendorf | 5430R Microcentrifuge" ;
definition: "Cross-over Centrifuge 5430 and 5430 R combine the best features of a microcentrifuge (small footprint) and multipurpose centrifuge (versatility) in one instrument. These centrifuges spin rotors for Eppendorf tubes and PCR strips as you would expect from any microcentrifuge. But that's not all. In a compact size, Centrifuge 5430 and 5430 R also accommodate rotors for microplates and 15/50 mL conical tubes. Now, the rotor program has been expanded with additional Eppendorf QuickLock rotors. This includes 48-place rotors (1.5/2.0 mL), a 16-place rotor for Eppendorf Tubes 5.0 mL and a swing-bucket rotor (24 × 1.5/2.0 mL). With their unmatched versatility, Centrifuge 5430 and Centrifuge 5430 R are the flagship products among the Eppendorf microcentrifuge portfolio. Available as keypad or knob variant" .
SCR:019850 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_H1200" ;
rdfs:label "EMCorp | H1200 Vibratome" ;
definition: "ibrVating blade microtome that is capable of preparing sections in the range of 10 to 1000 micrometres from a wide variety of both biological and materials specimens. The blade is clamped at a pre-set angle on a horizontally disposed ram which runs on precision engineered cross roller linear bearings." .
SCR:019851 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Dioxin Analyzer Mass Spectrometry System" ;
NIFRID:synonym "Thermo Scientific Dioxin Analyzer" ;
definition: "Thermo Scientific Dioxin Analyzer to deliver quantitation of dioxins and dl-PCBs in food samples in compliance with EU regulations. Ensures quantitation of polychlorinated dibenzo p dioxins PCDDs, polychlorinated dibenzo furans PCDFs and dioxin like polychlorinated biphenyls dl PCBs in food and feed samples. Dioxin Analyzer includes Thermo Scientific TSQ 9000 Triple Quadrupole GC-MS/MS, consumables, system suitability check standard solutions, e-workflow with acquisition method, data processing software, isotope dilution calculation, and reporting methods in compliance with EU regulations." .
SCR:019852 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5424R" ;
rdfs:label "Eppendorf | 5424R Microcentrifuge" ;
definition: "Eppendorf centrifuge 5424 (Eppendorf microcentrifuge models 5424 and 5424R) are versatile 24-place centrifuges that set new standards for silence, speed, and simplicity in operation. The fixed-angle rotor is best for standard applications and centrifugation of biohazardous or radioactive samples. The miniprep spin column rotor features an extra-high rim to support open tube lids. The PCR tube rotor is best in \"knockdown\" spin applications for liquids after reaction setup. Certified aerosol-tight rotors have red screw-tops for easy identification. These are the direct replacements for the legendary models 5415D and 5415R." .
SCR:019853 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_D30" ;
rdfs:label "Eppendorf | Biophotometer D30 Photometer" ;
definition: "Spectrophotometer that processes data, records at fixed wavelengths and evaluates results. For specific methods, additional measurements are recorded and displayed as graph, making impurities quick to identify." .
SCR:019854 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5430" ;
rdfs:label "Eppendorf | 5430 Microcentrifuge" ;
definition: "Cross-over Centrifuge 5430 and 5430 R combine the best features of a microcentrifuge (small footprint) and multipurpose centrifuge (versatility) in one instrument. These centrifuges spin rotors for Eppendorf tubes and PCR strips as you would expect from any microcentrifuge. But that's not all. In a compact size, Centrifuge 5430 and 5430 R also accommodate rotors for microplates and 15/50 mL conical tubes. Now, the rotor program has been expanded with additional Eppendorf QuickLock rotors. This includes 48-place rotors (1.5/2.0 mL), a 16-place rotor for Eppendorf Tubes 5.0 mL and a swing-bucket rotor (24 × 1.5/2.0 mL). With their unmatched versatility, Centrifuge 5430 and Centrifuge 5430 R are the flagship products among the Eppendorf microcentrifuge portfolio. Available as keypad or knob variant" .
SCR:019855 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5810R" ;
rdfs:label "Eppendorf | 5810R" ;
definition: "Centrifuge for medium to high-throughput laboratories with swing-bucket rotors and adapters accommodate tubes and bottles from 0.2 mL to 750 mL with a centrifugation speed of up to 14,000 rpm." .
SCR:019856 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CellTram_4r" ;
rdfs:label "Eppendorf | CellTram 4r Air/Oil Injector" ;
definition: "Pneumatic injector that is used for oil free micromanipulation and gentle holding of cells in suspension. It is also suitable for uptake and injection of cells, like sperm or ES cells." .
SCR:019857 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_epMotion_5070" ;
rdfs:label "Eppendorf | epMotion 5070 Automated Pipetting" ;
definition: "Automated pipetting workstation that is used for serial dilutions, reagent distribution, sample transfer from tubes to plates, and sample normalization." .
SCR:019858 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_epMotion_5070f" ;
rdfs:label "Eppendorf | epMotion 5070f Automated Pipetting" ;
definition: "Automated pipetting workstation that allows for the automation of key processes such as seeding cells, media changes, or performing assays e.g. cytotoxicity. It enables you to handle 6, 24 or 48 well plate or even denser formats from 96 to 384 wells." .
SCR:019859 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_epMotion_5073l" ;
rdfs:label "Eppendorf | epMotion 5073l Automated Pipetting" ;
definition: "Automated pipetting workstation that with 6 deck positions, gripper option and automatic exchange of 2 tools for automatic PCR setup in the 96 or 384 plate formats." .
SCR:019860 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5804R" ;
rdfs:label "Eppendorf | 5804R Centrifuge" ;
definition: "Centrifuge for medium capacity needs that allows for molecular applications in tubes up to 250 mL and offers additional swing bucket and fixed angle rotors as well as deepwell plate capacity for versatility. It has a centrifugation speed of up to14,000 rpm." .
SCR:019861 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5810" ;
rdfs:label "Eppendorf | 5810 Centrifuge" ;
definition: "Centrifuge that is used for medium to high throughput laboratories and combines versatility and capacity for both tubes and plates with compact footprint." .
SCR:019862 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5073m",
"SCR_019871" ;
rdfs:label "Eppendorf | epMotion 5073m Automated Pipetting system" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 3, 2023. Automated pipetting workstation that is tailored for nucleic acid purification, but can be used for other liquid handling tasks. Integrated magnetic finger and ThermoMixer module is used for magnetic bead based purifications." .
SCR:019863 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_epMotion_5075l" ;
rdfs:label "Eppendorf | epMotion 5075l Automated Pipetting" ;
definition: "Automated pipetting workstation with 15 worktable positions that is used for applications such as the purification of nucleic acids with magnetic beads or routine applications with several plates" .
SCR:019864 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_epMotion_5073m_NGS" ;
rdfs:label "Eppendorf | epMotion 5073m NGS Solution Automated Pipetting" ;
definition: "Automated pipetting workstation that is used for low throughput Next Generation Sequencing library preparation of up to 24 samples." .
SCR:019865 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_epMotion_5075m" ;
rdfs:label "Eppendorf | epMotion 5075m Automated Pipetting" ;
definition: "Automated pipetting workstation that combines magnetic finger module and ThermoMixer to facilitate magnetic bead separation, mixing, and temperature control in one deck position." .
SCR:019866 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5804" ;
rdfs:label "Eppendorf | 5804 Centrifuge" ;
definition: "Centrifuge 5804/5804 R is a high speed centrifuge for medium capacity needs. It allows for molecular applications in tubes up to 250 mL and offers additional swing,bucket and fixed,angle rotors as well as deepwell plate capacity for increased versatility. Eppendorf Centrifuge 5804/5804 R with its renowned quality and reliability offers you the most cost efficient solution for your medium throughput applications,now and in the future. It allows for molecular applications in tubes up to 250 mL and offers additional swing-bucket and fixed-angle rotors as well as deepwell plate capacity for increased versatility." .
SCR:019867 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_epMotion_5075t_NGS" ;
rdfs:label "Eppendorf | epMotion 5075t NGS Solution Automated Pipetting" ;
definition: "Automated pipetting workstation that combines automated liquid handling and software features with accessories and consumables for Next Generation Sequencing library preparation and NGS kit flexibility." .
SCR:019868 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_epMotion_5075t" ;
rdfs:label "Eppendorf | epMotion 5075t Automated Pipetting" ;
definition: "Automated pipetting workstation that includes a proprietary module to mix, heat or cool samples and reagents. The module can be loaded and unloaded with the gripper and pipetting to the mixer is possible before and after mixing steps." .
SCR:019869 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_epMotion_5075v" ;
rdfs:label "Eppendorf | epMotion 5075v Automated Pipetting" ;
definition: "Automated pipetting workstation that allows walk away automation of purification protocols that rely on vacuum filtration performing applications, such as nucleic acid purification or solid phase extraction away from workbench." .
SCR:019870 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4i" ;
rdfs:label "Eppendorf | FemtoJet 4i" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 14,2023. Eppendorf's electronic microinjectors FemtoJet 4i and FemtoJet 4x with their operation menu and a range of functionalities are perfectly suited for injecting small to intermediate volumes. With a built-in compressor, the FemtoJet 4i is the tool of choice for injecting aqueous solutions into adherent cells and suspension cells. If your research demands injecting volumes greater than 100 pL and/or longer series at higher pressures, FemtoJet 4x with its external pressure supply (not included) delivers the precise and continuous pressure required. Featuring the same quality design and compatibility features as the FemtoJet 4i, the FemtoJet 4x is the \"heavy duty\" device for those more demanding applications. Both the FemtoJet 4i and FemtoJet 4x, form the system with Eppendorf micromanipulators, yet they integrate just as easily with non-Eppendorf micromanipulation systems. The electronic connection between FemtoJet 4i or 4x and TransferMan 4r or InjectMan 4 guarantees simple, rapid and reproducible microinjections into cells, simplifying your daily work and speeding up your workflow. The FemtoJet 4i/ 4x injectors are for research use only." .
SCR:019872 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FemtoJet" ;
rdfs:label "Eppendorf | FemtoJet injector" ;
definition: "Microscope accessory that is suited for injecting small to intermediate volumes, up to 100 pL, featuring wide range of functionality, simple operation and built in compressor to independently deliver required pressure. Ideal for injecting aqueous solutions into adherent cells and suspension cells." .
SCR:019873 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_epMotion_96" ;
rdfs:label "Eppendorf | epMotion 96 and 96xl Automated Pipetting" ;
definition: "Automated pipetting workstation that automates multichannel pipetting, with reproducibility of results from cell based assays, ELISA, cell seeding, nucleic acid quantification, plate reformatting, or other applications." .
SCR:019874 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Incucyte" ;
rdfs:label "Essen | IncuCyte ZOOM System" ;
definition: "IncuCyte ZOOM system is a live-cell imaging and analysis platform that enables automated quantification of cell behavior over time (from hours to weeks) by automatically gathering and analyzing images around the clock. The system provides insight into active biological processes in real-time which is not possible using single-point and end-point measurements. The system resides within the controlled environment of a standard cell incubator. All imaging is completely non-invasive and non-perturbing to cell health. The system can process multiple plates, flasks and dishes in parallel and does not depend on shuttling plates into and out of the incubator." .
SCR:019876 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Vacufuge_Plus" ;
rdfs:label "Eppendorf | Vacufuge Plus Concentrator" ;
definition: "Benchtop concentrator that provides vacuum concentration of DNA and RNA, nucleotides, proteins and other liquid or wet samples. Coated lid provides chemical resistance against aggressive acids and organic solvents, like TFA and DMSO." .
SCR:019877 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NB24" ;
rdfs:label "Excella | NB24 Shaking Incubator" ;
definition: "Biological shaker with heavy-duty drives that provide long life and quiet operation under moderate loads and at speeds up to 400 rpm." .
SCR:019878 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MX-20" ;
rdfs:label "Faxitron | MX-20 Cabinet X-Ray System" ;
definition: "MX-20 Cabinet X-ray System is utilized to produce highly detailed radiographs of seed and grain to inspect for viability, infestation, damage or contamination. The system is available with either our large 12 cm x 12 cm DC-12 camera or our smaller, less expensive 5 cm x 5 cm DC-5 camera. Both provide 10 lp/mm spatial resolution in contact mode. Magnification allows for spatial resolution of up to 50 lp/mm. The 20 �m nominal focal spot and up to 5X additional geometric magnification provide ultra high-contrast and high spatial resolution images. If a larger field of view is required, the MX-20 can be used with a CR plate and small, upright CR reader to obtain a field of view up to 10� x 12�." .
SCR:019879 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Apreo" ;
rdfs:label "FEI | Apreo SEM (Scanning Electron Microscope) for Life Sciences" ;
definition: "Scanning electron microscope that provides a sub-nanometer or all-around nanometer resolution performance on materials spanning from catalysts, powders, nanoparticles, and bulk magnetic samples to nanodevices." .
SCR:019880 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Aquilos 2" ;
rdfs:label "Thermo Fisher | FEI Aquilos 2 Cryo-FIB for Life Sciences" ;
definition: "Sample preparation tool used for the preparation of thin, electron transparent lamellas for high resolution cryo electron tomography or MicroED of micro crystals." .
SCR:019881 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_flexProber" ;
rdfs:label "FEI | flexProber System for Semiconductors" ;
definition: "Nanoprobing platform that provides electrical characterization and fault isolation capabilities for process development, device design debug, and failure analysis." .
SCR:019882 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ExSolve Wafer" ;
rdfs:label "FEI | ExSolve Wafer TEM Prep DualBeam" ;
definition: "Sample preparation workflow that is used for transmission electron microscopy (TEM) analysis." .
SCR:019883 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Glacios" ;
rdfs:label "FEI | Glacios Cryo-TEM (Transmission Electron Microscope) for Life Sciences" ;
definition: "Microscope that features 200 kV XFEG optics and ensures a robust and contamination-free pathway throughout the entire workflow, from sample preparation and optimization to image acquisition and data processing." .
SCR:019884 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LX-60" ;
rdfs:label "Faxitron | LX-60 X-Ray Machine" ;
definition: "LX-60 Specimen Radiography System is best for imaging larger animals and more dense specimens, due to its cabinet size and energy range of up to 60 kV. The system's large 12 cm x 12 cm camera offers 10 lp/mm spatial resolution. Magnification allows for spatial resolution of up to 60 lp/mm. The 10-12 �m typical focal spot and up to 6X additional geometric magnification provide ultra high-contrast and high spatial resolution images. If a larger field of view is required, the LX-60 can be used with a CR plate and small, upright CR reader to obtain a field of view up to 10� x 12� (25.4 cm x 30.5 cm)." .
SCR:019885 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Hyperion_II" ;
rdfs:label "FEI | Hyperion II System" ;
definition: "Electrical failure analysis system for semiconductors that offers transistor probing for electrical characterization and fault localization in support of semiconductor technology development, yield engineering and device reliability improvement." .
SCR:019886 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NanoLab 1200AT" ;
rdfs:label "FEI | Helios NanoLab 1200AT DualBeam for Semiconductors" ;
definition: "Wafer analysis system that can create site-specific transmission electron microscope (TEM) samples thin enough to capture a single transistor at the 10nm node, from wafers up to 300mm in diameter." .
SCR:019887 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Krios G4" ;
rdfs:label "FEI | Krios G4 Cryo-TEM" ;
definition: "Transmission electron microscope that is used for automated applications such as single particle analysis, cryo-electron tomography, and micro electron diffraction." .
SCR:019888 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Meridian_7" ;
rdfs:label "FEI | Meridian 7 System for Semiconductors" ;
definition: "Electrical failure analysis system for semiconductors that provides visible laser voltage imaging and probing and dynamic laser stimulation on sub-10nm devices." .
SCR:019889 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Meridian_V" ;
rdfs:label "FEI | Meridian V System for Semiconductors" ;
definition: "Electrical failure analysis system for semiconductors with optimized dynamic LSM platform that supports automated test equipment docking and back side analysis with laser voltage probing, laser voltage imaging, and laser simulation for critical path analysis." .
SCR:019890 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Meridian_WS_DP" ;
rdfs:label "FEI | Meridian WS-DP System for Semiconductors" ;
definition: "Electrical failure analysis system for semiconductors that enables faster defect localization by using production testers, load boards, and probe cards." .
SCR:019891 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ELITE" ;
rdfs:label "FEI | ELITE System for Semiconductors" ;
definition: "Semiconductor with enhanced lock in thermal emission that provides better signal to noise ratio, increased sensitivity and higher feature resolution than steady state thermography." .
SCR:019892 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Meridian_IV" ;
rdfs:label "FEI | Meridian IV System for Semiconductors" ;
definition: "Electrical failure analysis system for low-voltage, high-density semiconductor devices with the ability to diagnose wide ranging failure modes, including parametric failures and those resulting from design-process marginalities." .
SCR:019893 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Metrios" ;
rdfs:label "FEI | Metrios TEM for Semiconductors" ;
definition: "Transmission electron microscope that provides fast, precise measurements for semiconductor manufacturers to develop and control their wafer fabrication processes." .
SCR:019894 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_nProber_III" ;
rdfs:label "FEI | nProber III System for Semiconductors" ;
definition: "Electrical failure analysis system for semiconductors with fault localization and transistor characterization that allows users to characterize individual transistor performance down to 7nm node." .
SCR:019895 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_OptiFIB" ;
rdfs:label "FEI | OptiFIB Taipan for Semiconductors" ;
definition: "Focused ion beam system that for semiconductors that enables a highly controlled beam profile and current, accurate navigation and ion beam placement, and reliable end-pointing." .
SCR:019896 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Phenom GSR" ;
rdfs:label "FEI | Phenom GSR Desktop SEM" ;
definition: "Desktop scanning electron microscope that is used to scan sample and find suspect gunshot residue particles. If suspect particle is found, Energy Dispersive Spectroscopy technique is used to identify elements in that particle." .
SCR:019897 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Meridian_M" ;
rdfs:label "FEI | Meridian M System for Semiconductors" ;
definition: "Electrical failure analysis system for semiconductors that uses high sensitivity broadband DBX photon emission and Static Laser Stimulation techniques to pinpoint the location of electrical faults." .
SCR:019898 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Phenom_ProX" ;
rdfs:label "FEI | Phenom ProX SEM" ;
definition: "Desktop scanning electron microscope that offers fast, high-resolution imaging in addition to an integrated energy-dispersive X-ray diffraction (EDS) detector for elemental analysis." .
SCR:019899 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Phenom Pure" ;
rdfs:label "FEI | Phenom Pure Desktop SEM" ;
definition: "Desktop scanning electron microscope that provides high-quality images and features autofocus and automated source alignments." .
SCR:019900 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Phenom_XL" ;
rdfs:label "FEI | Phenom XL SEM" ;
definition: "Desktop scanning electron microscope with increased chamber size for large samples up to 100 mm x 100 mm." .
SCR:019901 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Quattro_ESEM" ;
rdfs:label "FEI | Quattro ESEM" ;
definition: "Scanning electron microscope that combines a field emission gun (FEG) and three vacuum modes (high vacuum, low vacuum, and ESEM) to provide the flexibility to accommodate a wide range of samples, including those that are outgassing or otherwise not vacuum-compatible." .
SCR:019902 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Phenom Pro" ;
rdfs:label "FEI | Phenom Pro Desktop SEM" ;
definition: "Desktop scanning electron microscope with CeB6 source that offers high brightness while requiring low maintenance. It allows sample structures to be physically examined and their elemental composition determined." .
SCR:019903 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_F200C" ;
rdfs:label "FEI | Talos F200C TEM and STEM (Scanning/Transmission Electron Microscope)" ;
definition: "Microscope that is designed for performance and productivity across a wide range of samples and applications, such as 2D and 3D imaging of cells, organelles, asbestos, polymers, and soft materials, both at ambient and cryogenic temperatures." .
SCR:019904 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Prisma E" ;
rdfs:label "FEI | Prisma E SEM" ;
definition: "Scanning electron microscope that is used for industrial research and development with environmental SEM capability." .
SCR:019905 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Talos Arctica" ;
rdfs:label "FEI | Talos Arctica Cryo-TEM" ;
definition: "Transmission electron microscope that is built for delivering high-resolution 3D characterization of biological samples and biomaterials in cell biology, structural biology, and nanotechnology research." .
SCR:019906 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_F200S" ;
rdfs:label "FEI | Talos F200S G2 TEM and STEM" ;
definition: "TEM and STEM microscope for dynamic microscopy." .
SCR:019907 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_F200X" ;
rdfs:label "FEI | Talos F200X G2 TEM and STEM" ;
definition: "Transmission electron microscope that combines high-resolution STEM and TEM imaging with energy dispersive X-ray spectroscopy signal detection." .
SCR:019908 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_L120C" ;
rdfs:label "FEI | Talos L120C TEM and STEM" ;
definition: "Transmission electron microscope that is designed for performance and productivity across a wide range of samples and applications, such as 2D and 3D imaging of cells, cell organelles, asbestos, polymers, and soft materials, both at ambient and cryogenic temperatures." .
SCR:019909 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Themis S" ;
rdfs:label "FEI | Themis S S/TEM for Semiconductors" ;
definition: "Scanning/transmission electron microscope that is designed for high-speed imaging and analysis of semiconductor devices." .
SCR:019910 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Themis Z" ;
rdfs:label "FEI | Themis Z for Materials Science" ;
definition: "Next generation, ultra-high resolution, aberration corrected, scanning transmission electron microscope delivering the ultimate optical performance and flexibility with unprecedented reproducibility." .
SCR:019911 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Talos_F200i" ;
rdfs:label "Thermo Fisher | Talos F200i Transmission Electron Microscope" ;
NIFRID:synonym "FEI Talos F200i TEM",
"Talos F200i TEM",
"Thermo Scientific Talos F200i TEM" ;
definition: "Thermo Scientific Talos F200i is an integrated (S)TEM to perform both Transmission Electron Microscopy (TEM) and Scanning Transmission Electron Microscopy (STEM) in a single system. It acts as a 20-200 kV field emission instrument designed for high-resolution 2D/3D imaging, in situ observation, and EDX analysis.Designed for performance and productivity across a wide range of Materials Science samples and applications. Its standard X-Twin pole piece gap combined with a reproducibly performing electron column opens opportunities for high-resolution 2D and 3D characterization, in situ dynamic observations, and diffraction applications." .
SCR:019912 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_V400ACE" ;
rdfs:label "FEI | V400ACE Focused Ion Beam for Semiconductors" ;
definition: "Focused ion beam system that can be configured for backside editing with an optional IR microscope and bulk silicon trenching package." .
SCR:019913 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Volumescpe 2" ;
rdfs:label "FEI | Volumescope 2 SEM" ;
definition: "Microscope that is used for large volume samples with serial block face imaging and multi energy deconvolution." .
SCR:019914 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Verios 5" ;
rdfs:label "FEI | Verios 5 XHR SEM" ;
definition: "Microscope that is used for characterization of nanomaterials with sub nanometer resolution and high material contrast SEM." .
SCR:019915 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4x" ;
rdfs:label "Eppendorf | FemtoJet 4x electronic microinjector" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 14, 2023. Eppendorf electronic microinjectors FemtoJet 4i and FemtoJet 4x with their operation menu and a range of functionalities are perfectly suited for injecting small to intermediate volumes. With a built-in compressor, the FemtoJet 4i is the tool of choice for injecting aqueous solutions into adherent cells and suspension cells. If your research demands injecting volumes greater than 100 pL and/or longer series at higher pressures, FemtoJet 4x with its external pressure supply (not included) delivers the precise and continuous pressure required. Featuring the same quality design and compatibility features as the FemtoJet 4i, the FemtoJet 4x is the \"heavy duty\" device for those more demanding applications. Both the FemtoJet 4i and FemtoJet 4x, form the system with Eppendorf micromanipulators, yet they integrate just as easily with non-Eppendorf micromanipulation systems. The electronic connection between FemtoJet 4i or 4x and TransferMan 4r or InjectMan 4 guarantees simple, rapid and reproducible microinjections into cells, simplifying your daily work and speeding up your workflow. The FemtoJet 4i/ 4x injectors are for research use only." .
SCR:019916 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CyTOF_Helios",
"SCR_019917" ;
rdfs:label "Fluidigm | CyTOF Helios Mass Cytometer" ;
NIFRID:synonym "CyTOF Helios",
"CyTOF Helios Mass Cytometer" ;
definition: "Mass cytometer that enables deep profiling of translational and clinical research samples across range of cell surface and intracellular markers. Helios represents newer, more advanced iteration with improvements in throughput, detection range, and software capabilities." .
SCR:019917 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Helios" ;
rdfs:label "Fluidigm | Helios Cell Mass Cytometer" ;
definition: "Helios, a CyTOF system, comprises the most recent advances in mass cytometry and is designed to provide a new and improved tool for bioanalytical single-cell detection and analysis. This high-performance mass cytometer, from the CyTOF family of instruments, enables the analysis of more than 40 markers and ly allows their quantitative determination with negligible spectral overlap, a result of exquisite resolution between mass detection channels. Helios provides users with 135 detection channels that can simultaneously resolve multiple elemental probes at high acquisition rates, thereby maximizing the per-cell information obtained from a single sample. The expanded mass range of 75 209 amu and superior mass resolution provide researchers with the ability to differentiate adjacent peaks. The Helios system provides fast instrument startup, an easyto-use pneumatic sample loading system, an improved cell detection rate, and enhanced data storage capabilities. These attributes provide researchers with an unparalleled ability to generate high-resolution phenotypic and functional profiles of cells from normal and diseased states" .
SCR:019918 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Themis ETEM" ;
rdfs:label "FEI | Themis ETEM (Titan Environmental Transmission Electron Microscope)" ;
definition: "Environmental transmission electron microscope that is used for in situ observation of structure dynamics at nanostructure-characteristic length scales." .
SCR:019919 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Flexstation II" ;
rdfs:label "Molecular Devices | Flexstation II Dual Monochromator Fluorescence Kinetics Flexstation" ;
definition: "Molecular Devices FlexStation II is a benchtop scanning fluorometer and integrated fluid transfer workstation capable of conducting endpoint, kinetic, lambda scan and well scan experiments in a multi-well plate format (6, 12, 24, 48 and 96-well) and fluidics transfer experiments in 96-well format. The FlexStation II is best for measuring the activity of Gq-coupled receptors via the detection of intracellular calcium release. In addition, kits are available for the measurement of fatty acid uptake, cyclic GMP and AMP levels, potassium ion channel flux, and membrane potential. The dual monochromator optical bench design allows the user to choose multiple wavelengths and to optimize excitation and emission wavelengths for most fluorometric assays. Allow the user to obtain real-time kinetic data milliseconds before and after fluid transfer events. The dual monochromator optical bench design enables the user to choose multiple wavelengths and to optimize both excitation and emission wavelengths for most fluorometric assays." .
SCR:019920 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Formulator" ;
rdfs:label "Formulatrix | Formulator liquid handler for preparing crystallization reservoirs" ;
definition: "Liquid handler specifically designed for Protein Crystallography that uses patented microfluidic technology to dispense up to 34 different ingredients. A 96-nozzle dispensing chip can dispense any volume of any ingredient of any viscosity into any well." .
SCR:019921 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Steri-Cycle" ;
rdfs:label "Thermo Fisher | Forma Steri-Cycle CO2 Incubators" ;
definition: "Incubator that features an in-chamber HEPA air filtration system, which provides continuous protection against unwanted airborne contaminants, along with an on-demand, high-temperature sterilization cycle that simplifies routine cleaning." .
SCR:019923 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Mantis" ;
rdfs:label "Formulatrix | Mantis Automated Liquid Handler" ;
definition: "Automated liquid handler with a diaphragm-based chip design that dispenses aqueous and organic solutions. It will dispense in any SBS template from 6 to 1536 well plates, and can be easily programmed to dispense to custom designs as needed." .
SCR:019924 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BioContinuum" ;
rdfs:label "Gatan | BioContinuum Imaging Filter Transmission Electron Microscope (TEM) Imaging and Spectroscopy" ;
definition: "Microscope imaging filter that is optimized for cryo-EM and cryo-ET to gain further insight into system function and disease progression at the molecular level." .
SCR:019926 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ChromaCL2" ;
rdfs:label "Gatan | ChromaCL2 iBSED Detector Scanning Electron Microscope (SEM) Imaging and Spectroscopy" ;
definition: "Detector that is used for live color cathodoluminescence imaging in scanning electron microscopes." .
SCR:019927 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_930" ;
rdfs:label "Gatan | 930 Cryoplunge 3 Cryo Preparation System" ;
definition: "Cryoplunge 3 system with GentleBlot technology is used for the preparation of frozen hydrated specimens for cryo-electron microscopy (cryo-EM). GentleBlot technology optimizes blotting force and pressure to provide gentle 1- and 2-sided blotting to minimize breakage of fragile specimen supports. Humidified plunging chamber safeguards the specimen from drying during the blotting process. Temperature controlled pot maintains the condensed ethane at its melting point. Specially designed quick disconnect mechanism on plunge rod allows fast and easy attachment of the plunge tweezers to facilitate specimen handling. Removable liquid nitrogen workstation provides a contamination free environment to protect the frozen hydrated specimen" .
SCR:019928 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Dimple_Grinder_II" ;
rdfs:label "Gatan | Dimple Grinder II Transmission Electron Microscope (TEM) Specimen Preparation" ;
definition: "Instrument that prepares TEM specimens with mechanical method of pre-thinning to near electron transparency to greatly reduce ion milling times and uneven thinning." .
SCR:019929 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_3View" ;
rdfs:label "Gatan | 3View System Scanning Electron Microscope (SEM) Imaging and Spectroscopy" ;
definition: "Imaging system that automates sectioning and image capture of 3D ultrastructure using serial block face scanning electron microscopy." .
SCR:019931 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DigiScan_II" ;
rdfs:label "Gatan | DigiScan II System Transmission Electron Microscope (TEM) Imaging and Spectroscopy" ;
definition: "Detector and control system that uses digital beam control and image processing to enhance the photographic quality of digital images." .
SCR:019932 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_626" ;
rdfs:label "Gatan | Gatan | 626 Cryotransfer Holder" ;
definition: "Single tilt liquid nitrogen cryo transfer holder that is designed for low temperature transfer and subsequent recording of electron beam sensitive, frozen hydrated specimens in TEM. Tilt ranges and compatibility of specimen holders vary according to TEM manufacturer, model, pole piece gap, and presence of in gap accessories." .
SCR:019933 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Continuum_and_Continuum_S" ;
rdfs:label "Gatan | GIF Continuum and Continuum S Transmission Electron Microscope (TEM) Imaging and Spectroscopy" ;
definition: "Microscopy system that is used for both EELS and EFTEM applications and has spectral acquisition rates as high as 8000 spectra per second." .
SCR:019934 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ilion_II" ;
rdfs:label "Gatan | Ilion II System Scanning Electron Microscope (SEM) Specimen Preparation" ;
definition: "Microscope accessory that is used for low energy surface preparation for SEM cross section viewing." .
SCR:019935 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_K3_IS" ;
rdfs:label "Gatan | K3 IS Camera Transmission Electron Microscope (TEM) Imaging and Spectroscopy" ;
definition: "Large format camera for in-situ transmission electron microscopy." .
SCR:019936 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Murano" ;
rdfs:label "Gatan | Murano In-Situ Stages Scanning Electron Microscope (SEM) Specimen Stages" ;
definition: "SEM specimen heating stage that is specifically designed to enable in-situ research and designed to be compatible with geometrical requirements of different detectors including electron backscatter diffraction (EBSD) for dynamic observations." .
SCR:019937 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_K3" ;
rdfs:label "Gatan | K3 Camera Transmission Electron Microscope (TEM) Imaging and Spectroscopy" ;
definition: "Camera that is optimized for low-dose electron microscopy (EM) applications in both life science and materials science research and captures 1,500 full frames per second." .
SCR:019938 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_OneView" ;
rdfs:label "Gatan | OneView Camera Transmission Electron Microscope (TEM) Imaging and Spectroscopy" ;
definition: "Camera that captures 16 MP images and video in all TEM applications." .
SCR:019939 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PECS_II" ;
rdfs:label "Gatan | PECS II System Scanning Electron Microscope (SEM) Specimen Preparation" ;
definition: "Argon ion polishing system that is designed to polish and coat samples for SEM imaging and analytical techniques." .
SCR:019940 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Monarc CL" ;
rdfs:label "Gatan | Monarc CL Detector Scanning Electron Microscope (SEM) Imaging and Spectroscopy" ;
definition: "Cathodoluminescence detector that can determine the emission polarization properties of deep sub-wavelength structures like optical nanoantenna, nano-cavities, and photonic crystals." .
SCR:019941 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_STEMPack" ;
rdfs:label "Gatan | STEMPack Spectrum Imaging Transmission Electron Microscope (TEM) Imaging and Spectroscopy" ;
definition: "Imaging system that supports the acquisition of data from a broad range of detectors, including: electron energy loss (EELS), characteristic x-ray emission (EDS), cathodoluminescence emission (CL), absorbed / induced current (EBAC/EBIC), and electron diffraction" .
SCR:019942 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Solarus_II" ;
rdfs:label "Gatan | Solarus II Plasma Cleaner Transmission Electron Microscope (TEM) Specimen Preparation" ;
definition: "Plasma cleaner that can remove hydrocarbon contamination from TEM and SEM samples and holders." .
SCR:019943 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Rio" ;
rdfs:label "Gatan | Rio Camera Transmission Electron Microscope (TEM) Imaging and Spectroscopy" ;
definition: "CMOS camera with scintillator and 1:1 fiber optic coupling to maximize light generation and collection." .
SCR:019944 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_STEMx" ;
rdfs:label "Gatan | STEMx System Transmission Electron Microscope (TEM) Imaging and Spectroscopy" ;
definition: "4D STEM diffraction system that enables a wide variety of 4D STEM experiments, including strain mapping, indexing, orientation mapping, virtual apertures, and differential phase contrast." .
SCR:019945 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Auto ITC 200" ;
rdfs:label "GE | AutoITC 200 Isothermal Titration Calorimeter" ;
definition: "Isothermal titration calorimeter that can characterize molecular interactions of small molecules, proteins, antibodies, nucleic acids, lipids and other biomolecules. It can also be used to measure enzyme kinetics." .
SCR:019946 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Typhoon_Trio",
"SCR_020871" ;
rdfs:label "GE: Healthcare | Typhoon Trio Variable Mode Imager System" ;
definition: "Variable mode imager that produces digital images of radioactive, fluorescent, or chemiluminescent samples and contains three internal lasers (blue, green, and red)." .
SCR:019947 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GoldSeal_DPX_Bravo" ;
rdfs:label "GE: Healthcare | GoldSeal DPX Bravo" ;
definition: "DPX Bravo provides you with tools for basic bone health assessment. Its footprint is smaller than most other DXA tables 186cm 74� long by 86cm 34� wide. feature, WHO FRAX fracture risk assessment tool allows you to accurately predict 10 year probability of patient suffering major fracture. It offers you you dual energy X ray absorptiometry DXA technology in small, space saving footprint. It also provides you with essential, bone densitometry applications, such as AP spine, dual femur and forearm." .
SCR:019948 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PIPS II" ;
rdfs:label "Gatan | PIPS II System; Transmission Electron Microscope (TEM)" ;
definition: "Transmission electron microscope that uses precision ion polishing system for precise centering, control, and reproducibility of the milling process." .
SCR:019949 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Discovery RF180" ;
rdfs:label "GE: Healthcare | Discovery RF180; Radiography and Fluoroscopy System" ;
definition: "Remote imaging system that can perform tomo, Auto Image Paste, DSA, and bariatric exams. It also includes variable SID to conduct chest exams and has a 705 lb (or 325 kg) weight capacity." .
SCR:019950 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Infinia Hawkeye" ;
rdfs:label "GE: Healthcare | GoldSeal Infinia Hawkeye 4; Imaging system" ;
definition: "Dual detector SPECT/CT imaging system with extra large rectangular FOV detectors that incorporates hybrid imaging technology to help enable confident diagnosis, disease detection and precise localization." .
SCR:019951 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Precision 600FP" ;
rdfs:label "GE: Healthcare | Precision 600FP; Imaging System" ;
definition: "Flat panel radio-fluoroscopy system that provides ultra vivid imaging with frame rates ranging from 15 to 1 frames per second." .
SCR:019952 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_OEC Elite CFD" ;
rdfs:label "GE: Healthcare | OEC Elite CFD; Imaging system" ;
definition: "System is bestly suited for range of surgical needs including vascular, cardiac, orthopedics, gastrointestinal, endoscopic, urologic, critical care, pain management and emergency procedures.It has efficient image capture with SmartView 180 180 pivot joint on Ergo C arm model. It consists of CFD CMOS Flat Detector. Enhanced imaging control and planning with Live Zoom, Digital Pen, measurements and annotations. Six dose control options that can be used alone or in various combinations Digital Spot, Digital Cine Pulse, High Level Fluoroscopy, Standard Fluoroscopy, Low Dose, Pulse" .
SCR:019953 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Uroview 8K" ;
rdfs:label "GE: Healthcare | Uroview 8K;Imaging system" ;
definition: "Uroview 8K provides large field of view along with robust imaging platform to show you exact imaging detail. Designed to provide diagnostic image quality using dose saving strategies.Large field of view 17 inch x 17 inch dynamic digital flat panel detector.Superb resolution and grayscale with 2880 x 2880 resolution and 16 bit image processing. It has 32\" inch high resolution LCD display monitor with picture in picture capability on articulating arms.Adjustable low table height 25.2 inches with near 360 degree SmartAccess." .
SCR:019954 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Biacore_3000_Goldseal" ;
rdfs:label "GE: Healthcare | Biacore 3000 Real-time Biomolecular Interaction Analyzer" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8th,2024. Biacore 3000 processing unit is an established, label-free system for detailed studies of biomolecular interactions. The system delivers comprehensive characterization of the interaction, answers questions about the rate constants, affinity, specificity, and determines the active concentration of components. The ability to recover and transfer interaction partners directly to MALDI targets for identification and further characterization makes the system highly applicable to fast identification of unknown interactants." .
SCR:019956 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_OMX SR" ;
rdfs:label "GE: Healthcare | OMX SR Imaging System" ;
definition: "Compact imaging system that provides a stable platform for structured illumination microscopy (SIM) super resolution technology." .
SCR:019957 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_9500" ;
rdfs:label "GE | 9500 Biomolecular Imaging System" ;
definition: "Typhoon FLA 9500 is a robust and versatile laser scanner that is bestly suited to multiuser environments. Biomolecular imaging applications include sensitive and quantitative measurements of Western blots, multiplex fluorescence, and radioisotopic labels by storage phosphor as well as digitization of colorimetric stains. The system is flexible and can be customized with lasers, filters and detectors for multiplex near infrared fluorescence with IRDye. Typhoon FLA 9500 provides 457/532/635 nm excitation and up to 10 �m resolution for gel, blot, tissue and array imaging. The system can be customized with 685/785 nm excitation, customized filters and detectors for multiplex and near infrared fluorescence applications." .
SCR:019958 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AKTA" ;
rdfs:label "GE | AKTA FPLC System, Protein Purification System" ;
definition: "Purification system intended for microgram-scale protein purifications in Tricorn columns up to milligram-scale using HiTrap and HiScreen columns. For fast protein liquid chromatography of tens of grams of protein,can be used with flow rates up to 150 mL/min. This high flow rate is necessary when working with high-flow resins in large columns. Columns can even be packed at flow rates as high as 300 mL/min. System reduces hands-on time so that you can spend less time purifying proteins and more time focusing on your results. Easily switch between different users and applications. To get you up and running quickly, methods are easily created by dragging and dropping predefined templates in UNICORN 7. Purification of protein to sufficiently high yield and purity can be a time- and resource-consuming process. To address fast and efficient protein purification, Can be set up in different ways to handle multistep purification. With an additional column valve up to 10 columns can be connected enabling automation of several samples and steps." .
SCR:019959 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QPix II" ;
rdfs:label "Genetix | QPixII Colony Picking Robot" ;
definition: "QPixII offers high precision benchtop colony picking, gridding, and rearraying technology that has been specifically designed for high throughput genomics. It allows for automatic picking of 3500 colonies or plaques per hour. Constructed within a welded steel framework, the main bed is capable of holding 15 microtitre plates and 2 bioassay trays. The unit includes a sterilization bath and heated-air drier to ensure cleaning and drying of picking/gridding heads between the cycles. Colonies or plaques are visualized via CCD camera and picked from bioassay trays (QTrays) by a 96-pin picking head and inoculated into pre-filled 96 or 384 well QPlates. High accuracy picking, control and management at every step. Macroarrays are easily generated using the robots gridding software and accessories. Rearraying of clones can also be performed. The minimum computing requirements include WindowsTM software and an Intel Pentium III processor (600 MHz), 128 MB of RAM, and a 4 MB, 256 color video card. The unit is supplied with two picking/rearraying heads, one gridding head, and QSoft software including picking, gridding, and rearraying modules. Dimensions: 56.30\"w x 28.74\"d x 31.50\"h." .
SCR:019960 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XPS" ;
rdfs:label "Molecular Devices | Gemini XPS Microplate Reader" ;
definition: "Reader with top-read capability measures fluorescence on variety of sample formats from 6- to 384-well microplates in endpoint, kinetic, spectral scan, and well-scan modes." .
SCR:019961 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MR750" ;
rdfs:label "GE | 3.0T MR750 Magnetic Resonance Imager" ;
definition: "Magnetic resonance imager that is built around a third-generation, short-bore, superconducting 3.0T magnet and can generate multiple image contrasts in a single MRI scan including T1, T2, STIR, T1 FLAIR, T2 FLAIR* and PD contrasts of the brain in a single acquisition." .
SCR:019962 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Homogenizor" ;
rdfs:label "VWR | Genie Homogenizor" ;
definition: "Disruptor is available in analog or digital models, allows for Hands-Free disruption of up to twelve 1.5 or 2.0ml microtubes with timer from 0-15 minutes or continuous for analog models, and from 0-99 minutes or continuous for Digital models. Provides multi-directional action, which simultaneously agitates and vortexes at high speed, dramatically increasing cell disruption or sample resuspension efficiency. Suitable for use in cold rooms or incubators. best for difficult glass bead procedures - cell disruption/homogenization of yeast, bacteria, plant and animal tissue or anything that requires extremely violent high speed agitation. Digital model incorporates an adjustable speed alarm. Remove microtube holder and attach the supplied Pop-off Cup for high speed vortexing of single test tubes. The patented Disruptor Genie provides multi-directional action, which simultaneously agitates and vortexes at high speed, dramatically increasing cell disruption or sample resuspension effeciency." .
SCR:019965 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RT STARlet" ;
rdfs:label "Hamilton | RT STARlet Assay Ready Workstation" ;
definition: "Assay ready workstation that combines qPCR setup and qPCR on one platform." .
SCR:019966 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GenoGrinder" ;
rdfs:label "Cole-Parmer | GenoGrinder High Throughput Sample Homogenizer (SPEX)" ;
definition: "Geno/Grinder is an automated high-throughput plant & animal tissue homogenizer and cell lyser. It is equipped with an adjustable clamp that accommodates a full range of sample vials from 2mL to 50mL centrifuge tubes or up to six deep-well titer plates. It is specifically designed for rapid cell disruption, cell lysis and tissue homogenization through bead beating. This enables fast and efficient extraction of nucleic acids, proteins and other molecules. The new model Geno/Grinder incorporates a password protected, touch screen control panel, enabling the user to program run time, rate, cycles and pause time. A full range of Kryotech accessories are available to preserve temperature sensitive samples such as proteins and RNA. The Geno/Grinder is also recognized as an excellent automatic axial extractor. It is the best tool for the QuEChERS method used for extracting pesticide residues and other organic compounds. The Geno/Grinder enables increased throughput, improved extraction efficiency and reproducibility over traditional sample preparation methods. A full range of pre-loaded sample vials for different sample types is also available for fast and set up." .
SCR:019967 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MPE 2" ;
rdfs:label "Hamilton | [MPE]2 Solid Phase Extraction Device" ;
definition: "Positive pressure module that automates positive pressure processes, such as solid-phase extraction (SPE) and other positive-pressure applications with high reproducibility." .
SCR:019968 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Aliquot_STARlet" ;
rdfs:label "Hamilton | Aliquot STARlet Assay Ready Workstation" ;
NIFRID:synonym "Hamilton Aliquot STARlet" ;
definition: "Fully automates source-target sampling of blood and other homogeneous and heterogeneous biological samples for downstream applications. The walkaway process safely removes and replaces stoppers from a variety of commercial blood collection-type tubes, mixes the samples, and precisely aliquots daughter samples in under two minutes per tube. Up to 64 source tubes and 256 target tubes may be processed at once." .
SCR:019969 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AutoLys_STAR" ;
rdfs:label "Hamilton | AutoLys STAR Assay Ready Workstation" ;
definition: "Assay ready workstation that fully automates cell lysis and differential separation of DNA from biological evidentiary samples contained in specialized, barcoded spin-basket/filter type AutoLys Tubes." .
SCR:019970 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Aliquot" ;
rdfs:label "Hamilton | Aliquot STARlet Assay Ready Workstation" ;
definition: "Assay ready workstation that fully automates source target sampling of blood and other homogeneous and heterogeneous biological samples for downstream applications." .
SCR:019971 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BiOS",
"SCR_019974" ;
rdfs:label "Hamilton | BiOS Automated Ultra Low Temperature Freezer system" ;
definition: "BiOS is automated bio freezer storage system specifically designed to store sensitive biological samples. This ultra low temperature freezer is capable of reaching temperatures as low as minus 80°C, ensuring biological specimen integrity. BiOS can be scaled to fit your laboratory needs as a premier option for storing biological samples.Automated sample storage platforms run on INSTINCT S software." .
SCR:019973 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_easyBlood STARlet" ;
rdfs:label "Hamilton | easyBlood STARlet and STAR Assay Ready Workstation" ;
definition: "Assay ready workstation that fully automates image based blood fraction detection and aliquoting steps." .
SCR:019975 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BioTrode" ;
rdfs:label "Hamilton | BioTrode Laboratory Sensor" ;
definition: "Laboratory pH sensor that is commonly used for microtiter plate applications (especially solutions containing protein) with a slim tip that allows for immersion depth of only 7 mm." .
SCR:019976 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ELISA NIMBUS" ;
rdfs:label "Hamilton | ELISA NIMBUS Assay Ready Workstation" ;
definition: "Assay ready workstation that automates ELISA processing of up to eight 96 well microplates in parallel." .
SCR:019977 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Genomic_STARlet" ;
rdfs:label "Hamilton | Genomic STARlet Assay Ready Workstation" ;
definition: "Assay ready workstation that was developed in collaboration with MACHEREY-NAGEL for their vacuum based chemistry to quickly isolate high quality nucleic acids." .
SCR:019978 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LabElite Decapper SL" ;
rdfs:label "Hamilton | LabElite DeCapper SL Benchtop Automated Sample Mangament Device" ;
definition: "Automated Screw Cap Tube Decapping" .
SCR:019979 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LabElite Decapper" ;
rdfs:label "Hamilton | LabElite DeCapper Benchtop Automated Sample Management Device" ;
definition: "Automated Screw Cap Tube Decapping" .
SCR:019980 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_High_Temperature_GC_Septa" ;
rdfs:label "Hamilton | High Temperature GC Septa" ;
NIFRID:synonym "Hamilton High Temperature GC Septa Laboratory Products" ;
definition: "High temperature septa that is made of preconditioned PTFE/silicone rubber and is 3.175 mm (0.125 in) thick. The average life of these septa is up to 100 injections with a 26s gauge needle. The maximum operating temperature is 212C." .
SCR:019981 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_easuPunch STARlet" ;
rdfs:label "Hamilton | easyPunch STARlet Assay Ready Workstation" ;
definition: "Assay ready workstation that simplifies pre-PCR workflows from evidentiary and DNA databasing biological samples collected via FTA cards." .
SCR:019982 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LabElite_DeFroster" ;
rdfs:label "Hamilton | LabElite DeFroster Benchtop Automated Sample Management Device" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8th,2024. Automated Rack Frost Remover." .
SCR:019983 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LabElite_Integrated I.D._Capper" ;
rdfs:label "Hamilton | LabElite Integrated I.D. Capper" ;
NIFRID:synonym "Hamilton LabElite Integrated I.D. Capper Benchtop Automated Sample Managment Device" ;
definition: "Automated Screw Cap Decapping for Integration. Features all of utility of standalone version and allows users to seamlessly integrate these features with their Hamilton Microlab STAR. With the addition of extended linear rail, tube racks and cap holder racks can be presented directly onto the deck of the STAR allowing for easy automation of tube processing workflows. Easily swap decapping heads to decap tubes in 24-, 48-, and 96-format tube racks, all on a single device." .
SCR:019984 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_magEX" ;
rdfs:label "Hamilton | MagEX STARlet Assay Ready Workstation" ;
definition: "Assay ready workstation used for magnetic bead based nucleic acid extraction and isolation of pathogen RNA from SARS CoV 2, which causes Coronavirus Disease 2019. It is designed to be used with variety of kit chemistries from leading partners, including those that are FDA approved, and can process up to 96 samples at time." .
SCR:019985 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Low_Bleed_High_Temperature_GC_Septa" ;
rdfs:label "Hamilton | Low Bleed High Temperature GC Septa" ;
NIFRID:synonym "Hamilton Low Bleed High Temperature GC Septa Laboratory Products" ;
definition: "Low bleed high temperature septa that is designed for lowest bleed possible at temperatures up to 400 degrees C. They can be used in combination with Mass Spectrometers or in applications where septa bleed interferes with trace analysis." .
SCR:019986 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NIMBUS" ;
rdfs:label "Hamilton | foodInspect NIMBUS for 3M Molecule Detection System Assay Ready Workstation" ;
definition: "Molecular detection system that uses air displacement technology for precision, accuracy and reproducibility to detect pathogens from food samples." .
SCR:019987 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MassSTAR" ;
rdfs:label "Hamilton | MassSTAR Assay Ready Workstation" ;
definition: "Assay ready workstation used for fully automated CE-IVD certified mass spectrometry sample preparation." .
SCR:019988 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LabElite ID Capper" ;
rdfs:label "Hamilton | LabElite I.D. Capper Benchtop Automated Sample Management Device" ;
definition: "An automated I.D. capper that combines capping, decapping, and high-speed barcode reading in one device." .
SCR:019989 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Long_Life_GC_Septa" ;
rdfs:label "Hamilton | Long Life GC Septa" ;
NIFRID:synonym "Hamilton Long Life GC Septa Laboratory Products" ;
definition: "Autosampler septa that is designed for use with GC Autosamplers and uses a pre-pierced center depression to guide the syringe needle to the same injection point, which extends septa life. These septa are ideal for standard manual-injection GC and GC-MS." .
SCR:019990 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_microlab 600" ;
rdfs:label "Hamilton | Microlab 600 Stand Alone Syringe Pumps Laboratory Products" ;
definition: "Syringe pump that is available as a standalone pump with single and dual syringe configurations. The standalone pump offers two communication capabilities Ethernet and RS-232." .
SCR:019991 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Microlab" ;
rdfs:label "Hamilton | Microlab Prep Automated Liquid Handling" ;
definition: "Compact automated liquid handler made for convinience and efficiency." .
SCR:019992 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Microlab_600_Diluter" ;
rdfs:label "Hamilton | Microlab 600 Diluter" ;
NIFRID:synonym "Hamilton Microlab 600 Diluters Laboratory Products" ;
definition: "Syringe pump that quickly performs analytical dilutions of standards and samples." .
SCR:019993 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Microlab STAR" ;
rdfs:label "Hamilton | Microlab STAR Automated Liquid Handling" ;
definition: "STAR Automated Liquid Handling uses pipetting technology to achieve high accuracy, precision, and repeatability from sub-microliter to large volumes." .
SCR:019994 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Microlab_600_Dispenser" ;
rdfs:label "Hamilton | Microlab 600 Dispenser" ;
definition: "Syringe dispenser that can perform aliquot, serial dispense, and titrate dispensing." .
SCR:019995 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_STAR" ;
rdfs:label "Hamilton | NGS STAR for Library Prep Asssay Ready Workstation" ;
definition: "NGS STAR for Library Prep is used for Massive Parallel Sequencing." .
SCR:019996 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Microlab_Vantage" ;
rdfs:label "Hamilton | Microlab VANTAGE Automated Liquid Handling" ;
definition: "Automated Liquid Handling is used for precision engineering, performance, and craftsmanship." .
SCR:019997 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NIMBUS Select Assay" ;
rdfs:label "Hamilton | NIMBUS Select Assay Ready Workstation" ;
definition: "NIMBUS Select is used for high throughput, automated gel electrophoresis and nucleic acid size selection." .
SCR:019998 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NIMBUS Presto" ;
rdfs:label "Hamilton | NIMBUS Presto and ID NIMBUS Presto Assay Ready Workstation" ;
definition: "NIMBUS Presto and ID NIMBUS Presto optimize automated KingFisher magnetic bead based particle workflows." .
SCR:019999 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MiniTrode" ;
rdfs:label "Hamilton | MiniTrode Laboratory Sensor" ;
definition: "pH electrode with 3 mm shaft that is used for general measurements in vials and test tube applications." .
SCR:020000 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_STARWorks_GlycoWorks" ;
rdfs:label "Hamilton | STARWorks for Water GlycoWorks Assay Ready Workstation" ;
definition: "STARWorks for Waters GlycoWorks streamlines and automates your N glycan workflows." .
SCR:020001 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Microlab NIMBUS" ;
rdfs:label "Hamilton | Microlab NIMBUS Automated Liquid Handling" ;
definition: "Compact, multi channel automated liquid handler with speed, flexibility, and easy usage." .
SCR:020002 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PCR_Prep_STARlet" ;
rdfs:label "Hamilton | PCR Prep STARlet" ;
NIFRID:synonym "Hamilton PCR Prep STARlet Assay Ready Workstation" ;
definition: "PCR Prep STARlet assay ready workstation automates CDC authorized and FDA cleared testing kits for detection of SARS CoV 2." .
SCR:020004 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_M3Z" ;
rdfs:label "Leica | Heerbrugg M3Z Stereomicroscope" ;
definition: "Leica/Wild M3Z Stereo Microscope that has been serviced by a qualified microscope tech and meets factory specs. It has its Wild 10X, high eyepoint widefield eyepieces and a 1.0X bottom objective. In my opinion, the M-Series by Leica is the best stereomicroscope available. I like Zeiss as well, but have never had a Leica optical element delaminate. The M-Series is the microscope you want if you spend a lot of time looking through the eyepieces, want the brightest, flattest field and highest resolution. Built for demanding users, the Wild/Leica M-series is built to last." .
SCR:020005 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Three_Layer_GC_Septa" ;
rdfs:label "Hamilton | Three Layer GC Septa" ;
NIFRID:synonym "Hamilton Three Layer GC Septa Labratory Products" ;
definition: "Made of preconditioned silicone rubber and is 3.81 mm (0.150 in) thick. The average life of these septa is up to 100 injections with a 26s gauge needle. The maximum operating temperature is 200° C." .
SCR:020006 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Verso",
"SCR_020011" ;
rdfs:label "Hamilton | Verso Automated Freezer Sample Storage System" ;
NIFRID:synonym "Hamilton Verso" ;
definition: "Hamilton Verso is modular compound management system for automated storage at temperatures from ambient to minus 20°C for high-throughput applications. This compound storage system can easily be configured to meet your needs." .
SCR:020007 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MC4000" ;
rdfs:label "Hatteras Instruments | MC4000 Blood Pressure and Heart Rate Analyzer" ;
definition: "MC4000 Multi Channel Blood Pressure Analysis System helps researchers obtain accurate blood pressure measurements on mice and rats." .
SCR:020009 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VIOS 250i" ;
rdfs:label "Thermo Fisher | Heraeus Biofuge Stratos Centrifuge Series" ;
definition: "Centrifuge eliminates imbalances, provides reproducible results and delivers speed and flexibility." .
SCR:020010 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_STARWorks_ProteinWorks" ;
rdfs:label "Hamilton | STARWorks for Waters ProteinWorks" ;
NIFRID:synonym "Hamilton STARWorks for Water ProteinWorks Assay Ready Workstation",
"STARWorks for Water ProteinWorks Assay Ready Workstation",
"STARWorks for Waters ProteinWorks" ;
definition: "STARWorks for Waters ProteinWorks simplifies protein bioanalysis workflow and quantifies proteins in serum or plasma." .
SCR:020012 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8100" ;
rdfs:label "Hitachi | 8100 Transmission Electron Microscope" ;
definition: "Hitachi H-8100 TEM is a research grade scanning/transmission electron microscope (STEM) with analytical and high resolution imaging capabilities. Systematic theoretical instruction combined with practical hands-on training is the best way to thoroughly understand the utility and capabilities of this complex and delicate instrument. These instructions are meant only as a guide to the basic, daily alignments and operations of the H-8100, i.e. general imaging and diffraction. It is by no means a comprehensive guide to all operations of the microscope including ultra-high resolution imaging, SEM, EDX, cryo, and the various diffraction techniques. These advanced, specialized techniques will be dealt with on an as-need basis after mastery of the basic operations has been demonstrated." .
SCR:020013 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_3400N" ;
rdfs:label "Hitachi | 3400N Environmental Scanning Electron Microscope" ;
definition: "Hitachi S-3400N SEM is a high performance, user-friendly scanning electron microscope. Features include: VP-mode that allows microscopy of wet, oily and non-conductive samples in their natural state without the need of conventional sample preparation." .
SCR:020014 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8800" ;
rdfs:label "Hitachi | 8800 Amino Acid Analyzer" ;
definition: "Hitachi L-8800 Amino Acid Analyzer Hitachi L8800 professionally deinstalled and under service watch until such time used. Hitachi has manufactured over 1800 Amino Acid Analyzers for over 35 years. The L-8800 is capable of analyzing physiological fluids and protein hydrolysates. Hitachi offers the best solution to amino acid analysis." .
SCR:020015 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VeriSeq" ;
rdfs:label "Hamilton | VeriSeq NIPT Microlab STAR Assay Ready Workstation" ;
definition: "Veriseq NIPT Microlab STAR automates PCR free whole genome sequencing during NGS MPS based non invasive prenatal testing." .
SCR:020016 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_950FS" ;
rdfs:label "Drew Scientific | HemaVet 950FS Blood Analyzer" ;
definition: "HEMAVET 950FS can perform automated blood counts including; hemoglobin, hematocrit, white blood cells, platelets, differentials, and red blood cell indices for six animals." .
SCR:020017 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2030i" ;
rdfs:label "Thermo Fisher | Heratherm Advanced Protocol Security Microbiological Incubators" ;
definition: "Thermo Scientific� Heratherm� Advanced Protocol Security Microbiological Incubators, which include a unique 140�C decontamination routine, lockable incubator door with alarm for restricted access, and automatic over- and under-temperature alarms." .
SCR:020018 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_S-4800-II" ;
rdfs:label "Hitachi | S-4800-II with Leica Cryo Stage" ;
definition: "Hitachi S-4800-II Cold Field Emission SEM with Windows XP Pro OS. (Windows 7 optional). Fully refurbished with warranty and located in Northern California." .
SCR:020019 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_S4700" ;
rdfs:label "Hitachi | S4700 Field Emission Scanning Electron Microscope" ;
definition: "Hitachi S-4700 is a field emission scanning electron microscope (FE-SEM). More than a standard SEM, the S-4700, under optimal conditions, can magnify images upwards of 500,000 times and resolve features to 2 nanometers. In addition, a cathodoluminescence detector, backscatter electron detector and energy dispersive x-ray spectrographic detector accompany the microscope., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:020020 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HM_430" ;
rdfs:label "Thermo Fisher | HM 430 Sliding Microtome" ;
definition: "Ensures operation with automatic or manual fine sectioning abilities of Thermo Scientific HM 430 Sliding Microtome." .
SCR:020021 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_51" ;
rdfs:label "Horiba | 51 Series Explosion-proof Gas Analyzer" ;
definition: "Explosion proof analyzers that provide safe, and accurate measurements when analyzing flammable gases or operating in explosive environments." .
SCR:020022 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HT7700" ;
rdfs:label "Hitachi | HT7700 Transmission Electron Microscope" ;
definition: "HT7700 Transmission Electron Microscope with Dual-Mode objective lens features superior high-contrast and high-resolution performance together with analytical capabilities for biological and materials science. Digital design and sophisticated automation increase throughput for both novice and advanced users. Maximize contrast by lowering the high voltage through the 120-40 kV range and continue operation seamlessly. Configure the HT7700 to meet all of your advanced sample analysis needs, with customization options for BF-/DF-STEM, EDX, in-situ, cryo-microscopy, and electron tomography." .
SCR:020023 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HM_550" ;
rdfs:label "Thermo Fisher | HM 550 Cryostats Detach Block with Six Positions" ;
definition: "Defrost and detach tissue from specimen stage outside cryo chamber with Thermo Scientific HM 550 Cryostats Detach Block, featuring six positions marked with letters A to F." .
SCR:020024 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_APMC-370" ;
rdfs:label "Horiba | APMC-370 Air Pollution Multigas Calibrator" ;
definition: "Air pollution multigas calibrator that is designed to calibrate gas analyzers manually, remotely controlled or automatically. It is installed in air pollution monitoring stations for quality assurance in laboratory and also in production of gas analyzers." .
SCR:020025 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AP-370" ;
rdfs:label "Horiba | AP-370 Series Air Pollution Monitor" ;
definition: "Highly sesitive ambient air pollutions monitors that give precise, realiable measurements, and are easy to maintain." .
SCR:020026 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1000M" ;
rdfs:label "Horiba | 1000M Series Long Focal Length Spectrometer" ;
definition: "Large focal length monochromators for spectroscopy applications such as Raman, Plasma Emission, and LIBS." .
SCR:020027 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HD2300" ;
rdfs:label "Hitachi | HD2300 Transmission Electron Microscope" ;
definition: "Hitachi HD-2300 Dual EDS Cryo STEM (HD 2300) is a versatile Scanning Transmission Electron Microscope used for imaging and elemental analysis. The HD 2300 actually has three different electron detectors for different imaging modes (Transmitted Electron Detector, Annular Detector, and a Secondary Electron Detector) and features an electron Energy Loss Spectroscopy detector (EELS) and two EDS detectors (Energy Dispersive X-ray Spectroscopy) for elemental analysis and elemental mapping of a given sample. Overall, the HD 2300 is a multipurpose instrument for anyone who is looking to do research in material science, life science, chemistry and nanoscience." .
SCR:020028 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AQMS" ;
rdfs:label "Horiba | AQMS Air Quality Monitoring System" ;
definition: "Air quality monitoring system that measures metrological parameters such as wind speed, wind direction, rainfall, radiation, temperature, barometric pressure and ambient parameters. It also integrates series of ambient analyzers to monitor concentration of air pollutants continously." .
SCR:020029 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_S3000N" ;
rdfs:label "Hitachi | S3000N Scanning Electron Microscope" ;
definition: "Hitachi S-3000N scanning electron microscope (SEM) is a PC controlled variable pressure SEM with the ability to switch between the high vacuum and variable pressure modes. It has a high density frame memory of 1280x960 pixels and an advanced image capture and archiving system. Four quadrant solid state backscatter allows imaging in the compositional, 3D and topographic modes by manipulating from each segment of the detector." .
SCR:020030 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Auto SE" ;
rdfs:label "Horiba | Auto SE Spectroscopic Ellipsometer for Thin Film Measurement" ;
definition: "Thin film measurement tool that allows full automatic analysis of thin film samples with push button operation. It includes automatic XYZ stage, real time imaging of measurement site and automatic selection of spot size." .
SCR:020031 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CMA-200A/210A" ;
rdfs:label "Horiba | CM-200A/210A Hydrofluoric Acid Monitor" ;
definition: "CM 200A 210A hydrofluoric acid monitors have been developed specifically to meet stringent demands of semiconductor manufacturing. CM 200A 210A provides real time read out of hydrofluoric acid concentration by measuring electric conductivity of sample solution. These superior units offer high repeatability even at low concentrations. CM 200A 210A can be used for variety of purposes ranging from monitoring etched wafer cleaning processes to any other industrial application of hydrofluoric acid." .
SCR:020032 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Aqualog" ;
rdfs:label "Horiba | Aqualog Water Treatment Plant Analyzer" ;
definition: "Water treatment plant analyzer that simultaneously measure both absorbance spectra and fluorescence Excitation Emission Matrices." .
SCR:020033 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Camsizer P4" ;
rdfs:label "Horiba | Camsizer P4 Dynamic Image Analysis System Particle Size" ;
definition: "Digital image processing particle size and shape analysis system that provides rapid and precise particle size and particle shape distributions for dry powders and bulk material in size range from 20 um to 30 millimeters. This technique provides wide variety of information about sample, from general size measurement, to shape parameters that can be closely correlated to specific performance characteristics. This also allows correlation to existing data from techniques as diverse as sieving, microscopy, and hand caliper measurement." .
SCR:020034 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CEMS" ;
rdfs:label "Horiba | CEMS Continuous Emission Monitoring System" ;
definition: "Continuous Emission Monitoring System CEMS is integrated system to measure fuel flow, dust, and concentrations of air pollutants such as SO2, NOx, CO, CO2, THC and O2 in accordance with applicable regulations for emission source." .
SCR:020035 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6870" ;
rdfs:label "Horiba | Cryogenic Grinder 6870 Large Cryogenic Mill" ;
definition: "Large cryogenic mill for cryogenic grinding and pulverizing tough and or temperature sensitive samples immersed in liquid nitrogen. It can be used for sample sizes ranging from 0.1 to 50 grams." .
SCR:020036 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CS_100" ;
rdfs:label "Horiba | CS-100 Series Stand-alone Type Chemical Concentration Monitor" ;
definition: "Chemical concentration monitors that measure real time concentrations of various types of chemical solutions and control timing of automatic chemical spiking. Air is used for reference spectral measurements to be taken without abnormalities in solution flow." .
SCR:020037 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_785" ;
rdfs:label "Horiba | CiCi-Raman-NIR Spectrometer" ;
definition: "CiCi Raman 785 is high performance spectrometer featuring aberration corrected concave holographic grating configured with Horiba Scientific's Syncerity TE cooled CCD camera with VIS NIR 2048 x 70 detector, in TE cooled Head at 50 degrees C." .
SCR:020038 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PH1200" ;
rdfs:label "Horiba | Benchtop LAQUA PH1200 Water Quality Meters" ;
definition: "Benchtop model developed to provide simplicity with on site usability, from operation and maintenance to troubleshooting in water quality analysis." .
SCR:020039 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CC-55" ;
rdfs:label "Horiba | CC-55 Imaging Spectrometer" ;
definition: "CC 55 Imaging Multichannel Spectrometer Simultaneous acquisition 10 26 Fiber Inputs with diameters in range of 100 400 mic Interline CCD, may allow shutter free set up Call us Line imaging on tall Sony ICX285AL CCD." .
SCR:020040 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Camsizer X2" ;
rdfs:label "Horiba | Camsizer X2 Dynamic Image Analysis System Particle Size" ;
definition: "Dynamic image analysis system that provides particle size and shape distribution analysis needed for quality control of fine powders and suspensions, measuring 0.8 um to 8 mm." .
SCR:020041 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CS_100_F4" ;
rdfs:label "Horiba | CS-100 F4 Multi-point Chemical Solution Monitor" ;
definition: "Multi point chemical solution monitor with multipoint chemical measurement into single units used in etching and cleaning processes for semiconductor manufacturing." .
SCR:020042 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CS_600F" ;
rdfs:label "Horiba | CS-600F Fiber Optic Type Chemical Concentration Monitor" ;
definition: "Fiber optic type chemical concentration monitor for manufacturing, such as in line measurement of high temperature chemical solutions in various applications, such as semiconductor wet process." .
SCR:020043 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CVS_ONE" ;
rdfs:label "Horiba | CVS-ONE Constant Volume Sampler" ;
definition: "Designed for measurement of diluted emissions from vehicles and engines. Can be used to measure low emission levels such as SULEV." .
SCR:020044 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CS_700" ;
rdfs:label "Horiba | CS-700 Chemical Concentration Monitor" ;
definition: "Chemical concentration monitor for measurement of individual chemical constituents of complex chemistries used in Semiconductor Manufacturing Processes." .
SCR:020045 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DeltaRAM_X" ;
rdfs:label "Horiba | DeltaRAM X Random Access Monochromator" ;
definition: "DeltaRAM X microscope fluorescence illuminator is used for quantitative intracellular ion research. It utilizes galvanometer based Random Access Monochromator that can switch between any wavelength in 2 milliseconds." .
SCR:020046 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DeltaDiode" ;
rdfs:label "Horiba | DeltaDiode Pulsed Laser and LED Light Sources" ;
definition: "DeltaDiodes utilizes laser diode and LED technology to generate short optical pulses over very wide range of repetition rates and wavelengths." .
SCR:020047 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DeltaFlex" ;
rdfs:label "Horiba | DeltaFlex TCSPC Lifetime Fluorometer" ;
definition: "Designed for measurement of luminescence lifetimes ranging over 11 orders of magnitude, without need to change cables or cards." .
SCR:020048 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DeltaPro" ;
rdfs:label "Horiba | DeltaPro TCSPC Lifetime Fluorometer" ;
definition: "Enables seamless measurement of luminescence lifetimes from picoseconds to 1 second, using DeltaHub timing electronics. Takes advantage of interchangeable pulsed laser-diode and LED light-sources." .
SCR:020049 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Duetta" ;
rdfs:label "Horiba | Duetta Fluorescence and Absorbance Spectrometer" ;
definition: "Spectrofluorometer that combines, simultaneously, functions of fluorescence and absorbance spectrometers. Can acquire full spectrum from 250 nm to 1,100 nm in less than one second." .
SCR:020050 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DeltaTime" ;
rdfs:label "Horiba | DeltaTime TCSPC Lifetime Kit" ;
definition: "DeltaTime integrates monochromators, polarizers, and other accessories with widest array of sources, like LEDs, laser diodes, supercontinuum lasers, and detectors, including NIR, providing lifetime coverage from 25ps to 1sec over wavelengths spanning UV to NIR." .
SCR:020051 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DT_Dyno" ;
rdfs:label "Horiba | DT Dyno Hydraulic Dynamometers" ;
definition: "DT type Hydraulic dynamometers are available with large variety of power ranges. Standard range extends from 700 kW up to 4,500 kW." .
SCR:020052 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DYNAS3" ;
rdfs:label "Horiba | DYNAS3 AC Dynamometer" ;
definition: "DYNAS3 dynamometers are designed for use in engine test stands. Combination of powerful DYNAS AC machine with variable frequency drive, fine tuned test stand controller and proven safety module produces reliable and accurate results." .
SCR:020053 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EasyRatioPro" ;
rdfs:label "Horiba | EasyRatioPro Ca++ Imaging System" ;
definition: "Comprehensive system for measuring intracellular calcium, sodium, magnesium ion concentrations or pH and membrane potential. Includes tools required for image acquisition, analysis and calibration of intracellular dyes or intrinsic fluorophores." .
SCR:020054 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EC_5000" ;
rdfs:label "Horiba | EC-5000 Series Exhaust Pressure Controller" ;
definition: "Exhaust pressure controller can maintain consistent pressure within the chamber. High resolution stepper motor and butterfly valve ensures fast, sensitive response to any pressure changes." .
SCR:020055 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EasyLife_X" ;
rdfs:label "Horiba | EasyLife X Lifetime Fluorescence Spectrometer" ;
definition: "Time resolved fluorometer for lifetimes down to 150 ps with 10 percent binding efficiency, ANS binding to bovine serum albumin monitored with EasyLife X equipped with a 370 nm LED, and ratio of free ANS to BSA bound ANS, 9 to 1, can be determined from double exponential fit to fluorescence decay." .
SCR:020056 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Eco_Web" ;
rdfs:label "Horiba | Eco Web Data Management and Reporting Software" ;
definition: "Data management and reporting software for use in Ambient Air Quality and Meteorological monitoring. Software package provides data collection, management, analysis and reporting." .
SCR:020057 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EasyLife_L" ;
rdfs:label "Horiba | EasyLife L Phosphorescence Lifetime Spectrometer" ;
definition: "Low cost phosphorescence spectrometer from few microseconds to 300 milliseconds." .
SCR:020058 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EMGA_930" ;
rdfs:label "Horiba | EMGA-930 Oxygen/Nitrogen/Hydrogen Analyzer" ;
definition: "Oxygen, nitrogen, and hydrogen elemental analyzer with high accuracy and repeatability suiting to cutting edge technology's R and D, as well as quality control in market of steel, new materials, and catalyst. New generation model optimized to fit to user's requests." .
SCR:020059 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EMGA_921" ;
rdfs:label "Horiba | EMGA-921 Hydrogen Analyzer" ;
definition: "Hydrogen elemental analyzer with high accuracy and repeatability suiting to cutting edge technology's R and D, as well as quality control in market of steel, new materials, and catalyst. New generation model optimized to fit to user's requests." .
SCR:020060 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EMIA_Pro" ;
rdfs:label "Horiba | EMIA-Pro Carbon/Sulfur Analyzer" ;
definition: "Carbon and Sulfur Analyzer is based on expertise in Non Dispersive Infrared technology. It offers improved cleaning efficiency, enhanced software, durability, operability and maintenance to ensure efficient measurements and its shortened cycle time accelerates development and manufacturing speed." .
SCR:020061 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Fluorolog-3" ;
rdfs:label "Horiba | Fluorolog-3 Spectrofluorometer" ;
definition: "Fluorolog-3 is a , modular system which allows the researcher to interchange a wide range of accessories to correspond precisely with the characteristics of a given sample. From analysis of steady-state or molecular dynamics to IR probes, the Fluorolog-3 comes equipped with a wide range and limitless configuration of accessories to enhance the accuracy and speed of it's performance. The Fluorolog-3 series enables you to customize your spectrofluorometer's performance to meet your research needs. It can also perform (TCSPC) Time Correlated Single Photon Counting lifetime measurements like the FluoroMax-4 and QM800." .
SCR:020062 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EMGA_920" ;
rdfs:label "Horiba | EMGA-920 Oxygen/Nitrogen Analyzer" ;
definition: "Oxygen and nitrogen elemental analyzer with high accuracy and repeatability suiting to cutting edge technology's R and D, as well as quality control in market of steel, new materials, and catalyst. New generation model optimized to fit to user's requests." .
SCR:020063 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FTX_ONE" ;
rdfs:label "Horiba | FTX-ONE FTIR Exhaust Gas Analyzer" ;
definition: "Fast response and compact size FTIR analyzer for simultaneous measurement of multiple components of engine exhaust gases." .
SCR:020064 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Fluoromax 4" ;
rdfs:label "Horiba | FluoroMax 4 Spectrofluorometer" ;
definition: "FluoroMax family, with its all reflective optics and photon counting was the first to bring the sensitivity of a modular fluorometer to a tabletop fluorescence instrument. It's a compact spectrofluorometer, yet offers the ultimate sensitivity in fluorescence investigations as well as features not found in most table-top fluorescence detection systems. The FluoroMax series consists of the FluoroMax-4, the latest generation of the original, high performance tabletop fluorometer, which offers extended performance with detection of emission spectra out to 1700 nm and (TCSPC) Time Correlated Single Photon Counting lifetime measurements as short as 25ps." .
SCR:020065 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Gemini_180" ;
rdfs:label "Horiba | Gemini 180 Double Monochromator" ;
definition: "Fully automated, double additive grating scanning monochromator. Incorporation of toroidal optics provides for optimum throughput and spectral resolution." .
SCR:020066 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2020" ;
rdfs:label "Horiba | Geno Grinder 2020 Automated Tissue Homogenizer" ;
definition: "Automated plant and tissue homogenizer that integrates with most robotic systems and platforms. Its vertical grinding motion prepares plant and animal tissue for extractions of DNA, RN or proteins in less than two minutes." .
SCR:020067 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GA_370" ;
rdfs:label "Horiba | GA-370 Trace Gas Monitor" ;
definition: "Provides constant, ultra high sensitivity and high precision monitoring of trace impurities, like CO, CO2 and CH4, for quality control at gas manufacturing facilities." .
SCR:020068 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EMIA_Expert" ;
rdfs:label "Horiba | EMIA-Expert Carbon/Sulfur Analyzer" ;
definition: "Carbon and Sulfur Analyzer is based on expertise in Non Dispersive Infrared technology. It offers improved cleaning efficiency, enhanced software, durability, operability, and maintenance to ensure efficient measurements and its shortened cycle time accelerates development and manufacturing speed." .
SCR:020069 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GIANT_8000" ;
rdfs:label "Horiba | GIANT 8000 Series Brake Test Systems" ;
definition: "Has NVH test system providing with testing conditions for all types of vehicles. Test brake fixtures could be tested with complete wheel suspension system." .
SCR:020070 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GIANT_6000" ;
rdfs:label "Horiba | GIANT 6000 Series Multi-Purpose Brake Dynamometers" ;
definition: "Product line is multi purpose, full size inertia brake dynamometer for performance and NVH tests of brake systems from passenger vehicles to truck brakes, commercial vehicle assemblies and high speed railway applications." .
SCR:020071 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2010" ;
rdfs:label "Horiba | Geno Grinder 2010 High-throughput tissue homogenizer" ;
definition: "High throughput plant and tissue homogenizer with adjustable clamp that accommodates variety of formats ranging from deep well titer plates to centrifuge tubes. Designed for rapid cell disruption, lysis and tissue homogenization while preserving temperature sensitive samples." .
SCR:020072 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_H_CLUE" ;
rdfs:label "Horiba | H-CLUE Versatile Hyperspectral Cathodoluminescence" ;
definition: "Direct coupled solution offers ultimate performance for Cathodoluminescence Imaging and Spectroscopy analysis." .
SCR:020073 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GIANT_Evo" ;
rdfs:label "Horiba | GIANT Evo Brake Test Systems" ;
definition: "Brake testing machine forms base of inertia brake dynamometers portfolio. All components are specifically tailored to needs of passenger car market segment." .
SCR:020074 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GI_700" ;
rdfs:label "Horiba | GI-700 Series Stack Gas Analyzer" ;
definition: "Gas analyzer is designed to continuously measure concentrations of nitrogen oxides, sulfur dioxide, carbon monoxide, carbon dioxide, oxygen, and ammoni in stack flue gas streams." .
SCR:020075 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GR_300" ;
rdfs:label "Horiba | GR-300 Series Wafer Back Side Cooling System" ;
definition: "Can control gases used to cool back side of wafers that are fixed in position by electrostatic chuck system." .
SCR:020076 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_H30_UVL" ;
rdfs:label "Horiba | H30-UVL Vacuum Spectrometer" ;
definition: "H30 UVL allows working either in monochromator mode using exit slit or in flat field spectrograph mode using CCD detector." .
SCR:020077 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GIANT_9000" ;
rdfs:label "Horiba | GIANT 9000 Series Brake Test Systems" ;
definition: "Brakes can be exposed to either stop brakings or endurance brakings according to standardized NVH test matrix." .
SCR:020078 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HC_200F" ;
rdfs:label "Horiba | HC-200F Fluoride Ion Concentration Meter" ;
definition: "Industrial simplified fluoride ion concentration meter that is suitable for fluoride ion monitoring in effluent from factories and those of semiconductor FPD and glass manufacturers. 0 to 10,000 mg L wide measuring range, with 10 range switching." .
SCR:020079 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_H20_UVL" ;
rdfs:label "Horiba | H20-UVL Vacuum Spectrometer" ;
definition: "Based on single holographic concave aberration corrected grating, H20 UVL is monochromator covering range 100 600 nm." .
SCR:020080 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_H1034B" ;
rdfs:label "Horiba | H1034B OEM Imaging Scanning Spectrometer Monochromator" ;
definition: "Ion Etched gratings combine advantages of holographic gratings with high efficiency. Aberration corrected concave gratings permit one piece opticsl design with imaging properties." .
SCR:020081 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HD_200FL" ;
rdfs:label "Horiba | HD-200FL Industrial Dissolved Oxygen Analyzer" ;
definition: "Realizes both cartridge method membrane replacement and membrane internal liquid replacement regeneration system. Responds to wide range of measurements, like boiler, water, rivers, and aeration treatments." .
SCR:020082 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HD_200" ;
rdfs:label "Horiba | HD-200 Industrial Dissolved Oxygen Analyzer" ;
definition: "Industrial dissolved oxgen analyzer that realizes both cartridge method membrane replacement and membrane internal liquid replacement regeneration system. Responds to wide range of measurements, like boiler, water, rivers, and aeration treatments." .
SCR:020083 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HC_300F" ;
rdfs:label "Horiba | HC-300F Fluoride Ion Concentration Meter" ;
definition: "Industrial simplified fluoride ion concentration meter that is suitable for fluoride ion monitoring in effluent from factories and those of semiconductor FPD and glass manufacturers." .
SCR:020084 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HC_200NH" ;
rdfs:label "Horiba | HC-200NH Ammonia Nitrogen Meter" ;
definition: "HC 200NH is ammoni nitrogen meter using ion electrode method which is designed for aeration control in wastewater treatment." .
SCR:020085 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HD_300" ;
rdfs:label "Horiba | HD-300 Industrial Dissolved Oxygen Analyzer" ;
definition: "Realizes both cartridge method membrane replacement and membrane internal liquid replacement regeneration system. Responds to wide range of measurements, like boiler, water, rivers, and aeration treatments." .
SCR:020086 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EC1100" ;
rdfs:label "Horiba | LAQUA EC1100 Benchtop Water Quality Meters" ;
definition: "Developed to provide simplicity with on site usability, from operation and maintenance to troubleshooting." .
SCR:020087 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_i_CLUE" ;
rdfs:label "Horiba | i-CLUE Fast Imaging Cathodoluminescence" ;
definition: "Offers up to 10 times higher sensitivity compared to standard CL imaging solutions due to performance of high numerical aperture and low roughness collection mirror coupled to optimized acquisition chain and detection." .
SCR:020088 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EC220" ;
rdfs:label "Horiba | LAQUA EC220 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing. Meter can be used for long periods, even in dark places." .
SCR:020089 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_F_72" ;
rdfs:label "Horiba | LAQUA F-72 Benchtop Water Quality Meters" ;
definition: "Developed to provide simplicity with on site usability, from operation and maintenance to troubleshooting." .
SCR:020090 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_F_74" ;
rdfs:label "Horiba | LAQUA F-74 Benchtop Water Quality Meters" ;
definition: "High end benchtop model developed to provide simplicity with on site usability, from operation and maintenance to troubleshooting in water quality analysis." .
SCR:020091 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PC210" ;
rdfs:label "Horiba | LAQUA PC210 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing. Meter can be used for long periods, even in dark places, making it ideal for field measurements in rivers and lakes." .
SCR:020092 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_F_73" ;
rdfs:label "Horiba | LAQUA F-73 Benchtop Water Quality Meters" ;
definition: "High end benchtop model developed to provide simplicity with on site usability, from operation and maintenance to troubleshooting in water quality analysis." .
SCR:020093 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EC210" ;
rdfs:label "Horiba | LAQUA EC210 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing. Meter can be used for long periods, even in dark places." .
SCR:020094 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HD_480" ;
rdfs:label "Horiba | HD-480 Industrial Dissolved Oxygen Analyzer" ;
definition: "Industrial dissolved oxygen meter that takes sequential measurements of concentration of dissolved oxygen, which is indicator used in management of activated sludge tanks in waste water processing, and quality of water in boilers, or rivers and waterways." .
SCR:020095 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PC1100" ;
rdfs:label "Horiba | LAQUA PC1100 Benchtop Water Quality Meters" ;
definition: "High end benchtop model developed to provide simplicity with on site usability, from operation and maintenance to troubleshooting in water quality analysis." .
SCR:020096 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PH1100" ;
rdfs:label "Horiba | LAQUA PH1100 Benchtop Water Quality Meters" ;
definition: "High end benchtop model developed to provide simplicity, from operation and maintenance to troubleshooting in water quality analysis." .
SCR:020097 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PH1300" ;
rdfs:label "Horiba | LAQUA PH1300 Benchtop Water Quality Meters" ;
definition: "High end benchtop model developed to provide simplicity, from operation and maintenance to troubleshooting in water quality analysis." .
SCR:020098 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PD210" ;
rdfs:label "Horiba | LAQUA PD210 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing. Meter can be used for long periods, even in dark places, making it ideal for field measurements in rivers and lakes." .
SCR:020099 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_WQ_320_K" ;
rdfs:label "Horiba | LAQUA WQ-320-K Handheld Water Quality Meters" ;
definition: "Dual channel handheld water quality meter that has large colour graphic LCD screen, measuring 70 x 52 mm, with backlight and built in foldable meter stand. It is IP67 waterproof and dustproof, battery and USB powered, eco friendly, shock proof, scratch resistant, and non slip." .
SCR:020100 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PC220" ;
rdfs:label "Horiba | LAQUA PC220 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing. Meter can be used for long periods, even in dark places, making it ideal for field measurements in rivers and lakes." .
SCR:020101 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PD220" ;
rdfs:label "Horiba | LAQUA PD220 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing. Meter can be used for long periods, even in dark places, making it ideal for field measurements in rivers and lakes." .
SCR:020102 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_WQ_310_K" ;
rdfs:label "Horiba | LAQUA WQ-310-K Handheld Water Quality Meters" ;
definition: "Single channel handheld water quality meter that has large colour graphic LCD screen, measuring 70 x 52 mm, with backlight and built in foldable meter stand. It is IP67 waterproof and dustproof, battery and USB powered, eco friendly, shock proof, scratch resistant, and non slip." .
SCR:020103 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DO120" ;
rdfs:label "Horiba | LAQUAact DO120 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing, Meter can be used for long periods, even in dark places." .
SCR:020104 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PH210" ;
rdfs:label "Horiba | LAQUA PH210 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing. Meter can be used for long periods, even in dark places, making it ideal for field measurements in rivers and lakes." .
SCR:020105 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PH220" ;
rdfs:label "Horiba | LAQUA PH220 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing. Meter can be used for long periods, even in dark places, making it ideal for field measurements in rivers and lakes." .
SCR:020106 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EC110" ;
rdfs:label "Horiba | LAQUAact EC110 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing, Meter can be used for long periods, even in dark places." .
SCR:020107 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DO110" ;
rdfs:label "Horiba | LAQUAact DO110 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing. Meter can be used for long periods, even in dark places." .
SCR:020108 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_WQ_330_K" ;
rdfs:label "Horiba | LAQUA WQ-330-K Handheld Water Quality Meters" ;
definition: "Triple channel handheld water quality meter that has large colour graphic LCD screen, measuring 70 x 52 mm, with backlight and built in foldable meter stand. It is IP67 waterproof and dustproof, battery and USB powered, eco friendly, shock proof, scratch resistant, and non slip." .
SCR:020109 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PH110" ;
rdfs:label "Horiba | LAQUAact PH110 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing, Meter can be used for long periods, even in dark places." .
SCR:020110 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PD110" ;
rdfs:label "Horiba | LAQUAact PD110 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing, Meter can be used for long periods, even in dark places." .
SCR:020111 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EC120" ;
rdfs:label "Horiba | LAQUAact EC120 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing, Meter can be used for long periods, even in dark places." .
SCR:020112 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PH120" ;
rdfs:label "Horiba | LAQUAact PH120 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing, Meter can be used for long periods, even in dark places, making it ideal for field measurements in rivers and lakes." .
SCR:020113 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PC110" ;
rdfs:label "Horiba | LAQUAact PC110 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing, Meter can be used for long periods, even in dark places." .
SCR:020114 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ca_11" ;
rdfs:label "Horiba | LAQUAtwin Ca-11 Pocket Water Quality Meters" ;
definition: "Compact meter integrates electrode, display and sample container to enable on site testing by direct measurement from single drops." .
SCR:020115 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EMIA_Step" ;
rdfs:label "Horiba | EMIA-Step Carbon/Sulfur Analyzer" ;
definition: "Tubular electric resistance heating furnace type realizes accurate and sensitive analysis, and its variable heating temperature function enables quantitative analysis by separating it by temperature and condition and whole quantity analysis." .
SCR:020116 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_800PS" ;
rdfs:label "HP | 800PS Mass Spectrometer" ;
definition: "HP designjet 800ps printer (42-inch model) is a large-format 42 inch printer for architects, engineers and GIS professionals working in technical departments. Network ready printer, a \"virtual-computer\" inside processes files, quickly freeing up the computer." .
SCR:020117 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Bead Xpress" ;
rdfs:label "Illumina | Bead Xpress In Vitro Assay" ;
definition: "Illumina Beadstation 500 is a high performance benchtop system designed for genetic analysis, particularly single nucleotide polymorphism (SNP) genotyping. High quality BeadArray technology provides the utmost in sensitivity thanks to a built in 30 fold redundancy and unparalleled quality control for every single feature on each array. Manual and automated processing is possible for both RNA- and DNA- based applications, and is made easy when the instrument is used in conjunction with liquid handlers and system software. For flexibility, the platform can be integrated with various other systems and robotics for meeting the requirements of many protocols. Reliability and reproducibility are ensured thanks to the scanner of the Beadstation. Additionally, sample throughput is adjustable. For gene expression (focused set), the unit can process 16 samples on one individual Sentrix BeadChip or 96 samples on a single Sentrix Array Matrix (SAM). For a 96 bundle matrix, processing times are as fast as 90 minutes or less. With a multiplex capability of as many as 1,536 plex, this system also provides great efficiency without sacrificing precision. Image resolution is less than one micron, and throughput can range from 16 to 192 (1536 SNP loci per array) per eight hour day for genotyping and 6 to 54 whole genome expression samples for gene expression. Minimal sample requirement (about 250 ng of DNA per assay for genotyping protocols and 50 ng to 100 ng total RNA for gene expression protocols) makes this system best for applications that use biopsies, fine needle aspirates, or preserved samples that are typically impossible to replace or are too low in quantity to meet the minimum input requirements of comparable instruments." .
SCR:020118 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EC_11" ;
rdfs:label "Horiba | LAQUAtwin EC-11 Pocket Water Quality Meters" ;
definition: "Compact meter integrates electrode, display and sample container to enable on site testing by direct measurement from single drops." .
SCR:020119 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_iCyte" ;
rdfs:label "ThorLabs | iCyte Automated Imaging Cytometer" ;
definition: "iCyte Automated Imaging Cytometer combines digital microscopy with image processing and the real time population data analysis of analytical cytometry to produce high levels of information content with minimal investigation time.The iCyte combines the advantages of flow and image cytometry into a single system that provides unparalleled flexibility and power for rapid measurements of biochemical constituents or evaluating cell morphologies. It comes packaged with our iGen software for data acquisition and analysis. The system houses four lasers that are available in five different wavelengths (see Specs tab for more details) for laser-spot scanning illumination. The detection system, which combines PMTs for fluorescence detection and photodiodes for absorbance and scatter detection, offers excellent quantitative cytometric performance and imaging capabilities. iCyte provides fully automated operation for analysis of cellular and tissue samples that have been stained with fluorescent or chromatic dyes. Fluorescent excitation, laser light absorbance by chromatic dyes, and scatter signals may all be acquired simultaneously. This quantitative image analysis system enables both walk-away high-throughput applications (e.g., cell cycle screens on a 96-well plate in under ten minutes) and high-content analysis (where scanning and analysis can take longer depending on the level of multiplexing required, desired resolution and size of the scan area). It automatically segments and quantifies cellular and subcellular events. The automated analysis allows for the study of morphometric and fluorescent measurement correlations on thousands of cells per specimen. The iBrowser software automates the analysis of the measurement for quick and easy to understand analysis." .
SCR:020120 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Bead Station 500GX" ;
rdfs:label "Illumina | Beadstation" ;
definition: "Illumina Beadstation 500 is a high performance benchtop system designed for genetic analysis, particularly single nucleotide polymorphism (SNP) genotyping. High quality BeadArray technology provides the utmost in sensitivity thanks to a built in 30 fold redundancy and unparalleled quality control for every single feature on each array. Manual and automated processing is possible for both RNA- and DNA- based applications, and is made easy when the instrument is used in conjunction with liquid handlers and system software. For flexibility, the platform can be integrated with various other systems and robotics for meeting the requirements of many protocols. Reliability and reproducibility are ensured thanks to the scanner of the Beadstation. Additionally, sample throughput is adjustable. For gene expression (focused set), the unit can process 16 samples on one individual Sentrix BeadChip or 96 samples on a single Sentrix Array Matrix (SAM). For a 96 bundle matrix, processing times are as fast as 90 minutes or less. With a multiplex capability of as many as 1,536 plex, this system also provides great efficiency without sacrificing precision. Image resolution is less than one micron, and throughput can range from 16 to 192 (1536 SNP loci per array) per eight hour day for genotyping and 6 to 54 whole genome expression samples for gene expression. Minimal sample requirement (about 250 ng of DNA per assay for genotyping protocols and 50 ng to 100 ng total RNA for gene expression protocols) makes this system best for applications that use biopsies, fine needle aspirates, or preserved samples that are typically impossible to replace or are too low in quantity to meet the minimum input requirements of comparable instruments." .
SCR:020121 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EC_22" ;
rdfs:label "Horiba | LAQUAtwin EC-22 Pocket Water Quality Meters" ;
definition: "Compact meter integrates electrode, display and sample container to enable on site testing by direct measurement from single drops." .
SCR:020122 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PH130" ;
rdfs:label "Horiba | LAQUAact PH130 Handheld Water Quality Meters" ;
definition: "Designed for use with one hand and with IP67 waterproof rating and shock resistant casing, Meter can be used for long periods, even in dark places." .
SCR:020124 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BeadArray Reader" ;
rdfs:label "Illumina | BeadArray Reader BeadArray Reader" ;
definition: "BeadArray microarray technology is based on 3-micron silica beads that self assemble in microwells on either of two substrates: fiber optic bundles or planar silica slides. When randomly assembled on one of these two substrates, the beads have a uniform spacing of ~5.7 microns. Each bead is covered with hundreds of thousands of copies of a specific oligonucleotide that act as the capture sequences in a given Illumina assay." .
SCR:020126 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HiScan SQ" ;
rdfs:label "Illumina | HiScan SQ Microarray Scanner" ;
definition: "HiScanSQ system (Figure 1) integrates the power and resolution of next-generation sequencing with the high-throughput capacity of genotyping, gene expression, and methylation arrays, delivering unprecedented flexibility for experimental design. The instrument features two distinct components, the HiScan Reader and the SQ Module. The HiScan Reader functions as a high-speed, precision imaging scanner for Illumina sequencing and microarray-based analyses. The SQ Module is a reagent handling fluidics device needed to perform Illumina next-generation sequencing." .
SCR:020130 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HiSeq2000",
"SCR_020132" ;
rdfs:label "Illumina | HiSeq2000 Sequencing System" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15, 2023. HiSeq 2000 sequencing system for sequencing and fastest data generation rate." .
SCR:020140 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NextSeq_1000" ;
rdfs:label "Illumina | NextSeq 1000 Sequencing System" ;
definition: "Benchtop sequencer that allows to explore new science across variety of current and emerging applications, with higher efficiency and fewer restraints." .
SCR:020144 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ion_Proton_Sequencer" ;
rdfs:label "Ion Torrent | Ion Proton Sequencer" ;
definition: "Powered by Ion Torrent semiconductor chip technology, Ion Proton Sequencer is benchtop next generation sequencer to offer fast, affordable human genome and human exome sequencing. Powered by next generation of semiconductor sequencing technology, offers similar single day workflow to Ion PGM Sequencer." .
SCR:020145 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_J-815" ;
rdfs:label "Jasco | J-815 Spectropolarimeter" ;
definition: "Circular dichroism (CD) spectroscopy measures differences in the absorption of left-handed polarized light versus right-handed polarized light that arise due to structural asymmetry. The absence of regular structure results in zero CD intensity, while an ordered structure results in a spectrum which can contain both positive and negative signals." .
SCR:020146 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_100CX II",
"SCR_020153" ;
rdfs:label "JEOL | JEM-100CX II Transmission Electron Microscope" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 5,2023.JEOL JEM-100CX II transmission electron microscope is an electron microscope with imaging capabilities at low to high magnifications (90X to 800, 000X). A 10M-pixel HAMAMASTU C4742-95 digital camera is integrated to the system for high- image acquisition." .
SCR:020147 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_J-1500" ;
rdfs:label "Jasco | 1500 1500" ;
definition: "J-1500 allows for the maximum flexibility to upgrade your CD system with different measurement techniques. While the standard measurement modes are CD, LD, and absorbance, up to four simultaneous modes can be measured when combined with a wide range of sampling accessories. These accessories can measure a variety of samples, from liquids to films to solid-states. Temperature control systems can be coupled with multi-position cells to run thermal melts, providing researchers with CD and thermodynamic data sets for conformational and folding studies. Automated high-throughput CD can obtain measurements on up to 192 samples without user intervention, saving both time and money. Kinetic and protein dynamics studies can be performed with our dedicated stopped-flow systems that can measure both CD and fluorescence. The wavelength range has also been significantly extended, allowing measurements to be obtained in both the vacuum-UV and NIR spectral regions using the standard PMT detector (163 950 nm) and an optional InGaAs detector (up to 1600 nm). Additional features now allow researchers to optimize their parameter specifications in order to obtain data with the highest resolution and S/N performance for a specific application set." .
SCR:020148 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_inSPIRE" ;
rdfs:label "Thermo Fisher | Ion Max Source Mass Spectrometer Accessories" ;
definition: "Ion Max source's design imparts performance, allows interchangeability, and provides commonality between many different Thermo Scientific LC MS systems. Universal Thermo Scientific Ion Max source features rapidly interchangeable electrospray ionization ESI and atmospheric pressure chemical ionization APCI probes." .
SCR:020149 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Countess" ;
rdfs:label "Thermo Fisher: Invitrogen | Countess Countess" ;
definition: "Countess Automated Cell Counter from Invitrogen is a benchtop automated cell counter. It can perform cell counts as well as viability and cell calculations. The Countess has a touch screen display and allows data to be transferred via USB drive to a computer for data access and storage." .
SCR:020151 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GCxGC" ;
rdfs:label "JEOL | AccuTOF GCxGC Mass Spectrometer" ;
definition: "Mass spectrometer that offers both chromatographic separation and high resolution mass spectra. Offers variety of ion sources and features Instrument Detection Limit of 16 fg, statistically calculated from repeated injections of 100 fg octafluoronaphthalene." .
SCR:020152 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_400_800_MHZ" ;
rdfs:label "JEOL | 400-800 MHz Magnets" ;
definition: "Superconducting magnets including actively shielded magnets from 400 to 800 MHz, and ultra high field magnets from 900 to 930 MHz. Magnets feature low cryogen consumption cryostats, extremely small B0 drift characteristics and homogeneity." .
SCR:020154 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LC_plus_4G" ;
rdfs:label "JEOL | AccuTOF LC-plus 4G Time-of-Flight Mass Spectrometer" ;
definition: "Mass spectrometer with analyzer design that employs elegant ion optics and ADC based digitizer to deliver dynamic range exceeding 4 orders of magnitude, without compromising resolution or mass accuracy." .
SCR:020155 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2100F" ;
rdfs:label "JEOL | 2100F Transmission Electron Microscope" ;
definition: "JEM-2100F is a multipurpose, 200 kV FE (Field Emission) analytical electron microscope. Variety of versions is provided to adapt user's purposes. The FE electron gun (FEG) produces highly stable and bright electron probe that is never achieved with conventional thermionic electron gun. This feature is essential for ultrahigh resolution in scanning transmission microscopy and in an analysis of a nano-scaled sample. Various analytical instruments and/or cameras such as EDS (Energy Dispersive X-ray Spectrometer) or EELS (electron energy loss spectrometer) or CCD cameras are ready for integration with a PC system of the microscope control." .
SCR:020156 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AccuTOF_DART" ;
rdfs:label "JEOL | AccuTOF-DART 4G Mass Spectormeter" ;
definition: "Mass spectrometer that provides solutions for wide variety of fields with interchangeable atmospheric and ambient ionization sources" .
SCR:020157 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GCx_plus" ;
rdfs:label "JEOL | AccuTOF GCx-plus Mass Spectrometer" ;
definition: "Mass spectrometer with high resolution and high mass accuracy that enables accurate elemental composition determination of unknown compounds and impurities" .
SCR:020158 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BS-80011BPG" ;
rdfs:label "JEOL | BS-80011BPG Plasma Source" ;
definition: "Plasma source that can be used as Ion Plating for thin films, especially optical thin films and with Film quality such as density, adhesion, flatness, index of refraction and absorption are improved by comparison with usual vacuum deposition method" .
SCR:020159 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ECX_300" ;
rdfs:label "JEOL | ECX-300 Console" ;
definition: "Available from 300 to 500 MHz console is designed around modular, digital NMR electronics chassis controlled by intelligent acquisition computer. Both workstation and spectrometer may be connected to standard network, allowing seamless remote operation anywhere in world." .
SCR:020160 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EBG-300UA" ;
rdfs:label "JEOL | EBG-300UA High Power Electron Beam Source" ;
definition: "High power electron beam source that is designed to uniformly deposit metal oxides onto wide plastic films or steel plates in continuous feed such as in magnetic tape manufacture for high density recording or in wrapping film manufacture with oxide barrier function" .
SCR:020161 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CRYO ARM 200" ;
rdfs:label "JEOL | CRYO ARM 200 Transmission Electron Microscope" ;
definition: "Transmission elecctron microscope that achieves unprecedented resolution and stability allowing for automatic and unattended acquisitoin of image data for Single Particle Analysis" .
SCR:020162 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ElementEye JSX-1000S XRF" ;
rdfs:label "JEOL | ElementEye JSX-1000S XRF Fluorescence Spectrometer" ;
definition: "Fluoresence spectormeer that analyzes major to trace components on most sample types solids, powders, liquids with little or no sample preparation" .
SCR:020163 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CRYO ARM 300" ;
rdfs:label "JEOL | CRYO ARM 300 Transmission Electron Microscope" ;
definition: "Transmission electron microscope field emission cryo electron microscope that allows for automated detection of holes on specimen grid for automated, unattended acquisition of high resolution images" .
SCR:020164 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IB_29500VED_IB_29510VET" ;
rdfs:label "JEOL | IB-29500VED/IB-29510VET Vacuum Evaporator Sample Preparation Tool" ;
definition: "High vacuum specimen sample preparation tool. Preparation device that makes it easy to prepare samples for imaging and analysis with with electron microscopes." .
SCR:020165 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GC_Mate_II" ;
rdfs:label "JEOL | GC Mate II Mass Spectrometer" ;
definition: "Benchtop double focusing magnetic sector mass spectrometer operating in electron ionization mode with TSS 2000 software." .
SCR:020166 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JBX-3050MV" ;
rdfs:label "JEOL | JBX-3050MV Electron Beam Lithography System" ;
definition: "Electron beam lithography system for mask reticle fabrication that meets design rule of 45 to 32 nm and pattern writing with high speed, high accuracy and high reliability, achieved by high end technology" .
SCR:020167 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_InfiTOF" ;
rdfs:label "JEOL | InfiTOF Multi-Turn Time-of-Flight Mass Spectrometer" ;
definition: "Mass spectrometer that can determine elemental compositions for ions within range of m/z 1 to 1,000. Hydrogen ion H plus can be detected with multi turn and multi segment that obtains high resolution with small ion flight path design." .
SCR:020168 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JAMP_9510F" ;
rdfs:label "JEOL | JAMP-9510F Elecrostatic hemispherical analyzer (HSA)" ;
definition: "Electrostatic hemispherical analyzer with multi channel detector optimally designed for Auger analysis that provides user selectable energy resolution for high throughput high resolution and high sensitivity." .
SCR:020169 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JEBG-1000UB" ;
rdfs:label "JEOL | JEBG-1000UB High Power Electron Beam Source" ;
definition: "High power electron beam source that is designed to uniformly deposit metal oxides onto wide plastic films or steel plates in continuous feed such as in magnetic tape manufacture for high density recording or in wrapping film manufacture with oxide barrier function" .
SCR:020170 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JBX_8100FS" ;
rdfs:label "JEOL | JBX-8100FS Electron Beam Lithography System" ;
definition: "Electron beam lithography system that writes ultrafine patterns at faster rate of speed while minimizing idle time, especially during exposure process, thus increasing throughput." .
SCR:020171 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JBX_9500FS" ;
rdfs:label "JEOL | JBX-9500FS Electron Beam Lithography System" ;
definition: "Electron beam lithography system that is versatile in its applications from basic research of elements to test production of optical elements to research and development for masks for high accelerating voltage exposure." .
SCR:020172 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JEBG-3000UB" ;
rdfs:label "JEOL | JEBG-3000UB High Power Electron Beam Source" ;
definition: "A high power electron beam source that is designed to uniformly deposit metal oxides onto wide plastic films or steel plates in continuous feed such as in magnetic tape manufacture for high density recording or in wrapping film manufacture with oxide barrier function" .
SCR:020173 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JEM-2100Plus" ;
rdfs:label "JEOL | JEM-2100Plus Transmission Electron Microscope" ;
definition: "Multipurpose transmissoin electron microscope ombining optic system of original JEM 2100 with advanced control system for enhanced ease of operation." .
SCR:020174 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JEM-ARM300F" ;
rdfs:label "JEOL | JEM-ARM300F Transmission Electron Microscope" ;
definition: "Transmission electron microscope that is designed to meet most advanced materials development requirements for atom by atom characterization and chemical mapping" .
SCR:020175 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JEM-F200 F2" ;
rdfs:label "JEOL | JEM-F200 F2 Transmission Electron Microscope" ;
definition: "Transmission scanning electron microscope that offers Cold Field Emission Gun and dual Silicon Drift Detectors" .
SCR:020176 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JES_X310" ;
rdfs:label "JEOL | JES-X310 Electron Spin Resonance (ESR) Spectrometer" ;
definition: "Electron spin resonance spectrometer that is user friendly and provides high sensitivity, resolution, and stability." .
SCR:020177 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JES_X320" ;
rdfs:label "JEOL | JES-X320 Electron Spin Resonance (ESR) Spectrometer" ;
definition: "Electron spin resonance spectrometer that is user friendly and provides high sensitivity, resolution, and stability." .
SCR:020178 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JIB-4000PLUS" ;
rdfs:label "JEOL | JIB-4000PLUS Focused Ion Beam" ;
definition: "Focused ion bean that is milling and imaging system featuring high performance ion optical column" .
SCR:020179 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JEOL JEM-1400Flash" ;
rdfs:label "JEOL | JEOL | JEM-1400Flash Transmission Electron Microscope" ;
definition: "Transmission electron microscope that can be used to first view samples at low magnification before studying fine structures of interest at high magnification." .
SCR:020180 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JCM-7000 NeoScope Benchtop" ;
rdfs:label "JEOL | JCM-7000 NeoScope Benchtop Scanning Electron Microscope (SEM)" ;
definition: "Scanning electron microscope that is equipped with large chamber, high and low vacuum modes, secondary and backscatter electron detectors, real time 3D imaging, highly advanced auto functions and option to add fully embedded EDS with real time, Live, analysis." .
SCR:020181 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JMS_TQ4000GC" ;
rdfs:label "JEOL | JMS-TQ4000GC Triple-Quadrupole Mass Spectrometer" ;
definition: "Mass spectrometer that accurately measures trace or residual pesticides in agricultural materials, trace levels of regulated chemicals in tap water, and simplifies quantitative analysis of persistent environmental pollutants such as dioxins and PCB's." .
SCR:020182 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JMS_Q1500GC" ;
rdfs:label "JEOL | JMS-Q1500GC Single-Quad Mass Spectrometer" ;
definition: "Mass spectrometer that can be used for wide range of applications such as environmental analysis for agrichemicals and mold odor, material analysis, and aroma analysis." .
SCR:020183 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JNM_ECZR" ;
rdfs:label "JEOL | JNM-ECZR Nuclear Magnetic Resonance (NMR) Spectrometer" ;
definition: "Nuclear magnetic resonance spectormeter that enables highly sophisticated measurements to be carried out while most routine measurement operations can be performed automatically." .
SCR:020184 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JNM_ECZS" ;
rdfs:label "JEOL | JNM-ECZS Nuclear Magnetic Resonance (NMR) Spectrometer" ;
definition: "Nuclear magnetic resonance spectormeter that incorporates ultra high accuracy RF circuitry utilizing latest digital high frequency technology. Compact spectrometer equipped with functions normally only found on research models and supports most advanced NMR experiments." .
SCR:020185 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JES_X330" ;
rdfs:label "JEOL | JES-X330 Electron Spin Resonance (ESR) Spectrometer" ;
definition: "Electron spin resonance spectrometer that is user friendly and provides high sensitivity, resolution, and stability." .
SCR:020186 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JSM_IT200" ;
rdfs:label "JEOL | JSM-IT200 InTouchScope Scanning Electron Microscope (SEM)" ;
definition: "Scanning electron microscope that is compact and versatile and delivers high resolution imaging with unsurpassed low kV performance and high sensitivity solid state BSE detector included with LV models." .
SCR:020187 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JSM-F100 Field Emission" ;
rdfs:label "JEOL | JSM-F100 Field Emission Scanning Electron Microscope (SEM)" ;
definition: "Scanning electron microscope that offers high spatial resolution imaging and analysis at nanoscale" .
SCR:020188 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JIB-4700F" ;
rdfs:label "JEOL | JIB-4700F Focused Ion Beam" ;
definition: "Focused ion beam that can be used in morphological observations, elemental and crystallographic analyses of variety of specimens." .
SCR:020189 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JSM-IT500HR InTouchScope" ;
rdfs:label "JEOL | JSM-IT500HR InTouchScope Scanning Electron Microscope (SEM)" ;
definition: "Scanning Electron Microscope that provides high resolution imaging along with high sensitivity and high spatial resolution analysis" .
SCR:020190 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JSM-7610FPlus Field Emission" ;
rdfs:label "JEOL | JSM-7610FPlus Field Emission Scanning Electron Microscrope (SEM)" ;
definition: """Scaning electron microscope with semi in lens detector with integrated electron energy filter r filter and in lens Schottky field emission gun to deliver
ultrahigh spatial resolution with wide range of probe currents for all applications""" .
SCR:020191 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JSM_7900F" ;
rdfs:label "JEOL | JSM-7900F Field Emission Scanning Electron Microscope (SEM)" ;
definition: "Scanning electron microscope with flexible platform that combines high resolution imaging with nano scale microanalysis." .
SCR:020192 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JXA_iHP200F" ;
rdfs:label "JEOL | JXA-iHP200F Field Emission Electron Probe Microanalyzer (EPMA)" ;
definition: "Electron probe microanalyzer that provides both high imaging resolution and analytical resolution with very high and stable probe current for analytical performance." .
SCR:020193 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MStation" ;
rdfs:label "JEOL | MStation Mass Spectrometer" ;
definition: "Mass spectrometer with ion optics design that permits rapid and auto tuning with minimal operator intervention, even under high resolution conditions." .
SCR:020194 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Monochromated ARM 200F" ;
rdfs:label "JEOL | Monochromated ARM 200F Transmission Electron Microscope" ;
definition: "Transmission electron microscope that provides ultrahigh energy resolution EELS analysis of materials at atomic scale" .
SCR:020195 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MALDI_SpiralTOF" ;
rdfs:label "JEOL | MALDI SpiralTOF Time-of-Flight (TOF) Mass Spectrometer" ;
definition: "Mass spectormeter that has levels of mass resolution and sensitivity and system that has been acknowledged for its distinctive capabilities in various scientific studies." .
SCR:020196 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Soft X-Ray Emission Spectormeter" ;
rdfs:label "JEOL | Soft X-Ray Emission Spectormeter Scanning Electron Microscope (SEM)" ;
definition: "Scanning electron microscope that provides excellent light element detection and superb sensitivity that is best for chemial shift analysis of light elements" .
SCR:020197 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NEOARM" ;
rdfs:label "JEOL | NEOARM Transmission Electron Microscope" ;
definition: "Transmission electron microscope that enables atomic resolution imaging" .
SCR:020198 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JXA_iSP100" ;
rdfs:label "JEOL | JXA-iSP100 Electron Probe Microanalyzer (EPMA)" ;
definition: "Electron probe microanalyzer that provides both high imaging resolution and analytical resolution with very high and stable probe current for analytical performance with new algorithms for auto functions of both SEM column and optical microscope." .
SCR:020199 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ROYAL_HFX" ;
rdfs:label "JEOL | ROYAL HFX Nuclear Magnetic Resonance (NMR) Probe" ;
definition: "NMR probe that has capability to switch between single tune and dual tune modes on high frequency coil." .
SCR:020201 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SpiralTOF_plus" ;
rdfs:label "JEOL | SpiralTOF-plus MALDI TOF/TOF Mass Spectrometer" ;
definition: "Mass spectrometer with long flight path that results in ultrahigh resolving power greater than 75,000 and sub ppm mass accuracy." .
SCR:020202 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_M2BIO" ;
rdfs:label "Kramer Scientific | M2Bio M2BIO" ;
definition: "M2Bio is the original hybrid stereo-compound fluorescence microscope available to customers worldwide from Kramer Scientific. It is the go-to microscope for genetic research, cell biology, neuroscience, and developmental biology. The continuous zoom capabilities in both stereo and compound make it for transgenic sorting and observation needs. While copied by others, the M2BIO still offers the best value and flexibility for those needing true stereo for picking with a compound light path for resolving more faint fluorescence markers." .
SCR:020205 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6" ;
rdfs:label "Kent Scientific | 6 Blood Pressure System" ;
definition: "CODA mouse rat tail-cuff system was designed to allow accurate blood pressure measurement in mice and rats. Blood pressure is measured in the tail of the mouse or rat using Volume Pressure Recording (VPR) sensor technology. The included software allows you to continuously view data in real-time.CODA High Throughput System with 6 Activated Channels." .
SCR:020206 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_3050S" ;
rdfs:label "Leica | 3050S Cryostat" ;
definition: "Primarily designed for the demanding needs of cryosectioning in biomedical, neuro-anatomical and pharmaceutical research. The Leica CM3050 S cryostat features superior user comfort with excellent safety standards for practically all types of cryosectioning applications. It is the instrument of choice for all research applications and for advanced clinical cryosectioning needs. Particularly when working with delicate specimens for example brain samples in neuroscience the precise specimen orientation and the specimen feed system guarantees reproducible, thin, serial sections of maximum quality." .
SCR:020207 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AXIS-165 XPS" ;
rdfs:label "Kratos | AXIS-165 XPS Surface Analylsis System" ;
definition: "AXIS Nova combines XPS imaging and spectroscopic capabilities with a highly automated, large sample handling system and is the next generation of AXIS Nova spectrometer. The AXIS Nova is based on Kratos, AXIS technology comprising: magnetic and electrostatic transfer lenses; co-axial electron-only charge neutralisation; spherical mirror and hemispherical electron energy analysers. Kratos developed innovations such as the delay-line detector for spectroscopy and imaging modes and high energy X-ray excitation sources ensure the AXIS Nova is capable of performing in the most demanding research and development environments." .
SCR:020208 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ROYAL" ;
rdfs:label "JEOL | ROYAL Nuclear Magnetic Resonance (NMR) Probe" ;
definition: "Probe that combines performance of broadband probe for heteronuclear measurements and inverse probe for 1H and 19F measurements." .
SCR:020209 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_APO S8" ;
rdfs:label "Leica | APO S8 Microscope" ;
definition: "Greenough stereo microscope, Leica S8 APO with apochromatic 8:1 zoom and 75mm working distance allows easy access to specimen even at high magnification up to 80x which is best for quality control, cell sorting and microinjection applications. Ergonomic 38 viewing angle provides comfort, which helps increase productivity, reduce fatigue related inspection errors and acquire precise positioning while working with incident or transmitted light. Adjustable zoom stops allows fast, easy, repeatable measurements and inspections. The Integrated Documentation port allows to connect digital cameras." .
SCR:020210 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ACE900" ;
rdfs:label "Leica | ACE900 Freeze Fracturing System" ;
definition: "Vitrified frozen structures are extremely sensitive to environmental influences and need to be protected from the formation of artefacts. Prepare your samples for detailed image evaluation under optimal conditions: Cold shield around the sample avoids water molecules freezing onto your sample, Accurate temperature control during the complete process, Clean Knife fresh blade for each cut avoids contamination, Instant, fast e-beam coating, which captures detailed surface information, and Protected vacuum transfer to other analysis systems." .
SCR:020211 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_S8 APO" ;
rdfs:label "Leica | APO S8 S8 APO" ;
definition: "Greenough stereo microscope, Leica S8 APO with apochromatic 8:1 zoom and 75mm working distance allows easy access to specimen even at high magnification up to 80x which is best for quality control, cell sorting and microinjection applications. Ergonomic 38 viewing angle provides comfort, which helps increase productivity, reduce fatigue related inspection errors and acquire precise positioning while working with incident or transmitted light. Adjustable zoom stops allows fast, easy, repeatable measurements and inspections. The Integrated Documentation port allows to connect digital cameras." .
SCR:020212 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Autostainer XL" ;
rdfs:label "Leica | Autostainer XL Automated Slide Stainer" ;
definition: "Autostainer XL continues to provide reproducible, consistent, high-quality staining and increased workload throughput. Plus, combine it with the CV5030 Glass Coverslipper to create a workstation that eliminates the manual handling of slide racks between staining and coverslipping. Can be used stand-alone or integrated with the Leica CV5030 Glass Coverslipper to create a ‘walk-away, staining/coverslipping workstation. Upgrade at anytime to match your laboratory's specific needs." .
SCR:020214 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CM3050 S" ;
rdfs:label "Leica | CM3050 Cryostat" ;
definition: "Leica CM3050 S is a cryostat for routine as well as research applications in biology, medicine and industry. The instrument has been designed for rapid freezing and sectioning of tissue samples. The instrument has not been designed for unattended storage of tissue material." .
SCR:020215 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DFC 452" ;
rdfs:label "Leica | DFC 452 Microscope Camera" ;
definition: "Leica DFC495 is a digital camera with 8 Megapixel CCD that quickly captures high-resolution images microscopy in life science.. The scan preview in SXGA resolution provides up to 18 frames per second (fps) and allows the sample to be adjusted and focussed directly on the computer screen. The Peltier cooling reduces noise for imaging in low light conditions." .
SCR:020217 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DFC495" ;
rdfs:label "Leica | DFC495 Microscope Camera" ;
definition: "Leica DFC495 is a digital camera with 8 Megapixel CCD that quickly captures high-resolution images microscopy in life science.. The scan preview in SXGA resolution provides up to 18 frames per second (fps) and allows the sample to be adjusted and focussed directly on the computer screen. The Peltier cooling reduces noise for imaging in low light conditions. ." .
SCR:020218 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CM1900" ;
rdfs:label "Leica | CM1900 Cryostat" ;
definition: "Leica CM1900 is a rapid sectioning cryostat for advanced routine diagnostics in histology and clinical histopathology. This Leica cryostat offers extremely rapid specimen freezing and frequent changes in specimen temperature, meeting even the highest demands for smooth operation and enhanced safety. With the CM1900's overall engineering and ergonomic concept, the system provides accurate results for any cryostat application. The CM1900 is equipped with an ergonomically positioned handwheel for extremely smooth movement and easy locking in the upper position. The model also provides a functional control panel, which includes self-explanatory single-function keys and easily readable LEDs to prevent operating errors. The motorized coarse advance is ergonomically positioned in the arm rest at the left and operated via push buttons." .
SCR:020221 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CM1800" ;
rdfs:label "Leica | CM1800 Cryostat" ;
definition: "Leica CM1800 is a cryostat for routine and research applications in biology, medicine and industry. It has been designed for rapid freezing and sectioning of tissue samples." .
SCR:020222 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EM_AFS2",
"SCR_020230" ;
rdfs:label "Leica | EM AFS2 Freeze Substitution and Low Temperature Embedding System" ;
NIFRID:synonym "Leica EM AFS2" ;
definition: "System for Light and Electron Microscopy. Performs freeze substitution and progressive lowering of temperature techniques and allows low temperature embedding and polymerization of resins. Leica EM FSP (freeze substitution processor), automatic reagent handling system combined with Leica EM AFS2, dispenses reagents for both freeze substitution and PLT applications. The LED illumination from within the chamber and the attached stereomicroscope for viewing and positioning of samples ensures ease of use." .
SCR:020223 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DM2000" ;
rdfs:label "Leica | DM2000 Histology Microscope" ;
definition: "Leica DM2000 microscopes are best for complex tasks in pathology and cytology. For special diagnostics requirements, the microscope is certified for in-vitro-diagnostics (IVD) like in-vitro-fertilization (IVF)." .
SCR:020224 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DM2500" ;
rdfs:label "Leica | DM2500" ;
definition: "Leica DM2500 & DM2500 LED optical microscopes are two optical microscopes wih different illumination: DM2500 LED is equipped with LED illumination for transmitted light, DM2500 works with halogen. Both types of illumination render a realistic impression of the colors of the sample." .
SCR:020225 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DM1000" ;
rdfs:label "Leica | DM1000 Histology Microscope" ;
definition: "Leica DM1000 LED Histology Microscope features long-life LED illumination that provides near daylight, bright illumination with constant color temperature and emits less heat.. Users of the Leica DM1000 LED benefit from the system's ability to adapt to every user. the microscope is certified for in-vitro-diagnostics (IVD) like in-vitro-fertilization (IVF)." .
SCR:020226 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_UC6b" ;
rdfs:label "Leica | EM FC6 UC6b Ultramicrotome" ;
definition: "Leica Ultracut EM UC6 is an advanced ultramicrotome that features a Touch Screen Control Panel or a Keypad Control Panel. Both options enable fast and safer alignment of knife and specimen, and the programmable knife and cutting movements make trimming easy. With Leica's AutoTrim, you can automatically trim a specimen to a predetermined level in the block face, best for morphometric studies. Three dependent, built-in, brightness- controlled LED light sources provide outstanding illumination for top light, back light, and specimen transillumination." .
SCR:020227 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1150H" ;
rdfs:label "Leica | EG1150H Heated Paraffin Embedding Module" ;
definition: "Leica EG1150 H is a heated, paraffin dispensing module with 3-liter capacity and a heated work surface with storage areas for both cassettes and molds. All functions of the EG1150 H are controlled via an easy-to-read LED display, including the temperature settings for left and right hand warming trays, paraffin reservoir, and working surface." .
SCR:020229 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RM2255" ;
rdfs:label "Leica | RM2255 Automated Microtome" ;
definition: "Leica RM2255 rotary microtome is designed for fully motorized sectioning of both paraffin- and the Leica RM2255 in routine and in histology. Its two-in-one design concept, which allows motorized and manual sectioning, provides reproducible high-quality sections." .
SCR:020231 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TCS SP2 AOBS" ;
rdfs:label "Leica | TCS SP2 Confocal Laser Scanning Microscope" ;
definition: "Leica TCS SP2 is a spectral confocal laser scanning microscope with 405 UV laser 3CHDIC digital emission 400-800nm range designed to acquire high spatial resolution images of fluorescently labeled materials and for analysis of these images. The confocal principle utilizes a pinhole (confocal aperture) to eliminate out-of-focus light from fluorescently labeled specimens (i.e., provide “optical sectioning�). Lasers provide intense, point illumination that is scanned over the preparation and the fluorescence at each point is quantified and used to construct a representation of the object brightness (an image). This method provides high resolution for the x and y planes as well as vertically (z plane). The SP2 is an advanced confocal system with nine laser excitation lines spanning the spectrum from UV to near IR. The following laser lines are available: 405nm, 458, 476, 488, 496, 514, 543, 594, and 633, all fiber coupled and controlled by AOTFs." .
SCR:020232 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LMD7000" ;
rdfs:label "Leica | LMD7000 Laser Microdissection System" ;
definition: "Specimen collection by gravity contact-free and contamination-free. Laser Microdissection (LMD) makes it possible to distinguish between relevant and non-relevant cells or tissues. It enables the researcher to obtain homogeneous, ultra-pure samples from heterogeneous starting material. Researcher can selectively and routinely analyze regions of interest down to single cells from all kinds of tissues, even living cells from cell culture, to obtain results that are relevant, reproducible, and specific." .
SCR:020233 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TCS SP5" ;
rdfs:label "Leica | TCS SP5 Broadband Confocal Laser Scanning Microscope" ;
definition: "Leica TCS SP5 is a broadband confocal microscope that provides the full range of scan speeds at the a high resolution. With its SP detection (five channels simultaneously) and optional AOBS (Acousto Optical Bream Splitter), the Leica TCS SP5 delivers bright, noise-free images with minimal photo damage at high speed. The system is also the platform for the new Leica DM6000 CFS (Confocal Fixed Stage) for physiological and electrophysiological experiments and for the new super resolution Leica TCS STED confocal microscope." .
SCR:020234 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultracut S" ;
rdfs:label "Leica | Ultracut S Ultramicrotome" ;
definition: "Reichert/Leica UltraCut S ultramicrotome is designed for extremely precise cutting, and achieves consistent high quality ultra thin sections for electron microscopy, or semi-thin sections for light microscopy. It features a continuous feed range from 0 to 2.5 microns and has adjustable cutting speeds of 0.1 to 50 mm/sec. It has a 6V, 10W halogen illumination system." .
SCR:020235 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_4Pi" ;
rdfs:label "Leica | TCS 4Pi 4Pi" ;
definition: "4Pi microscopy uses a special phase- and wavefront-corrected double-objective imaging system linked to a confocal scanner to enable 4-7 fold increased axial resolution over confocal & two photon microscopy. Even in living specimens, axial sections of ~100 nm are obtained. The system maintains all advantages of fast scanning, Acousto-Optical Beam Splitting (AOBS) and Spectral Detection of the Leica TCS SP2 AOBS for routine operation. The first marked leap in resolution in commercial 3D fluorescence microscopy opens up new dimensions for research in cell and developmental biology. The Leica TCS 4PI system was developed in close cooperation with Prof. Stefan Hell, Head of the NanoBiophotonics Department at the Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany and was in part funded by the German Ministry of Education and Research (BMBF)." .
SCR:020237 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ACE600" ;
rdfs:label "Leica | EM ACE600 High Vacuum Sputter Coater" ;
definition: "EM ACE600 sputter coater is a versatile high vacuum film deposition instrument for your FE-SEM and TEM applications." .
SCR:020238 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QuantStudio 3" ;
rdfs:label "Thermo Fisher: Life Technologies | QuantStudio 3 Real Time PCR System" ;
NIFRID:synonym "Applied Biosystems QuantStudio 3 Real Time PCR System" ;
definition: "System designed for users who need easy-to-use real-time PCR system that doesn't compromise performance and quality. Using OptiFlex technology (featuring 4 coupled channels and white LED) and featuring three independent Veriflex temperature zones, the QuantStudio 3 system enables improved data accuracy and sensitivity for broad range of genomic applications." .
SCR:020239 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QuantStudio 6" ;
rdfs:label "Thermo Fisher | Life Technologies QuantStudio 6 Real Time PCR System" ;
definition: "QuantStudio 6 Flex system accommodates the interchange of a 96-well, 96-well Fast, or 384-well block. The system is delivered with one block type (a 96-well block in this case); other block types may be purchased separately. For a system that also supports TaqMan array cards, as well as automation, please see our QuantStudio 7 Flex system. The QuantStudio 6 Flex system can also be upgraded to a QuantStudio 7 Flex system at a later date, as your needs change. For the ultimate in productivity, consider the QuantStudio 12K Flex system, which also accommodates TaqMan OpenArray plates." .
SCR:020240 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QuantStudio 5" ;
rdfs:label "Thermo Fisher: Life Technologies | QuantStudio 5 Real Time PCR System" ;
definition: "Carry out rapid food protection testing with the Applied Biosystems QuantStudio 5 Food Safety Real-Time PCR System. The and easy-to-use system is best for users who need superior performance, maximum dye versatility, and security options in a real time PCR system. The QuantStudio5 Food Safety System is a high performance benchtop platform combining ease-of-use and system connectivity. Benefit from the flexibility of a 6-channel, 96-well, cloud-enabled open platform suitable for running our full range of PCR solutions for food safety, authenticity, and quality testing." .
SCR:020241 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultracut E",
"SCR_020426" ;
rdfs:label "Leica | Reichert-Jung Ultracut E Microtome" ;
definition: "Ultracut E microtome is designed for extremely precise cutting, and achieves consistent high quality ultra thin sections for electron microscopy, or semi-thin sections for light microscopy. It features a continuous feed range from 0 to 2.5,m and has adjustable cutting speeds of 0.1 to 50 mm/sec. Comes with a control box with power cord, a microtome sectioning unit, and a microscope assembly with AO Stereostar 570 zoom body (0.7X - 4.2X) with attached 10X eyepieces. It has a 6V, 10W halogen illumination system." .
SCR:020242 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Vacuum_Oven" ;
rdfs:label "Thermo Fisher | Lindberg/Blue M Vacuum Oven Accessories" ;
definition: "Configure Thermo Scientific Lindberg Blue M Vacuum Oven Accessories with vacuum oven for more effective lab tool." .
SCR:020243 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VT1200S" ;
rdfs:label "Leica | VT1200S vibrating microtome" ;
definition: "Vibrating blade microtome for sectioning by Leica Biosystems used in neurophysiology, neuropathology, experimental pathology, botany. Fully automated Leica VT1200 S vibrating blade microtome for cutting fresh and fixed tissue in Neuroscience. To achieve sections of the highest quality that retain viable cells on the section surface, the vertical deflection of the blade can be measured by Leica's Vibrocheck measurement device and minimised with the blade holder. The instrument was designed in collaboration with Prof. Dr. Peter Jonas and his group at the Physiology Department, Freiburg Germany." .
SCR:020245 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QuantStudio 7" ;
rdfs:label "Thermo Fisher: Life Technologies | QuantStudio 7 Real Time PCR System" ;
definition: "Applied Biosystems QuantStudio 7 Flex Real-Time PCR System advances your research further by enabling a broad range of real-time PCR-based applications through its multiplexing capabilities and interchangeable block formats. With a simplified workflow, software, automation capabilities, and touch-screen interface, the QuantStudio 7 Flex system offers reproducibility with minimal well-to-well and instrument-to-instrument variation." .
SCR:020246 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1200C" ;
rdfs:label "Thermo Fisher | Lindberg/Blue M 1200C Split-Hinge Tube Furnaces" ;
definition: "Configure Thermo Scientific Lindberg Blue M 1200 degrees C Split Hinge Tube Furnaces for horizontal or vertical use." .
SCR:020249 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model 80604" ;
rdfs:label "Bussey-Saksida Rat Touch Screen Chamber Package Model 80604" ;
NIFRID:synonym "Bussey-Saksida Rodent TouchScreen Operant System",
"Bussey-Saksida Rodent Touchscreen System" ;
definition: "Designed for efficient and high throughput cognitive evaluation of rodents. System contains multiple cognitive paradigms, prewritten to include the entire battery of tasks necessary to habituate, shape, and bring the animal to criteria on that particular application, as well as collect and analyze prepared Data Analysis Sets using the ABET II software." .
SCR:020250 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "thesugarscience" ;
definition: "Interactive digital platform helping scientists who study type 1 diabetes connect, collaborate, and gain funding for their best ideas. All volunteer team has received much positive support from the global population of scientists studying type 1 diabetes, as well as from Beyond Type 1, JDRF, and IPITA. Provides curated conversations, events and technology to scientific T1D focused audience. Non profit entity funded by donations and sponsorships with industry and academic partners to provide unique collaborative benefits and programs to researchers in the T1D academic research community." .
SCR:020251 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CalcuSyn" ;
NIFRID:synonym "CalcuSyn Version 2.0" ;
definition: "Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools." .
SCR:020252 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Guava_Muse" ;
rdfs:label "CyTekBio | Guava Muse Cell Analyzer" ;
NIFRID:synonym "Cytek Guava Muse Cell Analyzer",
"Luminex Guava Muse Cell Analyzer" ;
definition: "Analyzer packs 3-parameter analysis into compact benchtop device, making flow cytometry accessible to anyone, anytime. A user-friendly touchscreen interface, cell analysis software, and optimized assays work to simplify your research." .
SCR:020253 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CCD165" ;
rdfs:label "mar ccd | CCD165 Detector" ;
definition: "Single CCD chip based area detector and has a read-out time of three (3) seconds for a 2k x 2k image. Some other features of the marCCD 165 are: Very low noise, Fast read-out, Peltier cooled detector, Monolithic design with no gaps. and Computer controlled data collection." .
SCR:020254 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_16" ;
rdfs:label "Maxwell | 16 DNA purification system" ;
definition: "Nucleic Acid and Protein Purification instrument that provides consistent, automated purification of high-quality DNA, RNA, viral total nucleic acid, or recombinant proteins using paramagnetic particles. There are no Clogs or Drips, Optimal Capture, Washing, and Elution of Target Material, Purifier Can Configure as an SEV or LEV Instrument, Preprogrammed Purification Protocols, For Purification of High-Quality DNA, RNA, and More. It works as a particle processor, not a liquid handler, so there are no clogs or drips, allowing optimal capture, washing, and elution of target material. Purification protocols are preprogrammed into the instrument and can be combined with purification kits containing prefilled reagent cartridges to maximize simplicity and convenience. The purifier can be configured as an SEV Instrument (Standard Elution Volume, 200 400 �L) for maximum yield or an LEV Instrument (Low Elution Volume, 30 100 �L) for maximum concentration. Accessories information: Kits are sold separately and contain enough materials to run 48 preps each." .
SCR:020256 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2010/M" ;
rdfs:label "Metricon | 2010/M Prism Coupler" ;
definition: "Refractometer that utilizes advanced optical waveguiding techniques to rapidly and accurately measure both the thickness and the refractive index/birefringence of dielectric and polymer films as well as refractive index of bulk materials. The 2010/M offers advantages over conventional refractometers and instruments based on ellipsometry or spectrophotometry: Completely General no advanced knowledge of optical properties of film/substrate required, Routine index resolution of �.0005 (accuracy of up to �.0001 available for many applications see specifications), Routine index resolution of �.0003 (resolution of up to �.00005 available for many applications see specifications), High accuracy index measurement of bulk, substrate, or liquid materials including birefringence/anisotropy, Rapid (20-second) characterization of thin film or diffused optical waveguides or SPR sensor structures, measurement of index vs wavelength, Options to measure index vs temperature (dn/dT), and waveguide loss, and Wide index measurement range (1.0-3.35)." .
SCR:020258 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DS50" ;
rdfs:label "Zeiss | Microm DS50 Slide Stainer" ;
definition: "Zeiss-Microm DS-50 slide stainer is fully programmable and meets the requirements of histology, hematology, cytology, microbiology and pathology laboratories. The Zeiss-Microm DS-50 slide stainer offers the efficiency, safety features and ease of operation customers have come to expect from Carl Zeiss. Equally important, the system's flexibility allows you to define your own protocols and remain consistent with your laboratory's individual procedures and requirements." .
SCR:020259 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HM325" ;
rdfs:label "Thermo Fisher | Microm HM325 Microtome" ;
definition: "Cut paraffin sections without a power supply with the robust Thermo Scientific HM 325 Rotary Microtome. The HM 325 features retraction at the return travel to protect the specimen and manual coarse advance for fast working." .
SCR:020263 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MACSQuant" ;
rdfs:label "Miltenyi | Bioscience MACSQuant Analyzer 16" ;
definition: "Automated flow cytometer with expanded fluorescence capabilities, enabling measurement of up to 16 parameters." .
SCR:020265 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MicroMax 007HF",
"SCR_020445" ;
rdfs:label "Rigaku | MicroMax-007 HF generator" ;
definition: "Microfocus rotating anode X ray generator.Used for Protein crystallography, small molecule crystallography, SAXS, micro diffraction, phase contrast imaging. Home lab X-ray source for protein crystallography and a popular source for small molecule crystallographers who need the additional flux of a rotating anode generator. The original MicroMax 007 introduced the world to the concept of a sub-100 micron focal spot size along the increased brilliance that can be more effectively used to illuminate small crystals. The current HF version increases the power loading by 50% over the original model providing an X-ray source that rivals second generation synchrotron sources - but with better beam stability and, of course, easy access." .
SCR:020267 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_gentleMACS",
"SCR_020280",
"SCR_025922" ;
rdfs:label "Miltenyi | gentleMACS Dissociator" ;
NIFRID:synonym "Miltenyi Biotec gentleMACS Dissociator",
"Miltenyi GentleMACS",
"Miltenyi gentleMACS Dissociator Tissue Dissociator" ;
definition: "Benchtop instrument for semi automated dissociation of tissues into single cell suspensions or thorough homogenates. Single sample or two samples in parallel can be processed." .
SCR:020268 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MACS Quant 10" ;
rdfs:label "Miltenyi | Bioscience MACSQuant Analyzer 10" ;
definition: "MACSQuant Analyzer 10 brings to life the versatility and power required for modern flow cytometry applications. Whether mining for rare cells, analyzing the efficiency of your cell manufacturing process or investigating signaling pathways, you are equipped for the task at hand. With a range of automated features, this flow cytometer lays the foundation for true automation present in all instruments belonging to the MACSQuant Family of flow cytometers." .
SCR:020269 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_gentleMACS_M" ;
rdfs:label "Miltenyi | gentleMACS M Tubes Tubes" ;
definition: "Used in combination with gentleMACS Dissociators for automated tissue homogenization, in order to isolate biomolecules like mRNA or total RNA, or to extract proteins." .
SCR:020270 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_gentleMACS_C" ;
rdfs:label "Miltenyi | gentleMACS C Tubes Tubes" ;
definition: "Used in combination with gentleMACS Dissociators for automated dissociation of tissues to obtain single cell suspensions with high viability rate." .
SCR:020271 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_gentleMACS_Octo_Heaters" ;
rdfs:label "Miltenyi | gentleMACS Octo Dissociator with Heaters Tissue Dissociator" ;
definition: "Benchtop instrument for fully automated and standardized tissue dissociation or homogenization of up to eight samples. Equipped with eight individual heating units and gentleMACS Programs." .
SCR:020272 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_gentleMACS_Octo" ;
rdfs:label "Miltenyi | gentleMACS Octo Dissociator Tissue Dissociator" ;
definition: "Benchtop instrument for semi automated and standardized tissue dissociation or homogenization of up to eight samples. Single cell suspensions or thorough homogenates from virtually any tissues are reproducibly obtained using uniquecanTubes or M Tubes." .
SCR:020289 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Prodigy" ;
rdfs:label "Miltenyi | Prodigy Cell Manufacturing Platform" ;
definition: "Offers advanced integrated solutions to streamline cell processing workflows from cell separation through cell culture to formulation of final product. Offers flexible platform for cell processing applications enabling magnetic separation of different cell types and customized cell processing protocols." .
SCR:020294 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ImageXpress" ;
rdfs:label "Molecular Devices | ImageXpress High Content Confocal Imaging System" ;
definition: "ImageXpress Micro Confocal system is a high-content solution that can switch between widefield and confocal imaging of fixed and live cells. It can capture high quality images of whole organisms, thick tissues, 2D and 3D models, and cellular or intracellular events. The spinning disc confocal and sCMOS camera enable imaging of fast and rare events like cardiac cell beating and stem cell differentiation. With MetaXpress software and flexible options like water immersion objectives to choose from, the system enables many confocal imaging applications from 3D assay development to screening." .
SCR:020296 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SpectraMax Gemini XS" ;
rdfs:label "Molecular Devices | SpectraMax Gemini XS Microplate Spectrofluorometer" ;
definition: "SPECTRAmax GEMINI XS Dual-Scanning Microplate Spectrofluorometer can perform a variety of fluorescent applications as well as some time-resolved fluorescent and luminescent assays. The extreme flexibility and high sensitivity of the SPECTRAmax GEMINI XS make it appropriate for applications within the fields of biochemistry, cell biology, immunology, molecular biology, and microbiology. The SPECTRAmax GEMINI XS uses two holographic diffraction grating monochromators which allow for individual optimization of wavelengths for both excitation and emission. The dual-scanning capability can also be used to determine excitation and emission settings for new fluorescent probes. Mirrored optics focus the light into the sample volume and cutoff filters are used to reduce stray light and minimize background interference. The light source is a highpowered Xenon flashlamp; additional flexibility is provided by allowing a variable number of lamp flashes per read. Microplates having 6, 12, 24, 48, 96, and 384 wells can be used in the SPECTRAmax GEMINI XS. Fluorescent detection is achieved from the top, through the entire depth of sample in the microplate well. Detection of species collected on membrane plates is also possible. Two plate carrier adapters are provided with the instrument. The blue adapter is required for optimum performance with standard 96- and 384-well format microplates. The red adapter has been optimized for use with Cliniplate 384 microplates." .
SCR:020297 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SpectraMax M2e",
"SCR_020527" ;
rdfs:label "Molecular Devices | Spectramax M2e Microplate Reader" ;
definition: "Multidetection microplate readers with dualmonochromators, dual-mode cuvette ports, and top- and bottom-reading capability. Detection modalities include absorbance (UV-Vis Abs) and fluorescence intensity (FI). Endpoint, kinetic, spectrum and area-well scanning read types and the PathCheck Sensor allow homogeneous and heterogeneous microplate assays to be performed in one flexible system. SpectraMax M2 readers provide for easy conversion and optimization of very-low-throughput to medium-high-throughput assays, faster, more precise results and reagent savings. In addition, combined absorbance and fluorescence intensity assays can be run by issuing a single read command." .
SCR:020298 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SpectraMax Gemini EM" ;
rdfs:label "Molecular Devices | SpectraMax Gemini Microplate Reader" ;
definition: "Microplate reader built on Gemini platform delivering high quality top and bottom reading for both solution and cell based assays. The Gemini EM can sample a variety of formats, from 6- to 384-well microplates, in different modes, such as endpoint, spectral scan, kinetic, and well scan. This reader's dual monochromators for excitation and emission cover the wavelength selection from 250 to 850 nm. Utilize both top and bottom fluorescence reading for the best optical sensitivity, and read up to four wavelength pairs in endpoint and kinetic measurements. The Gemini EM offers superb accuracy and reproducibility of results, possible with AutoPMT electronics, calibration for comparing RFUs between samples, consistent temperature regulation, programmable Automix, gentle movement, seamless automation, and comprehensive reader validation. Applications for the Gemini EM include enzyme assays, protein quantitation, microbial growth, ELISAs and immunoassays, transporter assays, nucleic acid quantitation, phosphotases/kinases, reporter gene assays, and cell viability, proliferation, and cytotoxicity." .
SCR:020299 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8600" ;
rdfs:label "Molecular Devices | Molecular Dynamics 8600 Imager" ;
definition: "Typhoon 8600 Variable Mode Imager unites storage phosphor autoradiography technology with fourcolour fluorescent labelling techniques for maximum data quality in a single, high-throughput system." .
SCR:020300 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SpectraMax M5" ;
rdfs:label "Molecular Devices | SpectraMax M5 Multimode Plate Reader" ;
definition: "Microplate Reader delivers single mode reader performance and can be equipped to read volumes as low as 2uL in one multimode reader package. The dual monochromator optics allow the widest range of applications to be utilized for bioresearch and drug discovery applications, all without the need to change filters. For fluorescence intensity, time resolved fluorescence, and fluorescence polarization assays, the SpectraMax M5 Microplate Reader optical design provides the highest level of flexibility. Users can select from top or bottom read modes for improved sensitivity for solution and cell-based assays. Assays can be better optimized by scanning across a range of wavelengths in increments as small as 1 nm. Up to 4 wavelength pairs can be read in one protocol for endpoint and kinetic measurements, allowing for fast setup of FRET and TR-FRET assays. For luminescence, the SpectraMax M5 Microplate Reader utilizes a dedicated luminescence photomultiplier tube (PMT), providing the user the maximum signal and lowest background possible for glow luminescence reporter gene assays. The SpectraMax M5 utilizes a single monochromator design for UV/VIS Absorbance, allowing the user to maximize sensitivity and tunability, and also uses patented PathCheck Pathlength Measurement Technology: the only temperature independent pathlength correction for microplates. The M5 can read volumes down to 2uL with the uMax Low Volume Plate." .
SCR:020302 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DS4208" ;
rdfs:label "Motorola | DS4208 Barcode Scanner" ;
definition: "General purpose imager that delivers the speed typical of laser scanners on both 1D and 2D barcodes, accommodating 2D barcodes without sacrificing performance. Users never need to take time to align the barcode with the scanner or pause between scans. Since the DS4208 can scan barcodes printed on paper labels or on mobile phone displays, users can drive revenue by attracting the millions of customers who are using their cell phones to better manage their lives. Retailers can accommodate customers who download mobile coupons, mobile loyalty cards and more. Quick service restaurants can accept mobile coupons at the register. Hotels can allow guests to use electronic loyalty cards stored on their cell phones, eliminating the need to carry physical cards. And since theaters, theme parks and stadiums can scan mobile tickets as easily as a paper ticket, they can offer customers an added convenience: paperless ticketing." .
SCR:020303 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SpectraMax 340PC384" ;
rdfs:label "Molecular Devices | SpectraMax 340PC384 Microplate Reader" ;
definition: "Microplate reader from Molecular Devices provides everything needed to measure absorbance in the visible range, including temperature control, a robotics-compatible interface and SoftMax Pro Data Acquisition and Analysis Software." .
SCR:020304 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SQ 120" ;
rdfs:label "MESO | QuickPlex SQ 120" ;
definition: "QuickPlex instrument is the newest multiplexing instrument from MSD, offering access to high-performance, electrochemiluminescence immunoassays. This compact system has been engineered for reliability, ease of use, and low cost of ownership. The combination of rapid read times and the ability to perform multiple, simultaneous tests on a single sample increases productivity, saves sample, and delivers results quickly. The QuickPlex has a wide menu of commercially available assay kits and a full line of components and reagents for developing your own assays." .
SCR:020305 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Class_II" ;
rdfs:label "Thermo Fisher | MSC-Advantage Class II Biological Safety Cabinets" ;
definition: "Conserve energy with Thermo Scientific MSC Advantage Class II Biological Safety Cabinets, which combine design and value with energy efficiency. Units feature 60 percent less energy consumption and heat output and cabinets are certified to EN 12469 safety standard." .
SCR:020306 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XC 47" ;
rdfs:label "Princeton Cryo | MVE XC 47/11-6 Cryogenic Tank" ;
definition: "Cryogenic tank for Specimen Sample Storage.This item includes the XC 47/11-6 dewar, cork/cover, and (6) 11\" hanging round canisters. All other accessories sold separately. MVE XC Series tanks have capacities ranging from 700-5000 straws and 210 to over 1000 vials. ." .
SCR:020307 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SpectraMax M2" ;
rdfs:label "Molecular Devices | SpectraMax M2 Microplate Reader" ;
definition: "Multidetection microplate readers with dualmonochromators, dual-mode cuvette ports, and top reading capability. Detection modalities include absorbance (UV-Vis Abs) and fluorescence intensity (FI). Endpoint, kinetic, spectrum and area-well scanning read types and the PathCheck Sensor allow homogeneous and heterogeneous microplate assays to be performed in one flexible system. SpectraMax M2 readers provide for easy conversion and optimization of very-low-throughput to medium-high-throughput assays, faster, more precise results and reagent savings. In addition, combined absorbance and fluorescence intensity assays can be run by issuing a single read command." .
SCR:020308 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Versa XRM-500" ;
rdfs:label "SelectScience | Nano CT scanner: Xradia VersaXRM-500" ;
definition: "VersaXRM-500 from Xradia VersaXRM family is the latest generation of 3D X-ray microscopy (XRM) solutions optimized for non-destructive micro tomography. The VersaXRM-500 advances industry and science with a versatile combination of world-leading resolution and contrast, sample flexibility and the large working distance required to address emerging research challenges. The system's source technology and high resolution detector provide unmatched sub-micron resolution, even for large samples." .
SCR:020309 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2000c" ;
rdfs:label "Thermo Fisher | NanoDrop 2000c Spectrophotometer" ;
NIFRID:synonym "NanoDrop 2000c Spectrophotometer" ;
definition: "Full-spectrum, UV-Vis spectrophotometer used to quantify and assess purity of DNA, RNA, Protein and more.NanoDrop 2000c combines micro-volume pedestal technology and cuvette capability in single instrument.Provides expanded measurement options for all types of samples.Provides broader concentration range for measuring very low concentrations and very high concentrations. Cuvette capability allows for kinetics (time or time/temperature studies) and cell culture (OD 600) measurements." .
SCR:020310 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NS500" ;
rdfs:label "Malvern Panalytical | Nanosight NS500 Analyzer" ;
definition: "Malvern Panalytical NanoSight NS500 instrument provides an easy-to-use, reproducible platform for nanoparticle characterization. The NS500 provides detailed and analysis of the size distribution and concentration of all types of nanoparticles from 10nm to 2000nm in diameter, depending on the instrument configuration and sample type being analyzed. Single particle zeta potential measurements on the NS500 provide inherent high resolution zeta distributions which can be measured simultaneously with other NTA measurements parameters like size, particle concentration and can even operate whilst in fluorescence mode." .
SCR:020311 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Qubit 3.0" ;
rdfs:label "Thermo Fisher | Nanodrop Qubit 3 Fluorometer" ;
definition: "Benchtop fluorometer that can be used for the quantitation of DNA, RNA, microRNA, and protein using the highly sensitive and accurate fluorescence-based Qubit quantitation assays. Additionally, Ion Sphere Particle quality can be evaluated on the Qubit 3.0 Fluorometer using the Ion Sphere Quality Control Kit prior to performing a sequencing run on the Ion Personal Genome Machine (PGM) Sequencer. You can also use the Qubit 3.0 Fluorometer to directly measure the fluorescence of samples or to create new assay(s) using the MyQubit software pre-programmed into the instrument." .
SCR:020312 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5000" ;
rdfs:label "Nikon | 5000 Film Scanner" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10, 2024. Professional 135/IX240 film scanner is a scanner that satisfies the need for quality and speed. 4,000-dpi true optical-resolution scanning,16-bit A/D converter featuring 16-/8-bit output for crisp, color-true images. Exclusive Scanner Nikkor ED high-performance lens elements for reduced color aberration and minimized image distortion. Proprietary LED illumination technology ensures consistently accurate color reproduction. Amazingly fast scanning (approx. 20 seconds including image transfer to display) at 4,000 dpi Newly-developed, high-quality 2-line CCD sensor Improved image processing algorithm for significant boost in scan quality of color negative film Multi-sample scanning capability of up to 16 passes for faithful reproduction and smoother gradation Quick AF & Quick Preview enhance operability and High-speed USB 2.0 interface for fast, easy image transfer Compatible with various film formats (35mm [135], IX240, etc.) Enhanced Color Management System for higher precision, in compliance with ICC (International Color Consortium) version 4 standards." .
SCR:020313 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Innova 4230" ;
rdfs:label "Marshall Scientific | New Brunswick Innova 4230 Incubator" ;
definition: "Refrigerated Incubator Shaker has a heavy gauge stainless steel frame, both refrigeration and heating capabilities, and a internal shaking platform, this Refrigerated incubator is fully capable of handling just about any sample parameters. The internal Cabinet of the 4230 is composed of sturdy heavy gauge stainless steel and has a double paned glass window on the outside to allow internal sample viewing. The cabinet contains two adjustable stainless steel shelves and a fluorescent light for improved visibility. The 4230 also includes an internal AC receptacle for the sole purpose of the powering of internal devices. The built in shaker features an audible and visible alarm, control, display, timer and other onboard installations. The internal shaker drive is a triple eccentric counter balanced drive with 9 sealed for life ball bearings and has a motion of � circular standard. The rpm range is between 25 and 400 non stacked, and 25-300 stacked. The onboard timer has a time range of up to 99.9 hours setable in 0.1 hours. The temperature of the 4230 ranges from 20C below ambient with a minimum of 4C to maximum of 75C for 50 Hz units or 80C for 60 Hz units. Temperature alarms provide indication when temperature deviates > 1.0C" .
SCR:020316 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_C24KC" ;
rdfs:label "Marshall Scientific | New Brunswick C24KC Incubator Shaker" ;
definition: "New Brunswick C24KC Incubator Shaker microprocessor controls allow for uniform heating, motion and accurate regulation of shaking speed. Audible and visual alarms come standard with built-in timer. Speed ranges from 50 to 400 RPM and temperature ranges from 5 to 60 C." .
SCR:020317 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_A1R" ;
rdfs:label "Nikon | A1R Confocal Laser Scanning Microscope" ;
definition: "A1R model incorporates a hybrid scanner system utilizing a high speed resonant galvanometer capable of acquisitions up to 240 frames per second. Both scanners can be used simultaneously for experiments requiring acquisition and photoactivation by concurrently scanning the specimen. This supports advanced research methods using photoactivation fluorescence proteins and facilitates high-speed, live-cell work with a huge array of new imaging strategies. A spectral imaging detector further enables the A1 and A1R models to obtain up to 32 discreet spectral bandwidths of data in one acquisition, with spectral unmixing capabilities. The total system is controlled through NIS-Elements C applications software, which also enables full control of the Nikon Ti-E research inverted microscope equipped with Nikon's Focus System (PFS), widefield CCD cameras and an array of hardware devices." .
SCR:020318 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_A1" ;
rdfs:label "Nikon | A1 Confocal Laser Scanning Microscope System" ;
definition: "Basic confocal system consisting of a separate scan head, standard 5 PMT detectors, control module, and laser module. The A1 has a new multi-detector unit with 2 GaAsp PMT detectors to give brighter signals, enhanced signal-to-noise, and allow less phototoxicity.Fully automated A1 offers standard paired galvanometers with high resolution scanning at up to 4096 x 4096 pixels." .
SCR:020319 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_A1RMP" ;
rdfs:label "Nikon | A1R MP Confocal Microscope" ;
definition: "Nikon A1R MP is a multiphoton imaging system featuring a high resolution galvanometer scanner and a high speed resonant scanner that is capable of frame rates from 30 fps at 512 x 512 pixels to as fast as 420 fps in band scan mode. New 4 channel non-descanned detectors with higher sensitivity, reduced dark current and broad spectral range allow for real time unmixing of closely spaced probes for accurate and high-contrast spectral imaging. This is especially important in multiphoton microscopy because of the overlap of emission spectra of probes and autofluorescence, which is often unavoidable when using a single laser line." .
SCR:020320 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_E400" ;
rdfs:label "Nikon | Eclipse E400" ;
definition: "E400 standard microscope is optimized for comfort in extended clinical applications." .
SCR:020321 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_55i" ;
rdfs:label "Nikon | 55i Upright Microscope" ;
definition: "Versatile Eclipse 55i clinical microscope offers optical capabilities, unsurpassed ergonomic features and is optimized for digital imaging. Its white LED illumination system provides a homogenous and bright distribution of illumination across the field for optimal viewing and digital imaging, resulting in spectacular, vivid, true-to-life colors. ergonomic features, like the stay-in-position stage handle and tilting/telescoping ergonomic eyepiece tube ensure best viewing posture, enabling long hours of observations to be carried out in comfort." .
SCR:020323 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_800" ;
rdfs:label "Nikon | Eclipse 800 Widefield Microscope" ;
definition: "Eclipse 800 Microscope is a premier member of Nikon's advanced research microscope line. The E800 series incorporates Nikon's CFI60 optical system that (according to them) alleviates the limitations of conventional optics, allowing for very long working distances (for a tutorial on Nikon's CFI60 Optical System, click here). This system corrects chromatic aberrations over the entire field of view, generating a very sharp, clear image over the broadest magnification range. One can also put in a broad range of accessories without affecting optical quality. The microscope is designed so that the scientist can work with ease, especially in the dark, requiring little movement to operate the control knobs and handles. The CFI60 Optical System offers a 60mm objective parfocal distance, a 25mm objective thread size and a standard 25mm field of view all of which combine to provide a higher optical quality." .
SCR:020324 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TS-100F" ;
rdfs:label "Nikon | Eclipse TS100-F Eclipse" ;
definition: "Nikon Eclipse TS100-F Inverted Microscope comes from a long line of microscopes. The Halogen bright-field lamp provides enough light for phase contrast and NAMC viewing. The Eclipse TS100-F Inverted Microscope Sidentopf eye piece from Nikon delivers constant brightness throughout the entire field of view. This microscope is best for applications such as tissue culture, plaque measurement and blood typing. Used in combination with Narishige manipulators, also available from Nikon, these microscopes can be used for a range of micromanipulation techniques necessary for cyto-engineering, developmental and genetic engineering, electrophysiology, pharmacology and neurochemistry. Eco-illumination provides a long lifetime of 60,000 hours and reduces the frequency of lamp replacement. Nikon Eclipse TS 100 highly acclaimed CFI60 optical system is used, providing flat, sharp and clear images, while achieving longer working distances and higher numerical apertures. The Eclipse TS100 is also outfitted for phase contrast applications with a phase ring slider and filter, and is camera mount ready. The compact high-performance inverted Nikon ECLIPSE TS100-F Microscope uses Eco-illumination, a newly developed LED illumination. Eco-illumination provides enough brightness for phase contrast and NAMC observations on the Nikon Eclipse TS100 F. With a fly-eye lens, uniform brightness is provided in the entire field of view. LEDs are an environmentally friendly low-power-consumption light source. Eco-illumination provides a long lifetime of 60,000 hours and reduces the frequency of lamp replacement. Nikon's highly acclaimed CFI60 optical system is used, providing flat, sharp and clear images, while achieving longer working distances and higher numerical apertures. The Nikon Eclipse TS100F is best for applications such as tissue culture, plaque measurement and blood typing. Used in combination with Narishige manipulators, also available from Nikon, these microscopes can be used for a range of micromanipulation techniques necessary for cyto-engineering, developmental and genetic engineering, electrophysiology, pharmacology and neurochemistry." .
SCR:020326 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_E800" ;
rdfs:label "Nikon | E800" ;
definition: "Building upon the success of the popular CFI60 optical system (60-millimeter parfocal distance and 25-millimeter objective thread size) first installed on the Eclipse E600, Nikon has moved a step further by introducing ultra-low magnification objectives and has increased the standard field of view to 25 millimeters. Introduced with the Eclipse E800 was a plan 0.5x magnification objective, which accommodates a 50-millimeter field of view at the unprecedented magnification of 0.5x. When coupled with a 2x projection lens, the 0.5x objective permits macrophotography at 1:1 magnification (in effect, actual size documentation). The new macro objective lens is particularly useful for investigating large specimens such as brain slices, developing embryos, and extensive tissue sections. This objective is easily accommodated into the microscope without major re-configuration, and is interchangeable with other objectives on a standard rotating nosepiece." .
SCR:020328 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Nikon_SMZ-1B" ;
rdfs:label "Nikon | SMZ-1 Microscope" ;
definition: "Nikon SMZ-1 and SMZ-1B zoom stereo microscopes offer legendary Nikon stereo performance. Developed to fit a variety of applications and OEM needs, these advanced-design stereo microscopes have the features and image quality you expect from Nikon. High-performance optics and a 6V/10W halogen illuminator deliver images with excellent contrast, resolution, and brightness. The SMZ-1 and SMZ-1B are human-engineered to allow long periods of operation without fatigue. Mechanical design is yet rugged for daily trouble-free operation in industrial, laboratory, and classroom environments. All controls are easy to use. Nikon's versatile modular approach allows the SMZ-1/1B to be easily adapted to various configurations such as stand, arm, or table mounting. Similarly, the illuminator can be fixed to the instrument stand, placed in a diascopic base, or attached externally for oblique lighting. The SMZ-1/1B use a Nikon-designed twin-lens objective system inclined at 12o. Only the center of the lenses is used to provide the sharpest three-dimensional image and enable the operator to work more accurately and efficiently for prolonged periods without eye strain." .
SCR:020329 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TE300" ;
rdfs:label "Nikon | TE300 Inverted Fluorescence Microscope" ;
definition: "Advent of the infinity-corrected CFI60 optical system spurred Nikon design engineers to upgrade their research-caliber inverted microscope from the Diaphot 300 to the Eclipse TE300 in 1997. The vastly improved instrument provides longer working distances that accommodate a wide variety of culture vessels and thick specimens, while maintaining high numerical apertures to ensure suitable levels of brightness, imaging contrast, resolution, and sharpness. The paired oculars of the instrument provide a standard 22-millimeter field of view, but like other microscopes in the Eclipse line, the Nikon TE300 is highly modular and provides several options for binocular and trinocular tubes, condensers, stages, and illumination systems. The standard condenser system fabricated for the Nikon TE300 microscope consists of a series of condenser top lenses and a five-position turret assembly with components for phase, differential interference, and Hoffman modulation contrast techniques. Also, Nikon designers patented a video enhancement contrast system for the microscope that features special polarizers and analyzers that enable the visualization of low contrast minutiae that would ordinarily go unnoticed by traditional video imaging methods." .
SCR:020331 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Nunc Cell Factory Shaker GEN 2" ;
definition: "Automated system to perform horizontal, continuous accelerated and decelerated movement to Cell Factory System.Eliminates the need for manual methods of cell detachment, such as shaking and pounding." .
SCR:020332 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TMS" ;
rdfs:label "Nikon | TMS Inverted Phase Contrast Microscope" ;
definition: "Nikon TMS Inverted Phase Contrast Microscope produces high quality images for tissue culture labs, readily meeting biological and metallurgical research needs. This Nikon microscope offers operation with an easy-to-maintain inverted microscope frame. This inverted phase microscope is configured with 4x achromat, 10x Ph1, and 20x Ph2 objectives with critical halogen illumination. The TMS can accommodate a variety of Nikon CF objectives on its revolving triple nosepiece, along with multiple other accessories, such as stage adapters and extenders, sliders and rings, and extra long working condensers. The 4x achromat objective provides a lower magnification for a wider field of view, primarily best for when needing to view a large portion of a slide for study. The 10x Ph1 provides phase contrast low-power magnification, while the 20x Ph2 provides medium-power magnification with a larger aperture." .
SCR:020333 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SMZ800" ;
rdfs:label "Nikon | SMZ800 Stereomicroscope" ;
definition: "Offers higher magnification than conventional models, enabling high-resolution observation of minute structures. In combination with the new objective series, its improved chromatic aberration correction provides bright and sharp images through the entire viewfield. The parallel optics design allows ergonomic accessories and observation attachments to be used in a wide range of applications." .
SCR:020334 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Nunc Cell Factory Systems with Active Gassing Bioprocessing System" ;
definition: "Flow system helps to ensure controlled, contamination free atmosphere in each culture tray by equally distributing user specified gas mixture. Available in 4,10 and 40 tray models." .
SCR:020335 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_90i" ;
rdfs:label "Nikon | Eclipse 90i Upright Microscope" ;
definition: "Nikon Eclipse 90i is a fully motorized upright microscope configured to image in transmitted light, DIC and epi-fluorescence modes. Fluorescence cubes available for DAPI, GFP, RFP, and HYQ Cy5. Fluorescence illumination is provided by a Lumencor Sola Light Engine. You can do timelapse, XYZ position, Z stacks, multiple excitation or emission wavelengths, and tiling experiments. Equipped with a Hamamatsu Orca Flash 4.0 v2 CMOS monochrome camera and a Nikon D2-Fi2 color camera running on Nikon Elements software." .
SCR:020336 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AX70" ;
rdfs:label "Olympus | AX70 Upright Fluorescence Microscope" ;
definition: "Upright Fluorescence Microscope with automatic photomicrography system.Using the AX70 together with the U-PHOTO Universal Photo System provides a very advanced level of microscope performance and sophisticated photomicrography capabilities. Combining the mainframe and its corresponding auto focus function with the U-AFPHOTO and motorized units integrates technology with a system that fully supports automated photomicrography. This combination offers fast auto focus in brightfield, darkfield, fluorescence*, and Nomarski Differential Interference Contrast*, and provides automatic light intensity adjustment for the objective in use as well as automatic observation light path selection." .
SCR:020337 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FV1000" ;
rdfs:label "Olympus | FV1000 Confocal Microscope" ;
definition: "Next generation imaging system designed for high resolution, confocal observation of both fixed and living cells.FV1000 offers advances in confocal system performance while providing the speed and sensitivity required for live cell imaging with minimal risk of damage to living specimens.In addition, the FV1000 offers a revolutionary synchronized laser scanning system called the SIM Scanner. While one laser stimulates, the second laser simultaneously provides high-resolution imaging. This coordination of laser stimulation and imaging makes the FV1000 an ideal choice for FRAP, FLIP and photoactivation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:020338 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BH-2" ;
rdfs:label "Olympus | BH-2 Fluorescence Microscope" ;
definition: "Goal of the BH2 was superior optics and customizability, and it soon became very well known for both. Standard equipment on this microscope included 10x widefield high eyepoint eyepieces having a field number of 20, precentered halogen lamps, aspherical collector lenses, and fully enclosed light paths designed to exclude dirt and dust. Auxiliary components for the microscope included photoeyepieces, an automatic exposure photomicrography system, and a wide range of objectives covering the entire range of correction and magnification. In addition, both mechanical and circular stages were offered as were binocular and trinocular observation tubes. Contrast enhancing equipment included phase contrast, differential interference contrast, darkfield, fluorescence, and polarized light." .
SCR:020339 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FV300",
"SCR_020345" ;
rdfs:label "Olympus | FluoView 300 Confocal Microscope" ;
definition: "Confocal microscopy can improve conventional fluorescence images by recording fluorescence generated from the focal plane within the sample, while rejecting all other light coming from above or below the focal plane. The efficient point-scan/pinhole-detection confocal optics of the FluoView systems virtually eliminate out of focus light to produce high-contrast images with superb resolution. The FluoView systems are fully integrated workstations that incorporate user-friendly image acquisition and image analysis software with high-resolution confocal optics that require no user alignment. An , Windows-based graphic user interface allows new users to quickly generate images in various scan modes, such as XY, XZ, XT, XYZ, XYT, and XYZT. Standard image formats, including TIFF and AVI, permit easy, direct export of FluoView images to off-line analysis packages. XY scanning is performed with a pair of galvanometric mirrors, yielding a wide scanning range to cover up to a field number of 20. The optical zoom (up to 10x magnification) can be performed by narrowing the scanning range while maintaining the maximum pixel resolution of up to 2048 x 2048 pixels." .
SCR:020340 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FV500" ;
rdfs:label "Olympus | FV500 laser scanning microscope" ;
definition: "Olympus launched FV500/300 laser scanning biological microscopes in 1998, shortly after releasing the AX, BX, and IX series of microscopes that featured infinity-corrected UIS optics. The FV500/300 produce 2048 x 2048-pixel images." .
SCR:020341 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IX 81" ;
rdfs:label "Olympus | IX 81 Inverted Fluorescence Automated Live cell Microscope" ;
definition: "Olympus IX81 Inverted Fluorescense Phase Contrast Live cell Inverted microscope." .
SCR:020343 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BX61" ;
rdfs:label "Olympus | BX61 Upright Wide Field Microscope" ;
definition: "BX61 Upright Wide Field Microscope is specially designed to work with the Olympus laser based autofocus unit. With precise focus and active tracking, users can speed up routine inspections. Additional settings such as illumination level, lens selection and aperture setting can be set using push buttons on the microscope frame, a keypad or via the PC. A variety of motorized modules including nosepieces and illuminators are available to provide you with full flexibility in configuring your system." .
SCR:020344 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IX83" ;
rdfs:label "Olympus | IX83 Automated Fluorescence Microscope" ;
definition: "The Olympus IX83 inverted microscope has been integrated into our IXplore systems. IXplore Systems are designed to provide solutions-based packages that suit your research application needs." .
SCR:020346 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IX73" ;
rdfs:label "Olympus | IX73 Inverted Microscope" ;
definition: "Olympus IX73 inverted microscope has been integrated into our IXplore systems. IXplore Systems are designed to provide solutions-based packages that suit your research application needs." .
SCR:020350 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Atomfab" ;
rdfs:label "Oxford |Atomfab ALD Plasma Technology" ;
definition: "Uses remote source specifically designed for atomic scale processing. Has low damage for sensitive substrates, fast cycle times and reliablity with uniform plasma exposure and film deposition, short plasma times, 250ms, short strike time, 80ms, for high throughput, and reproducible strike time and low reflected power for high yield." .
SCR:020351 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ES" ;
rdfs:label "Oxford |Cypher ES Environmental AFM" ;
definition: "Asylum Research Cypher ES builds on performance of Cypher S and adds full environmental control features. Same resolution, speed and stability are maintained while operating in controlled gas or liquid environments, at temperatures from 0 to 250 degrees C." .
SCR:020352 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FlexAL" ;
rdfs:label "Oxford |FlexAL ALD System Plasma Technology" ;
definition: "FlexAL systems provide newrange of flexibility and capability in engineering of nanoscale structures and devices by offering remote plasma atomic layer deposition processes and thermal ALD within single ALD systems." .
SCR:020353 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ES_Polymer" ;
rdfs:label "Oxford |Cypher ES Polymer Edition AFM" ;
definition: "Configuration of Cypher ES AFM designed for polymer science research, comes standard with blueDrive photothermal excitation, three techniques from NanoMechPro toolbox for nanomechanical characterization, and high temperature polymer heater." .
SCR:020354 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VRS" ;
rdfs:label "Oxford |Cypher VRS AFM" ;
definition: "Full featured video rate atomic force microscope. This high speed AFM allows researchers to measure nanoscale dynamic processes at video frame rates." .
SCR:020355 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Integra" ;
rdfs:label "Oxford |Integra Superconducting Magnet System" ;
definition: "Helium magnet system. Wide range of superconducting magnet systems up to 22 T, cooled by liquid helium. Ideal for highly vibration sensitive experiments." .
SCR:020356 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IntegraAC" ;
rdfs:label "Oxford |IntegraAC Helium Magnet System" ;
definition: "IntegraAC range of recondensing helium systems has been developed to reduce consumption of liquid helium. By recondensing helium gas evaporated within system, this minimises running costs and conserves this limited resource. It is also compatible with wide range of superconducting magnets." .
SCR:020357 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ionfab_300_IBE" ;
rdfs:label "Oxford |Ionfab 300 IBE Plasma Technology" ;
definition: "Ion beam etch offers flexibility coupled with uniformity and is suitable for wide range of applications. Systems have flexible hardware options including open load, single substrate load lock and cassette to cassette. System specifications are closely tuned to applications, enabling faster and repeatable process results." .
SCR:020358 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ionfab" ;
rdfs:label "Oxford |Ionfab Ion Beam Plasma Technology" ;
definition: "Ion beam etch and deposition system is used for high quality material processing. Systems have flexible hardware options including open load, single substrate load lock, and cassette to cassette." .
SCR:020359 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_100_Polaris" ;
rdfs:label "Oxford |PlasmaPro 100 Polaris Plasma Technology" ;
definition: "PlasmaPro 100 Polaris single wafer etch system offers solutions to produce etch results needed to maintain competitive edge, with experience of etching materials such as GaN, SiC and Sapphire." .
SCR:020360 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Jupiter_XR" ;
rdfs:label "Oxford |Jupiter XR AFM" ;
definition: "Large sample AFM that offers high speed imaging and extended range in single scanner. Jupiter provides complete 200 mm sample access and delivers resolution, results, and versatility for academic research and industrial R and D laboratories." .
SCR:020361 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MercuryiPS" ;
rdfs:label "Oxford |MercuryiPS Power Supply System" ;
definition: "Magnet power supply system enables automated control of wide range of superconducting magnets, including NMR, high field, beamline and Vector Rotate magnet systems. MercuryiPS is bi polar and has high stability, four quadrant power supply with incorporated quench protection." .
SCR:020362 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ionfab_300_IBD" ;
rdfs:label "Oxford |Ionfab 300 IBD Plasma Technology" ;
definition: "Ion beam deposition products produce deposited films with high quality, dense and smooth surfaces. Ion beam technology provides approach to etch and deposition by offering single tool and maximising system utilisation, which includes open load, single substrate load lock, and cassette to cassette." .
SCR:020363 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MercuryiTC" ;
rdfs:label "Oxford |MercuryiTC Cryogenic Environment Controller" ;
definition: "Cryogenic environment controller that includes single channel 24 bit high resolution temperature measurement circuit, which supports all standard cryogenic sensors, like ruthenium oxide, cernox, silicon diodes, platinum, thermocouple and RhFe. With constant voltage mode, it enables accurate temperature measurement using negative temperature sensors down to below 250 mK." .
SCR:020364 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_P80" ;
rdfs:label "Oxford |Instruments P 80 Plasma Etcher" ;
definition: "PlasmaPro 800 offers a flexible solution for Plasma Enhanced Chemical Vapour Deposition (PECVD) processes on large wafer batches and 300mm wafers, in a compact footprint, open-loading system. The large wafer platen allows for production scale batch processing and 300mm wafer handling." .
SCR:020366 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BIO" ;
rdfs:label "Oxford |MFP-3D-BIO AFM" ;
definition: "Integrates AFM and optical microscopy for bioscience research. Bio AFM that uses AFM imaging resolution, force measurement performance, and application versatility while integrating optical techniques." .
SCR:020367 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Origin_plus" ;
rdfs:label "Oxford |MFP-3D Origin+ AFM" ;
definition: "Features same core performance as MFP 3D Origin but includes support for complete range of innovative MFP 3D accessories." .
SCR:020368 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Nanonis_Tramea" ;
rdfs:label "Oxford |Nanonis Tramea Measurement System" ;
definition: "Measurement system used for quantum transport measurements. In conjunction with cryogenic research tools, it offers multi channel measurements to for quantum technologies." .
SCR:020369 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Origin" ;
rdfs:label "Oxford |MFP-3D Origin AFM" ;
definition: "Features Asylum Research performance and quality and offers high resolution imaging, supports large samples, most imaging modes, and many accessories." .
SCR:020370 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_OmniProbe_400" ;
rdfs:label "Oxford |OmniProbe 400 Electron Microscope" ;
definition: "Ninth generation of nanomanipulator, OmniProbe 400 uses piezo actuation for nanoscale positioning. Nanomanipulator with high resolution and high throughput applications." .
SCR:020371 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_100_Cobra" ;
rdfs:label "Oxford |PlasmaPro 100 Cobra Plasma Technolgy" ;
definition: "PlasmaPro 100 Cobra ICP utilises high density plasma to achieve etching and deposition rates. Process modules offer uniformity, high throughput, high precision and low damage processes for wafer sizes up to 200mm." .
SCR:020372 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_100_ALE" ;
rdfs:label "Oxford |PlasmaPro 100 ALE Plasma Technology" ;
definition: "PlasmaPro 100 ALE delivers precise process control to create and manipulate thinner layers through specialised hardware including precise control of gas dose, repeatability of low power RF delivery, and switching enabled by fast PLC." .
SCR:020373 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_100_Estrelas" ;
rdfs:label "Oxford |PlasmaPro 100 Estrelas Plasma Technology" ;
definition: "Platform is designed to give total flexibility for Deep Silicon Etch applications. Serves diverse set of process requirements across Micro Electro Mechanical Systems and Advanced Packaging and Nanotechnology markets." .
SCR:020374 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_100_PECVD" ;
rdfs:label "Oxford |PlasmaPro 100 PECVD Plasma Technology" ;
definition: "PECVD process modules are designed to produce uniformity and high rate films, with control of film properties such as refractive index, stress, electrical characteristics and wet chemical etch rate." .
SCR:020375 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_100_ICPCVD" ;
rdfs:label "Oxford |PlasmaPro 100 ICPCVD Plasma Technolgy" ;
definition: "ICPCVD process module is designed to produce films at low growth temperatures, enabled through high density remote plasmas that achieves film quality with low substrate damage." .
SCR:020376 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_100_RIE" ;
rdfs:label "Oxford |PlasmaPro 100 RIE Plasma Technology" ;
definition: "PlasmaPro 100 RIE modules deliver anisotropic dry etching. Being compatible with all wafer sizes up to 200mm, it has rapid change between wafer size, uniformity, high throughput and high precision processes, in situ chamber cleaning and end pointing, and wide temperature range electrode, from 150 degrees C to 400 degrees C." .
SCR:020377 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_80_ICP" ;
rdfs:label "Oxford |PlasmaPro 80 ICP Plasma Technology" ;
definition: "PlasmaPro 80 ICP is compact, small footprint system offering ICP etch solutions with open loading. Open load design allows fast wafer loading and unloading, ideal for research, prototyping and low volume production. It enables high performance processes using optimised electrode cooling and substrate temperature control." .
SCR:020378 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_80_ICPCVD" ;
rdfs:label "Oxford |PlasmaPro 80 ICPCVD Plasma Technology" ;
definition: "PlasmaPro 80 is compact, small footprint system offering etch and deposition solutions with open loading. Open load design allows fast wafer loading and unloading, ideal for research, prototyping and low volume production. It enables high performance processes using optimised electrode cooling and substrate temperature control." .
SCR:020379 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_800_PECVD" ;
rdfs:label "Oxford |PlasmaPro 800 PECVD Plasma Technology" ;
definition: "PlasmaPro 800 offers solution for Plasma Enhanced Chemical Vapour Deposition processes on large wafer batches and 300mm wafers, in compact footprint, open loading system. Large wafer platen allows for production scale batch processing and 300mm wafer handling." .
SCR:020380 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_80_PECVD" ;
rdfs:label "Oxford |PlasmaPro 80 PECVD Plasma Technology" ;
definition: "PlasmaPro 80 is compact, small footprint system offering etch and deposition solutions with open loading. Open load design allows fast wafer loading and unloading, ideal for research, prototyping and low volume production. It enables high performance processes using optimised electrode cooling and substrate temperature control." .
SCR:020381 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_80_RIE" ;
rdfs:label "Oxford |PlasmaPro 80 RIE Plasma Technology" ;
definition: "PlasmaPro 80 reactive ion etch is compact, small footprint system offering etch and deposition solutions with open loading. Open load design allows fast wafer loading and unloading, ideal for research, prototyping and low volume production. It enables high performance processes using optimised electrode cooling and substrate temperature control." .
SCR:020382 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SpectromagPT" ;
rdfs:label "Oxford |SpectromagPT Superconducting Magnet System" ;
definition: "Split pair, horizontal field magneto optical Cryofree superconducting magnet system. It provides optical access to sample in variable magnetic field and low temperature environment." .
SCR:020383 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Proteox" ;
rdfs:label "Oxford |Proteox Dilution Refrigerator" ;
definition: "Self supporting Secondary Insert that enhances adaptability, enabling rapid exchange of full experimental setups for multi user, multi experiment system. Upgradeable Secondary Inserts are cross compatible and transferrable between ProteoxTM family systems. Has large experimental volume and abundant line of sight access." .
SCR:020384 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_100_Nano" ;
rdfs:label "Oxford |PlasmaPro 100 Nano Plasma Technology" ;
definition: "Chemical Vapour Deposition and PECVD tools for growth of 1D and 2D nanomaterials and heterostructures. PlasmaPro 100 Nano delivers performance growth of nanomaterials with in situ catalyst activation and process control, with flexible temperatures up to 1,200 degrees C." .
SCR:020385 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TeslatronPT" ;
rdfs:label "Oxford |TeslatronPT Superconducting Magnet System" ;
definition: "Integrated Cryofree® superconducting magnet system with variable temperature inserts. Has standard magnetic fields up to 14 T in compact geometry, integrated variable temperature insert providing sample temperatures between 1.5 K and 300 K, and range of high performance sample rods with height adjustment and rotation options." .
SCR:020386 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TritonXL" ;
rdfs:label "Oxford |TritonXL Dilution Refrigerator" ;
definition: "TritonXL is used for research applications where sample temperatures below 5 mK is required, for integrating larger numbers of signal lines or very high magnetic fields. Has two integrated 1.5 W pulse tube coolers, decoupled with flexible braids and bellows to minimize vibrations." .
SCR:020387 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Oxford_PlasmaPro_1000" ;
rdfs:label "Oxford |PlasmaPro 1000 Stratum Plasma Technology" ;
NIFRID:synonym "Oxford PlasmaPro 1000 Stratum" ;
definition: "Maximised large area etching and deposition production solutions available in load lock or cluster configurations with up to 3 chambers and vacuum load lock as standard with cluster capability options." .
SCR:020388 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultim_Extreme" ;
rdfs:label "Oxford |Ultim Extreme Electron Microscopy" ;
definition: "Ultra high resolution FEG SEM application and delivers solutions beyond micro and nano analysis. It uses radical geometry for both imaging and EDS performance in ultra high resolution FEG SEMs while working at low kV and short working distance, with EDS resolution that approaches that of SEM." .
SCR:020390 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Symmetry" ;
rdfs:label "Oxford |Symmetry Electron Microscopy" ;
definition: "Symmetry uses customised CMOS sensor to unlock combination of speed, sensitivity and diffraction pattern detail." .
SCR:020393 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7000" ;
rdfs:label "Perkin Elmer | 7000 Automated Confocal Microscope" ;
definition: "Optima 7000 DV brings advanced technology to laboratories requiring flexibility and excellent analytical performance for varied and moderate sample loads.Totally eliminating peak search algorithms, the UV sensitive, backside illuminated CCD array detector allows you to collect a complete analyte spectrum at speeds that far exceed competitive systems.Automatic dual viewing ensures the lowest detection limits and the widest working ranges." .
SCR:020394 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Chemagic 360" ;
rdfs:label "Perkin Elmer | Chemagic 360 Genetic isolation Workstation" ;
definition: "Nucleic Acid Extractor for Medium to High Throughput. Based on our patented chemagen magnetic bead technology the chemagic 360 instrument represents the best solution for nucleic acid isolation in a huge variety of research market segments including but not limited to Biobanking/Human Genetics, HLA Typing, Virus and Bacteria Detection. Experience the revolutionary compact benchtop design of our newly developed chemagic 360 Nucleic Acid Extractor. Based on the well-established chemagen Technology, the system offers a flexible solution for different sample processing and throughput needs. Configurable with three kinds of chemagic Rod Heads (see table below) the system can process sample volumes from 10 �l 10 ml." .
SCR:020395 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EP3" ;
rdfs:label "Perkin Elmer | EP3 Pipetting System" ;
definition: "Evolution Precision Pipetting System as flexible automated liquid handler for both low and high throughput microplate applications using 96 or 384 channel disposable tip dispense heads. EP3 can be configured for many common applications." .
SCR:020396 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_easiGlow" ;
rdfs:label "SelectScience | PELCO easiGlow Glow Discharge Cleaning System" ;
definition: "System uses automated and quick cycle with fully selectable parameters.Microprocessor controlled system also offers full manual control for all parameters and an advanced protocol programming feature for custom designed glow discharge applications. Parameters and protocols can be stored to facilitate consistent glow discharge results. Open the shipping box, plug it in, and you can start. The PELCO easiGlow Glow Discharge Cleaning System is a compact, quick and easy to use standalone system. It is primarily designed for cleaning TEM grids and hydrophilization of TEM carbon support films, which have the tendency to be hydrophobic. A glow discharge treatment with air will make a carbon film surface negatively charged (hydrophilic) which allows aqueous solutions to spread easily." .
SCR:020398 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_800_RIE" ;
rdfs:label "Oxford |PlasmaPro 800 RIE Plasma Technology" ;
definition: "PlasmaPro 800 offers solution for reactive ion etching processes on large wafer batches and 300mm wafers, in compact footprint, open loading system. Large wafer platen allows for production scale batch processing and 300mm wafer handling." .
SCR:020399 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Nexion 300Q" ;
rdfs:label "Perkin Elmer | Nexion 300Q Inductively-Coupled Plasma-Optical Emission Mass Spectrometer" ;
definition: "NexION 300Q Inductively-Coupled Plasma-Optical Emission Mass Spectrometer the best solution for analyses requiring accepted interference-correction capabilities. This configuration does not include cell technology but it can be field upgraded to include a Universal Cell at any time. The NexION 300Q is best suited for markets such as geochemical analysis. The PerkinElmer NexION 300 offers three modes of operation (Standard, Collision and Reaction) and can be quickly switched from one mode to another. The PerkinElmer NexION is the only ICP-MS that lets you maximize productivity without compromising sensitivity or performance. For the first time ever, a single ICP-MS instrument offers both the simplicity and of a collision cell and the detection limits of a true reaction cell." .
SCR:020400 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Scanarray Express" ;
rdfs:label "Perkin Elmer | Scanarray Microarray Scanner" ;
definition: "Packard ScanArray Express Line of Microarray Scanners from PerkinElmer Life Sciences with easy to use software, breakthrough technology and uncompromising data quality. With the introduction of the first commercial microarray scanner, originally by GSI Lumonics, the ScanArray line offered the only upgradeable 2-wavelength scanner, the only scanning instrument to have patents that covered acquisition, barcoding and automation, and today is the brand most often found in microarray labs worldwide. Only the ScanArray family can visualize the spotting process on each array before hybridization. Without the use of special reagents or any change to your protocol, if salts are used in the spotting buffer, the user simply scans the array using the red laser and a PerkinElmer standard equipment filter. ScanArray Express and Express HT scanners equipped with PerkinElmer's blue laser readily display immobilized DNA on microarrays. Using ethidium bromide, which is easily washed off, there is no fluorophore cross-talk or interference with hybridization." .
SCR:020401 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MultiProbe II" ;
rdfs:label "Perkin Elmer | MultiProbe II Robotic Liquid Handler" ;
definition: "8 tip robotic liquid handling system designed for the efficient automation of sample preparation procedures utilized in Drug Discovery and Molecular Biology. The MultiPROBE II HT system is controlled by WinPREP applications software, a package which operates under Windows NT operating system. This easy-to-use graphical user interface allows programming of even complex liquid handling protocols." .
SCR:020402 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Analyte" ;
rdfs:label "Teledyne | Photon Machines Analyte Excite Laser Ablation Source Analyte" ;
definition: "Laser ablation system that offers excimer technology at 193 nm with all the analytical capabilities you require, and a price you can afford. The Excite delivers finely controlled, homogenizer-flat ablations with high sensitivity and split second response. Fire-on-the-fly lasing that is synchronized to the stage motion, combined with fast washout ablation cells, make precision depth profiling of spots, lines and areas possible and enables high spatial resolution elemental mapping. The Excite is equipped with a high definition, color GigE camera on a high magnification, optical zoom, video-microscope capable of resolving 2 �m features. Transmitted, reflective and ring illumination, cross polarizers plus software selectable camera settings give the user enhanced viewing capabilities. The combination of ultra-short pulse length and 193 nm wavelength is unsurpassed in coupling efficiency. The Excite ablates all materials, from opaque to highly transparent, including delicate powders, hard quartz and resilient carbonates with depth penetration in the tens of nanometers per shot. The beam energy profile is homogenized to ensure uniform ablations across the entire range of spot sizes and on a wide range of materials." .
SCR:020403 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Pippin Prep" ;
rdfs:label "Sage Science |Pippin Prep" ;
definition: "Facilitates library construction system for NGS platforms, and is recommended by Illumina and Ion Torrent for certain workflows. The platform features the ability to collect narrow and even fragment distributions, as well as the flexibility to collect wide ranges of fragments with minimal effort. Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer. Up to 5 samples per gel cassette may be run, with no possibility of cross contamination." .
SCR:020404 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Milo" ;
rdfs:label "Bio-Techne | Protein Milo Single Cell Western Milo" ;
definition: "Milo is Single-Cell Western platform. Milo measures protein expression in thousands of single cells in a single run so you can profile heterogeneity in your samples. Just load your cell suspension and the scWest chip captures ~1,000 single-cells. Milo then does a fast, 1 minute SDS-PAGE separation on each single-cell lysate on-chip. Then just probe with your favorite conventional Western antibodies to measure ~12 proteins per cell using a variety of multiplexing strategies. Use Single-Cell Westerns to unlock the single-cell proteome and measure more of the proteome than is possible with any other single-cell technique." .
SCR:020405 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Perkin Elmer | UltraView ERS" ;
definition: "PerkinElmer UltraVIEW system (PerkinElmer Life Sciences Inc., MA, USA) is a Yokogawa (Yokogawa Corp. Japan) Nipkow Spinning Disk Confocal System. It uses a spinning disk with multiple pinholes to achieve confocality (e.g. the rejection of out-of-focus light). Emission light from the sample passes through the pinholes to generate a confocal image of the sample that can be detected with an EMCCD (Electron Multiplification Charge-Coupled Device) camera. Spinning disk confocal systems have 2 main advantages over conventional Laser Scanning Confocal Microscopes (LSCM): Higher imaging speed: up to 360frames/sec compared to 0.5-1 frames per second in a LSC and Lower photo-toxicity: around 5 times less than a LSCM, probably due to the fact that the system splits the laser light into thousands of minibeams." .
SCR:020406 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PeggySue" ;
rdfs:label "Bio-Techne | Protein PeggySue Protein Analyzer" ;
definition: "Peggy Sue lets you separate and analyze proteins by size or charge from 2-440 kDa either by immunoassay or total protein." .
SCR:020408 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Tribute" ;
rdfs:label "GYROS PROTEIN Technologies | Tribute" ;
definition: "Protein Technologies peptide synthesizers are designed to cover synthesis scales from 0.005 to 200 mmol." .
SCR:020410 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QIA Cube" ;
rdfs:label "Qiagen | QIAcube Connect" ;
definition: """For fully automated nucleic acid extraction with QIAGEN's spin column kits.Automates over 80 QIAGEN kits with over 140 standard protocols for most frequently used applications
Optional protocol customization expands use to virtually any application.Allows automated DNA, RNA and protein sample processing.Eliminates manual processing steps.Generates standardized results .Enables quick response times and remote run monitoring through provided tablet.QIAcube Connect is redefining benefits of automating sample processing. With advanced digital capabilities and connectivity QIAcube Connect with its accessories and consumables allows research labs to fully automate and track their well known QIAGEN spin column extraction and purification protocols at push of button..QIAcube Connect offers augmented user interface that provides new dimension of utility. Researchers can stay connected to their instrument through built in screen and also remotely with tablet included, containing pre installed QIAcube Connect App, enabling quick response times and ability to monitor runs while away from QIAcube Connect.""" .
SCR:020411 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Phillips_CM12" ;
rdfs:label "Philips | CM12 Transmission Electron Microscope" ;
definition: "General purpose analytical transmission/scanning transmission electron microscope (TEM/STEM). It was used to visualize the structure, chemical composition, and arrangement of atoms in thin, extraordinary small specimens." .
SCR:020412 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_M48" ;
rdfs:label "Qiagen | BioRobot M48" ;
definition: "Automated nucleic acid purification workstation with liquid handling capabilities that purifies the DNA via magnetic separation within the pipette tips. It's pipettor head contains 6 syringe pumps that dispense 25-1000 microliters at a time." .
SCR:020415 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NEP2320" ;
rdfs:label "Pressure BioSciences | NEP2320 Barocycler" ;
definition: "Barocycler uses the Pressure Cycling Technology (PCT) platform based on repeated cycles of hydrostatic pressure between ambient (14.7 psi) and ultra-high levels (up to 45,000 psi). These rapid changes in pressure are used to control biomolecular interactions for applications such as accelerated proteolytic digestion and improved extraction of cellular components, including proteins and lipids. The PCT platform allows for a high degree of safety, speed, reproducibility, and in modern sample preparation protocols. Advantages of the PCT technology include:" .
SCR:020416 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EZ1 Advanced XL" ;
rdfs:label "Qiagen | EZ1 Advanced XL" ;
definition: """For automated purification of nucleic acids from up to 14 human, forensic, or molecular diagnostics samples High quality genomic DNA and RNA from range of sample materials Viral RNA DNA and bacterial DNA from biomedical samples Throughput of up to 14 samples per run Effortless data management with full traceability
UV lamp to help minimize contamination risk The EZ1 Advanced XL performs automated nucleic acid purification for wide range of sample types relevant for molecular diagnostics, human identity testing, forensics, biomedical research, and gene expression analysis.""" .
SCR:020419 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QIACube HT" ;
rdfs:label "Qiagen | QIAcube HT" ;
definition: """Instrument for automated mid to high throughput nucleic acid purification in 96 well format DNA, RNA and miRNA extraction from virtually any sample type.Mid to high throughput solution with dedicated purification kits saves costs and time.User friendly software allows for easy data management and documentationdesign features increase safety and minimize cross contamination.Convenient, flexible and easy to use instrument with small footprint.QIAcube HT enables automated mid to high throughput nucleic acid purification in 96 well format using silica membrane technology. variety of QIAcube HT Purification Kits lets users quickly and easily purify DNA, RNA and miRNA from almost any type of sample including cells, tissues and stool samples, as well as from bacteria and viruses in animal samples. Automated protocols and dedicated accessories and consumables increase reliability and and save valuable time. system provides same high quality results as other trusted QIAGEN purification technologies.
""" .
SCR:020422 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rainin | Classic Pipette PR-1000" ;
definition: "Rainin Classic manual single-channel pipette, 100-1000 uL, uses universal-fit tips. Finger hook, light springs, silicone shock absorber, accurate, precise, economical (PR-1000)" .
SCR:020423 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_E4XLS Electronic Multipipette" ;
rdfs:label "Rainin | E4 Electronic Pipette, LTS E4-20XLS+" ;
definition: "E4 XLS electronic single-channel pipette, 2-20 uL, uses LTS LiteTouch tips." .
SCR:020424 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RDT_1000" ;
rdfs:label "RainDance | RDT 1000 Analyzer" ;
definition: "DNA Sequence Analyzer RDT 1000 incorporates RainStorm microdroplet based technology to amplify hundreds to thousands of genomic loci with high specificity and uniformity. It leverages the sensitivity and specificity of polymerase chain reaction (PCR) methodology.Allows to isolate specific regions of the genome for subsequent sequencing." .
SCR:020425 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Q Exactve HF" ;
rdfs:label "Thermo Fisher | Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer Q Exactive" ;
definition: "Identifies and quantifies proteins, peptides, lipids, glycans and small molecules. Combines segmented quadrupole for high performance precursor ion selection with high resolution, accurate mass, ultra high field Orbitrap mass analyzer to deliver combination of scan speed, resolving power, mass accuracy, spectral quality and sensitivity." .
SCR:020427 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MM400" ;
rdfs:label "Retsch | mixer mill MM 400" ;
definition: "Compact versatile bench top unit, which has been developed specially for dry, wet and cryogenic grinding of small amounts of sample.It can mix and homogenize powders and suspensions in only a few seconds. It is also perfectly suitable for the disruption of biological cells as well as for DNA/RNA and protein extraction. With its high performance and great flexibility" .
SCR:020428 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Tissue Lyzer LT" ;
rdfs:label "Qiagen | Tissue Lyzer LT" ;
definition: "RNA/DNA purification small bead mill for disruption of up to 12 samples at the same time. Disruption and homogenization occurs through high-speed shaking of samples in 2 ml microcentrifuge tubes with stainless steel or glass beads. The TissueLyser LT must be used in combination with the coolable TissueLyser LT Adapter, which holds tubes during the disruption process." .
SCR:020429 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BioSAXS-2000 Nano" ;
rdfs:label "Rigaku | BioSAXS-2000" ;
definition: "Small angle x ray scattering SAXS krakty camera system. Small angle scattering of macromolecules." .
SCR:020430 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Max-Flux" ;
rdfs:label "Rigaku | Confocal Max-Flux X-Ray Optic" ;
definition: "Custom focusing CMF X ray optics for X ray diffraction." .
SCR:020431 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Single Channel Pipette Lite PR-2" ;
rdfs:label "Rainin | Classic Pipette PR-2" ;
definition: "Manual single-channel pipette, 0.1-2 ?L, uses universal-fit tips. Finger hook, light springs, silicone shock absorber, accurate, precise, economical (PR-2)" .
SCR:020432 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DSC8231" ;
rdfs:label "Rigaku | DSC8231 Differential Scanning Calorimeter" ;
definition: "Quantifies energy changes in reactions such as melting, transition, crystallization and glass transition temperature." .
SCR:020433 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Automate II" ;
rdfs:label "Rigaku | AutoMATE II" ;
definition: "Micro area residual stress measurement system that helps detect residual stress and lifetime of products." .
SCR:020434 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DSCvesta" ;
rdfs:label "Rigaku | DSCvesta calorimeter" ;
definition: "Differential scanning calorimeter. Used to characterize heat gain or loss associated with phase transitions." .
SCR:020435 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EIGER R" ;
rdfs:label "Rigaku | EIGER R detector" ;
definition: "High resolution photon counting x ray detector from Dectris. X ray detector for single crystal X ray diffraction.Small Molecule Crystallography Product." .
SCR:020436 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EUV" ;
rdfs:label "Rigaku | EUV Optics" ;
definition: "Multilayer optics for extreme UV lithography patterning of semiconductor wafers. High efficiency multilayer optics for 13.5 nm, 6.x nm wavelengths." .
SCR:020437 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_KT-100S" ;
rdfs:label "Rigaku | KT-100S Handheld LIBS" ;
definition: "Handheld LIBS metal alloy analyzer for metal grade identification.Used for for fast and accurate metal grade identification." .
SCR:020438 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FR-X" ;
rdfs:label "Rigaku | FR-X generator" ;
definition: "High intensity microfocus rotating anode X-ray generator." .
SCR:020439 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AZX 400" ;
rdfs:label "Rigaku | AZX 400" ;
definition: "Sequential wavelength dispersive XRF spectrometer for large samples film thickness and composition measurements on large and heavy samples, wafers, and media disks." .
SCR:020440 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MFM310" ;
rdfs:label "Rigaku | MFM310" ;
definition: "X-ray metrology tool to perform high throughput measurements on product and blanket wafers ranging from ultrathin single layer films to multilayer stacks." .
SCR:020441 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Max-Flux XRD" ;
rdfs:label "Rigaku | Max-Flux XRD monochromator" ;
definition: "Parallel beam graded multilayer monochromator for XRD. Maximizes intensity for parallel X ray beam and high resolution diffraction." .
SCR:020442 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CR-1012" ;
rdfs:label "Rigaku | CR-1012 scanner" ;
definition: "Computed radiography mobile imaging plate scanner." .
SCR:020443 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6000HE" ;
rdfs:label "Rigaku | HyPix-6000HE detector" ;
definition: "Hybrid photon counting x ray detector large area. Hybrid Photon Counting detector for single crystal X ray diffraction." .
SCR:020444 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Micro-Z" ;
rdfs:label "Rigaku | Micro-Z ULS analyzer" ;
definition: "Wavelenght Dispersive X-ray Fluorescence Sulfur analyzer. Measures ultra low sulfur ULS in petroleum fuels by ASTM D2622 10 and background intensity." .
SCR:020446 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Max-Flux TXRF" ;
rdfs:label "Rigaku | Max-Flux TXRF Optic monochromator" ;
definition: "Focusing graded multilayer monochromator for TXRF. Maximizes intensity on sample within total external reflection angle for TXRF." .
SCR:020447 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MicroMax-003" ;
rdfs:label "Rigaku | MicroMax-003" ;
definition: "Microfocus high intensity sealed tube X ray source. X ray source component for X ray diffraction and crystallography." .
SCR:020448 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HyPix-3000" ;
rdfs:label "Rigaku | HyPix-3000 detector" ;
definition: "Compact Photon Counting X-ray detector.Two dimensional semiconductor X-ray detector." .
SCR:020449 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Mini-Z" ;
rdfs:label "Rigaku | Mini-Z analyzer" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10,2024. Benchtop single element wavelength dispersive XRF analyzer with high precision and high sensitivity elemental analysis." .
SCR:020450 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Mini-Z_Sulfur" ;
rdfs:label "Rigaku | Mini-Z Sulfur analyzer" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10,2024. Wavelength dispersive x ray fluorescence sulfur analyzer that measures ultra low sulfur in petroleum fuels ULSD." .
SCR:020451 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MiniFlex" ;
rdfs:label "Rigaku | MiniFlex analyzer" ;
definition: "Benchtop powder x ray diffraction instrument that gives qualitative and quantitative phase analysis of polycrystalline materials." .
SCR:020452 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_nano3DX" ;
rdfs:label "Rigaku | nano3DX microscope" ;
definition: "X ray microscope with microtomography of large samples at high resolution." .
SCR:020453 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NANOPIX Mini" ;
rdfs:label "Rigaku | NANOPIX Mini analyzer" ;
definition: "Benchtop small angle X-ray scattering instrument designed for nano structure analyses.Non-destructive measurement of particle size and size distribution." .
SCR:020454 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NANOPIX" ;
rdfs:label "Rigaku | NANOPIX analyzer" ;
definition: "Small angle and wide angle x ray scattering instrument Advanced SAXS WAXS for nanostructure analysis." .
SCR:020455 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Onyx" ;
rdfs:label "Rigaku | Onyx 3000" ;
definition: "Hybrid XRF and optical metrology fab tool. Used for thickness, composition, defect identification and sizing of films and structures on blanket and patterned wafers." .
SCR:020456 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NanoMAX" ;
rdfs:label "Rigaku | NanoMAX" ;
definition: "Modernized 2D Kratky system that eliminates data corrections required of traditional systems." .
SCR:020457 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ovonyx" ;
rdfs:label "Rigaku | Ovonyx analyzer" ;
definition: "Light element analyzer for laboratory XRF instruments.Enables light element analysis in laboratory XRF Instruments." .
SCR:020458 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MultiMax-9" ;
rdfs:label "Rigaku | MultiMax-9 generator" ;
definition: "Multi-purpose rotating anode X-ray generator. X-ray source component for X-ray diffraction and crystallography." .
SCR:020459 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Progenty ResQ FLX" ;
rdfs:label "Rigaku | Progeny ResQ FLX Raman analyzer" ;
definition: "Advanced narcotics analyzer. Identifies narcotics, including opiods and fentanyl analysis, in seconds." .
SCR:020460 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PILATUS3 R" ;
rdfs:label "Rigaku | PILATUS3 R Detector" ;
definition: "Photon counting X-ray detectors from Dectris.Hybrid pixel array detector HPAD for X ray crystallography." .
SCR:020461 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_R-Axis_HCT" ;
rdfs:label "Rigaku | R-Axis HTC X-Ray detector" ;
definition: "R-AXIS HTC was designed with speed in mind. High throughput crystallography requires an area detector that can measure accurate data rapidly. The R-AXIS HTC combines the data quality that is achieved with an imaging plate area detector with data acquisition speed that approaches that of an electronic detector. It combines three large active area imaging plates with minimal dead-time and a wide dynamic range, making it best for collecting fast, accurate diffraction data from the widest ranges of samples in the home laboratory. High dynamic range is achieved through use of a dual photomultiplier configuration that allows high intensities to be measured by a second, attenuated photomultiplier." .
SCR:020462 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Progeny ResQ" ;
rdfs:label "Rigaku | Progeny ResQ Raman analyzer" ;
definition: "Original 1064 NM handheld raman for chemical threat analysis. Used for rapid chemical identification of unknown substances." .
SCR:020463 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Nanohunter II" ;
rdfs:label "Rigaku | NANOHUNTER II spectrometer" ;
definition: "Next generation benchtop total reflection X ray fluorescence TXRF spectrometer. Rapid trace elemental analysis and thin film characterization." .
SCR:020464 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RF-200SPS" ;
rdfs:label "Rigaku | RF-200SPS generator" ;
definition: "Small, light weight non destructive testing X ray generator. Performs inspections by X ray radiography in narrow or high places." .
SCR:020465 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_R-Axis_IV" ;
rdfs:label "Rigaku | R-Axis IV X-Ray detector" ;
definition: "R- AXIS IV is a two- dimensional X- ray detector which collects diffracted X- ray data used for small or macromolecular crystal structure analysis. A complete X-ray detector system consists of the X- ray generator, optics, R-AXIS IV main body, R-AXIS IV controller, and control/data processing software (com-puter)." .
SCR:020466 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RF-300EGM2" ;
rdfs:label "Rigaku | RF-300EGM2" ;
definition: "300 kV microcomputerized directional industrial X ray system" .
SCR:020467 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RF-200EGM2" ;
rdfs:label "Rigaku | RF-200EGM2" ;
definition: "200 kV microcomputerized directional industrial X ray system." .
SCR:020468 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RV-5020" ;
rdfs:label "Rigaku | RV-5020" ;
definition: "Foreign object X ray inspection instrument." .
SCR:020469 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ResQ CQL" ;
rdfs:label "Rigaku | ResQ CQL Raman detector" ;
definition: "New 1064 NM handheld raman analyzer for explosives and narcotics detection fast chemical detection" .
SCR:020470 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RV-5030B" ;
rdfs:label "Rigaku | RV-5030B" ;
definition: "Foreign object X ray inspection instrument. Metals checks in shoes, bags, general merchandise and apparel products by X ray." .
SCR:020471 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Progeny" ;
rdfs:label "Rigaku | Progeny Handheld Raman spectrometer" ;
definition: "Advanced 1064 NM handheld raman spectrometer for raw material identification, material verification and authentication." .
SCR:020472 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Simultix 15" ;
rdfs:label "Rigaku | Simultix 15 spectrometer" ;
definition: "Tube above simultaneous wavelength dispersive X-ray fluorescence spectrometer.Used for high-throughput elemental analysis of solids, powders and alloys." .
SCR:020473 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SmartLab" ;
rdfs:label "Rigaku | SmartLab diffractometer" ;
definition: "Automated multipurpose X-Ray diffractometer with guidance software. Power diffraction, thin film metrology, SAXS, in plane scattering, and operando measurements." .
SCR:020474 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SmartSite RS" ;
rdfs:label "Rigaku | SmartSite RS analyzer" ;
definition: "Non destructive portable stress analyzer for field and indoor use." .
SCR:020475 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SmartLab_SE" ;
rdfs:label "Rigaku | SmartLab SE" ;
definition: "Multipurpose X-ray diffraction system with built in intelligent guidance that includes powder diffraction, thin film diffraction, SAXS, pole figure, and residual stress and non ambient experiments." .
SCR:020476 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TG-DTA" ;
rdfs:label "Rigaku | TG-DTA/HUM Thermal Analyzer" ;
definition: "Humidity Controlled TG-DTA.Compact humidity generator HUM 1 is connected to TG DTA for measurements under constant relative humidity water vapor atmosphere. Measures weight changes and endothermic or exothermic reactions." .
SCR:020477 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RV-5020DV" ;
rdfs:label "Rigaku | RV-5020DV" ;
definition: "Foreign object X ray inspection instrument." .
SCR:020478 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TXRF 3760" ;
rdfs:label "Rigaku | TXRF 3760" ;
definition: "Surface contamination metrology. Used to measure elemental contamination at discrete points or with full wafer maps." .
SCR:020479 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TG-DTA8122" ;
rdfs:label "Rigaku | STA8122 Thermal Analyzer" ;
definition: "Simultaneous Thermal Analyzer.Measures weight changes and endothermic or exothermic reaction." .
SCR:020480 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TMA/HUM" ;
rdfs:label "Rigaku | TMA/HUM Thermal Analyzer" ;
definition: "Humidity controlled TMA.Measurement of mechanical property change with respect to temperature and humidity." .
SCR:020481 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TXRF310 Fab" ;
rdfs:label "Rigaku | TXRF310Fab" ;
definition: "Wafer surface contamination metrology by TXRF with measurement of trace elemental surface contamination." .
SCR:020482 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultima IV" ;
rdfs:label "Rigaku | Ultima IV diffractometer" ;
definition: "Automated multipurpose diffractometer. Powder diffraction, thin film diffraction, SAXS, pole figure, and residual stress and in plane experiments." .
SCR:020483 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Supermini200" ;
rdfs:label "Rigaku | Supermini200 spectrometer" ;
definition: "High power benchtop sequential WDXRF spectrometer.Used for elemental analysis of solids, liquids, powders, alloys and thin films." .
SCR:020484 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TXRF-V310" ;
rdfs:label "Rigaku | TXRF-V310" ;
definition: "Wafer surface contamination metrology by VPD TXRF with measurement of ultra trace elemental surface contamination." .
SCR:020485 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_UltraX 18" ;
rdfs:label "Rigaku | UltraX 18 generator" ;
definition: "18 kW rotating anode X-ray generator. A high powered X-ray source that can produce point or line focus X-ray beams." .
SCR:020486 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TMA8311" ;
rdfs:label "Rigaku | TMA8311 Thermal Analyzer" ;
definition: "Thermomechanical analyzer. Measurement of a mechanical property change with respect to temperature." .
SCR:020487 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_WaferX 310" ;
rdfs:label "Rigaku | WaferX 310 spectrometer" ;
definition: "In line, simultaneous WDXRF spectrometer film thickness and composition measurements on blanket wafers." .
SCR:020488 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VariMax DW" ;
rdfs:label "Rigaku | VariMax DW" ;
definition: "Dual wavelength Confocal Max Flux CMF optics for single crystal X ray diffraction. Focuses and monochromatizes two different X ray wavelengths for single crystal X ray diffraction applications." .
SCR:020489 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_WDA-3650" ;
rdfs:label "Rigaku | WDA-3650 spectrometer" ;
definition: "Simultaneous WDXRF spectrometer film thickness and composition measurements on wafers and media disks." .
SCR:020490 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TXRF 3800e" ;
rdfs:label "Rigaku | TXRF 3800e" ;
definition: "Surface contamination metrology that measures elemental contamination at discrete points or with full wafer maps." .
SCR:020491 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Mini II" ;
rdfs:label "Rigaku | XtaLAB Mini II diffractometer" ;
definition: "Benchtop single crystal x ray diffractometer." .
SCR:020492 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_X-Sight" ;
rdfs:label "Rigaku | Xsight Micron FC" ;
definition: "Compact 2D X ray camera for topography and imaging applications X ray and EUV detector." .
SCR:020493 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XtalCheck" ;
rdfs:label "Rigaku | XtalCheck diffractometer" ;
definition: "Automated in situ x ray crystallography that screens protein crystals on single crystal X ray diffractometer." .
SCR:020494 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XSight" ;
rdfs:label "Rigaku | XSight Micron LC" ;
definition: "Compact 2D X ray camera with micron and sub micron resolution for imaging." .
SCR:020495 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_zSX Primus III" ;
rdfs:label "Rigaku | ZSX Primus III spectrometer" ;
definition: "Tube above sequential WDXRF spectrometer with elemental analysis of solids, liquids, powders, alloys and thin films,from Oxygen fhrough Uranium." .
SCR:020496 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ZSX Primus 400" ;
rdfs:label "Rigaku | ZSX Primus 400 spectrometer" ;
definition: "Sequential WDXRF spectrometer for large samples with elemental analysis of solids, liquids, powders, alloys and thin films." .
SCR:020497 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ZSX Primus" ;
rdfs:label "Rigaku | ZSX Primus spectrometer" ;
definition: "Sequential WDXRF spectrometer with elemental analysis of solids, liquids, powders, alloys and thin films, from beryllium Be through uranium U" .
SCR:020498 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_F3" ;
rdfs:label "Thermo Fisher | CRS F3 Robot Arm and C500C Controller" ;
definition: "Thermo Scientific CRS F3 Robot Arm and C500C Controller is designed for light payload applications and provides an articulated robot arm with six degrees of freedom, plus a powerful, multitasking controller. The system sets a new standard for \"human-scale\" robots, delivering a combination of high speed, reliability, ease of use, and value. It dramatically increases walk-away time and reduces human error by automating container handling for a wide variety of instruments and devices. The F3 can carry payloads up to 3kg, enabling it to carry multiple containers at once. The arm of the system communicates with its external controller, sensors and other devices along a dedicated communication network, eliminating the masses of wires required by traditional robots. The F3 arm can store position data for up to eight weeks, even if the robot and controller are disconnected." .
SCR:020499 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Roche | Elecsys 2010 Immunoassay Analyzer" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. April 10,2024. Roche Diagnostics Elecsys 2010 has the power and efficiency to meet the needs of medium and large volume testing facilities. Roche Elecsys 2010, which is available in the form of sample disk or a rack handling system, can be operated in both continuous and random access modes. The throughput rate of this analyzer is 86 tests per hour and on-board capacity is of 15 tests. Elecsys 2010 disk and Elecsys 2010 rack holds 30 and 100 positions for samples respectively. With Roche Elecsys 2010 system at your workstation, you can attain benefits such as easy and trouble free operation, workflow flexibility, faster turnaround times, broad measuring ranges, and more." .
SCR:020500 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XPIN" ;
rdfs:label "Rigaku | xPIN X-Ray Detector" ;
definition: "PIN diode based X-ray detector.Applications ranging from alignment and testing of laboratory devices to long term precision monitoring of X-ray intensity." .
SCR:020501 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VariMAX" ;
rdfs:label "Rigaku | VariMax" ;
definition: "Confocal x ray optical assembly that focuses and monochromatizes X ray beam for single crystal X ray diffraction." .
SCR:020503 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ZSX Primus IV" ;
rdfs:label "Rigaku | ZSX Primus IV" ;
definition: "Tube above sequential WDXRF spectrometer with elemental analysis of solids, liquids, powders, alloys and thin films, from beryllium Be through uranium U" .
SCR:020505 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BluePippin" ;
rdfs:label "Sage Science | BluePippin system" ;
definition: "Used for DNA Size Selection for Next-Gen Sequencing, with Pulsed-Field (100bp � 50kb).BluePippin has the DNA capabilities of the Pippin Prep, plus the extra benefit of pulsed-field electrophoresis for resolving and collecting high molecular weight DNA. For long-range genomic applications, high-pass filtering allows users to collect all fragments above a size threshold set by the user. Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer. Up to 5 samples/gel cassette may be run, with no possibility of cross contamination." .
SCR:020506 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Magnalyzer" ;
rdfs:label "Roche | MagNA Lyser" ;
definition: "MagNA Lyser Instrument is a benchtop device that automatically disrupts cells or other biological materials. The instrument facilitates the production of a supernatant containing nucleic acids (NA) and proteins suitable for subsequent purifi cation, extraction or analysis. During a MagNA Lyser Instrument run, the rotor, which is fi lled with special tubes, rapidly oscillates." .
SCR:020509 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MCO-19AIC" ;
rdfs:label "Marshall Scientific | Sanyo MCO-19AIC UV CO2 Incubator" ;
definition: "Incubator features humidity and temperature control technology, which provides both stability control for cultures. The direct heat and air jacket system eliminate the inconvenient use of water in the incubator and provides heat from the door, side, and bottom of the unit. The Sanyo MCO-19AIC utilizes a dual detector infrared CO2 sensor, which is not affected by changes in humidity or temperature, maintains constant conditions via the microprocessor control, and automatically calibrates using room air temperature as reference. Also features Safe Cell UV contamination control system." .
SCR:020510 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LCMS_8030" ;
rdfs:label "Shimadzu | 8030 LC/MS mass spectrometer" ;
definition: "Shimadzu 8030 triple quadrupole mass spectrometer is for targeted quantitation applications." .
SCR:020511 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8040" ;
rdfs:label "Shimadzu | 8040 Triple Quadrupole Liquid Chromatograph Mass Spectrometer" ;
definition: "Spectrometer delivers scan speeds of up to 15,000 u/second with a 0.1 Dalton step width." .
SCR:020513 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VivaCT40" ;
rdfs:label "Scanco | VivaCT40 Microcomputed Tomography Scanner" ;
definition: "vivaCT 40 is a fast and flexible in-vivo microCT (micro-computed tomography) scanner for preclinical studies. The low X-ray dose allows serial measurements of individuals. Whole-body scans or scans from selected regions of mice can be made, while head and hind limbs of larger rodents can be scanned using beds supplied with the system. A range of beds for in-vivo use as well as specimen scans are supplied. ." .
SCR:020514 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2000" ;
rdfs:label "Siemens | 2000 Immunoassay System" ;
definition: "Immunoassay analyzer with a maximum throughput of 200 tests per hour. Immunoassay system is designed specifically for optimum efficiency and consolidation in medium- and high-volume laboratories. The IMMULITE 2000 software, and graphical user interface, offers streamlined information management, from remote test ordering to sophisticated analysis of results." .
SCR:020515 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8060" ;
rdfs:label "Shimadzu | LCMS-8060 Triple Quadrupole Liquid Chromatograph Mass Spectrometer" ;
definition: "LCMS-8060 is a mass spectrometry helping to transform LC/MS/MS data quality." .
SCR:020516 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Single Channel Pipette Lite PR-20" ;
rdfs:label "Rainin | Single Channel Pipette PR-20" ;
definition: "Rainin Classic manual single channel pipette, 2-20 uL, uses universal-fit tips. Finger hook, light springs, silicone shock absorber, accurate, precise, economical.." .
SCR:020517 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QTRAP_5500" ;
rdfs:label "SCIEX | QTRAP 5500 Mass Spectrometer" ;
definition: "QTRAP 5500 system Performs multiple reaction monitoring (MRM) for quantitation using this high-sensitivity triple quadrupole system. Identify, characterize, and quantitate metabolites more quickly and easily.Discover and quantitate targeted biomarkers. Enable high-sensitivity full-scan MS, MS/MS, and MS3 with high-selectivity from true triple quadrupole precursor ion (PI) and neutral loss (NL) scans." .
SCR:020518 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CSU10" ;
rdfs:label "Yokogawa | Solarmere CSU10 Fluorescence Confocal Spinning Disk Microscope" ;
definition: "Solarmere CSU10 Fluorescence Confocal Spinning Disk Microscope is a confocal microscopy that has enabled z-axis resolution of a thick specimen by employing pin-point illumination. Now, as fast as 360 frames/sec. scanning speed and high S/N design of Yokogawa Model CSU10 enables direct viewing of clear-cut confocal images of fluorescent specimens in real time at its eyepiece. Discontinued." .
SCR:020519 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_100SE" ;
rdfs:label "Sorvall | 100SE Centrifuge" ;
definition: "Sorvall Discovery 100SE floor ultra-centrifuge." .
SCR:020520 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Legend RT" ;
rdfs:label "Sorvall | Legend RT Centrifuge" ;
definition: "Legend RT is a general-purpose tabletop centrifuge for biotechnological and pharmaceutic research. .The user-friendly \"QUIKset\" control panel permits easy selection of speed, RCF value, run time and deceleration profile, as well as temperature of the Legend RT. You can switch from speed to RCF display and vice versa, with a touch of a button and even during a run" .
SCR:020522 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SY3200",
"SCR_020528" ;
rdfs:label "Sony biotechnology | SY3200 Cell Sorter" ;
definition: "SY3200 cell sorter platform is expandable to a dual system layout, effectively enabling two systems in one." .
SCR:020523 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RC-6" ;
rdfs:label "Sorvall | RC-6 Centrifuge" ;
definition: "Thermo Scientific Sorvall RC 6 Plus Centrifuge has been discontinued. Please consider our recommended replacement: Thermo Scientific Sorvall LYNX Superspeed Centrifuge Series." .
SCR:020524 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6000" ;
rdfs:label "Sorvall | MT-RMC 6000 Ultra Microtome" ;
definition: "SORVALL MT-6000 improves the accuracy and reproducibility of the time-tested SORVALL mechanical advance system. Other improvements include a new fiber optics approach lighting system, a diffuse lighting and viewing system, a highly effective built-in vibration dampening system, precise digital speed and thickness controls, and the Visutrac system. All combine to make the MT-6000 an excellent microtome for electron or light microscopy." .
SCR:020525 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Storm 865" ;
rdfs:label "GE | Storm 865 Imager" ;
definition: "Multifunction phosphoimager/fluorimager laser scanner used to collect fluorescent or storage phosphor images from gels, membranes and phosphor screens." .
SCR:020526 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Mx3000P" ;
rdfs:label "Agilent | Stratagene Mx3000P Real Time PCR System" ;
definition: "Agilent Mx3000P QPCR System has been replaced with the AriaMx system. Used for gene expression analysis, microarray data validation, SNP genotyping, pathogen detection, DNA methylation analysis, and chromatin immuno-precipitation studies. Agilent qPCR software, MxPro, provides users with an interface, quick experiment design, data analysis and easy report generation." .
SCR:020529 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LectroPol-5" ;
rdfs:label "Struers | Lectro Pol 5 electropolisher" ;
definition: "LectroPol-5 is designed for automated electrolytic polishing and etching of metallographic specimens. A scanning function for easy determination of parameters, built-in safety features, and a database with methods for various materials enables short polishing times and maximum reproducibility. LectroPol-5 consists of two units, the control unit and the polishing unit. The two units can be separated from each other. LectroPol-5 features a scanning function that helps to determine the correct voltage for both polishing and etching, thus saving time and avoiding human error. LectroPol-5 displays the scan curve, while the user selects and sets the voltage. The LectroPol-5 comes with ten polishing/etching methods for various materials, enabling immediate preparation of a wide range of materials without any lengthy and time-consuming trials." .
SCR:020530 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Skyra" ;
rdfs:label "Siemens | 3T Magnetom Skyra MRI scanner" ;
definition: "Siemens 3T MAGNETOM Skyra scanner with new software that enables rapid imaging." .
SCR:020531 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Spectradyne nCS1" ;
rdfs:label "Spectradyne | Spectradyne nCS1 Particle Counter" ;
definition: "nCS1 particle counter is a tool for obtaining detailed size and concentration information about particle distributions in liquids." .
SCR:020533 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MA6" ;
rdfs:label "SUSS | MicroTek MA6/BA6 Mask Aligner" ;
definition: "MA/BA6 mask aligner is designed for all standard lithography applications and wafer sizes of up to 150 mm. For thick-resist MEMS applications, the MA/BA6 offers high resolution and optimum edge quality. The bottom side alignment option allows for pattern printing on both sides of the substrate. The MA/BA6 additionally provides tailored features for fragile III-V compounds, thinned or warped wafers, transparent substrates and pieces or single dies." .
SCR:020534 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_V240" ;
rdfs:label "Sun Microsystems V240 Server" ;
definition: "Powered by either 1 x 1.34 GHz or 2 x 1.5 GHz UltraSPARC IIIi processors, the Sun Fire V240 server is an entry-level, data center-class server. It provides high availability and expandability in a compact, 2U package. Four autonegotiating Gigabit Ethernet ports provide multiple connectivity for high-speed, high-bandwidth networking, while hot-swappable, front-accessible disk drives and redundant, hot-swappable power supplies (with independent cords) further enhance the Sun Fire V240 server's uptime. With expandability features such as three PCI slots, up to four disk drives, and 16 GB of memory, the rack-optmized Sun Fire V240 server easily scales to meet the needs of Tier 1 and Tier 2 applications. With a low-cost, integrated SSL option on the motherboard, the Sun Fire V240 server provides fast, secure Web transactions without sacrificing CPU cycles or a PCI slot. The standard System Configuration Card and serviceability features help enable quick upgrades and repairs, while the unit's Sun Advanced Lights Out Manager (ALOM) provides remote management to a large number of servers from virtually anywhere on the network." .
SCR:020535 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_P-10" ;
rdfs:label "Tencore | KLA P-10 Surface Profiler" ;
definition: "Computer controlled manual wafer load profilometer with Max wafer size of 8\"/200mm that measures roughness, waviness, step height, and other surface characteristics. Capabilities of this instrument include: Measurement of vertical features ranging from under 100Ã… (0.4 min.) to approximately 300 �m (11 mils), with a vertical resolution of 0.5, 2, or 10Ã…, A virtually unlimited number of data points per profile guarantee that the horizontal resolution is limited by the stylus radius and not by the number of data points, Measurement of many roughness and waviness parameters, with user-selectable cutoff filters to isolate roughness and waviness, Ability to fit and level a scan, allowing accurate step height measurements on curved surfaces, and the Ability to detect the edge or apex of a profile feature, allowing automated data analysis relative to the feature. The KLA P-10 to repeat a scan up to ten times and automatically calculate the average, thereby minimizing the effects of environmental noise on measurements. KLA-Tencor P10 can profile a variety of materials including: Semiconductor wafers, Thin-film heads, Precision-machined and polished surfaces, Ceramics for micro-electronics, Glass for flat panel displays, and Optical surfaces" .
SCR:020536 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Synergy HT" ;
rdfs:label "Agilent: BioTek | Synergy HT Plate Reader" ;
definition: "Luminescent assays are sensitive and quantitative tools commonly used for a variety of purposes in biomedical and pharmaceutical research. Quantitation of ATP can be used to detect and measure cellular growth, as well as bacterial contamination. Luminescent genetic reporting assays are widely used to study gene expression and cellular responses to external stimuli in Prokaryotic and Eukaryotic organisms. Dual-reporter assays use two independent reporter systems simultaneously to improve experimental accuracy. One reporter is used to measure the response resulting from the experimental conditions and is often referred to as the “experimental� reporter. The second reporter is designed not to respond to the experimental conditions, acting as an internal control from which data generated by the experimental reporter can be normalized. Normalization of the data serves to compensate for variability caused by differences in transfection efficiency, cell viability, cell lysis, and pipetting. Promega's Dual-Luciferase System uses the activities of luminescent proteins (luciferases) from the firefly (Photinus pyralis) beetle and the sea pansy (Renilla renformis) to serve as an experimental and a control reporter respectively (See Figure 1). The Synergy HT Multi-Detection Reader (BioTek Instruments, Winooski, VT) is a robotic compatible microplate reader that can measure absorbance, fluorescence, and luminescence in all plate formats up to 384-well plates with performance in all three detection modes, that has recently been optimized for luminescence measurements (Figure 2). The Synergy HT utilizes a dual optics design that has both a monochromator/xenon flash system with a silicone diode detector for absorbance and a tungsten halogen lamp with blocking interference filters and a photomultiplier tube (PMT) detector for fluorescence. Reagent addition is accomplished by an optional external injector module, which controls two independent injector syringes. Each syringe is connected to a separate injector tip. Emitted luminescence is captured using either the top or bottom probes and measured using the Synergy HT's low noise PMT operated in photon integration mode. Here we describe the use of a Synergy HT Multi-Detection Microplate Reader (BioTek Instruments) to perform dual-luciferase measurements with purified recombinant enzymes." .
SCR:020538 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2991" ;
rdfs:label "Terumo | BCT COBE 2991 Cell Processor" ;
definition: "COBE 2991 cell processor offers an alternative to labor-intensive methods for the separation of cell products, such as manually layering blood over a density gradient separation medium using conical tubes. These methods involve a large number of operator steps and manual pipetting techniques that require significant practice, introducing variability and the opportunity for operator error. Automated processing puts control at the user's fingertips. Protocols can be easily programmed for efficient, reproducible results while saving time and reducing the number of manual operating steps. For maximum flexibility, nearly all aspects of operation can be controlled manually. operation saves training time, requires little technical support and reduces the opportunity for operator errors." .
SCR:020539 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ALPS 3000" ;
rdfs:label "Thermo Fisher | 3000 Plate Sealer" ;
definition: "Quickly seal in heat with the Thermo Scientific ALPS 3000 Automated Microplate Heat Sealer. This compact sealer is designed for optimal robotic integration in high throughput labs, yet still allows for manual benchtop control." .
SCR:020542 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Capit-All" ;
rdfs:label "Thermo Fisher | Capit-All Screw Cap Tube Capper and Decapperr" ;
definition: "Maintain sample integrity with a hands-free method of capping and decapping tubes quickly and easily with the Thermo Scientific Capit-All Screw Cap Tube Capper/Decapper. Designed for benchtop or integrated use, Capit-All instruments cap and decap 24-, 48-, and 96- format Thermo Scientific Matrix and Thermo Scientific Nunc ScrewTop tubes with precision and ease. All instruments cap tubes to optimal torque." .
SCR:020543 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Infinite_200_Pro" ;
rdfs:label "Tecan | Infinite 200 PRO Multimode Microplate Reader" ;
NIFRID:synonym "Infinite 200 PRO",
"Tecan Infinite 200 PRO",
"Tecan Infinite 200 Pro" ;
definition: "Infinite 200 PRO is multimode plate reader family that offers affordable high performance detection solutions empowered by monochromator or filter based technologies. The six new tailored configurations provide excellence in ELISA assays, nucleic acid quantifications, reporter assay technologies, and drug discovery assays including HTRF and fluorescence polarization. This fully upgradeable reader family is designed to simplify your target applications." .
SCR:020544 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DHR-2" ;
rdfs:label "TA Instruments | DHR-2 Rheometer" ;
definition: "Discovery Series Hybrid Rheometer (DHR) system combines a patented advanced drag cup motor, a second generation magnetic bearing, force rebalance transducer (FRT), and the new patent-pending True Position Sensor (TPS) in a single-head Hybrid rheometer. The DHR has unprecedented performance specification and delivers unsurpassed direct strain control, direct stress control, and normal force measurement accuracy. The DHR features all popular TA innovations including patented Smart Swap geometries and the widest range of Smart Swap temperature systems and accessories commercially available. The result is the most advanced, versatile rheometer platform imaginable. The HR-2 is an outstanding general-purpose rotational rheometer for a wide range of analytical, research, and production uses. With performance characteristics suitable for the most demanding measurements and a track-record of reliability, the HR-2 is at home anywhere a rheometer is needed, from around-the-clock production control to cutting-edge research." .
SCR:020545 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_exactive orbitrap" ;
rdfs:label "Thermo Fisher | Q Exactive HF Orbitrap LC-MS/MS System" ;
definition: "Thermo Exactive benchtop Orbitrap operates with a Waters Acquity UPLC and generates high resolution, high mass accuracy full Mass Spectrometry data." .
SCR:020546 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CX7" ;
rdfs:label "Thermo Fisher | CellInsight CX7 High Content Screening Platform" ;
definition: "Integrated system for performance in screening and analysis.Provides the user a choice of imaging modes to extract the information you need from your samples. Use the entire fluorescence spectrum to optimize your assay, and select either widefield or confocal optics for any channel. You also have 4-color brightfield options for colorimetric analysis of tissue sections." .
SCR:020547 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Wellmate" ;
rdfs:label "Thermo Fisher | Wellmate Liquid Handler" ;
definition: "Liquid handler for all microplate filling needs. With a volume range of 1 to 2000 �l, the Matrix WellMate accommodates a wide selection of labware and improves cost-efficiency with disposable, presterilized and pre-calibrated tubing cartridges." .
SCR:020548 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LTQ Elite" ;
rdfs:label "Thermo Fisher | Orbitrap Elite Hybrid Ion Trap Orbitrap Mass Spectrometer" ;
definition: "Mass spectrometer for analyzing demanding proteomics, metabolomics, lipidomics and metabolism samples. This instrument combines a high-field Thermo Scientific Orbitrap mass analyzer and Thermo Scientific Velos Pro ion trap technology." .
SCR:020549 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LTQ Orbitrap XL" ;
rdfs:label "Thermo Fisher | LTQ Orbitrap XL ETD Hybrid Ion Trap-Orbitrap Mass Spectrometer" ;
definition: "Thermo Scientific LTQ Orbitrap XL ETD Hybrid Ion Trap-Orbitrap Mass Spectrometer can be used to identify, characterize and quantify proteins and peptides using. This instrument is a comprehensive solution for a range of proteomics applications including complex PTM analysis; intelligent sequencing of peptides; top-down and middle-down analysis; label-free quantitation; or quantitation using stable isotope labeling methods such as TMT and iTRAQ." .
SCR:020550 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LTQ Orbitrap" ;
rdfs:label "Thermo Fisher | Orbitrap Velos Mass Spectrometer" ;
definition: "Hybrid mass spectrometer with dual-pressure ion trap with the high resolution and outstanding mass accuracy of Orbitrap technology." .
SCR:020551 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LTQ_Discovery" ;
rdfs:label "Thermo Fisher | LTQ Orbitrap Discovery Mass Spectrometer" ;
definition: "Hybrid mass spectrometer that incorporates LTQ XL linear trap and Orbitrap. Consists of linear ion trap for sample ionization, selection, fragmentation, and AGC, intermediate storage device that is required for short pulse injection, and Orbitrap analyzer for Fourier transformation based analysis." .
SCR:020552 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Exactive Plus Orbitrap Mass Spectrometer" ;
definition: "Screen, identify and quantify compounds in complex samples rapidly and with confidence using the Thermo Scientific Exactive Plus Orbitrap Mass Spectrometer. This benchtop LC-MS system delivers high-resolution, accurate-mass (HR/AM) data and fast full-scan capabilities to increase your sample throughput and confidence in results. Easy-to-use and cost effective to operate, it is the best instrument for analytical laboratories performing food safety or environmental screening, clinical research, forensic toxicology, DMPK, metabolomics and biopharma (intact protein analysis) applications." .
SCR:020553 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Qubit" ;
rdfs:label "Thermo Fisher | Qubit 2.0 Fluorometer Qubit 2.0" ;
definition: "Invitrogen Qubit Flex Fluorometer can selectively, accurately measure the concentration of up to 8 samples of DNA, RNA or protein simultaneously. Compared to single sample microvolume fluorometers, using the Qubit Flex Fluorometer for multiple samples reduces your time to data by up to 50%, with time savings beginning with batches of as few as 8 samples. Combining the one-of-a-kind Qubit Flex Fluorometer and optimized Invitrogen Qubit reagents and tube strips offers a complete solution for DNA, RNA and protein quantification." .
SCR:020554 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LTQ XL" ;
rdfs:label "Thermo Fisher | LTQ XL Linear Ion Trap Mass Spectrometer" ;
definition: "Ion trap mass spectrometer with Agilent 1100 HPLC system is used for a variety of studies including metabolite identification, stability testing, degradation products, and high-abundance quantitation." .
SCR:020555 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QE-HFX" ;
rdfs:label "Thermo Fisher | Q Exactive HF-X Hybrid Quadrupole-Orbitrap Mass Spectrometer" ;
definition: "HFX is our newest addition to the proteomics resource. It offers the fastest scanning rate of our Orbitraps, which improves proteomic depth for discovery applications, and integrates well with targeted applications such as parallel reaction monitoring." .
SCR:020556 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Q Exactive Plus" ;
rdfs:label "Thermo Fisher | Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer" ;
definition: "Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer has increased performance and new options that enhance applications from confident DMPK qual/quan screening studies to characterization of intact monoclonal antibodies." .
SCR:020558 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Q Exactive HF" ;
rdfs:label "Thermo Fisher | Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer" ;
definition: "Identify and quantify more proteins, peptides, lipids, glycans and small molecules accurately and in less time with the Thermo Scientific Q Exactive HF hybrid quadrupole-Orbitrap mass spectrometer. The Q Exactive HF system combines a state-of-the-art segmented quadrupole for high-performance precursor ion selection with a high-resolution, accurate-mass (HR/AM) ultra-high-field Orbitrap mass analyzer to deliver a superior combination of scan speed, resolving power, mass accuracy, spectral quality and sensitivity. Identify, quantify and confirm in a single analysis with a single instrument with the Q Exactive HF mass spectrometer." .
SCR:020559 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Fusion" ;
rdfs:label "Thermo Fisher | Orbitrap Fusion Tribrid Mass Spectrometer" ;
definition: "Thermo Orbitrap Fusion Tribrid mass spectrometer and Waters M-Class Acquity nanoUPLC is a versatile platform. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments." .
SCR:020561 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ISQ 7000" ;
rdfs:label "Thermo Fisher | ISQ 7000 Single Quadrupole GC-MS System" ;
definition: "Thermo Scientific ISQ 7000 is a Single Quadrupole GC-MS system offers extended uptime and robustness to maximize sample throughput, along with routine easy-to-use smart tools to simplify operation and speed up instrument familiarization. Featuring a range of configurations at different level of performances, the ISQ 7000 GC-MS is a flexible fit-for-purpose platform, fully upgradable from base to advanced highly sensitive configuration to boost performance when needed and ready-to-fit with continuous changing in regulations." .
SCR:020562 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_C1200" ;
rdfs:label "Thermo Fisher | Orbitrap Fusion Lumos Tribrid Mass Spectrometer" ;
definition: "Spectrometer performs analysis including low level PTM analysis, multiplexed relative quantitation using isobaric tags, intact protein characterization, and MSn analysis of small molecules. System incorporates the brightest ion source, segmented quadrupole mass filter with improved selectivity and ion transmission, Advanced Vacuum Technology, and ETD HD." .
SCR:020564 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Q_Exactive_HF_X" ;
rdfs:label "Thermo Fisher | Q Exactive HF-X Hybrid Quadrupole-Orbitrap Mass Spectrometer" ;
definition: "Uses high capacity transfer tube for maximum ion loading, electrodynamic ion funnel that accomodates and transmits ions over broad mass range. These components enable identification and analysis of peptides, label free and TMT quantitation, top down proteomics analyses, sophisticated DDA and DIA, dynamic Retention Time PRM and BioPharma characterization." .
SCR:020565 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Q Exactive Hybrid" ;
rdfs:label "Thermo Fisher | Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer" ;
definition: "Identify, quantify and confirm more compounds rapidly and with confidence using the Thermo Scientific Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer. This benchtop LC-MS/MS system combines quadruple precursor ion selection with high-resolution, accurate-mass (HRAM) Orbitrap detection to deliver performance and versatility. The Q Exactive Mass Spectrometer is equally useful for untargeted or targeted screening and a broad range of qualitative and quantitative applications in drug discovery, proteomics, environmental and food safety, clinical research and forensic toxicology." .
SCR:020566 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Q_Exactive" ;
rdfs:label "Thermo Fisher | Q Exactive GC Orbitrap GC-MS/MS" ;
definition: "Orbitrap mass spectrometry System provides comprehensive characterization of samples in single analysis for highest confidence in compound discovery, identification, and quantitation. Offers quantitative power of GC triple quadrupole MS combined with high precision, full scan HRAM capabilities." .
SCR:020567 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Q Exactive Focus Hybrid" ;
rdfs:label "Thermo Fisher | Q Exactive Focus Hybrid Quadrupole-Orbitrap Mass Spectrometer" ;
definition: "The sensitivity, selectivity, flexibility, and ease-of-use provided by hybrid quadrupole-Orbitrap mass spectrometers set the standard for screening, quantitation, identification, and confirmation of targeted and untargeted compounds. The Thermo Scientific Q Exactive Focus hybrid quadrupole-Orbitrap MS makes this power accessible to environmental, food safety, clinical research, forensic toxicology, and pharmaceutical labs challenged by growing sample volumes and constrained by strict budgets. The Q Exactive Focus system simplifies method development, saving time and decreasing costs while reliably delivering unsurpassed results." .
SCR:020569 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Wellwash" ;
rdfs:label "Thermo Fisher | Wellwash Wellwash" ;
definition: "Microplate washer designed for 96-well plate format in both landscape and portrait orientation. 96-well plates and strips designed to be washed in 1x8 or 1x12 format and prepare plates for mainly enzyme-linked immunosorbent assay tests. Allows shaking and is controlled through the built-in graphical user interface and keypad." .
SCR:020570 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Finess_325" ;
rdfs:label "Thermo Fisher | Shandon Finess 325 Manual Microtome Finess" ;
definition: "Manual microcotme that ontains quick release cassette clamp and x y orientation head, disposable blades or standard microtome knives, Accu Feed System that provides reproducible sections throughout the length of specimen travel, specimen tilt and orientationusing X Y micro adjustment, free running flywheel with ergonomic design, and removable deep debris tray." .
SCR:020571 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Q Exactive" ;
rdfs:label "Thermo Fisher | Q Exactive UHMR Hybrid Quadrupole-Orbitrap Mass Spectrometer" ;
definition: "Perform the highest - quality native intact mass and top-down analysis in structural biology and biopharma research. The Thermo Scientific Q Exactive UHMR (Ultra-High Mass Range) Hybrid Quadrupole-Orbitrap Mass Spectrometer is the first UHMR MS to combine substantially increased sensitivity and mass resolution at high m/z, MS2, and psuedo-MS3 capabilities in a single platform." .
SCR:020572 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Finess" ;
rdfs:label "Thermo Fisher | Shandon Finesse Microtome Series Finesse" ;
definition: "Features models ranging from fully automated to precision manual that cuts wax or resin with ergonomic design and safe precision for cutting quality sections." .
SCR:020573 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Fusion_Tribrid" ;
rdfs:label "Thermo Fisher | Orbitrap Fusion Tribrid Mass Spectrometer" ;
definition: "Combines quadrupole, ion trap, and Orbitrap mass analysis into Tribrid architecture to provide depth of analysis. Enables analyzing of low-abundance, high-complexity samples to identify compounds and to quantify accurately and elucidate structures thoroughly." .
SCR:020574 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TSQ Vantage" ;
rdfs:label "Thermo Fisher | TSQ Vantage Mass Spectrometer" ;
definition: "Quantify small molecules, peptides, biosimilars, and biologics using the Thermo Scientific TSQ Vantage Triple Quadrupole Mass Spectrometer." .
SCR:020575 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Merlin M150 LR 400/50 CP55 L/LF RS232" ;
rdfs:label "Thermo Fisher | Merlin M150 LR 400/50 CP55 L/LF RS232 Recirculating Chiller" ;
definition: "Compact recirculating chiller that has a cooling capacity of up to 4,282 watts and delivers a continuous supply of it to your samples using a CP55 pump" .
SCR:020576 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Merlin M150 LR 230/60 CP55 L/LF RS232" ;
rdfs:label "Thermo Fisher | Merlin M150 LR 230/60 CP55 L/LF RS232 Recirculating Chiller" ;
definition: "Compact recirculating chiller that has a cooling capacity of up to 4,832 watts and delivers a continuous supply of it to your samples using a CP55 pump" .
SCR:020577 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Merlin M75 LR 208/60 PD2 FLUORINERT" ;
rdfs:label "Thermo Fisher | Merlin M75 LR 208/60 PD2 FLUORINERT Recirculating Chiller" ;
definition: "Compact recirculating chiller that has a cooling capacity of up to 1,800 watts and delivers a continuous supply of it to your samples using a PD2 pump" .
SCR:020578 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TSQ_Vantage" ;
rdfs:label "Thermo Fisher | Triple Quadrupole TSQ Vantage LC-MS system" ;
definition: "Vantage triple quad and Accela UPLC/MS specializes in quantitative work and selective assays of targeted analytes, including metabolites and other small molecules, and peptides from complex matrices such as serum, tissue, cell culture, and other biological sources." .
SCR:020579 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Matrix" ;
rdfs:label "Thermo Fisher | Matrix Tubing Set for Peristaltic Pump Head" ;
definition: "Additional tubing set to combine with Thermo Scientific Matrix PlateMate Peristaltic Pump Head." .
SCR:020580 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA Acrylic S6T" ;
rdfs:label "Thermo Fisher | SAHARA Acrylic S6T Heated Bath Circulators" ;
definition: "Heated bath circulator that provides efficient heating from ambient plus 13 degrees C to maximum of 80 degrees C, with maximum bath volume of 6 liters" .
SCR:020581 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Merlin M150 LR 230/60 T1 RS232" ;
rdfs:label "Thermo Fisher | Merlin M150 LR 230/60 T1 RS232 Recirculating Chiller" ;
definition: "Compact recirculating chiller that has a cooling capacity of up to 4,832 watts and delivers a continuous supply of it to your samples using a T1 pump" .
SCR:020582 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Nucleic Acid Extraction WorkStation" ;
rdfs:label "Thermo Fisher | Automated Nucleic Acid Extraction WorkStation" ;
definition: "Automate high speed purifications that enables faster, cleaner, more consistent nucleic acid extraction.Based on magnetic separation technology.Enables to process any sample from virtually any source with guaranteed sample integrity." .
SCR:020583 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S49 PC200" ;
rdfs:label "Thermo Fisher | SAHARA S49 PC200 Heated Bath Circulator" ;
definition: "Stainless steel heated bath circulator with a temperature range of Ambient +13� to 200�C and a voltage of 100/115 V" .
SCR:020584 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S49 AC200" ;
rdfs:label "Thermo Fisher | SAHARA S49 AC200 Heated Bath Circulator" ;
definition: "Stainless steel heated bath circulator with a temperature range of Ambient +13� to 200�C and a voltage of 100 V" .
SCR:020585 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S49 AC150" ;
rdfs:label "Thermo Fisher | SAHARA S49 AC150 Heated Bath Circulator" ;
definition: "Stainless steel heated bath circulator with a temperature range of Ambient +13� to 150�C and a voltage of 100 V" .
SCR:020586 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S49 SC100" ;
rdfs:label "Thermo Fisher | SAHARA S49 SC100 Heated Bath Circulator" ;
definition: "Stainless steel heated bath circulator with a temperature range of Ambient +13� to 100�C and a voltage of 100 V" .
SCR:020587 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Polar Series Accel 500 LC" ;
rdfs:label "Thermo Fisher | Polar Series Accel 500 LC Recirculating Chiller" ;
definition: "Chiller that offers 500 watts of cooling, with a working temperature range of 10� to 80�C" .
SCR:020588 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA_S49_SC150" ;
rdfs:label "Thermo Fisher | SAHARA S49 SC150 Heated Bath Circulator" ;
definition: "Stainless steel heated bath circulator with a temperature range of Ambient +13 to 150 C and a voltage of 100 V." .
SCR:020589 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S49 SC150L" ;
rdfs:label "Thermo Fisher | SAHARA S49 SC150L Heated Bath Circulator" ;
definition: "Stainless steel heated bath circulator with a temperature range of Ambient +13� to 150�C and a voltage of 100 V" .
SCR:020590 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S49 PC201" ;
rdfs:label "Thermo Fisher | SAHARA S49 PC201 Heated Bath Circulator" ;
definition: "Stainless steel heated bath circulator with a temperature range of Ambient +13� to 200�C and a voltage of 200/230 V" .
SCR:020591 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_II_LR_PD1" ;
rdfs:label "Thermo Fisher | ThermoChill II LR, 115V/60Hz, PD-1 RS232 Recirculating Chiller" ;
definition: "Recilculating chiller with a colling capacity of up to 1,000 watts and a flow rate of 1.2 gpm @ 60 psid" .
SCR:020592 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sample Preparation" ;
rdfs:label "Thermo Fisher | Sample Preparation Automated Liquid Handler" ;
definition: "Automated liquid handler designed to gain greater consistency through automation and allow lab staff to focus on results." .
SCR:020593 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_II_LR_PD2" ;
rdfs:label "Thermo Fisher | ThermoChill II LR, 115V/60Hz, PD-2 RS232 Recirculating Chiller" ;
definition: "Recirculating chiller with a colling capacity of up to 1,000 watts and a flow rate of 3.6 gpm @ 60 psid (13.6 lpm @ 4.1 bar)" .
SCR:020594 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_III_LR_PD1_RS_232" ;
rdfs:label "Thermo Fisher | ThermoChill III LR, 230V/ 50Hz, PD-1 RS 232 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 1,900 watts and temperature setpoints between -10C to +30C." .
SCR:020595 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill II LR 115V/60HZ MDCI" ;
rdfs:label "Thermo Fisher | ThermoChill II LR 115V/60HZ MDCI Recirculating Chiller" ;
definition: "Recirculating chiller with a colling capacity of up to 1,000 watts and a flow rate of 2.0 gpm @ 15 psid (7.6 lpm @ 1.0 bar" .
SCR:020596 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_III_LR_PD1" ;
rdfs:label "Thermo Fisher | ThermoChill III LR, 230V/50Hz, PD-1 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 1,900 watts and temperature set points between -10C to +30C." .
SCR:020597 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_II_LR_PD-2" ;
rdfs:label "Thermo Fisher | ThermoChill II LR, 230V/50Hz, PD-2 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 900 watts and a flow rate of 2.5 gpm @ 60 psid (9.4 lpm @ 4.1 bar)" .
SCR:020598 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill II 115V/ 60Hz PD-2" ;
rdfs:label "Thermo Fisher | ThermoChill II 115V/ 60Hz PD-2 Recirculating Chiller" ;
definition: "Recirculating chiller with a colling capacity of up to 1,000 watts and a flow rate of 3.6 gpm @ 60 psid (13.6 lpm @ 4.1 bar)" .
SCR:020599 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_III_LR_PD-2" ;
rdfs:label "Thermo Fisher | ThermoChill III LR, 230V/50Hz, PD-2 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 1,900 watts and temperature setpoints between -10C to +30C" .
SCR:020600 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_II_LR_PD-1" ;
rdfs:label "Thermo Fisher | ThermoChill II LR, 230V/50Hz, PD-1 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 900 watts and a flow rate of 1.2 gpm @ 60 psid (4.5 lpm @ 4.1 bar)" .
SCR:020601 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SampleArray Base Weight Station" ;
rdfs:label "Thermo Fisher | SampleArray Instrument" ;
definition: "RESOURCE IS DISCONTINUED; A base weight station that can Array sample tubes in 48-, 96-, or 384-format racks �quickly and easily for optimal downstream sample processing" .
SCR:020602 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_III_LR_MDCI_RS232" ;
rdfs:label "Thermo Fisher | ThermoChill III LR 208-230V/60HZ, MDCI, RS232 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 2,000 watts and temperature setpoints between -10C to +30C." .
SCR:020603 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_II_LR_PD-1_RS_232" ;
rdfs:label "Thermo Fisher | ThermoChill II LR, 230V/ 50Hz, PD-1 RS 232 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 900 watts and a flow rate of 1.2 gpm @ 60 psid (4.5 lpm @ 4.1 bar)" .
SCR:020604 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_III_LR_MDCI" ;
rdfs:label "Thermo Fisher | ThermoChill III LR, 208-230V/ 60Hz, MDCI Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 2,000 watts and temperature setpoints between -10C to +30C." .
SCR:020605 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_II_LR_MDCI_RS232" ;
rdfs:label "Thermo Fisher | ThermoChill II LR,115V/60HZ, MDCI RS232 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 1,000 watts and a flow rate of 2.0 gpm @ 15 psid (7.6 lpm @ 1.0 bar)" .
SCR:020606 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_II_LR_PD-2_RS_232" ;
rdfs:label "Thermo Fisher | ThermoChill II LR, 230V/50Hz, PD-2 RS 232 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 900 watts and a flow rate of 2.5 gpm @ 60 psid (9.4 lpm @ 4.1 bar)" .
SCR:020607 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_II_LR_PD-1_RS232" ;
rdfs:label "Thermo Fisher | ThermoChill II LR, 115V/60Hz, PD-1 RS232 Recirculating" ;
definition: "Recirculating chiller with colling capacity of up to 1,000 watts and flow rate of 1.4 gpm @ 60 psid 5.3 lpm @ 4.1 bar" .
SCR:020608 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill III LR 230V/50Hz",
"PD-2",
"RS 232" ;
rdfs:label "Thermo Fisher | ThermoChill III LR, 230V/50Hz, PD-2 RS 232 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 1,900 watts and temperature setpoints between -10�C to +30�C" .
SCR:020609 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_III_LR_PD-2_RS232" ;
rdfs:label "Thermo Fisher | ThermoChill III LR, 208-230V/ 60Hz, PD-2, RS232 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 2,000 watts and temperature setpoints between -10C to +30C." .
SCR:020610 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_III_LR_MDCI" ;
rdfs:label "Thermo Fisher | ThermoChill III LR, 230V/50HZ, MDCI Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 1,900 watts and temperature setpoints between -10C to +30C." .
SCR:020611 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_II_LR_MDCI_RS232" ;
rdfs:label "Thermo Fisher | ThermoChill III LR, 230V/50HZ,MDCI RS232 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 900 watts and a flow rate of 2.0 gpm @ 15 psid (7.6 lpm @ 1.0 bar)" .
SCR:020612 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_III_LR_PD-1_RS_232" ;
rdfs:label "Thermo Fisher | ThermoChill III LR, 208-230V/60Hz, PD-1 RS 232 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 2,000 watts and temperature setpoints between -10C to +30C." .
SCR:020613 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_III_LR_PD-2" ;
rdfs:label "Thermo Fisher | ThermoChill III LR, 208-230V/60Hz, PD-2 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 2,000 watts and temperature setpoints between -10C to +30C." .
SCR:020614 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_III_LR_PD-1" ;
rdfs:label "Thermo Fisher | ThermoChill III LR, 208-230V/60Hz, PD-1 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 2,000 watts and temperature setpoints between -10C to +30C." .
SCR:020615 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_III_PD2" ;
rdfs:label "Thermo Fisher | ThermoChill III, 208-230V/60Hz, PD2 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 2,000 watts and temperature setpoints between 5C to 30C." .
SCR:020616 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Toxicity Testing Workstation" ;
rdfs:label "Thermo Fisher | Toxicity Testing Workstation Automated Liquid Handler" ;
definition: "Automated liquid handler that is adaptable to both specific and common cytotoxity assays and can be used with any commom cells lines and primary cells" .
SCR:020617 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_III_LR_MDCI_RS232" ;
rdfs:label "Thermo Fisher | ThermoChill III LR, 230V/50HZ,MDCI RS232 Recirculating Chiller" ;
definition: "Recirculating chiller with a cooling capacity of up to 1,900 watts and temperature setpoints between -10C to +30C." .
SCR:020618 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Versette" ;
rdfs:label "Thermo Fisher | Versette Automated Liquid Handler" ;
definition: "Automated liquid handler that can support a wide range of applications, including high-throughput Mass Spectrometric Immunoassay (MSIA), plate stamping, plate reformatting, serial dilution and many other applications" .
SCR:020619 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AC 200 230V/50Hz (with bridge)" ;
rdfs:label "Thermo Fisher | AC 200 230V/50Hz with bridge Immersion Circulator" ;
definition: "MantainsT between 13� to 200�C with greater pumping performance, ramp programming, and application alarms" .
SCR:020620 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AC 200 100V/50-60Hz (with bridge)" ;
rdfs:label "Thermo Fisher | AC 200 100V/50-60Hz with bridge Immersion Circulator" ;
definition: "An immersion circulator that can maintain temperature between 13� to 200�C with greater pumping performance, ramp programming, and application alarms" .
SCR:020621 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AC150 100V/50-60Hz (without bridge)" ;
rdfs:label "Thermo Fisher | AC150 100V/50-60Hz (without bridge); Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 200�C" .
SCR:020622 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AC 200 115V/60Hz" ;
rdfs:label "Thermo Fisher | AC 200 115V/60Hz Immersion Circulator" ;
definition: "An immersion circulator that can maintain temperature between 13� to 200�C with greater pumping performance, ramp programming, and application alarms" .
SCR:020623 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AC150 115V/60Hz" ;
rdfs:label "Thermo Fisher | AC150 115V/60Hz; Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 200�C" .
SCR:020624 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AC150 230V/50Hz (with bridge)" ;
rdfs:label "Thermo Fisher | AC150 230V/50Hz (with bridge); Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 200�C" .
SCR:020625 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AC 200 230V/50Hz" ;
rdfs:label "Thermo Fisher | AC 200 230V/50Hz Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 200�C with greater pumping performance, ramp programming, and application alarms" .
SCR:020626 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AC 200 115V/60Hz (with bridge)" ;
rdfs:label "Thermo Fisher | AC 200 115V/60Hz with bridge Immersion Circulator" ;
definition: "An immersion circulator that can maintain temperature between 13� to 200�C with greater pumping performance, ramp programming, and application alarms" .
SCR:020627 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AC150 230V/50Hz" ;
rdfs:label "Thermo Fisher | AC150 230V/50Hz; Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 200�C" .
SCR:020628 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AC150 115V/60Hz (with bridge)" ;
rdfs:label "Thermo Fisher | AC150 115V/60Hz (with bridge); Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 200�C" .
SCR:020629 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AC150 100V/50-60Hz (with bridge)" ;
rdfs:label "Thermo Fisher | AC150 100V/50-60Hz with bridge Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 200�C" .
SCR:020630 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10 AC200 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10 AC200 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 6 liters" .
SCR:020631 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10 AC150 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10 AC150 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 6 liters" .
SCR:020632 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10 AC200 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10 AC200 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 6 liters" .
SCR:020633 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AC 200 100V/50-60Hz (without bridge)" ;
rdfs:label "Thermo Fisher | AC 200 100V/50-60Hz without bridge Immersion Circulator" ;
definition: "An immersion circulator that can maintain temperature between 13� to 200�C with greater pumping performance, ramp programming, and application alarms" .
SCR:020634 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10 AC200 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10 AC200 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 6 liters" .
SCR:020635 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10 AC150 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10 AC150 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 6 liters" .
SCR:020636 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10 AC150 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10 AC150 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 6 liters" .
SCR:020637 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10 SC150 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10 SC150 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 6 liters" .
SCR:020638 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10B AC150 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10B AC150 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 30 liters" .
SCR:020639 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10 SC100 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10 SC100 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 6 liters" .
SCR:020640 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10 SC150 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10 SC150 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 6 liters" .
SCR:020641 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10 SC150 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10 SC150 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 6 liters" .
SCR:020642 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10B AC200 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10B AC200 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 30 liters" .
SCR:020643 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10B AC150 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10B AC150 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 30 liters" .
SCR:020644 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10 SC100 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10 SC100 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 6 liters" .
SCR:020645 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10B AC200 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10B AC200 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 30 liters" .
SCR:020646 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10B SC150 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10B SC150 100V/50-60Hz Refrigerated Circulator" ;
NIFRID:synonym "ThermoFisher ARCTIC A10B SC150 100V/50-60Hz Refrigerated Bath Circulator" ;
definition: "Refrigerated water bath that features temperatures ranging from 10C to +100C and maximum bath volume of 30 liters." .
SCR:020647 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10B AC150 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10B AC150 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 30 liters" .
SCR:020648 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10B AC200 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10B AC200 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 30 liters" .
SCR:020649 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 AC150 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 AC150 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020650 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 AC150 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 AC150 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020651 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 AC200 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 AC200 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020652 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10B SC100 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10B SC100 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 30 liters" .
SCR:020653 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10B SC150 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10B SC150 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 30 liters" .
SCR:020654 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10B SC100 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10B SC100 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 30 liters" .
SCR:020655 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 AC200 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 AC200 115V/60Hz; Refrigerated Circulator" ;
definition: "Rfrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020656 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 SC100 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 SC100 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25 to +200 C and maximum bath volume of 12 liters" .
SCR:020657 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10B SC150 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10B SC150 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 30 liters" .
SCR:020658 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 PC200 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 PC200 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020659 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 AC150 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 AC150 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020660 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 SC100 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 SC100 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020661 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 PC200 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 PC200 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020662 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 PC200 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 PC200 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020663 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A10B SC100 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A10B SC100 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 10� to +100�C and maximum bath volume of 30 liters" .
SCR:020664 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 SC150L 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 SC150L 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020665 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 AC200 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 AC200 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020666 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 SC150L 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 SC150L 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020667 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 SC150 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 SC150 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020668 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 SC150 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 SC150 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020669 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 SC100 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 SC100 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25 to +200 C and maximum bath volume of 12 liters." .
SCR:020670 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25B AC150 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25B AC150 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 21 liters" .
SCR:020671 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 SC150 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 SC150 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020672 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25B AC150 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25B AC150 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 21 liters" .
SCR:020673 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25B AC150 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25B AC150 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 21 liters" .
SCR:020674 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25B SC100 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25B SC100 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 21 liters" .
SCR:020675 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25 SC150L 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25 SC150L 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 12 liters" .
SCR:020676 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25B AC200 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25B AC200 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 21 liters" .
SCR:020677 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25B SC150 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25B SC150 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 21 liters" .
SCR:020678 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 AC150 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 AC150 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020679 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 AC150 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 AC150 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020680 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25B SC100 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25B SC100 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 21 liters" .
SCR:020681 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25B SC100 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25B SC100 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25 to +200 C and maximum bath volume of 21 liters." .
SCR:020682 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 AC150 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 AC150 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020683 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25B AC200 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25B AC200 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 21 liters" .
SCR:020684 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 PC200 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 PC200 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020685 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 PC200 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 PC200 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020686 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25B SC150 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25B SC150 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 21 liters" .
SCR:020687 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25B SC150 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25B SC150 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 21 liters" .
SCR:020688 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 SC150 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 SC150 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020689 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 PC200 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 PC200 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020690 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A25B AC200 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A25B AC200 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 25� to +200�C and maximum bath volume of 21 liters" .
SCR:020691 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 AC200 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 AC200 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020692 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 AC200 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 AC200 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020693 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CW3 Cell Washer" ;
rdfs:label "Thermo Fisher | CW3 Cell Washer; Centrifuge" ;
definition: "Centrifuge that is designed to provide thorough, reproducible blood cell washing, up to 12-24 tubes per run" .
SCR:020694 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 SC150L 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 SC150L 100V/50-60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020695 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 SC150L 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 SC150L 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020696 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 SC150L 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 SC150L 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020697 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 SC150 115V/60Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 SC150 115V/60Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020698 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ARCTIC A40 SC150 230V/50Hz" ;
rdfs:label "Thermo Fisher | ARCTIC A40 SC150 230V/50Hz; Refrigerated Circulator" ;
definition: "Refrigerated circulator that features temperatures ranging from 40� to +200�C and maximum bath volume of 12 liters" .
SCR:020699 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Decapper 550" ;
rdfs:label "Thermo Fisher | Decapper 550; Lab Automation" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Lab automated tool with an integrated barcode reader that provides automated decapping and capping of Thermo Scientific Matrix and Nunc tubes with screw top closures in ANSI racks." .
SCR:020700 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EK 45" ;
rdfs:label "Thermo Fisher | EK 45; Immersion Cooler" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27th,2024. Immersion cooler that is used for the direct cooling of small samples with a temperature range of -45�C to +40�C" .
SCR:020701 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EK 90" ;
rdfs:label "Thermo Fisher | EK 90; Immersion Cooler" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Immersion cooler that is used for the direct cooling of small samples with a temperature range of -90C to +40C." .
SCR:020702 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Heraeus Megafuge 16" ;
rdfs:label "Thermo Fisher | Heraeus Megafuge 16; Centrifuge" ;
definition: "Centrifuge that is perfect for clinical protocols, cell culture applications and microplate processing, the refrigerated version is designed for handling temperature-sensitive sample processing" .
SCR:020703 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Decapper 500" ;
rdfs:label "Thermo Fisher | Decapper 500; Lab Automation" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Lab automated tool that provides automated decapping and capping of Thermo Scientific Matrix and Nunc tubes with screw top closures in ANSI racks." .
SCR:020704 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Heraeus Multifuge X3F" ;
rdfs:label "Thermo Fisher | Heraeus Multifuge X3F; Centrifuge" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Centrifuge that can process a range of general purpose applications including cell culture, microplate, bioproduction, blood separation and microbiology." .
SCR:020705 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EK45FP" ;
rdfs:label "Thermo Fisher | EK45FP; Immersion Cooler" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Immersion cooler that is used for the direct cooling of small samples with a temperature range of -45C to +40C." .
SCR:020706 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Heraeus Freso 21" ;
rdfs:label "Thermo Fisher | Heraeus Freso 21; Centrifuge" ;
definition: "Refrigerated microcentrifuge available with 7 different rotors and designed to provide acceleration up to 21,100xg" .
SCR:020707 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Heraeus Multifuge X1" ;
rdfs:label "Thermo Fisher | Heraeus Multifuge X1; Centrifuge" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Centrifuge that can handle a range of general-purpose processing, including cell culture, microplate, bioproduction, blood separation and microbiology." .
SCR:020708 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Heraeus Multifuge X3FR" ;
rdfs:label "Thermo Fisher | Heraeus Multifuge X3FR; Centrifuge" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Centrifuge that can process a range of general purpose applications including cell culture, microplate, bioproduction, blood separation and microbiology." .
SCR:020709 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Heraeus Pico 17" ;
rdfs:label "Thermo Fisher | Heraeus Pico 17; Centrifuge" ;
definition: "Ventilarted microcentrifuge that provides outstanding processing power, unique safety features and a broad array of microcentrifuge rotors and accessories for microcentrifuge tube processing" .
SCR:020710 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Heraeus Megafuge 8" ;
rdfs:label "Thermo Fisher | Heraeus Megafuge 8; Centrifuge" ;
definition: "Small benchtop centrifuge that can spin 50mL conical tubes at over 12,000 x g or a wide range of microtubes at speeds up to 30,279 x g" .
SCR:020711 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_F7 Industrial Robot" ;
rdfs:label "Thermo Fisher | F7 Industrial Robot; Lab Automation" ;
definition: "Lab automation robot that has,� 0.02 mm repeatability at full, 5 kg payload and full speed within the entire robot work envelope ensures maximum accuracy and superior positions" .
SCR:020712 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MicroCL 17R" ;
rdfs:label "Thermo Fisher | MicroCL 17R; Centrifuge" ;
definition: "Microcentrifuge that provide outstanding processing power, unique safety features and broad array of microcentrifuge rotors and accessories for microcentrifuge tube processing with refrigeration available." .
SCR:020713 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Medifuge" ;
rdfs:label "Thermo Fisher | Medifuge; Centrifuge" ;
definition: "Small benchtop centrifuge that can perform both routine clinical and life science separations" .
SCR:020714 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Heraeus Multifuge X1R" ;
rdfs:label "Thermo Fisher | Heraeus Multifuge X1R; Centrifuge" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 27,2024. Centrifuge that can handle a range of general-purpose processing, including cell culture, microplate, bioproduction, blood separation and microbiology" .
SCR:020715 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MicroCL 21" ;
rdfs:label "Thermo Fisher | MicroCL 21; Centrifuge" ;
definition: "Ventilated centrifuge with lightweight microcentrifuge rotors designed to provide acceleration up to 21,100xg in as little as 12 seconds" .
SCR:020716 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_F5 Robot System" ;
rdfs:label "Thermo Fisher | F5 Robot System; Lab Automation" ;
definition: "Lab automated robot with,�0.02mm repeatability at full, 5kg payload and full speed within the entire robot work envelope that ensures maximum accuracy and superior positioning (NA, RIA Cert. and EU, CE Cert.)" .
SCR:020717 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Heraeus Megafuge 8R" ;
rdfs:label "Thermo Fisher | Heraeus Megafuge 8R; Centrifuge" ;
definition: "Small benchtop centrifuge that can spin 50mL conical tubes at over 12,000 x g or a wide range of microtubes at speeds up to 30,279 x g" .
SCR:020718 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_inSPIRE Platform Bundle" ;
rdfs:label "Thermo Fisher | inSPIRE Platform Bundle; Lab Automation" ;
definition: "Lab automation system that integrates SmartShelves (3-6 Available with each bundle) and allows you to configure the right solution for your automated workflow" .
SCR:020719 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MicroCL 17" ;
rdfs:label "Thermo Fisher | MicroCL 17; Centrifuge" ;
definition: "Ventilated centrifuge that processes sample prep at up to 17,000 x g" .
SCR:020720 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PC 200 100-115V/50-60Hz" ;
rdfs:label "Thermo Fisher | PC 200 100-115V/50-60Hz; Immersion Circulator" ;
definition: "Immersion circulator that has an extreme temperature performance ranging from 13� to 300�C" .
SCR:020721 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Orbitor RS2 Microplate Robot" ;
rdfs:label "Thermo Fisher | Orbitor RS2 Microplate Robot; Lab Automation" ;
definition: "Lab automation microplate robot with Its innovative bi-directional telescoping arm that provides exceptional reach and precision; available with 3-6 Stacks, 3-6 Hotels, or a Mix of both 3-6 total" .
SCR:020722 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Multifuge X4R Pro-MD" ;
rdfs:label "Thermo Fisher | Multifuge X4R Pro-MD; Centrifuge" ;
definition: "Centrifuge that has nine acceleration speeds and can easily access and track all runs, rotor life and centrifuge health" .
SCR:020723 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PC 200 100-115V/50-60Hz (with bridge)" ;
rdfs:label "Thermo Fisher | PC 200 100-115V/50-60Hz (with bridge); Immersion Circulator" ;
definition: "Immersion circulator that has an extreme temperature performance ranging from 13� to 300�C" .
SCR:020724 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Heraeus Pico 21" ;
rdfs:label "Thermo Fisher | Heraeus Pico 21; Centrifuge" ;
definition: "Ventilated microcentrifuge available with 7 different rotors and designed to provide acceleration up to 21,100xg" .
SCR:020725 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PC 200 200-230V/50-60Hz" ;
rdfs:label "Thermo Fisher | PC 200 200-230V/50-60Hz; Immersion Circulator" ;
definition: "Immersion circulator that has an extreme temperature performance ranging from 13� to 300�C" .
SCR:020726 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Multifuge X4 Pro" ;
rdfs:label "Thermo Fisher | Multifuge X4 Pro; Centrifuge" ;
definition: "Centrifuge that has nine acceleration speeds and can easily access and track all runs, rotor life and centrifuge health" .
SCR:020727 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Multifuge X4 Pro-MD" ;
rdfs:label "Thermo Fisher | Multifuge X4 Pro-MD; Centrifuge" ;
definition: "Centrifuge that has nine acceleration speeds and can easily access and track all runs, rotor life and centrifuge health" .
SCR:020728 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PC 201 (with bridge)" ;
rdfs:label "Thermo Fisher | PC 201 (with bridge); Immersion Circulator" ;
definition: "Immersion circulator with an all stainless-steel pump that offers extreme temperature ranging from 13� to 300�C" .
SCR:020729 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Precision_SWB_15S",
"SCR_020735" ;
rdfs:label "Thermo Fisher | Precision SWB 15 Shaking Water Bath" ;
definition: "Shaking water bath with capacity of 15L that supports a range of sensitive life science. Precision Shallow form shaking bath has removable tray that allows for use with smaller sample containers. Precision Dubnoff shaking water baths are designed specifically for applications that require your samples to be incubated in controlled atmosphere." .
SCR:020730 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA PPO S14P AC150" ;
rdfs:label "Thermo Fisher | SAHARA PPO S14P AC150; Heated Bath Circulator" ;
definition: "Heated bath circulator that offers efficient heating from ambient 13� to 100�C with a max bath volume of 14 liters and a voltage of 100 V" .
SCR:020731 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PC 200 200-230V/50-60Hz (with bridge)" ;
rdfs:label "Thermo Fisher | PC 200 200-230V/50-60Hz (with bridge); Immersion Circulator" ;
definition: "Immersion circulator that has an extreme temperature performance ranging from 13� to 300�C" .
SCR:020732 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PC 300 (with bridge)" ;
rdfs:label "Thermo Fisher | PC 300 (with bridge); Immersion Circulator" ;
definition: "Immersion circulator with an all stainless-steel pump that offers extreme temperature ranging from 50� to 300�C" .
SCR:020733 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PC 201" ;
rdfs:label "Thermo Fisher | PC 201; Immersion Circulator" ;
definition: "Immersion circulator with an all stainless-steel pump that offers extreme temperature ranging from 13� to 300�C" .
SCR:020734 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Precision TSCIR35" ;
rdfs:label "Thermo Fisher | Precision TSCIR35; Circulating Water Bath" ;
definition: "Circulating water bath that can Achieve enhanced temperature uniformity with perimeter-directed water flow and has a max capacity of 35 L" .
SCR:020736 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA PPO S14P AC200" ;
rdfs:label "Thermo Fisher | SAHARA PPO S14P AC200; Heated Bath Circulator" ;
NIFRID:synonym "SAHARA PPO S14P Heated Bath Circulators" ;
definition: "Heated bath circulator that offers efficient heating from ambient 13 to 100 C with a max bath volume of 14 liters and a voltage of 100 V." .
SCR:020737 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA PPO S14P SC100" ;
rdfs:label "Thermo Fisher | SAHARA PPO S14P SC100; Heated Bath Circulator" ;
definition: "Heated bath circulator that offers efficient heating from ambient 13� to 100�C with a max bath volume of 14 liters and a voltage of 100 V" .
SCR:020738 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Precision SWB 27" ;
rdfs:label "Thermo Fisher | Precision SWB 27; Shaking Water Bath" ;
definition: "Water bath with a capacity of 27L that supports a range of sensitive life science and is designed specifically for applications that require your samples to be incubated in a controlled atmosphere" .
SCR:020739 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Precision DUB 15" ;
rdfs:label "Thermo Fisher | Precision DUB 15; Shaking Water Bath" ;
definition: "Shaking water bath with a capacity of 15L that supports a range of sensitive life science and is designed specifically for applications that require your samples to be incubated in a controlled atmosphere" .
SCR:020740 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA PPO S21P SC150" ;
rdfs:label "Thermo Fisher | SAHARA PPO S21P SC150; Heated Bath Circulator" ;
definition: "Heated bath circulator that offers efficient heating from ambient 13� to 100�C with a max bath volume of 21 liters and a voltage of 100 V" .
SCR:020741 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA PPO S21P AC200" ;
rdfs:label "Thermo Fisher | SAHARA PPO S21P AC200; Heated Bath Circulator" ;
definition: "Heated bath circulator that offers efficient heating from ambient 13� to 100�C with a max bath volume of 21 liters and a voltage of 100 V" .
SCR:020742 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Precision TSCIR89" ;
rdfs:label "Thermo Fisher | Precision TSCIR89; Circulating Water Bath" ;
definition: "Circulating water bath that can Achieve enhanced temperature uniformity with perimeter-directed water flow and has a max capacity of 89 L" .
SCR:020743 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PC 300" ;
rdfs:label "Thermo Fisher | PC 300; Immersion Circulator" ;
definition: "Immersion circulator with an all stainless-steel pump that offers extreme temperature ranging from 50� to 300�C" .
SCR:020744 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S12T AC150",
"SCR_020749" ;
rdfs:label "Thermo Fisher | SAHARA S12T AC150; Heated Bath Circulators" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13, 2024. Acrylic heated bath circulator that provides efficient heating from ambient plus 13C to a maximum of 80C, with maximum bath volume of 12 liters and a voltage of 100 V." .
SCR:020745 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Precision TSCIR19" ;
rdfs:label "Thermo Fisher | Precision TSCIR19; Circulating Water Bath" ;
definition: "Water bath that can Achieve enhanced temperature uniformity with perimeter-directed water flow and has a max capacity of 19 L" .
SCR:020746 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA PPO S21P AC150" ;
rdfs:label "Thermo Fisher | SAHARA PPO S21P AC150; Heated Bath Circulator" ;
definition: "Heated bath circulator that offers efficient heating from ambient 13� to 100�C with a max bath volume of 21 liters and a voltage of 100 V" .
SCR:020747 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA PPO S21P SC100" ;
rdfs:label "Thermo Fisher | SAHARA PPO S21P SC100; Heated Bath Circulator" ;
definition: "Heated bath circulator that offers efficient heating from ambient 13� to 100�C with a max bath volume of 21 liters and a voltage of 100 V" .
SCR:020748 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S13 AC150 100V" ;
rdfs:label "Thermo Fisher | SAHARA S13 AC150; 100V; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13 to 300C and a voltage of 100 V" .
SCR:020750 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S13 AC200" ;
rdfs:label "Thermo Fisher | SAHARA S13 AC200; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 300�C and a voltage of 100 V" .
SCR:020751 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S13 PC200" ;
rdfs:label "Thermo Fisher | SAHARA S13 PC200; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 300�C and a voltage of 100/115 V" .
SCR:020752 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA PPO S14P SC150" ;
rdfs:label "Thermo Fisher | SAHARA PPO S14P SC150; Heated Bath Circulator" ;
definition: "Heated bath circulator that offers efficient heating from ambient 13� to 100�C with a max bath volume of 14 liters and a voltage of 100 V" .
SCR:020753 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S12T SC100" ;
rdfs:label "Thermo Fisher | SAHARA S12T SC100; Heated Bath Circulators" ;
definition: "Acrylic heated bath circulator that provides efficient heating from ambient plus 13�C to a maximum of 80�C, with maximum bath volume of 12 liters and a voltage of 100 V" .
SCR:020754 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S13 PC300" ;
rdfs:label "Thermo Fisher | SAHARA S13 PC300; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 300�C and a voltage of 200/230 V" .
SCR:020755 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S12T AC200" ;
rdfs:label "Thermo Fisher | SAHARA S12T AC200; Heated Bath Circulators" ;
definition: "Acrylic heated bath circulator that provides efficient heating from ambient plus 13�C to a maximum of 80�C, with maximum bath volume of 12 liters and a voltage of 100 V" .
SCR:020756 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S13 SC100" ;
rdfs:label "Thermo Fisher | SAHARA S13 SC100; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 300�C and a voltage of 100 V" .
SCR:020757 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S21 SC150" ;
rdfs:label "Thermo Fisher | SAHARA S21 SC150; 100V; Heated Bath Circulator" ;
definition: "Stainless-steel heated bath circulator that has efficient heating from Ambient +13C to 150C, max bath volume of 19 liters, and a range voltage of 100 V." .
SCR:020758 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S19T SC100" ;
rdfs:label "Thermo Fisher | SAHARA S19T SC100; 100V; Heated Bath Circulator" ;
definition: "Heated bath circulator that offers efficient heating from ambient 13C to 80CC with a max bath volume of 19 liters and a voltage of 100 V." .
SCR:020759 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S13 PC201" ;
rdfs:label "Thermo Fisher | SAHARA S13 PC201; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 300�C and a voltage of 200/230 V" .
SCR:020760 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S13 SC150" ;
rdfs:label "Thermo Fisher | SAHARA S13 SC150; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 300�C and a voltage of 100 V" .
SCR:020761 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S13 SC150L" ;
rdfs:label "Thermo Fisher | SAHARA S13 SC150L; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 300�C and a voltage of 100 V" .
SCR:020762 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S21 AC200" ;
rdfs:label "Thermo Fisher | SAHARA S21 AC200; 100V; Heated Bath Circulator" ;
definition: "Stainless-steel heated bath circulator that has efficient heating from Ambient +13C to 200C, max bath volume of 19 liters, and a range voltage of 100 V." .
SCR:020763 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA_S19T_AC200" ;
rdfs:label "Thermo Fisher | SAHARA S19T AC200; 100V; Heated Bath Circulator" ;
definition: "Heated bath circulator that offers efficient heating from ambient 13C to 80C with a max bath volume of 19 liters and a voltage of 100 V." .
SCR:020764 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S45 AC150" ;
rdfs:label "Thermo Fisher | SAHARA S45 AC150; 100 V; Heated Bath Circulators" ;
definition: "Stainless-steel heated bath circulator with a temperature of ambient +13C to 150C, max bath volume of 41 liters, and range voltage of 100 V" .
SCR:020765 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S45 AC200" ;
rdfs:label "Thermo Fisher | SAHARA S45 AC200; Heated Bath Circulators" ;
definition: "Stainless-steel heated bath circulator with a temperature of ambient +13� to 200�C, max bath volume of 41 liters, and range voltage of 100 V" .
SCR:020766 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S19T SC150" ;
rdfs:label "Thermo Fisher | SAHARA S19T SC150; Heated Bath Circulator" ;
definition: "Heated bath circulator that offers efficient heating from ambient 13� to 80�C with a max bath volume of 19 liters and a voltage of 100 V" .
SCR:020767 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S5P SC100" ;
rdfs:label "Thermo Fisher | SAHARA S5P SC100; Heated Bath Circulator" ;
definition: "Heated bath circulator that can maintain temperatures from ambient +13� to 100�C, with maximum bath volume of 5 liters and voltage of 100 V" .
SCR:020768 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S19T AC150" ;
rdfs:label "Thermo Fisher | SAHARA S19T AC150; Heated Bath Circulator" ;
definition: "Heated bath circulator that offers efficient heating from ambient 13� to 80�C with a max bath volume of 19 liters and a voltage of 100 V" .
SCR:020769 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S45 SC150L" ;
rdfs:label "Thermo Fisher | SAHARA S45 SC 150L; Heated Bath Circulators" ;
definition: "Stainless-steel heated bath circulator with a temperature of ambient +13� to 150�C, max bath volume of 41 liters, and range voltage of 115 V" .
SCR:020770 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S21 SC100" ;
rdfs:label "Thermo Fisher | SAHARA S21 SC100; Heated Bath Circulator" ;
definition: "Stainless-steel heated bath circulator that has efficient heating from Ambient +13� to 100�C, max bath volume of 19 liters, and a range voltage of 100 V" .
SCR:020771 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S5P SC150" ;
rdfs:label "Thermo Fisher | SAHARA S5P SC150; Heated Bath Circulator" ;
definition: "Heated bath circulator that can maintain temperatures from ambient +13� to 100�C, with maximum bath volume of 5 liters and voltage of 100 V" .
SCR:020772 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S15 PC300" ;
rdfs:label "Thermo Fisher | SAHARA S15 PC300; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 300�C with a max bath volume of 17 liters and a voltage of 200/230 V" .
SCR:020773 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S21 AC150" ;
rdfs:label "Thermo Fisher | SAHARA S21 AC150; Heated Bath Circulator" ;
definition: "Stainless-steel heated bath circulator that has efficient heating from Ambient +13� to 150�C, max bath volume of 19 liters, and a range voltage of 100 V" .
SCR:020774 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S45 SC 150" ;
rdfs:label "Thermo Fisher | SAHARA S45 SC 150; Heated Bath Circulators" ;
definition: "Stainless-steel heated bath circulator with a temperature of ambient +13� to 150�C, max bath volume of 41 liters, and range voltage of 100 V" .
SCR:020775 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S45 SC100" ;
rdfs:label "Thermo Fisher | SAHARA S45 SC100; Heated Bath Circulators" ;
definition: "Stainless-steel heated bath circulator with a temperature of ambient +13� to 100�C, max bath volume of 41 liters, and range voltage of 100 V" .
SCR:020776 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S7 AC200" ;
rdfs:label "Thermo Fisher | SAHARA S7 AC200; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 200�C with a max bath volume of 8 liters and a voltage of 100 V" .
SCR:020777 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S7 AC150" ;
rdfs:label "Thermo Fisher | SAHARA S7 AC150; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 150�C with a max bath volume of 8 liters and a voltage of 100 V" .
SCR:020778 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S7 PC200" ;
rdfs:label "Thermo Fisher | SAHARA S7 PC200; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 200�C with a max bath volume of 8 liters and a voltage of 100/115 V" .
SCR:020779 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S7 PC201" ;
rdfs:label "Thermo Fisher | SAHARA S7 PC201; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 200�C with a max bath volume of 8 liters and a voltage of 200/230 V" .
SCR:020780 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S45 PC200" ;
rdfs:label "Thermo Fisher | SAHARA S45 PC200; Heated Bath Circulators" ;
definition: "Stainless-steel heated bath circulator with a temperature of ambient +13� to 200�C, max bath volume of 41 liters, and range voltage of 200/230 V" .
SCR:020781 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S7 SC100" ;
rdfs:label "Thermo Fisher | SAHARA S7 SC100; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 100�C with a max bath volume of 8 liters and a voltage of 100 V" .
SCR:020782 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S6T SC100" ;
rdfs:label "Thermo Fisher | SAHARA S6T SC100; Heated Bath Circulators" ;
definition: "Acrylic heated bath circulator that provides efficient heating from ambient plus 13�C to a maximum of 80�C, with maximum bath volume of 6 liters and a voltage of 100 V" .
SCR:020783 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S6T SC150" ;
rdfs:label "Thermo Fisher | SAHARA S6T SC150; Heated Bath Circulators" ;
definition: "Acrylic heated bath circulator that provides efficient heating from ambient plus 13�C to a maximum of 80�C, with maximum bath volume of 6 liters and a voltage of 100 V" .
SCR:020784 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC100 115V/60Hz" ;
rdfs:label "Thermo Fisher | SC100 115V/60Hz; Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 100�C" .
SCR:020785 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC_150L_230V/50Hz (with clamp)" ;
rdfs:label "Thermo Fisher | SC 150L 230V/50Hz (with clamp); Immersion Circulator" ;
definition: "Immersoin circulator that can maintain temperature up to +150 C while increasing immersion depth to accomodate larger or deeper baths." .
SCR:020786 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S7 SC150" ;
rdfs:label "Thermo Fisher | SAHARA S7 SC150; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 150�C with a max bath volume of 8 liters and a voltage of 100 V" .
SCR:020787 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S7 PC300" ;
rdfs:label "Thermo Fisher | SAHARA S7 PC300; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 200�C with a max bath volume of 8 liters and a voltage of 200/230 V" .
SCR:020788 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC 150L 100V/50-60Hz (with clamp)" ;
rdfs:label "Thermo Fisher | SC 150L 100V/50-60Hz (with clamp); Immersion Circulator" ;
definition: "Immersoin circulator that can maintain temperature up to +150�C while increasing immersion depth to accomodate larger or deeper baths" .
SCR:020789 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAHARA S7 SC150L" ;
rdfs:label "Thermo Fisher | SAHARA S7 SC150L; Heated Bath Circulator" ;
definition: "Stainles-steel heated bath circulator that offers efficient heating from ambient 13� to 150�C with a max bath volume of 8 liters and a voltage of 100 V" .
SCR:020790 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC100_100V/50-60Hz" ;
rdfs:label "Thermo Fisher | SC100 100V/50-60Hz; Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13 to 100 C." .
SCR:020791 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC 150L 115V/60Hz" ;
rdfs:label "Thermo Fisher | SC 150L 115V/60Hz; Immersion Circulator" ;
definition: "Immersoin circulator that can maintain temperature up to +150�C while increasing immersion depth to accomodate larger or deeper baths" .
SCR:020792 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC100 230V/50Hz" ;
rdfs:label "Thermo Fisher | SC100 230V/50Hz; Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 100�C" .
SCR:020793 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC100 230V/50Hz (with clamp)" ;
rdfs:label "Thermo Fisher | SC100 230V/50Hz (with clamp); Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 100�C" .
SCR:020794 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC 150L 230V/50Hz" ;
rdfs:label "Thermo Fisher | SC 150L 230V/50Hz; Immersion Circulator" ;
definition: "Immersoin circulator that can maintain temperature up to +150�C while increasing immersion depth to accomodate larger or deeper baths" .
SCR:020795 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC 150L 115V/60Hz (with clamp)" ;
rdfs:label "Thermo Fisher | SC 150L 115V/60Hz (with clamp); Immersion Circulator" ;
definition: "Immersoin circulator that can maintain temperature up to +150�C while increasing immersion depth to accomodate larger or deeper baths" .
SCR:020796 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC150 115V/60Hz (with clamp)" ;
rdfs:label "Thermo Fisher | SC150 115V/60Hz (with clamp); Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 150�C" .
SCR:020797 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC100 115V/60Hz (with clamp)" ;
rdfs:label "Thermo Fisher | SC100 115V/60Hz (with clamp); Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 100�C" .
SCR:020798 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC150 230V/50Hz (with clamp)" ;
rdfs:label "Thermo Fisher | SC150 230V/50Hz (with clamp); Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 150�C" .
SCR:020799 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC 150L 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | SC 150L 100V/50-60Hz; Immersion Circulator" ;
definition: "Immersoin circulator that can maintain temperature up to +150�C while increasing immersion depth to accomodate larger or deeper baths" .
SCR:020800 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC150 100V/50-60Hz" ;
rdfs:label "Thermo Fisher | SC150 100V/50-60Hz; Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 150�C" .
SCR:020801 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC100 100V/50-60Hz (with clamp)" ;
rdfs:label "Thermo Fisher | SC100 100V/50-60Hz (with clamp); Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 100�C" .
SCR:020802 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC150 115V/60Hz" ;
rdfs:label "Thermo Fisher | SC150 115V/60Hz; Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 150�C" .
SCR:020803 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall BP 16" ;
rdfs:label "Thermo Fisher | Sorvall BP 16; Centrifuge" ;
definition: "Centrifuge that is designed for blood banking and provides high-throughput sample processing" .
SCR:020804 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SL4 Plus-MD" ;
rdfs:label "Thermo Fisher | SL4 Plus-MD; Centrifuge" ;
definition: "Centrifuge with simple push-button operation for routine applications" .
SCR:020805 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC150 230V/50Hz" ;
rdfs:label "Thermo Fisher | SC150 230V/50Hz; Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13� to 150�C" .
SCR:020806 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall BP 8" ;
rdfs:label "Thermo Fisher | Sorvall BP 8; Centrifuge" ;
definition: "Centrifuge that is designed for blood banking and provides high-throughput sample processing" .
SCR:020807 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SC150_100V/50-60Hz (with clamp)" ;
rdfs:label "Thermo Fisher | SC150 100V/50-60Hz (with clamp); Immersion Circulator" ;
definition: "Immersion circulator that can maintain temperature between 13 to 150 C." .
SCR:020808 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SL 8R" ;
rdfs:label "Thermo Fisher | SL 8R; Centrifuge" ;
definition: "Small benchtop centrifuge that features innovative technologies with a smart, simple interface and the flexibility to meet your clinical and research processes and protocols, available in ventilated and refrigerated models" .
SCR:020809 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SL_8" ;
rdfs:label "Thermo Fisher | SL 8; Centrifuge" ;
definition: "Small benchtop centrifuge that features innovative technologies with a smart, simple interface and the flexibility to meet your clinical and research processes and protocols, available in ventilated and refrigerated models" .
SCR:020810 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall Legend Micro 21" ;
rdfs:label "Thermo Fisher | Sorvall Legend Micro 21; Centrifuge" ;
definition: "Ventilated centirfuge that offers productivity, versatility, safety and convenience in a compact, easy-to-use lab instrument" .
SCR:020811 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall Legend X1" ;
rdfs:label "Thermo Fisher | Sorvall Legend X1; Centrifuge" ;
definition: "Centrifuge that can process a variety of diverse laboratory applications" .
SCR:020812 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall MTX 150" ;
rdfs:label "Thermo Fisher | Sorvall MTX 150; Centrifuge" ;
definition: "Micro-ultracentrifuge that offers powerful separation technology in a quiet, compact, easy-to-use benchtop design that combines advanced functionality, rotor management and controlled access." .
SCR:020813 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall MX 120 Plus" ;
rdfs:label "Thermo Fisher | Sorvall MX 120 Plus; Centrifuge" ;
definition: "Micro-ultra centrifuge that combines high-speed performance, versatile rotor capacities and a compact footprint with excellent processing capacity and sample separation performance up to 1,048,000 × g" .
SCR:020814 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall MX 150 Plus" ;
rdfs:label "Thermo Fisher | Sorvall MX 150 Plus; Centrifuge" ;
definition: "Micro-ultra centrifuge that combines high-speed performance, versatile rotor capacities and a compact footprint with excellent processing capacity and sample separation performance up to 1,048,000 g" .
SCR:020815 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall RC4" ;
rdfs:label "Thermo Fisher | Sorvall RC4; Centrifuge" ;
definition: "Low-speed floor model refrigerated centrifuge that can process the optimal capacity for small to medium size blood processing centers with the ability to spin 4 or 8 blood bags in a wide range of bag configurations" .
SCR:020816 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall RC3BP Plus" ;
rdfs:label "Thermo Fisher | Sorvall RC3BP Plus; Centrifuge" ;
definition: "Low-speed centrifuge combines outstanding convenience with exceptional ease of use to expedite daily processing" .
SCR:020817 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall Legend X1R" ;
rdfs:label "Thermo Fisher | Sorvall Legend X1R; Centrifuge" ;
definition: "Centrifuge that can process a variety of diverse laboratory applications" .
SCR:020818 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall ST 16R" ;
rdfs:label "Thermo Fisher | Sorvall ST 16R; Centrifuge" ;
definition: "Centrifuge that can perform cell culture and blood processing applications" .
SCR:020819 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall ST 8R" ;
rdfs:label "Thermo Fisher | Sorvall ST 8R; Centrifuge" ;
definition: "Small benchtop centrifuge that provide exceptional capacity in a compact design with a smart, simple interface and the flexibility to support numerous applications" .
SCR:020820 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall ST 8" ;
rdfs:label "Thermo Fisher | Sorvall ST 8; Centrifuge" ;
definition: "Small benchtop centrifuge that provide exceptional capacity in a compact design with a smart, simple interface and the flexibility to support numerous applications" .
SCR:020821 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall ST4 Plus-MD" ;
rdfs:label "Thermo Fisher | Sorvall ST4 Plus-MD; Centrifuge" ;
definition: "Centrifuge with 13 available motors that provides high-power spins for sample preaparation" .
SCR:020822 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall ST 8FR" ;
rdfs:label "Thermo Fisher | Sorvall ST 8FR; Centrifuge" ;
definition: "Refrigerated floor-standing compact centrifuge that offers enhanced ergonomics and saves valuable bench space in your lab" .
SCR:020823 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall ST4R Plus-MD" ;
rdfs:label "Thermo Fisher | Sorvall ST4R Plus-MD; Centrifuge" ;
definition: "Centrifuge with 13 available motors that provides high-power spins for sample preaparation" .
SCR:020824 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall ST 16" ;
rdfs:label "Thermo Fisher | Sorvall ST 16; Centrifuge" ;
definition: "Centrifuge that can perform cell culture and blood processing applications" .
SCR:020825 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall ST4R Plus" ;
rdfs:label "Thermo Fisher | Sorvall ST4R Plus; Centrifuge" ;
definition: "Centrifuge with 13 available motors that provides high-power spins for sample preaparation" .
SCR:020826 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall X4R Pro-MD" ;
rdfs:label "Thermo Fisher | Sorvall X4R Pro-MD; Centrifuge" ;
definition: "Centrifuge that has nine acceleration speeds and can easily access and track all runs, rotor life and centrifuge health" .
SCR:020827 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall X4 Pro-MD" ;
rdfs:label "Thermo Fisher | Sorvall X4 Pro-MD; Centrifuge" ;
definition: "Centrifuge that has nine acceleration speeds and can easily access and track all runs, rotor life and centrifuge health" .
SCR:020828 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall_X4R_Pro" ;
rdfs:label "Thermo Fisher | Sorvall X4R Pro; Centrifuge" ;
definition: "Centrifuge that has nine acceleration speeds and can easily access and track all runs, rotor life and centrifuge health." .
SCR:020829 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall ST4 Plus" ;
rdfs:label "Thermo Fisher | Sorvall ST4 Plus; Centrifuge" ;
definition: "Centrifuge with 13 available motors that provides high-power spins for sample preaparation" .
SCR:020830 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_I_LR_MDCI" ;
rdfs:label "Thermo Fisher | ThermoChill I LR, 115V/ 60Hz MDCI; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from -10C to +30C." .
SCR:020831 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_I_LR_MDCI_RS232" ;
rdfs:label "Thermo Fisher | ThermoChill I LR, 115V/ 60Hz MDCI RS232; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from -10C to +30C." .
SCR:020832 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_I_LR_PD-1" ;
rdfs:label "Thermo Fisher | ThermoChill I LR, 115V/ 60Hz, PD-1; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from -10C to +30C." .
SCR:020833 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_I_LR_MDCI" ;
rdfs:label "Thermo Fisher | ThermoChill I LR, 230V/50Hz MDCI; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from -10C to +30C." .
SCR:020834 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sorvall X4 Pro" ;
rdfs:label "Thermo Fisher | Sorvall X4 Pro; Centrifuge" ;
definition: "Centrifuge that has nine acceleration speeds and can easily access and track all runs, rotor life and centrifuge health" .
SCR:020835 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_I_LR_PD-1_RS232" ;
rdfs:label "Thermo Fisher | ThermoChill I LR, 230V/50Hz, PD-1 RS232; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from -10C to +30C." .
SCR:020836 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoFlex 10000" ;
rdfs:label "Thermo Fisher | ThermoFlex 10000; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from -5�C to +90�C" .
SCR:020837 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_I_LR_PD-1" ;
rdfs:label "Thermo Fisher | ThermoChill I LR, 230V/50Hz, PD-1; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from -10C to +30C." .
SCR:020838 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Spinnaker Robot" ;
rdfs:label "Thermo Fisher | Spinnaker Robot; Lab Automation" ;
definition: "Lab automation robot that provides self-correcting precision as well as powerful sample tracking and inventory management" .
SCR:020839 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoFlex 20000 (new T9 pump)" ;
rdfs:label "Thermo Fisher | ThermoFlex 20000 (new T9 pump); Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from 5�C to 40�C" .
SCR:020840 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoFlex 15000 (new T9 pump)" ;
rdfs:label "Thermo Fisher | ThermoFlex 15000 (new T9 pump); Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from 5�C to 40�C" .
SCR:020841 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoFlex 24000 (new T9 pump)" ;
rdfs:label "Thermo Fisher | ThermoFlex 24000 (new T9 pump); Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from -5�C to +50�C" .
SCR:020842 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoFlex 3500" ;
rdfs:label "Thermo Fisher | ThermoFlex 3500; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from 5�C to 90�C" .
SCR:020843 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoChill_I_LR_MDCI_RS232" ;
rdfs:label "Thermo Fisher | ThermoChill I LR, 230V/50Hz MDCI RS232; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from -10C to +30C." .
SCR:020844 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoFlex 1400" ;
rdfs:label "Thermo Fisher | ThermoFlex 1400; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from 5�C to 90�C" .
SCR:020845 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoFlex 7500" ;
rdfs:label "Thermo Fisher | ThermoFlex 7500; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from 5�C to 90�C" .
SCR:020846 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoFlex 2500" ;
rdfs:label "Thermo Fisher | ThermoFlex 2500; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from -5�C to +90�C" .
SCR:020847 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ULT 179104241600" ;
rdfs:label "Thermo Fisher | ULT 179104241600; Bath Recirculator" ;
definition: "Refrigerated bath recirculators that is designed for circulating to external applications and has a temperature range of -95�C to -30�C" .
SCR:020848 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoFlex 900 (Low Noise)" ;
rdfs:label "Thermo Fisher | ThermoFlex 900 (Low Noise); Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from 5�C to 40�C" .
SCR:020849 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoFlex 900" ;
rdfs:label "Thermo Fisher | ThermoFlex 900; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from 5�C to 40�C" .
SCR:020850 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ULT_179106241600" ;
rdfs:label "Thermo Fisher | ULT 179106241600; Bath Recirculator" ;
definition: "Refrigerated bath recirculators that is designed for circulating to external applications and has a temperature range of -95 C to -30 C." .
SCR:020851 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ULT 180104201601" ;
rdfs:label "Thermo Fisher | ULT 180104201601; Bath Recirculator" ;
definition: "Refrigerated bath recirculators that is designed for circulating to external applications and has a temperature range of -80�C to +80�C" .
SCR:020852 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultra-low Temp G50 AC200 230 VOLT" ;
rdfs:label "Thermo Fisher | Ultra-low Temp G50 AC200 230 VOLT; Refrigerated/Heated Bath Circulator" ;
definition: "Refirgerated/heated bath circulator that delivers high heating and cooling capacities for rapid heat-up and cool-down times and has electrical requirements of 230 V" .
SCR:020853 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ULT 180106201601" ;
rdfs:label "Thermo Fisher | ULT 180106201601; Bath Recirculator" ;
definition: "Refrigerated bath recirculators that is designed for circulating to external applications and has a temperature range of -80�C to +80�C" .
SCR:020854 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ThermoFlex 5000" ;
rdfs:label "Thermo Fisher | ThermoFlex 5000; Recirculating Chiller" ;
definition: "Recirculating chiller that provides reliable temperature control with a temperature range from -5�C to +90�C" .
SCR:020855 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultra-low Temp G50 AC150 208-230 VOLT 60HZ" ;
rdfs:label "Thermo Fisher | Ultra-low Temp G50 AC150 208-230 VOLT 60HZ; Refrigerated/Heated Bath Circulator" ;
definition: "Refirgerated/heated bath circulator that delivers high heating and cooling capacities for rapid heat-up and cool-down times and has electrical requirements of 208/230 V 60 Hz" .
SCR:020856 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ULT 180104201600" ;
rdfs:label "Thermo Fisher | ULT 180104201600; Bath Recirculator" ;
definition: "Refrigerated bath recirculators that is designed for circulating to external applications and has a temperature range of --80�C to +10�C" .
SCR:020857 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VersaCool" ;
rdfs:label "Thermo Fisher | VersaCool; Refrigerated Circulating Bath" ;
definition: "Refrigerated circulating bath that can circulate fluid from the bath to specific applications with a temperature range of -20�C to +150�C" .
SCR:020858 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_E300" ;
rdfs:label "Sakura | Tissue-Tek E300 E300" ;
definition: "Tissue Tek VIP E300 is a tissue processor that features a self-calculation delay mode which coordinates completion of processing to enhance workflow. The computer monitors all steps in the processing sequence safeguarding your specimens and protecting your system. Precisely located heater elements provide uniform reagent temperatures throughout the retort during processing. Gentle tidal agitation ensures optimal reagent mixing while reducing tissue cross-contamination. Paraffin cleansing automatically degasses the paraffin while in the oven, eliminating additional retort cleaning cycles. The Tissue Tek VIP E300 tissue processor features a full-screen display for complete information at a glance and an easy-access control panel for complete system management. The basket design allows for upright placement of cassette specimens and fits all standard embedding consoles." .
SCR:020859 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultra-low Temp G50 PC200 208-230 VOLT 60HZ" ;
rdfs:label "Thermo Fisher | Ultra-low Temp G50 PC200 208-230 VOLT 60HZ; Refrigerated/Heated Bath Circulator" ;
definition: "Refirgerated/heated bath circulator that delivers high heating and cooling capacities for rapid heat-up and cool-down times and has electrical requirements of 200/230 V 60 Hz 200 V 50 Hz" .
SCR:020860 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_G8" ;
rdfs:label "Tosoh | G8 Hematology Analyzer" ;
definition: "G8 HPLC Hematology Analyzer is the Tosoh's industry HPLC testing systems for fast and accurate HbA1c results. Tosoh designed the G8 HPLC Analyzer from the user's perspective, enhancing overall safety and of operation. The system utilizes Ion-exchange HPLC testing method, which is the gold standard for HbA1c diabetes measurement. The system is used for in vitro diagnostic measurement of HbA1c in blood specimens. The G8 uses a non-porous column and microcomputer technology to quickly and accurately measure the stable portion of HbA1c as a percentage of the total amount of hemoglobin present in the sample. The G8 provides accurate and precise separation of HbA1c from other hemoglobin fractions. Off-line pretreatment is not required, and there is no interference from the labile portion of HbA1c." .
SCR:020861 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TissueLoc" ;
rdfs:label "Thermo Fisher | TissueLoc Tissue Cassettes" ;
definition: "Tissue Cassettes for specimen safety during processing and easy removal of cover while embedding with hinge design. Preassembled for added convenience." .
SCR:020862 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultra-low Temp G50 AC200 208-230 VOLT 60 HZ" ;
rdfs:label "Thermo Fisher | Ultra-low Temp G50 AC200 208-230 VOLT 60 HZ; Refrigerated/Heated Bath Circulator" ;
definition: "Refirgerated/heated bath circulator that delivers high heating and cooling capacities for rapid heat-up and cool-down times and has electrical requirements of 200/230 V 60 Hz 200 V 50 Hz" .
SCR:020863 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TBS-380" ;
rdfs:label "Turner BioSystems | TBS-380 Fluorometer" ;
definition: "TBS-380 Mini-Fluorometer is a dual-channel fluorometer designed for quick, easy, and accurate fluorescence measurements. When properly calibrated with a standard of known concentration, the TBS380 displays the actual concentration of the measured compound. The new Minicell adaptor design enables the user to measure compounds at a low concentration with a low assay volume (e.g. dsDNA at 1ng/mL using PicoGreen, and RNA at 1 ng/mL using RiboGreen)." .
SCR:020864 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Mosquito HTS" ;
rdfs:label "TTP Labtech | Mosquito HTS Automated Liquid Handler" ;
definition: "Both TTP Labtech's mosquito HTS and mosquito HV make assay miniaturisation simple, leading to significant savings on precious reagents and time. Both liquid handlers are best for multi-user labs as you can just walk up to either one and use it. mosquito HTS offers an accurate and easy-to-use-solution to miniaturising any assay within an automated, high-throughput setting. Volume range is 25 nL 1.2 ΜL, which can be expanded to cover 25 nL 5 ΜL in conjunction with mosquito HV. By using mosquito's positive displacement pipetting technology, dead volumes are minimised to under 0.3 ΜL. Using mosquito HTS means you can prepare “assay ready� plates containing test compounds direct from library stocks or dilution plates, as the disposable micropipettes guarantee zero carry-over between samples. mosquito HTS can aspirate from any source plate leaving dead volumes of less than 0.3 ΜL both critical cost areas to consider when capitalising on the savings of assay miniaturisation for high throughput screening assays. You can easily program mosquito HTS to perform traditional serial dilutions by aspirating, dispensing and mixing across a plate using miniaturised volumes ranging from 25 nL 1.2 ΜL. This allows you to effectively perform hit confirmation from high throughput screening assays using multiple compound concentrations." .
SCR:020865 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VaLet Robot" ;
rdfs:label "Thermo Fisher | VaLet Robot; Lab Automation" ;
definition: "Lab automated tool that automates applications from simple instrument loading to more complex, integrated workflows (with Plate Storage Only)" .
SCR:020866 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Mosquito HV" ;
rdfs:label "TTP Labtech | Mosquito HV Automated Liquid Handler" ;
definition: "TTP Labtech introduced the mosquito HV liquid handler to bridge the gap between nanolitre and microlitre pipetting. It provides accurate liquid handling for low volume serial dilutions and assay plate preparation across the intermediate volume range of 500 nL 5 �L. TTP Labtech's mosquito HV can be employed for a wide range of chemical and biological-based applications; including compound and small molecule screening, cell- or bead-based assays, enzyme kinetic assays, ELISAs, and molecular biology applications including rtPCR/qPCR set-up, RNAi screening and SNP genotyping." .
SCR:020867 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DxI 800 Access" ;
rdfs:label "Beckman Coulter | UniCel DxI 800 Access Immunoassay System" ;
definition: "Immunoassay system analyzer by Beckman Coulter with standardized test menus, assay protocols, instrument processes and reference ranges. Sample types include serum, plasma, urine, amniotic fluid, and whole blood." .
SCR:020868 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PowerLook_2100XL" ;
rdfs:label "UMAX | 2100XL Flat Bed Scanner" ;
NIFRID:synonym "UMAX PowerLook 2100XL" ;
definition: "UMAX PowerLook 2100XL is a scanner for graphics professionals who require high resolution and fast color scanning of any image in a small package. You can scan illustrations, newspapers, magazines, transparencies, color photos, and even x-rays, textiles, and negatives. The scanning area measures a full 12\" by 17\", despite the small footprint of just over 18\" by 24\" to fit on any desktop. The scan area can accommodate up to thirty-two 35mm slides when used with the transparency adapter. High 3.4Dmax captures fine details of shadow areas -- especially important when scanning transparencies. In addition, batch scanning increases productivity by scanning more than one image in a single pass." .
SCR:020869 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Varian_Prostar 210" ;
rdfs:label "Varian | Prostar 210 Solvent Delivery System" ;
NIFRID:synonym "Prostar 210 Solvent Delivery System" ;
definition: "High-Performance Liquid Chromatography (HPLC) solvent delivery module (pump). It is used in laboratories to precisely pump solvents at high pressures to separate, identify, and quantify the components of a chemical mixture." .
SCR:020872 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ Virsonic_100" ;
rdfs:label "Virtis | Virsonic 100 Ultrasonic Probe Homogenizer" ;
definition: "VirTis Virsonic 100 is an ultrasonic probe homogenizer, designed for cell disruption and fluid processing. Uses a variety of probes to process fluid volumes from 0.2 to 60 mL." .
SCR:020873 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Nanoscope IIIA" ;
rdfs:label "Roche | Veeco Nanoscope IIIA Atomic Force Microscope" ;
definition: "Veeco Multimode Nanoscope IIIa AFM has a resolution of ~ 0.3 nm with A scanner. The instrument is capable of imaging areas ~ 1 sq.,m (using the standard A scanner), ~12 sq.,m. (using vertical engagement EV scanner) and ~125 sq.,m (using vertical engagement JV scanner) in the XY direction. The scanning range in the Z direction for EV and JV scanner are ~ 2,m and ~ 5,m respectively. The AFM is capable of imaging in Contact mode and Tapping mode with Nanoindentation capabilities. Attachments include a Fluid Cell for imaging in liquids (Contact and Tapping mode) and an Anti-vibration suspension mount for atomic resolution imaging. A 15 mm sample disc is used to mount the samples with access to ~ 2-3 mm area at the center of the sample." .
SCR:020874 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Multimode 8" ;
rdfs:label "Bruker | |Veeco Multimode 8 Atomic Force Microscope" ;
definition: "MultiMode 8-HR is an atomic force microscope which is well suited for imaging in both air and fluid. Heating to 250C, cooling to -35C with temperature control accessories. Nanothermal analysis for local polymer phase transition temperatures up to 350C.. Atomic resolution electrochemistry with AFM, STM, and SECPM. Invent your own mode by accessing and modifying any signal, high or low voltage. A large variety of standard operating modes and many capabilities enable the MultiMode 8-HR AFM system to characterize everything from mechanical to electrical properties" .
SCR:020875 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1525" ;
rdfs:label "Waters | 1525 Binary HPLC Pump" ;
definition: "Itegrated, high-pressure, binary HPLC pump that feature on-board pulse dampening and efficient mixing. Their pulse-free solvent flow, from analytical to semi-preparative flow rates, makes them best for use with highly sensitive detectors. Designed for use with 2 to 4.6 mm I.D. columns in routine LC and LC/MS applications, these pumps have a programmable flow-rate range of 0.00 to 10.00 mL/min in 0.01 mL increments." .
SCR:020876 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2996" ;
rdfs:label "Waters | 2996 Photodiode Array Detector" ;
definition: "Waters 2996 PDA Detector can be used for in-vitro diagnostic testing to analyze many compounds, including diagnostic indicators and therapeutically monitored compounds. It also describes detector optics and the principles of Spectral Contrast used in the Millennium32 software for analyzing the data from the PDA detector." .
SCR:020878 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1450" ;
rdfs:label "Wallac | 1450 Liquid Scintillation Counter" ;
definition: "Wallac 1450 MicroBeta is a liquid scintillation counter and luminescence detector that can accommodate either 1, 2, 3, 6, or 12 detectors, each of which can count in 96- and 24- or 96- and 384-well plate formats. Samples may be counted in microplates, tubes, or on filters for added flexibility. The counter features dual photomultiplier tubes (PMT), with the first PMT set over the sample and the second located below. This method of coincidence counting provides optimal productivity for any compatible assay, including proximity and filtration assays among others." .
SCR:020880 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Waters_Synapt_G2" ;
rdfs:label "Waters | Synapt G2 Mass Spectrometer" ;
definition: "Synapt G2 Mass Spectrometry (MS) system is a hybrid, quadrapole/orthogonal acceleration, time-of-flight (oa-TOF) mass spectrometer controlled by MassLynx software. The Waters Synapt G2 is compatible with the Acquity UPLC and nanoAcquity UPLC systems. Hamilton STARplus liquid handling robot." .
SCR:020881 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Trio 2000" ;
rdfs:label "GE | VG Trio 2000 GE Healthcare Typhoon Trio Variable Mode Imager System" ;
definition: "Typhoon instrument is a variable-mode imager that produces digital images of radioactive, fluorescent, or chemiluminescent samples. The Typhoon instrument is available in several models. The Typhoon Trio instrument contains three internal lasers (blue, green, and red)." .
SCR:020882 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ProteinLynx" ;
rdfs:label "Waters | ProteinLynx 3.03 Server" ;
definition: "ProteinLynx Global SERVER (PLGS) is a fully integrated Mass-Informatics platform for quantitative and qualitative proteomics research. It is the central analytical platform for Waters proteomics systems. PLGS leverages the selectivity of exact mass measured data and the specificity of MSE analysis. Combined with intelligent filtering and scoring routines, this minimizes the occurrence of false positive results. PLGS is based on open/pluggable system architecture, providing scalable, automated workflow for your high-throughput data processing and data interpretation. PLGS also includes project and database management tools with integrated results visualization and reporting. Import sample information and data into PLGS through XML (mzData supported), which provides integration of the PLGS toolset into a LIMS or Data Management System such as Waters NuGenesis SDMS. The PLGS custom report generation utility also allows you to produce publication-ready result reports." .
SCR:020883 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Quattro_Premier" ;
rdfs:label "Waters | Quattro Premier LC/MS" ;
NIFRID:synonym "Quattro Premier Mass Spectrometer" ;
definition: "Micromass (now Waters) Quattro Premier triple quadrupole mass spectrometer operates with an Agilent 1100 HPLC and specializes in quantitative work and selective of targeted analytes including metabolites and other small molecules, and peptides from complex matrices such as serum, tissue, cell culture, and other biological sources." .
SCR:020884 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DynaPro" ;
rdfs:label "Wyatt | DynaPro Plate Reader" ;
definition: "Plate Reader for dynamic light scattering (DLS) and static light scattering (SLS) measurements of the size, molecular weight and interactions of proteins, nanoparticles and other macromolecules in situ in industry-standard microwell plates. No liquid handling occurs after dispensing into the plates, to maximize throughput and minimize sample carryover." .
SCR:020885 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Xevo G2" ;
rdfs:label "Waters | Xevo G2 Mass Spectrometer" ;
definition: "Mass spectrometer with selectivity, in-spectrum dynamic range, speed of analysis, quantitative accuracy and exact mass performance simultaneously, for any UPLC/MS or UPLC/MSE experiment." .
SCR:020887 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Calypso" ;
rdfs:label "Wyatt | Calypso Composition-Gradient Multi-Angle Light Scattering (CG-MALS)" ;
definition: "Composition-Gradient Multi-Angle Light Scattering machine that characterizes biomolecular interactions, label free and immobolization free. It is able to determine equilibrium dissociation constants self and hhetero association as well as more complex interactions." .
SCR:020888 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Eclipse AF4" ;
rdfs:label "Wyatt | Eclipse AF4 Field-Flow Fractionation system" ;
definition: "Eclipse AF4 is optimal for all standard asymmetric flow field flow fractionation AF4 separations as well as frit inlet channels and semi preparative AF4. Combined with HPLC equipment and Wyatt's multi angle light scattering detectors, Eclipse AF4 excels at characterizing difficult samples." .
SCR:020889 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Dynapro III" ;
rdfs:label "Wyatt | DynaPro III Plate Reader" ;
definition: "Plate Reader for dynamic light scattering (DLS) and static light scattering (SLS) measurements of the size, molecular weight and interactions of proteins, nanoparticles and other macromolecules in situ in industry-standard microwell plates. No liquid handling occurs after dispensing into the plates, to maximize throughput and minimize sample carryover." .
SCR:020890 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Xevo" ;
rdfs:label "Waters | Xevo TQ-XS" ;
definition: "Triple quadrapole mass spectrometer with both analytical and microflow UPLC separations. It can be used for MRM testing and has LC flow of up to 2 mL/min." .
SCR:020891 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_microOptilab" ;
rdfs:label "Wyatt | microOptilab Refractometer" ;
definition: "Refractive Index detector that offers high sensitivity and 50 times dynamic range of every other UHPLC RI detector. Like Optilab, it offers temperature control both above and below ambient, as well as measurement of absolute refractive index of solvents." .
SCR:020892 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Eclipse" ;
rdfs:label "Wyatt | Eclipse DualTec Field-Flow Fractionation system" ;
definition: "Field flow fractionation device supports both Hollow Fiber Flow FFF HF5 and Asymmetric Flow FFF AF4 in one instrument. Utilizing one HPLC stack and one set of Wyatt detectors, DualTec permits automated switching between any two of SEC, AF4 and HF5 separation followed by MALS and or DLS characterization." .
SCR:020893 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_microDAWN" ;
rdfs:label "Wyatt | microDAWN Multi-Angle Light Scattering Detector" ;
definition: "Multi Angle Light Scattering Detector that can be coupled to any UHPLC SEC system to determine absolute molecular weights and sizes of proteins, peptides, polymers or nanoparticles below 50 nm in radius directly, without resorting to column calibration or reference standards." .
SCR:020894 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Mobius" ;
rdfs:label "Wyatt | Mobius Dynamic Light Scatterer" ;
definition: "Dynamic Light Scattering device DLS measures electrophoretic light scattering ELS and DLS simultaneously to determine zeta potential or molecular charge, automated by autosampler or manually, under wide range of solvents." .
SCR:020895 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_miniDAWN" ;
rdfs:label "Wyatt | miniDAWN Multi-Angle Light Scattering Detector" ;
definition: "Multi Angle Light Scattering Detector used to determine absolute molar mass and size to characterize proteins, peptides, small polymers and nanoparticles in solution." .
SCR:020896 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DAWN" ;
rdfs:label "Wyatt | DAWN Multi-Angle Light Scattering Detector" ;
definition: "Multi Angle Light Scattering Detector most often used in conjunction with size exclusion chromatography SEC MALS or field flow fractionation FFF MALS to determine distributions of molecular weight, size and composition." .
SCR:020897 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Optiab" ;
rdfs:label "Wyatt | Optiab Refractometer" ;
definition: "Refractometer based on semiconductor photodiode technology and proprietary computer algorithms. Can be used for standard chromatographic applications and measurements such as high concentrations, determination of sample refractive increments dn dc and solvent refractive index." .
SCR:020898 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DynaPro_NanoStar" ;
rdfs:label "Wyatt | DynaPro NanoStar Dynamic Light Scattering Detector" ;
definition: "Dynamic Light Scattering device that may be utilized to measure not just size, size distributions, particle concentration and weight average molar mass, but also solution properties relevant to sample stability.cuvette-based DLS instrument used for the analysis of proteins, promiscuous inhibitors, micelles, quantum dots, liposomes, metallic nanoparticles and more." .
SCR:020899 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Viscostar" ;
rdfs:label "Wyatt | Viscostar Viscometer" ;
definition: "Differential viscometer used in conjunction with SEC MALS IV to determine size and conformation of all types of biopolymers, synthetic polymers and even proteins and peptides." .
SCR:020900 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_microViscostar" ;
rdfs:label "Wyatt | microViscostar Viscometer" ;
definition: "microViscoStar incorporates multiple novel technologies to provide highest sensitivity, stability and solvent compatibility of any available viscometer for UHPLC. Its ease of use and serviceability make it companion for Wyatt's microDAWN light scattering and microOptilab refractive index detectors for UHPLC." .
SCR:020901 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IVIS 100" ;
rdfs:label "Perkin Elmer | | Xenogen IVIS 100 Imaging System" ;
definition: "In vivo imaging system that combines 2D optical and 3D optical tomography in one platform. The system can be used for preclinical imaging research and development best for non-invasive longitudinal monitoring of disease progression, cell trafficking and gene expression patterns in living animals." .
SCR:020902 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cheetah EVO" ;
rdfs:label "YXLON | Cheetah EVO Series X-Ray" ;
definition: "X-ray inspection system for SMT, semiconductor, and laboratory assembly applications." .
SCR:020903 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FF20" ;
rdfs:label "YXLON | FF20 CT System" ;
definition: "Computed tomography system for 3D inspection results at high resolution. In electronics and material science industries can use it for R&D, defect analysis, process monitoring, or CT metrology." .
SCR:020904 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ultraDAWN" ;
rdfs:label "Wyatt | ultraDAWN Multi-Angle Light Scattering Detector" ;
definition: "Multi Angle Light Scattering Detector that measures multi angle light scattering and reports results weight average molecular weight Mw and rms radius Rg in real time." .
SCR:020905 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GX430T" ;
rdfs:label "Zebra | GX430T Barcode Label Printer" ;
definition: "Thermal transfer barcode printer with label, receipt and tag-handling capabilities that connects via USB, serial, or parallel port." .
SCR:020906 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cougar EVO" ;
rdfs:label "YXLON | Cougar EVO Series X-Ray" ;
definition: "X-ray machine for inspection of SMT, semiconductor, and laboratory assembly applications." .
SCR:020907 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CSU-22" ;
rdfs:label "Yokogawa | CSU-22 Spinning Disk Confocal Microscope" ;
definition: "Spinning disk confocal micrscope for observation of various life processes in living samples in real time, minimal photo bleaching and photo toxicity." .
SCR:020908 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FF70" ;
rdfs:label "YXLON | FF70 CL X-Ray System" ;
definition: "X ray inspection system has been developed to enable automated analysis for flaws in semi-conductors. Flaws can be found on wafer, on substrate, in strip in sub assembly or in final device." .
SCR:020909 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FF35" ;
rdfs:label "YXLON | FF35 CT System" ;
definition: "Computed tomography system available in single or dual tube configuration. It can be used for small to medium sized parts inspection in automotive, electronics, aviation, and material science industries." .
SCR:020910 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FF65" ;
rdfs:label "YXLON | FF65 CL 3D X-Ray" ;
definition: "X ray inspection system for automatic analysis of smallest and most demanding features within 3D IC, MEMS and sensors." .
SCR:020911 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_X-Strea 2000" ;
rdfs:label "Rigaku | X-Stream 2000 Cryo-freezing System" ;
definition: "Cryogenic Crystal Cooler is a self-contained apparatus designed for cooling crystals to a temperature within the range of -180C to 4C. The X-stream 2000 system takes room air, compresses it, and removes the impurities from it to produce clean, dry nitrogen. This gas is then cooled to nearly -196C, and then rewarmed to the desired temperature" .
SCR:020913 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_S4M" ;
rdfs:label "Zebra | S4M Barcode Label Printer" ;
definition: "Barcode label printer with 203 and 300 dpi print resolutions, multiple interface options (including serial, parallel, USB, Ethernet and 802.11b wireless connections). It has side-loading design and an 8\" label roll capacity." .
SCR:020914 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Auriga" ;
rdfs:label "Zeiss | Auriga Auriga" ;
definition: "Electron microscope with pulsed laser beam that creates images in high resolution in the nanometre range. This miscroscope allows the user to investigate your samples with X-ray analysis, rework interesting sample positions, and analyze non-conducting material and complex geometries." .
SCR:020915 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Axiovert" ;
rdfs:label "Zeiss | Axio Vert series Axiovert 200 inverted microscope" ;
definition: "Inverted microscope that is used for the examination of cell and tissue culture of sediments in culture flasks, Petri dishes, microtiter plates, etc. in transmitted and reflected light. It hass attachment possibilities for various tools (micromanipulation), different light sources, temperature control devices., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:020916 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_5-Live" ;
rdfs:label "Zeiss | 5-Live" ;
definition: "Visible confocal microscope that acquires the X dimension simultaneously on a line CCD detector while scanning only in the Y dimension. This allows users to increase the speed of image acquisition compared to traditional confocal systems. This system is equipped with two fluorescence detectors and 4 lasers lines at 405nm, 488nm, 561nm and 633nm. It is capable of scanning over 120 FPS for a large field of view." .
SCR:020917 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FF85" ;
rdfs:label "YXLON | FF85 CT System" ;
definition: "Computed tomography system with dual tube configuration for use with a wide variety of material types and parts size." .
SCR:020918 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Axioplan" ;
rdfs:label "Zeiss | Axioplan 2 imaginig system" ;
definition: "Upright microscopy imaging platform for complex research that is optimized for light transmission and extremely high contrast fluorescence imaging. This complete system comes fully configured for best performance, range and functionality." .
SCR:020919 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Zeiss_Lightsheet_Z.1" ;
rdfs:label "Zeiss | Lightsheet Z.1 Fluorescence Microscope" ;
NIFRID:synonym "Zeiss Lightsheet Z.1" ;
definition: "Light sheet fluorescence microscope for the imaging of large cleared specimens. Lightsheet Z.1 with Clr Plan-Apochromat 20x/1.0 Corr nd=1.38 is used to perform experiments with tissue cleared by Scale medium (Hama et al, Nat Neurosci. 2011), which has a refractive index of n=1.38." .
SCR:020920 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Libra" ;
rdfs:label "Zeiss | Libra 200MC Monochromator" ;
definition: "Monochromated field emitter that produces high resolution high contrast images due to the Zeiss proprietary electron gun monochromator (MC) and Kohler illumination system. The monochromator enables the operator to reduce the energy width of primary electrons to less than 0.2 eV and thereby allows for highest resolution in Electron Energy Loss Spectroscopy (EELS)." .
SCR:020921 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MU2000-D" ;
rdfs:label "YXLON | MU2000-D X-Ray System" ;
definition: "Industrial X ray and CT inspection system for broad applications in foundries, R&D, laboratories, universities, and educational institutions. system delivers image quality with digital flat panel detector and radioscopy." .
SCR:020922 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LSM 780" ;
rdfs:label "Zeiss | LSM 780 Confocal Laser Scanning Microscope" ;
definition: "Laser Scanning Microscopes (LSM) for high resolution imaging of biological or material samples. The compact scanning module can be fitted to an inverted (Axio Observer.Z1 RP or SP) or upright (Axio Imager.Z2, Axio Imager.M2 or Axio Examiner) microscope." .
SCR:020923 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LSM_5_LIVE" ;
rdfs:label "Zeiss | LSM 5 LIVE Confocal Microscope" ;
definition: "Confocal microscope that acquires the X dimension simultaneously on a line CCD detector while scanning only in the Y dimension. This system is equipped with two fluorescence detectors and 4 lasers lines at 405nm, 488nm, 561nm and 633nm. It is capable of scanning over 120 FPS for a large field of view." .
SCR:020924 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Zeiss_2000C" ;
rdfs:label "Zeiss | 2000C Stereomicroscope" ;
definition: "Optical stereomicroscope with 7.7:1 zoom range (pancratic system 0.65x to 5.0x) zooms in continuously or with click stop. It has an object field size of 35mm, with an 0.3x attachment lens system permitting object fields of up to 118mm to be viewed." .
SCR:020925 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LSM 880" ;
rdfs:label "Zeiss | LSM 880 with Airyscan Confocal Laser Scanning Microscope" ;
definition: "Fully enclosed laser scanning confocal imaging microscopefor heating and environmental control with media perfusion capabilities and CO2 control. It can be used for Live Cell Imaging, FRET and Anisotropy, FRAP and FLIP, FCS, Photoactivation/ -conversion., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:020926 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LSM_5_DUO" ;
rdfs:label "Zeiss | LSM 5 DUO Spectral Confocal Microscope" ;
definition: "Laser scanning microscope for the high resolution imaging of biological or material samples." .
SCR:020927 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Axioscan" ;
rdfs:label "Zeiss | Axio Scan.Z1 Slide Scanner" ;
definition: "Used to digitize specimens with the Axio Scan.Z1 slide scanner to create high-quality virtual slides. Axio Scan.Z1 tackles the most demanding virtual microscopy research tasks as easily as it handles your routine work. The software module ZEN slidescan is designed specifically for the workflow of capturing virtual slides, while ZEN image analysis tools prepare your data accurately. Organize your virtual slides with ZEN browser, the web-based database, then view your data from any location using any operating system , or share virtual microscopy images online with colleagues and organize your projects, even when you are on the go." .
SCR:020928 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sigma" ;
rdfs:label "Zeiss | Sigma VP Scanning Electron Microscope" ;
definition: "ZEISS SIGMA VP field emission scanning electron microscope (FE-SEM) for imaging of non-conducting samples. It images of bacteria, cells, plants and organisms. Uses ATLAS software and can be combined with 3View technology from Gatan Inc." .
SCR:020929 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MicroBeam" ;
rdfs:label "Zeiss | PALM MicroBeam PALM" ;
definition: "PALM MicroBeam scanning electron microscope for isolating uncontaminated source material simple." .
SCR:020930 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Supra" ;
rdfs:label "Zeiss | Supra 25 Field Emission Scanning Electron Microscope" ;
definition: "Field scanning electron microscope with analytical specimen chamber with choice of optional detectors and accessories. It has 5-axes motorised cartesian stage can handle multiple smaller specimens simultaneously. It can image bulky or irregular shaped specimens." .
SCR:020931 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scidetect" ;
definition: "Software tool for detecting automatically generated academic papers. Discovers text that has been generated with SCIgen and other fake paper generators like Mathgen and Physgen. Provides on open source version of the scigen detector." .
SCR:020932 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:haste_toolkit" ;
rdfs:label "HASTE-project" ;
NIFRID:synonym "HASTE Toolkit",
"Hierarchical Analysis of Spatial and TEmporal data",
"Hierarchical Analysis of Spatial and Temporal Data" ;
definition: "Software toolkit for rapid development of cloud native intelligent data pipelines for scientific data streams. Hierarchical approach to acquisition, analysis, and interpretation of image data. Developed in the project Hierarchical Analysis of Spatial and Temporal Data." .
SCR:020933 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Collect Earth Online" ;
NIFRID:abbrev "CEO" ;
definition: "Web tool for systematic reference data collection in land cover and use applications.Open source software tool for land monitoring. Systematic reference data collection tool for land cover and land use applications. Satellite image viewing and interpretation system developed by SERVIR joint efforts between NASA, FAO, US Forest Service and Google." .
SCR:020934 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MEND QC" ;
NIFRID:synonym "Mapped Exonic Non-Duplicate QC" ;
definition: "Software tool to calculate number of mapped exonic non duplicate reads in bam file containing RNA-Seq data." .
SCR:020935 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ImJoy" ;
rdfs:label "ImJoy" ;
definition: "Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers." .
SCR:020936 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Type 1 Diabetes Knowledge Portal" ;
NIFRID:synonym "T1D Knowledge Portal" ;
NIFRID:abbrev "T1DKP" ;
definition: "Portal for providing data and tools to promote understanding and treatment of type 1 diabetes and its complications.Enables browsing, searching, and analysis of human genetic information linked to type 1 diabetes and related traits, while protecting integrity and confidentiality of underlying data.Represents effort to coordinate collection and deposition of genomic and epigenomic data related to type 1 diabetes and its complications." .
SCR:020937 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Common Metabolic Diseases Knowledge Portal" ;
NIFRID:abbrev "CMDKP" ;
definition: "Portal enables browsing, searching, and analysis of human genetic information linked to common metabolic diseases and traits, while protecting integrity and confidentiality of underlying data. Aggregates and analyzes genetic association results, epigenomic annotations, and results of computational prediction methods to provide data, visualizations, and tools in open access portal." .
SCR:020938 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:fgsea" ;
rdfs:label "fgsea" ;
NIFRID:synonym "Fast Gene Set Enrichment Analysis",
"fast gene set enrichment analysis",
"FGSEA" ;
definition: "Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction." .
SCR:020939 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:MERMAID" ;
rdfs:label "MERMAID" ;
NIFRID:synonym "iMagE Registration via autoMAtIc Differentiation" ;
definition: "Registration toolbox written in pyTorch. Supports various image registration methods. Focuses on nonparametric registration approaches including stationary velocity fields and large discplacement diffeomorphic metric mapping models though simple affine registration is also possible. Allows for rapid prototyping of new image registration approaches and similarity measures." .
SCR:020940 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012397",
"r3d100013223" ;
rdfs:label "brainlife" ;
NIFRID:synonym "Brainlife" ;
definition: "Free cloud platform for secure neuroscience data analysis. Allows to manage data, processing and results, sharing projects privately with collaborators or publicly with brainlife.io community.Promotes engagement and education in reproducible neuroscience.You can share your neuroimaging data publicly or privately. Data on brainlife.io is organized as Datatypes to allow interoperability between Apps." .
SCR:020942 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Flowlogic" ;
NIFRID:synonym "Flowlogic Software",
"Flowlogic TM Software" ;
definition: "Software tool for flow cytometry data analysis by Miltenyi Biotec." .
SCR:020943 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MACSQuantify" ;
NIFRID:synonym "MACSQuantify Software",
"MACSQuantify TM Software" ;
definition: "Software provides user interface for data acquisition on MACSQuant Analyzer Flow Cytometer Instrument and also works as stand alone application for flow cytometry data analysis." .
SCR:020945 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MIRACL" ;
NIFRID:synonym "Multi modal Image Registration And Connectivity anaLysis" ;
definition: "Automated software resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling analysis of histological features across multiple fiber tracts and networks, and their correlation with in vivo biomarkers.Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Open source pipeline for automated registration of mice clarity data to Allen reference atlas, segmentation and feature extraction of mice clarity data in 3D, registration of mice multimodal imaging data to Allen reference atlas, tract or label specific connectivity analysis based on Allen connectivity atlas,comparison of diffusion tensort imaging/tractography, virus tracing using CLARITY and Allen connectivity atlas, statistical analysis of CLARITY and Imaging data, atlas generation and label manipulation." .
SCR:020946 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MITE-Hunter" ;
NIFRID:synonym "Miniature Inverted repeat Transposable Elements Hunter" ;
definition: "Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences." .
SCR:020947 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:mircat",
"biotools:siloco" ;
rdfs:label "UEA sRNA Workbench" ;
NIFRID:synonym "UEA small RNA Workbench" ;
definition: "Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals." .
SCR:020948 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:bs-seeker2" ;
rdfs:label "Bs-Seeker2" ;
NIFRID:synonym "Bisulfite Sequencing Seeker2",
"BS Seeker2" ;
definition: "Software tool as versatile aligning pipeline for bisulfite sequencing data. Used for mapping bisulfite sequencing data and generating DNA methylomes. Improves mappability over existing aligners by using local alignment. Maps reads from RRBS library by building special indexes with improved efficiency and accuracy. Provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing overestimation of DNA methylation levels." .
SCR:020949 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genomic Association Tester" ;
NIFRID:abbrev "GAT" ;
definition: "Software tool as simulation framework for testing association of genomic intervals. Used for estimating significance of overlap between multiple sets of genomic intervals. Estimates statistical significance based on simulation and controls for multiple tests using false discovery rate." .
SCR:020950 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cgmapotools" ;
definition: "Software package for DNA methylation analysis. Used for context-wise, gene-wise, bin-wise, region-wise and sample-wise analysis and visualizations. Used to improve precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data." .
SCR:020951 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "genBlastA" ;
NIFRID:synonym "GenBlastA" ;
definition: "Software tool to enable BLAST to identify homologous gene sequences. Graph based algorithm, which automatically filters High Scoring Pairs into well defined groups, each representing candidate gene in target genome.Used for identifying homologous sequences. Used for extracting relevant HSPs that represent candidate homologous genes from the entire HSP report." .
SCR:020952 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mapping the pancreas and its ecosystem at the cellular level in health and type 1 diabetes" ;
definition: "Portal for scRNA-seq study. Includes dendrogram visualization and clustering of all cells in scRNA-seq study as well as interactive filtered views for cell type, gene and/or donor group." .
SCR:020954 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Cell Methylation Viewer" ;
NIFRID:synonym "Neomorph: Brain Cell Methylation Viewer" ;
NIFRID:abbrev "mC Viewer" ;
definition: "Viewer for DNA Methylation Atlas of Mouse Brain at Single Cell Resolution. Browser to interactively explore single cell methylome dataset including exploration of methylation diversity of one gene at single-cell or cell-type level, exploration of cell type composition of adult mouse brain dissection regions and anatomical structures, explorartion of spatial distribution and methylation signature genes of one cell type." .
SCR:020955 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ACCURATE" ;
NIFRID:synonym "Accurate" ;
definition: "Software package for quantitative analysis of PET/CT studies. Quantitative oncology molecular analysis suite. Allows for DICOM input of both PET and CT data. It includes several image processing steps such as rebinning/resampling, cropping and smoothing. After loading and processing PET/CT images, lesions can be delineated using a range of segmentation." .
SCR:020956 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TCapture" ;
NIFRID:synonym "TCapture v.4.3.0.605" ;
definition: "Tucsen camera image acquisition, managing and processing software by Tucsen Photonics Co., Ltd. Professional imaging software application developed by Tucsen for full control of Tucsen cameras.Tucsen continually upgrades TCapture." .
SCR:020957 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SuperDecisions" ;
definition: "Educational software that implements Analytic Hierarchy Process and Analytic Network Process. Provides tools to create and manage AHP and ANP models, enter your judgments, get results and perform sensitivity analysis on results. Provides support for complex, multilevel Benefits Opportunities Costs Risks models." .
SCR:020958 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hugging Face" ;
definition: "Portal to build, train and deploy state of the art models powered by reference open source in natural language processing." .
SCR:020959 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MesKit" ;
NIFRID:synonym "Multi region exome sequencing analysis tool Kit" ;
definition: "Software R package for dissecting cancer evolution from multi region derived tumor biopsies via somatic mutations. Used for characterizing cancer genomic ITH and inferring history of tumor evolution via implementation of well established computational and statistical methods." .
SCR:020960 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Golddigger" ;
definition: "ImageJ macro to detect, mark and count electron dense markers like goldgrains or quantum dots in electron micrographs." .
SCR:020963 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GBRS" ;
definition: "Software suite of tools for reconstructing genomes using RNA-Seq data from multiparent population and for quantifying allele specific expression." .
SCR:020964 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Differential Gene Correlation Analysis" ;
NIFRID:abbrev "DGCA" ;
definition: "Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix." .
SCR:020966 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PAM" ;
NIFRID:synonym "PIE analysis with MATLAB",
"Pulsed Interleaved Excitation analysis with MATLAB",
"Pulsed interleaved excitation Analysis with Matlab" ;
definition: "Software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with focus on experiments using pulsed interleaved excitation. Open source software package written in MATLAB that offers workflow through its graphical user interface. Framework for integrated analysis of imaging, single-molecule, and ensemble fluorescence data.Supports most types of data collection modalities." .
SCR:020967 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1125" ;
rdfs:label "University of Leicester Advanced Imaging Facility" ;
NIFRID:synonym "Advanced Imaging Facility" ;
NIFRID:abbrev "AIF" ;
definition: "Open access light microscopy facility of College of Life Sciences. Offers wide range of confocal and conventional fluorescence microscopes and image analysis resources. AIF is part of Core Biotechnology Services CBS." .
SCR:020968 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1127" ;
rdfs:label "University of Freiburg Life Imaging Center Core Facility" ;
NIFRID:synonym "LIC - Life Imaging Center",
"University of Freiburg LIC - Life Imaging Center" ;
NIFRID:abbrev "LIC" ;
definition: "Central core facility open to members of all faculties and the university clinic. Consists of 14 rooms in the Center for Integrative Signalling Analysis with 9 microscopy rooms with 20 microscope set-ups (3D-STED, confocal FLIM, two 2-photon confocal microscopes, 4 conventional confocal microscopes, lightsheet microscope, 4 high-end widefield ratio-imaging set-ups, 4 fluorescence stereo microscopes, 3 special set-ups for screening. LIC microscopes are hosted in Biosafety level S2 and S1 environments, connected to a large wet lab area and a cell culture room, both Biosafety level S2 classified. Additionally, the LIC offers a large computer lab with 12 high-end workstations for image processing and analysis. The LIC also covers two additional rooms, hosting 3 LSM systems in a neighboring building of the Signalling Campus Freiburg (SCF)." .
SCR:020969 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus | LEXT OLS4100 laser confocal microscope" ;
definition: "Laser scanning digital microscope for non-contact 3D observations and measurements of surface features at 10 nanometer resolutions with fast image acquisition and high-resolution images over wider area. Z-drive moves in steps less than 1nm, accuracy and repeatability guaranteed by Olympus. The system includes 5 objectives: 5x/0.15, 10x/0.30, 20x/0.60, 50x/0.95, and 100x/0.95." .
SCR:020972 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DTUrtle" ;
NIFRID:synonym "Differential Transcript Usage-rtle" ;
definition: "Software R package to perform differential transcript usage analysis of bulk or single-cell RNA-seq data." .
SCR:020973 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1128" ;
rdfs:label "Clemson University Light Imaging Core Facility" ;
NIFRID:synonym "Clemson Light Imaging Facility" ;
NIFRID:abbrev "CLIF" ;
definition: "Core light microscopy facility located on main campus of Clemson University. Offers access to multiple Leica Microsystems instruments, including SP8X LIGHTNING confocal with STED,SPE confocal, DMi8 widefield/TIRF/GSD system,THUNDER model organism imager, LMD6500, M125 stereoscope, and DM750P polarized light microscope.We also house Olympus LEXT OLS4100 optical profiler, GE InCell 2500HS high content screener, and Biorad S3e cell sorter. Offers assistance with equipment selection, image analysis, and sample preparation. Offers prepared slides for 4 color fluorescence imaging and can also prepare custom slides." .
SCR:020974 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "City of Hope Department of Pathology Core Facility" ;
definition: "Department of Pathology at City of Hope combines state-of-the-art laboratories equipped with the latest diagnostic techniques and advanced instrumentation with superior investigative skills to accurately and rapidly identify even the rarest and most complex diseases. Our experts provide comprehensive services, from initial diagnosis to monitoring of prognostic indicators throughout the treatment process." .
SCR:020975 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Beckman Research Institute of City of Hope" ;
definition: "Not-for-profit medical research facility located at and partnering with the City of Hope National Medical Center in Duarte, CA, United States.Fields of research include Cancer, Diabetes, Metabolic disorder, HIV/AIDS." .
SCR:020976 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "BioTools:deep_transfer_graph_convolutional_network" ;
rdfs:label "Deep Transfer Graph Convolutional Network" ;
NIFRID:abbrev "DTGCN" ;
definition: "Software tool as novel deep learning approach for multi-stage malaria parasites recognition in blood smear images using deep transfer graph convolutional network. DTGCN model is based on unsupervised learning by transferring knowledge learnt from source images that contain discriminative morphology characteristics of multi stage malaria parasites." .
SCR:020977 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "triku" ;
definition: "Software tool as feature selection method based on nearest neighbors for single-cell data." .
SCR:020978 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "NEST Initiative" ;
NIFRID:synonym "Neural Simulation Technology Initiative" ;
definition: "Incorporated as non-profit member based organization promoting scientfic collaboration in computational neuroscience.Advances computational neuroscience by pushing limits of large scale simulations of biologically realistic neuronal networks." .
SCR:020979 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "webKnossos" ;
definition: "Web tool for 3D data annotation for connectomics.Open source tool for annotating and exploring large 3D image datasets. Web based data sharing, annotation and visualization software for large scale 3D images. Provides flight mode, single view egocentric reconstruction method enabling to reconstruct for axons and for dendrites in 3D electron microscopic data from mammalian cortex. Supports skeleton and volumetric annotations as well as data management functionality." .
SCR:020980 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ISA API" ;
NIFRID:synonym "Investigation Study Assay API" ;
definition: """Open platform for interoperable life science experimental metadata. Metadata framework
as set of community specifications and software tools for enabling discovery, exchange and publication of metadata from experiments in life sciences. Python library for creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats.Provides programmatic metadata handling functionality to support automation, common interface and interoperable medium between two ISA formats, as well as with other life science data formats required for depositing data in public databases.""" .
SCR:020981 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SnapATAC" ;
NIFRID:synonym "Single Nucleus Analysis Pipeline for ATAC-seq" ;
definition: "Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset." .
SCR:020982 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ArchR" ;
definition: "Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing." .
SCR:020983 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:artistoo" ;
rdfs:label "Artistoo" ;
NIFRID:synonym "Artificial Tissue Toolbox" ;
definition: "Software toolbox, formerly called CPMjs, as framework to build interactive, explorable simulation models of cells and tissues in web browser. JavaScript library to build interactive Cellular Potts Models as command line applications or in web browser." .
SCR:020984 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NPSV" ;
NIFRID:synonym "Non-Parametric Structural Variant Genotyper",
"Non-Parametric Structural Variant genotyper" ;
definition: "Software Python tool for standalone genotyping of deletion and insertion structural variants in short read whole genome sequencing data. Implements machine learning based approach for SV genotyping that employs NGS simulation to model the combined effects of the genomic region, sequencer and alignment pipeline." .
SCR:020985 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_431",
"SCR_020988" ;
rdfs:label "Rockefeller University Fisher Drug Discovery Core Facility" ;
NIFRID:synonym "Fisher Drug Discovery Resource Center",
"Fisher Drug Discovery Resource Center Core Facility",
"Rockefeller University Fisher Drug Discovery Resource Center Core Facility" ;
NIFRID:abbrev "DDRC" ;
definition: "Core guides researchers in drug discovery by improving efficiency of their bioassays, identifying compounds and targets of function, and in utilizing technologies for measurement of drug/receptor interactions.Center also has spectroscopic and calorimetric equipment for use in studies of interactions of drugs with their targets." .
SCR:020986 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_430" ;
rdfs:label "Rockefeller University Genomics Resource Center Core Facility" ;
NIFRID:synonym "Genomics Resource Center" ;
definition: "Core offers services and instruments to support genomics research. Houses Illumina NovaSeq, NextSeq, MiSeq sequencers, 10X Genomics Chromium Single Cell System, and Life Technologies QuantStudio 12K flex realtime PCR system. Provides several accessory instruments for sample quantity and quality validation: Agilent Bioanalyzer, Agilent TapeStation, NanoDrop spectrophotometer, and Qubit spectrophotometer.Offers full services for genomic DNA-Seq and RNA-Seq, specializing in preparation of libraries from very small amount of starting total RNA. Users can also prepare their own libraries and use the center�s sequencing-only services. Offers free consultations on experimental designs, library preparation options, sequencer choice, sequencing depth and coverage, and biological replicates.Performs initial sequencing data analysis for all users, and can assist with downstream analysis." .
SCR:020987 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1131" ;
rdfs:label "University of Manchester BioMS Core Facility" ;
NIFRID:synonym "University of Manchester UoM-BioMS",
"UoM-BioMS" ;
NIFRID:abbrev "BioMS" ;
definition: "Core offers mass spectrometry services and associated technologies to the University of Manchester and beyond with focus on biological molecules such as proteins and metabolites in proteomics and metabolomics areas.Provides support from experimental design to advanced sample preparation and data processing and interpretation." .
SCR:020989 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1132" ;
rdfs:label "Rockefeller University Gruss Lipper Precision Instrumentation Technologies Resource Center Core Facility" ;
NIFRID:synonym "Precision Instrumentation Technologies Resource Center",
"The Rockefeller University Gruss Lipper Precision Instrumentation Technologies Resource Center" ;
NIFRID:abbrev "PIT" ;
definition: "The Gruss Lipper Precision Instrumentation Technologies (PIT) Resource Center provides access to various fabrication and rapid prototyping tools for qualified users. The PIT allows users to design and build their own research tools by providing access to wide array of prototyping and fabrication equipment, as well as design and fabrication consultation. The PIT also provides full prototyping service (design through fabrication and testing)." .
SCR:020990 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ez" ;
definition: "Software statistical analysis R package used for easy analysis and visualization of factorial experiments. Provides interface to common analysis techniques, including analysis of variance and mixed effects modeling. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling." .
SCR:020991 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gorilla Experiment Builder" ;
definition: "Cloud based research platform that allows researchers and students to quickly and easily create and deploy behavioural experiments online. Online behavioral experiment builder for running behavioural studies." .
SCR:020992 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "spdurl" ;
NIFRID:synonym "spectral power distribution url" ;
definition: "Software tool as Javascript encoder and decoder to use spectral power distributions in URL." .
SCR:020993 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aperio ImageScope" ;
NIFRID:synonym "Aperio ImageScope 12.3.3",
"Aperio ImageScope 12.3.3.5048",
"Aperio ImageScope 12.4.6" ;
definition: "Software tool for pathology slide viewing. Used for access to color digital slide images to which you can adjust magnification, pan and zoom, compare different stains, annotate areas of interest, perform image analysis, and more. Allows to view slide images taken by Leica biosystems scanner." .
SCR:020994 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "luox" ;
definition: "Open access software platform to faciliate calculation of quantities related to light and lighting. Users can upload spectra and platform will calculate relevant quantites including luminance, chromaticity, and α-opic radiance and α-opic daylight luminances from spectra, generate visualisation of spectrum, and enable export of calculations in tabular form." .
SCR:020995 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MuscleJ" ;
definition: "Software tool to allow characterization of parameters analyzed in fundamental and clinical studies in skeletal muscle field. Running on open source Fiji software platform, simultaneously analyzes parameters from immunofluorescent staining, imaged by different acquisition systems in completely automated manner.Used to analyze muscle cross-sectional area, fiber typing, localization of nuclei within muscle fiber, number of vessels, fiber associated stem cells parameters simultaneously." .
SCR:020996 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_718" ;
rdfs:label "Northwestern University Feinberg School of Medicine Center for Advanced Microscopy Nikon Imaging Center Core Facility" ;
NIFRID:synonym "Center for Advanced Microscopy and Nikon Imaging Center",
"Northwestern University Center for Advanced Microscopy and Nikon Imaging Center" ;
NIFRID:abbrev "CAM" ;
definition: "Core offers instrumentation and services for study of biological processes at whole animal, tissue, cellular and subcellular levels. Services include electron microscopy, super resolution microscopy, fluorescent laser scanning and spinning disk microscopy, fluorescent lifetime imaging, automated high throughput tissue cytometry, atomic force microscopy, laser capture microdissection, mutliphoton imaging, and whole animal bioluminescent and fluorescent imaging. Additionally we provide microinjection equipment, chambers for stable live cell observation, and anesthesia equipment. Provides training on numerous different instrument platforms, consultation on experiment design, as well as digital image processing and image analysis. We are a reference site for several companies including TissueGnostics. CAM is one of three Nikon Imaging Centers in the US, allowing us access and excellent support from Nikon to develop innovative solutions for the cutting edge imaging needs of users. This relationship has allowed our users to push super-resolution technologies to permit multi-color, 3D and live-cell applications. Additionally, we have been working together with Nikon to add confocal laser scanning to a low magnification upright dissection microscope, which is particularly useful to researchers interested in visualizing thick samples (such as epidermal raft cultures) at increased cellular resolution. We are also currently expanding our full service electron microscopy offerings. We currently support TEM and SEM sample preparation, immunogold labeling, platinum replicas, and CLEM." .
SCR:020997 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_466" ;
rdfs:label "University of Minnesota University Imaging Centers Core Facility" ;
NIFRID:synonym "Minnesota University Imaging Centers",
"University Imaging Centers",
"University of Minnesota Imaging Centers" ;
NIFRID:abbrev "UIC" ;
definition: "Center composes network of core imaging facility locations for advanced optical imaging and basic electron microscopy located within the AHC/Medical School (1-151 Jackson Hall, Minneapolis) and College of Biological Sciences (23 Snyder Hall, St. Paul) on the University of Minnesota Twin Cities Campus.UIC cores serve internal and external research clients in design of imaging experiments, choice of and training on suitable imaging systems, and subsequent image processing, visualization and analysis.Provides advanced imaging systems including macro spectral confocal microscopy,wide-field light and fluorescence microscopy, spinning disk confocal, laser-scanning confocal microscopes, multi photon/Second Harmonic Generation microscopes, total internal reflectance microscope, laser capture micro-dissection, live cell imaging systems, scanning and transmission electron microscopy, whole animal fluorescence, bioluminescence and chemiluminescence imagers, gel, print and film scanners,poster printers, full sample preparation capabilities." .
SCR:020998 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_785" ;
rdfs:label "McGill University Primary Airway Cell Biobank Core Facility" ;
NIFRID:synonym "McGill University Primary Airway Cell Biobank",
"Primary Airway Cell Biobank" ;
NIFRID:abbrev "PACB" ;
definition: "Nonprofit facility providing researchers worldwide with standardized, high-quality primary airway cells from normal and large variety of airway diseased donors with different genetic backgrounds, are essential for improving our understanding of CF and other respiratory diseases and for translational research to develop new therapeutic agents.The PACB is certified by the UBC Office of Biobank Education and Research Biobank Certification Program." .
SCR:020999 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allen Mouse Brain Common Coordinate Framework" ;
NIFRID:synonym "The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas" ;
NIFRID:abbrev "Allen CCF",
"CCFv3" ;
definition: "3D reference atlas to use with online datasets or as standalone resources. Can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D. Intensity and shape population average template brain serves as basis of reference space and coordinate system. Average was constructed at 10 um voxel resolution by interpolating high resolution serial two photon tomography images from young adult C57BL/6J mice. Using multimodal reference data, entire brain was directly parcellated in 3D, labeling every voxel with brain structure from Allen Mouse Reference Atlas Ontology. In the 2017 release, the parcellation spanned 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures." .
SCR:021000 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allen Mouse Reference Atlas Ontology" ;
definition: "Developed for Allen Reference Atlas and follows terminology from Brain Maps: Structure for the Rat Brain (Swanson, 2004, 2018). The ontology has been subsequently extended and revised to also serve as structure ontology for Allen Mouse Common Coordinate Framework.Defines hierarchical partonomy of anatomical structures of adult mouse brain. At top level, brain is divided into gray matter, fiber tracts and ventricular systems. Gray matter is subdivided into cerebrum, brain stem, and cerebellum, which are themselves organized into subregions in hierarchical tree." .
SCR:021001 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mantis" ;
definition: "Software homology based protein function annotation tool that integrates multiple reference data sources. Custom reference data sources can also be added.Accepts as input aminoacids sequence fasta. Customizable and is available on Linux." .
SCR:021002 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:sciga" ;
rdfs:label "SCIGA" ;
NIFRID:synonym "SCIGA_v1.0.0.tar.gz" ;
definition: "Software Perl toolkit for 10X single cell immunoglobulin repertoires analysis. Uses raw reads or output of Cellranger as input and performs reads quality control, immunoglobulin sequence assembly, sequence annotation, heavy- and light- chain pairing, computing statistics and visualizing." .
SCR:021003 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Statulator" ;
definition: "Software tool as statistical calculator that conducts statistical analyses, interprets results, and makes suggestions for presenting results in reports, journal articles and dissertations." .
SCR:021004 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_021007" ;
rdfs:label "immuneML" ;
definition: "Open source Python platform for machine learning based analysis and classification of adaptive immune receptors and repertoires. Supported by ELIXIR Norway." .
SCR:021005 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xProhet" ;
NIFRID:synonym "xQuest/xProhet" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 15, 2021. Software tool for analysis of cross-linked peptides." .
SCR:021006 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xQuest" ;
definition: "Resource no longer available. Documented on March 15, 2021. Software tool to identify cross-linked peptides from complex samples and large protein sequence databases by combining isotopically tagged cross-linkers, chromatographic enrichment, targeted proteomics. Reduces search space by upstream candidate peptide search before recombination step.Search engine for cross-linked peptides from complex samples." .
SCR:021008 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mozak" ;
definition: "Scientific discovery game about neuroscience that helps to build models of brain cells." .
SCR:021009 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multilayer Connectome of Caenorhabditis elegans" ;
definition: "Networks of extrasynaptic aminergic and peptidergic interactions in C. elegans" .
SCR:021010 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xiNET" ;
NIFRID:synonym "Crosslink Network Maps With Residue Resolution" ;
definition: "Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains." .
SCR:021011 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biofactoid" ;
definition: "Web tool for creating digital profile of scientific discoveries in article and connecting them to related research. Authors describe molecular interactions supported by their results, letting researchers explore first hand account of article findings and connect to related articles and knowledge. Web based system for scientists to compose structured representation of networks of interactions between genes, their products, and chemical compounds, represented using power of formal ontology." .
SCR:021012 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PySyft" ;
definition: "Software Python library for secure and private Deep Learning. Decouples private data from model training, using Federated Learning, Differential Privacy, and Encrypted Computation and Homomorphic Encryption within main deep learning frameworks. Used for computing on data you do not own and cannot see." .
SCR:021013 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Translational Research in Neuroimaging and Data Science datasets" ;
NIFRID:synonym "TReNDS" ;
definition: "Neuroimaging datasets available from TReNDs including resting state MRI." .
SCR:021014 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Python based Relational Animal Tracking" ;
NIFRID:synonym "PyRAT animal facility" ;
NIFRID:abbrev "PyRAT" ;
definition: "Software tool for management of animal facility data by Scionics Computer Innovation GmbH. Used by laboratory animal facilities. Used by researchers, animal house managers, animal keepers and others to access their data from same source. Available in English, French, German, Italian, Portuguese and Spanish." .
SCR:021015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MARS Data Analysis Software" ;
NIFRID:synonym "MARS",
"MARS Data Analysis" ;
definition: "Proprietary software package for data analysis by BMG Labtech." .
SCR:021016 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aperio VERSA" ;
NIFRID:synonym "Aperio VERSA Digital Pathology Scanner Software" ;
definition: "Software tool designed to support Leica Biosystems Aperio VERSA scanner. Digital pathology scanning software. Used for diverse imaging needs for digital pathology." .
SCR:021017 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pysam" ;
definition: "Software tool as interface for reading and writing SAM files. Python module to read and manipulate mapped short read sequence data stored in SAM/BAM files. Lightweight wrapper of htslib C-API." .
SCR:021018 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pybedtools" ;
rdfs:label "pybedtools" ;
definition: "Software Python wrapper for bedtools. Wraps and extends BEDTools and offers feature level manipulations from within Python. Flexible Python library for manipulating genomic datasets and annotations." .
SCR:021019 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Analyze Complex Roots Tool" ;
definition: "Software tool to analyze morphological characteristics of complex roots." .
SCR:021020 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "volBrain" ;
NIFRID:synonym "MRI Brain Volumetry System",
"volBrain: online MRI segmentation" ;
definition: "Software tool as MRI brain segmentation system to obtain automatically volumetric brain information from RI data. Works in automatic manner and is able to provide brain structure volumes without any human interaction." .
SCR:021021 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "celltrackR" ;
definition: "Software R package to analyze immune cell migration data. Supports pipeline for track analysis by providing methods for data management, quality control, extracting and visualizing migration statistics, clustering tracks, and simulating cell migration.Available measures include displacement, confinement ratio, autocorrelation, straightness, turning angle, and fractal dimension. Measures can be applied to entire tracks, steps, or subtracks with varying length." .
SCR:021022 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyNIDM" ;
NIFRID:synonym "Neuroimaging Data Model in Python" ;
definition: "Software Python library to manipulate Neuroimaging Data Model." .
SCR:021023 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1056" ;
rdfs:label "University of Nebraska Medical Center Computational Chemistry Core Facility" ;
NIFRID:synonym "University of Nebraska Medical Center Computational Chemistry Core",
"UNMC Computational Chemistry Core" ;
definition: "Core offers wide variety of services, including access to the Schrodinger platform and high-throughput computing. Services include examining molecular structures and mechanisms in atomic detail and provide graphically rich analysis suitable for inclusion in publications and grants." .
SCR:021024 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1141" ;
rdfs:label "University of Nebraska Medical Center Nebraska Biobank Core Facility" ;
NIFRID:synonym "UNMC-Nebraska Biobank" ;
definition: "Nebraska Biobank is made up of residual blood samples from volunteer patients. Serum, Plasma, and DNA are recovered from the consented samples and stored for future research studies.Deidentified data from the Electronic Health Record (EHR) such as age range, diagnosis, and medications are linked to the stored samples. Any faculty member from the University of Nebraska system may request samples from the biobank for their research projects but all requests are subject to feasibility and scientific merit review.Offers sample management services to investigators for clinical trials and registries." .
SCR:021025 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1139" ;
rdfs:label "Laval University Proteomics Platform Core Facility" ;
NIFRID:synonym "ULaval_CHU_Proteomics Platform",
"Universit� Laval ULaval_CHU_Proteomics Platform" ;
definition: "Proteomics platform offers sample preparation, protein identification, post-translational modification (PTM) protein analysis, protein quantification (Label Free, Label based and tarteted proteomics by MRM or PRM) by mass spectrometry and statistical or functional bioinformatic analyses." .
SCR:021027 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Protein Cross-Linking Database" ;
NIFRID:synonym "Protein XL Database" ;
NIFRID:abbrev "Protein XL",
"ProXL",
"proxl" ;
definition: "Web application and database designed for sharing, visualizing, and analyzing protein cross-linking mass spectrometry data with emphasis on structural analysis and quality control. Includes public and private data sharing capabilities, project based interface designed to ensure security and facilitate collaboration among multiple researchers. Used for private collaboration and public data dissemination." .
SCR:021028 a NLX:63400,
owl:NamedIndividual .
SCR:021029 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Label3DMaize" ;
definition: "Software tool used to manually segment and label 3D point cloud of corn and other crops." .
SCR:021031 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Driftage" ;
definition: "Software tool as modular multi agent framework to detect concept drifts from batch or streaming data." .
SCR:021032 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Distributed Automated Parameter Testing" ;
NIFRID:abbrev "DAPT" ;
definition: "Software Python package enabling small teams to test parameter space in distributed and automated manner.Library to assist with running parameter sets across multiple systems. Provides tool set and pipeline that make organizing, running and analyzing large amount of parameters easier." .
SCR:021033 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Innovadyne Technologies | Nanodrop 2 Pipetting System" ;
definition: "Liquid handling system designed for high precision pipetting." .
SCR:021034 a NLX:152328,
owl:NamedIndividual ;
rdfs:label " FUJIFILM Wako Pure Chemical Corporation" ;
definition: "Provides laboratory chemicals, specialty chemicals, and clinical diagnostic reagents based on advanced technological development from academia, companies and medical fields." .
SCR:021035 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Scientifica" ;
definition: "Develops and distributes premium scientific equipment to enhance research of neurons, neuronal circuits and animal behaviour." .
SCR:021036 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ 75501C" ;
rdfs:label "Campden Instruments Ceramic Blades" ;
NIFRID:synonym "Ceramic Blades",
"Ceramic Blades Campden Instruments" ;
definition: "Specialized Ceramic blades for Campden Vibrating Microtomes. These blades are honed with single bevel for superior slicing, particularly in tissue from older animals. They also work with the VT100S, Leica Biosystems." .
SCR:021037 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Harvard Apparatus" ;
definition: "Major US manufacturer of specialized physiological research laboratory equipment with current headquarters in Holliston, Massachusetts.Now part of Harvard Bioscience family of companies." .
SCR:021038 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_1440A" ;
rdfs:label "Molecular Devices | DigiData 1440 digitizer" ;
NIFRID:synonym "DigiData 1440",
"Digidata 1440A" ;
definition: """Digitizer for electrophysiology experiments, to send and receive signals from microelectrode amplifiers, and to interact with peripheral instruments such as solution changers and stimulators. High resolution, low noise digitizer intended for precision scientific applications.
Digidata 1440A digitizer communicates with the host computer using USB 2.0.
It is plug and play device, so it is automatically recognized by Windows.""" .
SCR:021039 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multichannel Systems | MEA60 Amplifier" ;
NIFRID:synonym "MEA60 Amplifier for Upright Microscopes",
"MicroElectrode Array 60 amplifier" ;
definition: "MEA amplifier for upright microscopes.Raw data from up to 60 electrodes of microelectrode array is amplified by 60 channels of filter amplifiers that are built very small and compact using Surface Mounted Devices technology." .
SCR:021040 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MultiClamp_700A" ;
rdfs:label "Molecular Devices | MultiClamp 700A Microelectrode Amplifier" ;
NIFRID:synonym "MultiClamp 700A" ;
definition: "Computer controlled microelectrode current and voltage clamp amplifier for electrophysiology and electrochemistry. It is a versatile instrument capable of single-channel and whole-cell voltage clamping, current clamping, ionselective electrode recording, voltammetry and amperommetry." .
SCR:021041 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Digidata_1322A" ;
rdfs:label "Molecular Devices | Digidata 1322A Digitizer" ;
NIFRID:synonym "Digidata 1322A" ;
definition: "Digitizer intended for precision scientific applications.Digitizes at aggregate speed of 500 kHz. It provides sixteen multiplexed, 16-bit analog inputs and two nonmultiplexed, 16-bit analog outputs." .
SCR:021042 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_P1000" ;
rdfs:label "Sutter | P-1000 Next Generation Micropipette Puller" ;
definition: "P-1000 include diagnostic testing of all puller components, built in error detection of air pressure loss or filament burnout, easy access to ramp test, measurement of jaw temperature, and access to previous pull results with heat on times for each cycle of program.Help topics are pre-loaded to assist with on-site troubleshooting and built-in glossary includes text, pictures, and diagrams explaining terms used in micropipette fabrication. Rotary dial is offered as alternative to keypad for numerical entry." .
SCR:021043 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurasmus | BLINK system" ;
NIFRID:synonym "BLINK 2.0",
"BLINK 2.0 Eyeblink conditioning analysis",
"BLINK Eyeblink conditioning analysis",
"Nerasmus Blink system" ;
definition: "Scientific setup used for both eyeblink conditioning and prepulse inhibition of startle reflex in animals. Used to measure kinetic and frequency domain properties of conditioned and unconditioned eyelid responses in freely moving mice. Allows determination of eyelid movements in time and space while using air puff as unconditioned stimulus." .
SCR:021044 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ETL-200" ;
rdfs:label "ISCAN | ETL-200 Primate Eye Tracking Laboratory" ;
NIFRID:synonym "ETL-200",
"ETL-200 Primate Eye Tracking Laboratory",
"ISCAN ETL-200" ;
definition: "Images and tracks one eye of human subject or lower animal at operator selected sampling rate at 120 Hz or 240 Hz. Contains all components to record eye movements as subject views imagery presented on computer screen or other visual display device. Configured to track one eye and allows for up to approximately one to two inches of side to side or up and down head movement." .
SCR:021045 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Advent research materials LTD" ;
definition: "Supplier of high purity metals, alloys and polymers including Aluminium, Indium, Platinum, Silver, Gold, Copper, Indium, Iridium, Rhodium and Tantalum in multiple forms, dimensions and purities." .
SCR:021046 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Foredom" ;
NIFRID:synonym "Foredom Electric Co." ;
definition: "Manufacturer of flexible shaft rotary power tools including specialized motors, handpieces, attachments, and accessories." .
SCR:021047 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "HelloBio" ;
NIFRID:synonym "Hello Bio Ltd." ;
definition: "Manufactures range of high quality agonists, antagonists, inhibitors, activators, antibodies and fluorescent tools to support life science research." .
SCR:021048 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCMICRO" ;
definition: "Open source software tool as multiple choice microscopy pipeline for multiplexed whole slide imaging and tissue microarrays. Scalable, modular image processing pipeline for multiplexed tissue imaging. Used for performing sequential steps needed to transform large, multi channel whole slide images into single cell data." .
SCR:021049 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hypothesis Center" ;
definition: "dkNET service that assist researchers in generating research hypotheses. Brings together collection of online tools that will allow researchers to explore different dataset and utilize analytics and visualization tools. Hypothesis Center phenotype-genotype analytics module is currently performed utilizing data from Signaling Pathways Project , and Mouse Metabolic Phenotyping Centers, and it brings SPP and MMPC together to connect cellular signaling pathways and gene expression with physiological phenotypes. Used to find gene sets and signaling pathways relevant to mouse phenotypes for generating hypotheses." .
SCR:021050 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UnMICST" ;
NIFRID:synonym "UNet Model for Identifying Cells and Segmenting Tissue",
"Universal Models for Identifying Cells and Segmenting Tissue",
"UnMicst" ;
definition: "Software tool as set of deep learning nuclei instance and semantic segmentation models that have been trained on 6 human tissue types: tonsil, small intestine, ovary, and cancers of brain, colon, prostate, and lung stained with Hoechst 33342 and combination of lamin B2 and nucleoporin98. Includes manually curated annotations as well as novel concept of introducing intentionally defocused and saturated images for robustness." .
SCR:021051 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CONSORT TM" ;
NIFRID:synonym "CONSORT-TM" ;
definition: "Software tool as testbed for text mining methods that assess Randomized Controlled Trial transparency, rigor, and reliability, and support methods for peer review and authoring assistance." .
SCR:021052 a owl:NamedIndividual ;
rdfs:label "Exemplar Microscopy Images of Tissues" ;
NIFRID:synonym "Exemplar Microscopy Images of Tissues ( and Tumors)" ;
NIFRID:abbrev "EMIT" ;
definition: "Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets." .
SCR:021053 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRISMA2020" ;
definition: "Software R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams. ShinyApp for producing PRISMA 2020 compliant flow diagrams." .
SCR:021054 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Waters High Definition Imaging" ;
NIFRID:synonym "High Definition Imaging v1.5" ;
NIFRID:abbrev "HDI" ;
definition: "Software package contains data analysis and processing tools required for rapid and effective interrogation of imaging data. Allows for full integration of full spectrum molecular imaging experiments on SYNAPT family platforms, as well as DESI imaging on Xevo G2-XS QTof Mass Spectrometers, using single user interface." .
SCR:021055 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fluidigm CyTOF" ;
NIFRID:synonym "CyTOF Software v7.0" ;
definition: "Software for analyzing mass cytometry (CyTOF) data." .
SCR:021056 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DownSample" ;
definition: "Software tool to subset samples in FlowJo software.Reduces number of events in data matrix by generating subpopulation containing cells distributed regularly or randomly throughout selected parent population." .
SCR:021057 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ZebEyeTrack" ;
definition: "Open source software for zebrafish eye tracking and visual stimulation. Used to evoke and track zebrafish eye movement in multiple larvae.Modular software able to control multiple aspects of oculomotor experiment, from stimulus presentation and data acquisition to eye tracking and data analysis, or to simply track eyes in existing video of larval zebrafish. In both cases, eyes of up to six fish can be tracked in parallel.Users can choose to control several alternative setups and optional hardware." .
SCR:021058 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Gene Set Variation Analysis" ;
NIFRID:abbrev "GSVA" .
SCR:021059 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cellxgene" ;
definition: "Software tool as interactive explorer for single cell transcriptomics datasets. Used to explore and visualize high dimensional single cell datasets in interactive way. Can visualize gene expression at level of entire dataset or particular subset of cells to help identify cell types, which can in turn help identify diseases. Enables plotting gene expression level against another gene to compare how these different genes are expressed across dataset. Open source cell visualization tool integrates with tools like SciPy and Jupyter." .
SCR:021060 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openCARP" ;
definition: "Software tool as open simulation environment for cardiac electrophysiology. Cardiac electrophysiology simulator for in silico experiments. Offers single cell as well as multiscale simulations from ion channel to organ level. Includes functions for pre and post processing of data as well as visualization." .
SCR:021061 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VizANT" ;
definition: "Software tool to produce graph using Graphviz from Ant build files forked from sourceforge vizant." .
SCR:021062 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rentrez" ;
definition: "Software package provides R interface to NCBI EUtils API, to search databases like GenBank and PubMed, process of those searches. Provides functions that work with NCBI Eutils API to search, download data from, and otherwise interact with NCBI databases." .
SCR:021063 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pvclust" ;
definition: "Software R package for hierarchical clustering with p-values. Used for assessing uncertainty in hierarchical cluster analysis." .
SCR:021064 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RobotReviewer" ;
NIFRID:synonym "Automating Biomedical Evidence Synthesis" ;
definition: "Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials." .
SCR:021065 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1145" ;
rdfs:label "University of Michigan Center for Structural Biology Core Facility" ;
NIFRID:synonym "Center for Structural Biology",
"University of Michigan Center for Structural Biology",
"University of Michigan�Ann Arbor Center for Structural Biology" ;
NIFRID:abbrev "CSB" ;
definition: "Comprehensive structural biology resource.Provides high throughput protein laboratory for protein engineering, protein purification facilities for small- and large-scale protein production, macromolecular crystallization and crystallography laboratories for solving crystal structures of biological molecules, and X-ray facility with access to high energy synchrotron radiation. Provides expert guidance to researchers through every stage of project, collaborating and consulting with researchers who use the facilities. Service categories are Chemical, Material and Protein Characterization, Molecular Biology. Services include Cloning, Crystallization, Differential thermal analysis, Drug development, NMR (small molecule), PCR, Protein crystallography, Protein engineering, Protein production, Structure determination, Xray." .
SCR:021066 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pgAdmin" ;
definition: "Open source administration and development platform for PostgreSQL." .
SCR:021067 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PostgreSQL" ;
NIFRID:synonym "Postgres" ;
definition: "Open source object relational database system that uses and extends SQL language combined with many features that safely store and scale the most complicated data workloads. PostgreSQL runs on all major operating systems." .
SCR:021068 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ti2" ;
rdfs:label "Nikon | ECLIPSE Ti2 inverted microscope" ;
NIFRID:synonym "ECLIPSE Ti2",
"Nikon ECLIPSE Ti2" ;
definition: "Inverted microscope delivers unparalleled 25mm field of view. With this FOV, the Ti2 maximizes sensor area of large format CMOS cameras without making compromises, and significantly improves data throughput. Stable, drift free platform designed to meet demands of super resolution imaging with high speed imaging applications. Status of each sensor is automatically recorded during acquisition, providing quality control for imaging experiments and enhancing data reproducibility." .
SCR:021069 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hifiasm" ;
definition: "Software tool as haplotype resolved de novo assembler for PacBio Hifi reads. Can assemble human genome in several hours.Introduces new graph binning algorithm and achieves haplotype resolved assembly given trio data. Takes advantage of long high fidelity sequence reads to represent haplotype information in phased assembly graph. Preserves contiguity of all haplotypes." .
SCR:021070 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1148" ;
rdfs:label "University of Wisconsin-Madison Advanced Genome Editing Laboratory" ;
NIFRID:synonym "Genome Editing and Animal Models Core",
"Transgenic Animal Facility",
"University of Wisconsin Madison Advanced Genome Editing Laboratory",
"University of Wisconsin Madison Genome Editing Core Facility",
"University of Wisconsin Madison UW-Genome Editing & Animal Models",
"UW Biotechnology Center Advanced Genome Editing Laboratory",
"UW-Genome Editing & Animal Models" ;
NIFRID:abbrev "AGEL" ;
definition: "Provides services and expertise to unlock genome editing tools to advance your research. Routinely generates new genome edited models, particularly mouse, rats, swine, and cell lines, as well as supports in vivo editing, novel preclinical therapeutic strategies, pooled lentiCRISPR screening, and other applications." .
SCR:021071 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pediatric Obesity Microbiome and Metabolism Study" ;
NIFRID:abbrev "POMMS" ;
definition: "Biorepository of clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification.Biorepository is available as shared resource." .
SCR:021072 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoCAD" ;
NIFRID:synonym "Auto Computer Aided Design" ;
definition: "Software tool as computer aided design software that architects, engineers, and construction professionals rely on to create precise 2D and 3D drawings." .
SCR:021073 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Brand:Cooled",
"Manufacturer:Cooled" ;
rdfs:label "CoolLED | pE-300white" ;
NIFRID:synonym "pE-300white" ;
definition: "Compact and simple to use LED illuminator for microscopes. Provides broad spectrum of illumination, covering excitation bands of fluorophores such as DAPI, CFP, Aqua, FITC, TRITC, TxRed, Cy5 and many more. Operation is by manual control pod with instant on and off, irradiance control, with remote control available via USB or TTL trigger." .
SCR:021074 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Deepnote" ;
definition: "Software tool as data science notebook. Jupyter compatible with real time collaboration and running in the cloud." .
SCR:021075 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Solid Edge" ;
definition: "Portfolio of software tools that addresses all aspects of product development process 3D design, simulation, manufacturing, data management and more. Combines speed and simplicity of direct modeling with flexibility and control of parametric design." .
SCR:021076 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eido" ;
definition: "Software validation tool for Portable Encapsulated Projects or PEPs in python." .
SCR:021077 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pepr" ;
NIFRID:synonym "Portable Encapsulated Projects in R" ;
definition: "Software python package for reading Portable Encapsulated Projects or PEPs in R." .
SCR:021078 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "peppy" ;
definition: "Software python package for reading Portable Encapsulated Projects or PEPs in python." .
SCR:021079 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "seqpac" ;
definition: "Software R package for analysis of short sequenced reads. Framework for small RNA analysis in R using Sequence Based Counts.Can be applied on any type of data generated by large scale nucleotide sequencing, where user wish to maintain sequence integrity during whole analysis." .
SCR:021080 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phantom Camera Control " ;
NIFRID:abbrev "PCC" ;
definition: "Software application for Phantom cameras. Controls every camera function on every Phantom camera model. Fine-tune resolution, frame rate, exposure, memory segmentation, trigger modes and automatic functions prior to recording. PCC also makes it easy to work with synchronized cameras, manage Phantom Cine raw files and convert files to format for final project.Software is compatible with Windows 7 Pro and Windows 8.1 and Windows 10, for both 32 and 64-bit operating systems." .
SCR:021081 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Micro_C110" ;
rdfs:label "Phantom | Miro C110 camera" ;
NIFRID:synonym "Phantom Miro C110" ;
definition: "Small, sturdy camera with all standard Phantom features and image quality. Memory can be partitioned up to 63 times to deliver images from 1.3 Mpx sensor with 12-bit depth and tightly packed 5.6 micron pixel size. Miro C110 is capable of 1295 fps at 720p HD and up to 52445 fps at reduced resolutions." .
SCR:021082 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSpherix | C Shuttle Glove Box hood" ;
NIFRID:synonym "BioSpherix C-Shuttle Glove Box",
"C-Shuttle laboratory glove box",
"Hypoxic Glove Box" ;
NIFRID:abbrev "C-Shuttle" ;
definition: "Oxygen controlled hood for handling cells under physiologic or pathophysiologic conditions. Double door entry allows import/export of materials without perturbation of experimental conditions. Optional control of carbon dioxide as well. Receives C-Chamber Incubator Subchamber to transfer cells without exposure to room air." .
SCR:021083 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSpherix | I Glove Incubator and Oxygen Glovebox chamber" ;
NIFRID:synonym "Hypoxic Glove Box" ;
NIFRID:abbrev "I-Glove" ;
definition: "Oxygen controlled Glovebox for both incubation and handling of cells in controlled physiologic or pathophysiologic conditions when used together with third party incubator. Carbon dioxide control is optional. Hosts C-Chamber Incubator Subchamber for transport of cells without exposure to room air." .
SCR:021084 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Azimuth" ;
definition: "Web application that uses annotated reference dataset to automate processing, analysis, and interpretation of new single cell RNA-seq experiment. Azimuth leverages reference based mapping, pipeline that inputs counts matrix of gene expression in single cells, and performs normalization, visualization, cell annotation, and differential expression. All results can be explored within the app, and easily downloaded for additional downstream analysis." .
SCR:021085 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SimFFPE" ;
NIFRID:synonym "NGS Read Simulator for FFPE Tissue",
"Simulator for FFPE Tissue" ;
definition: "Software R package to simulate artifact chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissue. Simulates normal reads as well as artifact chimeric reads that are enriched in FFPE samples. These artifact chimeric reads can lead to large amounts of false positive structural variant calls." .
SCR:021086 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FilterFFPE" ;
definition: "Software R package to find and filter artificial chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissues. These artificial chimeric reads can lead to large number of false positive structural variant calls. Artifact chimeric read filter to improve SV detection in FFPE samples." .
SCR:021087 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_13120" ;
rdfs:label "Scoary" ;
definition: "Software tool that scores components of pan genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes.Designed to take gene presence absence.csv file from Roary as well as traits file created by user and calculate associations between all genes in accessory genome and traits. It reports list of genes sorted by strength of association per trait." .
SCR:021088 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pyani" ;
definition: """Software package and script for calculation of genome scale average nucleotide identity.
Python3 module that provides support for calculating average nucleotide identity and related measures for whole genome comparisons, and rendering relevant graphical summary output. Where available, it takes advantage of multicore systems, and can integrate with SGE/OGE-type job schedulers for the sequence comparisons.""" .
SCR:021089 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PanGP" ;
NIFRID:synonym "Pan Genome Profile Analyze Tool" ;
definition: "Software tool for analyzing bacterial pan genome profile.Used to calculate pan genome profile of population with dozens of or hundreds of strains at extremely low time cost." .
SCR:021090 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Panaroo" ;
NIFRID:synonym "Bacterial Pangenome Analysis Pipeline" ;
definition: "Software pipeline for pangenome investigation. Shares information between genomes to correct errors. Can call large structural variants.Fast and scalable to over 10k bacterial genomes." .
SCR:021091 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FastANI" ;
NIFRID:synonym "Fast Whole Genome Similarity Estimation" ;
definition: """Software tool for fast alignment free computation of whole genome Average Nucleotide Identity . Supports pairwise comparison of both complete and draft genome assemblies.
to calcualte the average nucleotide identity (ANI) between your samples.""" .
SCR:021092 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BactDating" ;
definition: """Software tool for Bayesian inference of ancestral dates on bacterial phylogenetic trees.
Performs Bayesian dating of nodes of bacterial phylogenetic tree. This typically involves simultaneous Bayesian estimation of molecular clock rate and coalescent rate. Additional features include inference of root location, lost sampling dates and different evolutionary models.""" .
SCR:021093 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Abricate" ;
NIFRID:synonym "ABRicate" ;
definition: """Software tool for mass screening of contigs for antimicrobial and virulence genes.
Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB.""" .
SCR:021094 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "survminer" ;
definition: "Software R package provides functions for facilitating survival analysis and visualization." .
SCR:021095 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ExpressionSuite" ;
NIFRID:synonym "ExpressionSuite Software",
"ExpressionSuite v1.3" ;
definition: "Software tool to quantify relative gene expression across large number of genes and samples. Allows to analyze gene expression data on any current Applied Biosystems real time PCR instrument." .
SCR:021096 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Applied Biosystems QuantStudio 12K Flex RT PCR Software" ;
NIFRID:synonym "QuantStudio 12K Flex Real Time PCR Software" ;
definition: "Software supports QuantStudio12K Flex Real Time PCR System to open and analyze experiments. Enables to set up experiments, send experiments to instrument, control thermal cycling process in instrument, collect data and analyze collected data." .
SCR:021097 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Verti" ;
rdfs:label "Thermo Fisher: Applied Biosystems | Veriti 96-Well Thermal Cycler" ;
NIFRID:synonym "Veriti 96-Well Thermal Cycler" ;
definition: "Thermocycles with added control of VeriFlex technology, with six independent temperature blocks that provide precise control over PCR optimization. Color touch screen simplifies setup and use. Optional setups for fast or standard PCR methods provide with flexibility to shorten your PCR cycling times. Equipped with astandard 0.2 mL block configuration.Will be discontinued on December 31, 2021." .
SCR:021098 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Applied Biosystems | QuantStudio 12K Flex RealTime PCR System" ;
NIFRID:synonym "QuantStudio 12K Flex Real-Time PCR System" ;
definition: "System can simultaneously run up to four 3072 reaction QuantStudio 12K Flex OpenArray plates in about four hours. When combined with the QuantStudio 12K Flex OpenArray AccuFill System, can produce up to 110000 data points or more in 8 hour day. Has touch screen interface and comprehensive software analysis tools for gene expression, genotyping, and digital PCR increase productivity. Has five interchangable block formats including: OpenArray plate, TaqMan Array card, 384-well, and 96-well (0.1 and 0.2 mL)." .
SCR:021099 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DecodingDynamic" ;
definition: "Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex." .
SCR:021100 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Opera_Phenix_Plus" ;
rdfs:label "Perkin Elmer | Opera Phenix Plus High Content Screening System" ;
NIFRID:synonym "Opera Phenix Plus" ;
definition: "Opera Phenix Plus system for high throughput high content assays, phenotypic screening, assays using complex disease models, such as live cells, primary cells and microtissues, and fast response assays like calcium flux or cardiomyocyte beating.Optical design lets you generate information through confocal imaging and at higher throughput through simultaneous acquisition. Delivers speed without compromising sensitivity. Uses Harmony High Content Imaging and Analysis Software to quantify complex cellular phenotypes. Harmony software is designed for PerkinElmer high content screening systems." .
SCR:021101 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_640" ;
rdfs:label "University of New Hampshire University Instrumentation Center Core Facility" ;
NIFRID:synonym "University Instrumentation Center",
"University of New Hampshire University Instrumentation Center" ;
NIFRID:abbrev "UIC" ;
definition: "University wide core facility offers NMR,SEM including FIB, EBS, EBSD, Tensile Stage,Confocal,X-Ray Photoelectron Spectroscopy,X-Ray Microscope aka Micro CT, Expert analysis of research and industrial samples,Training in scientific instrument operation and data analysis, Maintenance, repair, and calibration of instruments,Specialty instrument engineering design and application services,Facilitation of access to scientific instruments throughout the university." .
SCR:021102 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenAlEx" ;
NIFRID:synonym "GenAlEx 6.5",
"Genetic Analysis in Excel" ;
definition: "Software tool as cross platform package for population genetic analyses that runs within Microsoft Excel. Offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences.Originally developed as teaching tool to facilitate teaching population genetic analysis at graduate level." .
SCR:021103 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneMapper ID-X" ;
NIFRID:synonym "GeneMapper ID-X Software",
"GeneMapper ID-X Software v1.6" ;
definition: "Software developed for forensic data analysis. When combined with the Applied Biosystems 3500 Data Collection Software v4.0 and Applied Biosystems STR kits, helps enhance productivity and confidence, as well as IT support and compliance, in HID laboratory data interpretation workflow." .
SCR:021104 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_116" ;
rdfs:label "New York State Department of Health Wadsworth Center Advanced Light Microscopy and Image Analysis Core Facility" ;
NIFRID:synonym "Advanced Light Microscopy & Image Analysis Core",
"New York State Department of Health Wadsworth Center Advanced Light Microscopy and Image Analysis Core" ;
definition: "Core facility is designed for Imaging living cells or tissues, Fluorescence imaging, Image analysis. Provides imaging of adherent cells or tissue fragments,drug delivery using perfusion chamber, gas exchange for the growth media, Rose chambers for imaging, image processing and analysis software to assist in data analysis and interpretation." .
SCR:021105 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1154" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Flow Cytometry Core Facility" ;
NIFRID:synonym "Memorial Sloan Kettering Cancer Center MSKCC-FCCF",
"MSKCC-FCCF" ;
NIFRID:abbrev "MSKCC FCCF" ;
definition: "Provides advanced instrumentation as well as high level technical and scientific expertise in multi dimensional Flow Cytometry and Cell Sorting, to facilitate science, improve the quality, and advance the scope of MSK research." .
SCR:021106 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1157" ;
rdfs:label "East Tennessee State University Quillen College of Medicine Molecular Biology Core Facility" ;
NIFRID:synonym "ETSU Molecular Biology Core Facility" ;
definition: "Core provides Genomics, Transcriptomics and Proteomics Services to researchers." .
SCR:021107 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1156" ;
rdfs:label "University of Pennsylvania Penn Electronic Design Shop Core Facility" ;
NIFRID:synonym "Penn Electronic Design Shop" ;
definition: """Provides electronic design services and medical device development including Embedded systems (Firmware, Hardware, and Software solutions),
Electronic prototype design services,PLM (Product Life-cycle Management) for electronic design. Supports Product Management from concept to final customer deployment. Expertise to make electronic device complete consumer product that can be deployed for mass production,Sustaining and maintenance engineering for electronic products,Consulting services in the areas of CE/FCC compliance, EMI, and ESD for lab products and certain consumer electronics,Troubleshooting and repair of released electronic systems.""" .
SCR:021108 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSpherix | I-Hood Protective Incubator Hood" ;
NIFRID:synonym "I-Hood",
"I-Hood Protective Incubator Hood",
"Vent Hood" ;
definition: "Protective hood for removing fumes which may escape incubator." .
SCR:021109 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSpherix | OxyCycler C42 Controller" ;
NIFRID:synonym "OxyCycler C42",
"OxyCycler C42 Dynamic O2 and CO2 Subchamber Controller" ;
NIFRID:abbrev "C-42" ;
definition: "Incubator controls dynamic or static levels of O2 and CO2 and offers O2 and CO2 profiling. Dual channel and dual gas controller for incubators and C-Chambers. Oxygen and carbon dioxide control is managed via independently programmable channels for optimum control. Applications of OxyCycler C42 incubator controller include intermittent hypoxia, graded hypoxia, and timed hyperoxia.Comes with computer software for easy interface, real time trend charting, data logging, and remote operation." .
SCR:021110 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSpherix | OxyCycler GT41 Controller" ;
NIFRID:synonym "and RH Subchamber Controller System",
"CO2",
"OxyCycler GT41",
"OxyCycler GT41 Dynamic O2" ;
NIFRID:abbrev "GT41" ;
definition: "O2 and CO2 controller that also features relative humidity limit control and monitoring of temperature conditions when used in combination with C-Chamber Incubator subchamber from BioSpherix." .
SCR:021111 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSpherix | Oxycycler GT4181C Controller" ;
NIFRID:synonym "and Carbon Monoxide Subchamber Controller System",
"CO2",
"OxyCycler GT4181C",
"Oxycycler GT4181C Dynamic O2" ;
NIFRID:abbrev "GT4181C" ;
definition: "Carbon Monoxide, O2, and CO2 controller that also features limit control of relative humidity and monitoring of temperature conditions when used in combination with C-Chamber Incubator Subchamber from BioSpherix. This system also features secondary monitor for Carbon Monoxide and may be used in combination with I-Hood Incubator Hood from BioSpherix for ventilating fumes." .
SCR:021112 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSpherix | Oxycycler GT4181N Controller" ;
NIFRID:synonym "and Nitric Oxide Subchamber Controller System",
"CO2",
"OxyCycler GT4181N",
"Oxycycler GT4181N Dynamic O2" ;
NIFRID:abbrev "GT4181N" ;
definition: "Nitric Oxide, O2, CO2 controller with limit control of relative humidity and monitoring of temperature conditions when used in combination with C-Chamber incubator subchamber from BioSpherix. Features secondary monitor of Nitric Oxide and may be used in combination with I-Hood Incubator Hood from BioSpherix in order to ventilate fumes." .
SCR:021113 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSpherix | OxyCycler GT4181CN Controller" ;
NIFRID:synonym "and Nitric Oxide Subchamber Cell Culture System",
"Carbon Monoxide",
"CO2",
"OxyCycler GT4181CN",
"OxyCycler GT4181CN Dynamic O2" ;
NIFRID:abbrev "GT4181CN" ;
definition: """Carbon Monoxide, Nitric Oxide, O2, and CO2 controller with limit control of relative humidity and monitoring of temperature conditions when used in combination with
C-Chamber incubator subchamber from BioSpherix. Features secondary monitors for both Carbon Monoxide and Nitric Oxide and may be used in combination with I-Hood Incubator Hood from BioSpherix to ventilate fumes.""" .
SCR:021114 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1160" ;
rdfs:label "University of California, Santa Cruz Chemical Screening Center Core Facility" ;
NIFRID:synonym "Santa Cruz UCSC-CSC",
"UCSC Chemical Screening Center",
"University of California" ;
NIFRID:abbrev "UCSC-CSC" ;
definition: "Shared research facility dedicated to improving human health by finding next generation of therapeutic agents against wide variety of diseases. The CSC is driving innovation in drug discovery by bringing together experts in drug screening with cell and molecular biologists engaged in disease research. Has assembled diverse collection of compounds derived from marine organisms, setting our facility apart as a leader in the discovery of therapeutic natural products." .
SCR:021115 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BarensLab Mini-Atlas" ;
definition: "Phenotypic variation of transcriptomic cell types in mouse motor cortex.Repository contains analysis code and preprocessed data.Data includes exonic and intronic gene counts, extracted electrophysiological features, extracted morphological features and z-profiles. Datasets with recorded at room temperature and recorded at physiological temperature." .
SCR:021117 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SYCAMORE" ;
NIFRID:synonym "SYstems biology Computational Analysis and MOdeling Research Environment" ;
definition: "Web browser based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Allows database supported modelling, basic model checking and estimation of unknown kinetic parameters based on protein structures. Integrates different online applications as well as locally installed software. Provides user guidance for sequence of steps associated with model building, model checking, simulation and analysis of results." .
SCR:021118 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PottersWheel " ;
NIFRID:synonym "PottersWheel mathematical modeling" ;
definition: "Software MATLAB toolbox for mathematical modeling of time dependent dynamical systems that can be expressed as chemical reaction networks or ordinary differential equations. Allows to automatically calibrate model parameters by fitting model to experimental measurements.Fits model to several data sets at once (multi-experiment fitting). Accessible via graphical user interfaces, from command line and scripts,determines parameter identifiability and confidence intervals,imports and exports SBML models and supports biochemical network modeling." .
SCR:021119 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011928" ;
rdfs:label "FAIRDOMHub" ;
NIFRID:synonym "FAIR Data",
"Operating procedures and Models" ;
definition: "Initiative to develop community, and establish internationally sustained data and model management service to European Systems Biology community. Web accessible repository for storing and sharing data, models, protocols and publications relating to systems biology research projects.Repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) data, operating procedures and models.Contains data, SOPs models, publications and other research assets from large research programmes and independent projects, including SysMO consortium, ERASyAPP and Digital Salmon. Public service for users to upload and publish research assets." .
SCR:021120 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ALLMAP " ;
definition: "Software tool for computing scaffold ordering that maximizes colinearity across collection of maps including genetic, physical or comparative maps into final chromosome build. Robust scaffold ordering based on multiple maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with input maps. Used in building high quality genome assemblies." .
SCR:021121 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1159" ;
rdfs:label "Forsyth Institute Advanced Microscopy Core Facility" ;
NIFRID:synonym "Forsyth Institute Imaging Core",
"Forsyth-Advanced Microscopy Core",
"The Forsyth Institute Forsyth-Advanced Microscopy Core" ;
definition: "Offers microscopy imaging services to both internal and external users in the greater Boston area. The facility is equipped for live cell imaging, laser scanning confocal and super resolution microscopy. Common sample types imaged in the facility are live and fixed bacteria, biofilms, embedded soft tissue, cleared tissue, and mineralized tissue and samples can be labelled or label free. One area of expertise is imaging many fluorophores simultaneously using spectral imaging and linear unmixing. In addition to instrument training, we can also provide advice for sample preparation and image analysis. In some cases, we are able to provide full-service imaging for customers." .
SCR:021122 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MCR501" ;
rdfs:label "Anton Paar | MCR501 rheometer" ;
NIFRID:synonym "Modular Compact Rheometer 501",
"SMaRT – MCR501",
"SMaRT – MCR501 (Anton Paar)" ;
definition: "Stress controlled rheometer.THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 19,2026." .
SCR:021123 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1162" ;
rdfs:label "Penn State College of Medicine Genome Sciences Core Facility" ;
NIFRID:synonym "Genome Sciences and Bioinformatics Facility",
"Pennsylvania State University Genome Sciences and Bioinformatics Facility" ;
definition: "Provides consultation, instrumentation and services in genomic, epigenomic and transcriptomic studies, analysis of candidate SNPs and mRNAs to whole genome, exome, epigenome and transcriptome sequencing. Services are also available for variety of study designs extending from few laboratory samples to large clinical projects involving hundreds or thousands of samples.Bioinformatics service is available for data analysis.Facility receives either tissue, DNA/RNA or customer generated NGS libraries. Samples are processed based on agreement reached during consultations on design of experiment." .
SCR:021124 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ,
;
rdfs:label "Common Cell Type Nomenclature" ;
NIFRID:synonym "Allen Brain Map Cell Type Nomenclature CCN",
"Allen Cell Type Common Cell type Nomenclature" ;
definition: "Framework for creating brain cell type nomenclature, and include examples using published datasets. System allows designation of cell types with or without hierarchical organization. Nomenclature convention initially applied to brain cells and types, is intended to encompass existing naming strategies used in publications across diverse research teams. Allows tracking of many different taxonomies, including those from different organ systems or across diverse areas of bioscience." .
SCR:021125 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mononucleotide Repeat Frameshift Portal" ;
NIFRID:synonym "MOnonucleotide Repeat Frameshift",
"MORF portal" ;
NIFRID:abbrev "MORF" ;
definition: "Portal devoted to suite of MORF reporter mice labels of Cre positive neurons and glia distributed stochastically throughout brain and can be imaged with endogenous fluorescence (mNeonGreen in MORF1 and EGFP in TIGRE-MORF) or stained for multivalent immunoreporter (Spaghetti Monster fluorescent protein V5, or smFP-V5, in MORF3). MORF technology used to label and reconstruct thousands genetically defined cells per brain for large scale, unbiased classification and quantitative analyses of CNS cell types brainwide." .
SCR:021126 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microphysiology Systems Database" ;
NIFRID:synonym "MPS database" ;
NIFRID:abbrev "MPS-Db" ;
definition: "Open source database used for analyzing and modeling compound interactions with human and animal organ models.Platform for experimental design, data management, and analysis, and to combine experimental data with reference data, to enable computational modeling. Resource for relating in vitro organ model data to multiple biochemical, preclinical, and clinical data sources on in vivo drug effects." .
SCR:021127 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ProCO2 120" ;
rdfs:label "BioSpherix | ProCO2 120 Controller" ;
NIFRID:synonym "ProCO2 120",
"ProCO2 120 Compact CO2 Controller",
"ProCO2 120 Compact Controller" ;
NIFRID:abbrev "P120" ;
definition: "Controls CO2 levels for most physiologic concentrations and may be connected with either C-Chamber Incubator Subchambers or A-Chamber Animal Chambers from BioSpherix. May also be connected with chambers which are either home built or are available from other manufacturers. These include thermal incubators, flush boxes, culture chambers, glove boxes, and other semi sealed enclosures." .
SCR:021128 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IN Cell Analyzer 2000" ;
rdfs:label "GE | IN Cell Analyzer 2000 cell imaging system" ;
NIFRID:synonym "GE Healthcare IN Cell Analyzer 2000 cell imaging system" ;
NIFRID:abbrev "IN Cell Analyzer 2000" ;
definition: "Cell imaging system for entire high content analysis (HCA) workflow. Delivers high performance hardware, software, and expert support for cell analysis." .
SCR:021129 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ProOx 110" ;
rdfs:label "BioSpherix | ProOx 110 Controller" ;
NIFRID:synonym "BioSpherix ProOx 110 Compact O2 Controller" ;
NIFRID:abbrev "P110",
"ProOx 110" ;
definition: "Compact, versatile O2 controller.Controls Oxygen and may be used with either C-Chamber Incubator Subchamber or A-Chamber Animal Chamber from BioSpherix. May be used with home-built or other manufacturers chambers." .
SCR:021130 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ProOx 360" ;
rdfs:label "BioSpherix | ProOx 360 Controller" ;
NIFRID:synonym "ProOx 360",
"ProOx 360 High Infusion Rate O2 Controller" ;
NIFRID:abbrev "P360" ;
definition: "Versatile high infusion rate O2 controller.Controls Oxygen and may be used with BioSpherix C-Chamber Incubator Subchamber, C-Shuttle Glove Box, I-Glove Incubator Glove Box, Xvivo System Model X3 Cytocentric Cell Incubation and Handling Platfrom, or A-Chamber Animal Chamber. Featuring capability to infuse gas over range 1-140 SCFH, may be used together with chambers which are either home built or are available from other manufacturers." .
SCR:021131 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ProOx C21" ;
rdfs:label "BioSpherix | ProOx C21 Controller" ;
NIFRID:synonym "ProOx C21",
"ProOx C21 Oxygen and Carbon Dioxide Subchamber Controller" ;
NIFRID:abbrev "C21" ;
definition: "Compact O2 and CO2 Subchamber Controller used together with C-Chamber Incubator Subchamber from BioSpherix or chambers from other manufacturers." .
SCR:021133 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_794" ;
rdfs:label "Barrow Neurological Institute Flow Cytometry and NanoString Core Facility" ;
NIFRID:synonym "Barrow Neurological Institute Flow Cytometry and NanoString Facility",
"Flow Cytometry and NanoString Core Facility" ;
definition: "Offers RNA integrity measurements and gene expression assays.Ask us how NanoStrings direct measurement of target molecules can help you avoid amplification bias in your studies.Facility offers flow cytometry and cell sorting services. Staff can help with panel design all the way through data analysis and one-on-one education about flow theory and applications." .
SCR:021134 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1164" ;
rdfs:label "Penn State Hershey College of Medicine Flow Cytometry and Cell Sorting Core Facility" ;
NIFRID:synonym "Penn State Hershey College of Medicine PSU-College of Medicine Flow Cytometry Core",
"PSU-College of Medicine Flow Cytometry Core Hershey" ;
definition: "Offers Flow Cytometry analysis, Cell sorting, Flow Imaging analysis.Available cytometers include 4-color BD FACSCalibur,10-color BD FACSCanto 10-color Amnis ImageStream X Mk II imaging cytometer,Special-order 16-color BD LSR II,16-color BD LSR Fortessa,17-color BD FACS Aria SORP high-performance cell sorter,23-color BD FACSSymphony." .
SCR:021135 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1168" ;
rdfs:label "University of California at Santa Cruz Life Sciences Microscopy Center Core Facility" ;
NIFRID:synonym "UCSC Life Sciences Microscopy Center" ;
definition: "Core facility affiliated with Institute for Biology of Stem Cells.Provides imaging instrumentation to biology research community including personalized assistance on various aspects of imaging.Offers assistance in experimental design,training on shared microscopes, image visualization and image analysis." .
SCR:021136 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Zyla 5.5" ;
rdfs:label "Andor | Zyla 5.5 sCMOS" ;
definition: "Large field of view, high resolution 5.5 megapixel sCMOS camera, ideal for research and OEM usage. Zyla 5.5 offers 100 fps frame rate and ultra low noise performance, in compact design.USB 3.0 version is available, offering up to 40 fps and industry fastest ROI speeds." .
SCR:021137 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "survival" ;
definition: "Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models." .
SCR:021138 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "caret" ;
NIFRID:synonym "Classification And REgression Training" ;
definition: "Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality." .
SCR:021139 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggpubr" ;
definition: "Software R package provides functions for creating and customizing ggplot2 based publication ready plots.Used for creation of ggplot2 based graphs." .
SCR:021140 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "infercnv" ;
NIFRID:synonym "Infer Copy Number Variation" ;
definition: "Software R package to infer copy number variation from single-cell RNA-seq data." .
SCR:021141 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_UV-KUB 2" ;
rdfs:label "Kloe | UV-KUB 2 - UV-LED masking system" ;
NIFRID:synonym "UV-KUB 2",
"UV‑KUB 2 masking system" ;
definition: "Compact exposure masking system is UV-LED masking system equipped with LED based optical head, collimated and homogeneous.One level mask aligner. Its masking function enables to reach resolutions less than 1um. This system is compatible with any of photoresists such as AZ series, Shipley series, SU-8 and K-CL series." .
SCR:021142 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scikit-image" ;
definition: "Open source software tool as collection of image processing algorithms implemented in Python programming language.Image processing library that implements algorithms and utilities developed by active, international team of collaborators." .
SCR:021143 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fluigent | LineUp LINK" ;
NIFRID:synonym "LineUp LINK" ;
definition: "Provides connection of LineUp series modules to PC for software control to use Fluigent Software." .
SCR:021144 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fluigent | Flow Unit" ;
definition: "Flow sensor for use with any flow control system. Unit to monitor flow rates in any microfluidic system with precision and accuracy." .
SCR:021145 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Flow EZ" ;
rdfs:label "Fluigent | Flow EZ" ;
NIFRID:synonym "Flow EZ",
"Flow EZ module",
"LINEUP FLOW EZ" ;
definition: "System for pressure based flow control. Enables to control or monitor flow rate as well as dispense volume. When combined with LINK module capabilities are extended by using Fluigent software to benefit from automation or live monitoring and recording of data. Flow EZ modules, are available in different pressure and vacuum ranges." .
SCR:021146 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1166" ;
rdfs:label "Rockefeller University Cryo Electron Microscopy Resource Center Core Facility" ;
NIFRID:synonym "Rockefeller University Cryo Electron Microscopy Resource Center",
"The Evelyn Gruss Lipper Cryo-Electron Microscopy Resource Center" ;
NIFRID:abbrev "CEMRC" ;
definition: "Offers new cryo-electron microscopy tools available to University researchers, allowing for visualization of three-dimensional structures of molecules and macromolecular complexes in solution." .
SCR:021147 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1169" ;
rdfs:label "University of Manchester Electron Microscopy Core Facility" ;
NIFRID:synonym "University of Manchester UoM-FBMH_EM_Core_Facility",
"UoM-FBMH_EM_Core_Facility" ;
definition: "Offers expertise and equipment tailored for biological samples mostly. Houses four electron microscopes.Preparation laboratory includes range of specialised room temperature and cryo sample preparation equipment, ultramicrotomes and suite of computer workstations for image processing.Electron microscopy staff are available to train and assist." .
SCR:021148 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1170" ;
rdfs:label "University of Massachusetts Light Microscopy Core Facility" ;
NIFRID:synonym "UMass-Amherst Light Microscopy Facility",
"University of Massachusetts Amherst UMass-Amherst Light Microscopy Facility" ;
definition: "Core provides resources for imaging model organisms, tissue, cells, biomaterials, and artificial structures and houses equipment including almost every light microscopy imaging modality presently available. Cell culture facilities are also available nearby as well as other routine items necessary for biological imaging and material imaging. This facility has been designated Nikon Centers of Excellence, thus providing unique opportunity for training, demonstration, instrument development, and research.We excel in use of telemicroscopy through use of remote imaging sessions, remote control of all instruments, and remote data analysis sessions available to all users.Provides training to all users that plan to conduct experimentation. Following an initial consultation in which experimental requirements, expected outcomes, and careful scrutiny of feasibility, training and/or access is arranged through the Director." .
SCR:021149 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1171" ;
rdfs:label "University of California, Santa Cruz IBSC Flow Cytometry Core Facility" ;
NIFRID:synonym "Santa Cruz UCSC-Institute for the Biology of Stem Cells Flow Cytometry Facility",
"UCSC-Institute for the Biology of Stem Cells Flow Cytometry Facility",
"University of California" ;
definition: "Facility offers multicolor cell analysis by BD LSRII cell analyzer and single cell sorting by BD Biosciences FACS Aria cell sorter. Provides user training for self-op use of BD FACS LSRII analyzer 3-laser and Self-op and Assisted sorting on BD FACS Aria IIU 5-lasers." .
SCR:021150 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpikeInterface" ;
definition: "Software tool as unified framework for spike sorting. Python framework to unify preexisting spike sorting technologies into single codebase and to facilitate straightforward comparison and adoption of different approaches.Used to reproducibly run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs." .
SCR:021151 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NWB Explorer" ;
definition: "Web application and standalone application to read, visualize and explore content of NWB:N 2 files.Used to share neurophysiological data in Neurodata Without Borders format." .
SCR:021152 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CaImAn" ;
definition: "Software Python toolbox for large scale calcium imaging data analysis and behavioral analysis.Used for motion correction, source extraction, spike deconvolution, and component registration across multiple days. It is suitable for both two-photon and one-photon fluorescence microscopy data, and can be run in both batch and online modes. Contains some routines for analysis of behavior from video cameras." .
SCR:021153 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "calciumImagingAnalysis" ;
NIFRID:synonym "CIAtah" ;
definition: "Software package for analyzing one and two photon calcium imaging datasets.Can be used to create GUI-less, command line ready analysis pipelines. Supports Neurodata Without Borders data standard for reading/writing cell-extraction (e.g. outputs of PCA-ICA, CELLMax, CNMF, CNMF-E, EXTRACT, etc.). Supports reading and writing NWB movie files with continued integration planned. Supports most major imaging movie file formats: HDF5, NWB, AVI, ISXD [Inscopix], and TIFF." .
SCR:021154 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NWBwidgets" ;
definition: "of widgets for visualization NWB data in Jupyter notebook. Widgets allow you to navigate through hierarchical structure of NWB file and visualize specific data elements. Designed to work with NWB 2.0 files and to be easy to extend." .
SCR:021155 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EcogVIS" ;
definition: "Software timeseries visualizer and data processing tools for Electrocorticography (ECoG) signals stored in NWB files, for Python." .
SCR:021156 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MatNWB" ;
NIFRID:synonym "matnwb" ;
definition: "Software Matlab interface for reading and writing Neurodata Without Borders (NWB) 2.0 files." .
SCR:021157 a owl:NamedIndividual ;
definition: "Open source software tool as interactive image segmentation filter for multiplex microscopy that aids in identification and removal of cell segmentation instances corrupted by optical and image processing artifacts." .
SCR:021158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Signac" ;
definition: "Software framework for analysis of single cell chromatin data. Used for analysis, interpretation, and exploration of single cell chromatin datasets including datasets that co-assay DNA accessibility with gene expression, protein abundance, and mitochondrial genotype. Analysis of single-cell chromatin data including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis, and interactive visualization." .
SCR:021159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mgatk" ;
NIFRID:synonym "mitochondrial genome analysis toolkit" ;
definition: "Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays." .
SCR:021160 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Ranger ATAC" ;
definition: "Software tool as set of analysis pipelines that process Chromium Single Cell ATAC data. Cell Ranger ATAC includes four pipelines relevant to single cell chromatin accessibility experiments.Used to investigate number of chromatin-accessibility signatures." .
SCR:021161 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "r8s" ;
definition: "Software package for estimating absolute rates of molecular evolution and divergence times on phylogenetic tree. Divergence time estimation on phylogenies." .
SCR:021162 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TimeTree" ;
definition: "Public knowledge base for information on evolutionary timescale of life. Data from thousands of published studies are assembled into searchable tree of life scaled to time." .
SCR:021163 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11543" ;
rdfs:label "IQ TREE" ;
definition: "Software tool for phylogenomic inference." .
SCR:021164 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100010677" ;
rdfs:label "UniProtKB/Swiss-Prot" ;
NIFRID:synonym "Swiss-Prot",
"SwissProt" ;
definition: "Curated component of UniProtKB (produced by the UniProt consortium). It contains hundreds of thousands of protein descriptions, including function, domain structure, subcellular location, post-translational modifications and functionally characterized variants." .
SCR:021165 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eggNOG-mapper" ;
NIFRID:synonym "eggNOG v5.0",
"eggNOG-mapper v2" ;
definition: "Software tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed eggNOG v5.0 clusters and phylogenies." .
SCR:021166 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GUSHR " ;
definition: "Software tool for assembly free construction of UTRs from short read RNA-Seq data on basis of coding sequence annotation." .
SCR:021167 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProtHint" ;
definition: "Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences." .
SCR:021168 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dfam" ;
NIFRID:synonym "Dfam 3.2" ;
definition: "Open collection of Transposable Element DNA sequence alignments, hidden Markov Models, consensus sequences, and genome annotations.Dfam 3.2 provides early access to uncurated, de novo generated families." .
SCR:021169 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Repbase" ;
definition: "Database of repetitive DNA elements.Database of prototypic sequences representing repetitive DNA from different eukaryotic species. Used in genome sequencing projects worldwide as reference collection for masking and annotation of repetitive DNA." .
SCR:021170 a owl:NamedIndividual ;
rdfs:label "RECON" ;
definition: """a package for automated de novo identification of repeat families from genomic sequences
Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes.""" .
SCR:021171 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ALLMAPS" ;
definition: "Software tool for computing scaffold ordering that maximizes colinearity to collection of maps, including genetic, physical or comparative maps into final chromosome build.Robust scaffold ordering based on multiple maps." .
SCR:021172 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Juicebox" ;
definition: "Visualization and analysis software for Hi-C data." .
SCR:021173 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "purge dups" ;
NIFRID:synonym "purge_dups" ;
definition: "Software tool to purge haplotigs and overlaps in assembly based on read depth.Used for haplotypic duplication identification. Designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth." .
SCR:021174 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CCS" ;
definition: "Software tool to combine multiple subreads of same SMRTbell molecule using statistical model to produce one highly accurate consensus sequence, also called HiFi read, along with base quality values. This tool powers Circular Consensus Sequencing workflow in SMRT Link." .
SCR:021175 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_X3" ;
rdfs:label "BioSpherix | Xvivo System model X3" ;
NIFRID:synonym "X3",
"Xvivo System X3",
"Xvivo System X3 Cytocentric Cell Incubation and Handling Platform" ;
definition: "Hypoxia cell culture system includes hypoxia incubator and cell culture hood with glove sleeves." .
SCR:021176 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSpherix | OxyStreamer Controller" ;
NIFRID:synonym "OxyStreamer Controller",
"OxyStreamer O2 and CO2 Controller for Live Cell Microscopy" ;
definition: "Controller for live cell microscopy provides two identical streams of any mix of oxygen and carbon dioxide gas without use of premixed gas cylinders. Eliminates need for pre-mixed gas. Controller is used primarily to pre-condition perfusion media while simultaneously conditioning headspace above culture." .
SCR:021177 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSpherix | A-Chamber" ;
NIFRID:abbrev "A-Chamber",
"A-Chamber Animal Cage Enclosure" ;
definition: "Animal Cage Enclosures for use in in vivo models that require control of experimental gases such as O2, CO2, NO, or CO. May be used together with gas controllers from BioSpherix. Chamber is outfitted with adjustable ventilation holes which permit ventilation of animal vapors and gases while simultaneously ensuring stable control of experimental conditions within. Available in three standard sizes." .
SCR:021178 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1167" ;
rdfs:label "Penn State Hershey College of Medicine cryo-EM Core Facility" ;
NIFRID:synonym "Penn State College of Medicine cryo-EM facility",
"Penn State COM Cryo-EM" ;
definition: "Cryo-electron microscopy (cryo-EM) facility providesTitan Krios cryo-transmission electron microscope that is fully equipped for high-throughput data collection of the utmost quality possible. It has the ability to determine the atomic structure of a single protein or view molecules interacting in their cellular context. Provides guidance, training or data collection for researchers at the College of Medicine.Equipment includes Zeiss LSM 980 Cryo-Confocal Microscope,300 kV Krios Cryo-TEM for SPA and tomography, Equipped with Volta phase plates, bioquantum energy filter and K3 direct electron detector,200 kV thermionic JEOL 2100 for cryo-imaging, cryo-tomography, and standard imaging of stained grids." .
SCR:021179 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MicroED tools" ;
NIFRID:synonym "Microcrystal Electron Diffraction" ;
definition: "Software Python suite to convert electron diffraction images to SMV format. Used in three dimensional electron crystallography.Developed to accomplish tasks of unit-cell determination, indexing, background subtraction, intensity measurement and merging, resulting in data that can be carried forward to molecular replacement and structure determination." .
SCR:021180 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1173" ;
rdfs:label "Forsyth Institute Micro Computed Tomography Core Facility" ;
NIFRID:synonym "Forsyth-MicroCT Core" ;
NIFRID:abbrev "uCT" ;
definition: "Core offers micro 3D X-ray imaging of small samples in high resolution and provides images and quantitative analyses of internal structures of ex vivo samples without any destructive procedures.Scanco CT40 system allows for visualization, measurement, and quantification of the structure of mineralized specimens. Contrast reagents permit visualization of soft tissue structures such as blood vessels.System creates 3D model from stack of 2D X-ray images taken around single axis of rotation. High-resolution scanner can capture detail at resolution of 6 to 32 microns. Non- destructive nature of this technology allows investigators to carry out complementary analyses of the same sample. There are two dedicated workstations for analyzing microCT data, the SCANCO analysis software or the Amira software package with XImagePAQ extension." .
SCR:021181 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "trRosetta" ;
NIFRID:synonym "transformed restrained Rosetta" ;
definition: "Software tool for fast and accurate protein structure prediction. Builds protein structure based on direct energy minimizations with restrained Rosetta. Restraints include inter-residue distance and orientation distributions, predicted by deep residual neural network. Homologous templates are included in network prediction to improve accuracy for easy targets." .
SCR:021182 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_A41OV" ;
rdfs:label "BioSpherix | OxyCycler A41OV Controller" ;
NIFRID:synonym "A41OV OxyCycler A41OV Dynamic O2 Animal Chamber Controller",
"OxyCycler A41OV" ;
definition: "Provides either dynamic or static control of O2 condition for animal modeling when used in combination with A-Chamber Animal Chamber." .
SCR:021183 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_A42OC" ;
rdfs:label "BioSpherix | OxyCycler A42OC Controller" ;
NIFRID:synonym "OxyCycler A42OC Controller" ;
NIFRID:abbrev "OxyCycler A42OC" ;
definition: "Provides either dynamic or static control of O2 and CO2 conditions for animal modeling when used in combination with one or two A-Chamber Animal Chamber(s)." .
SCR:021184 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_A44C" ;
rdfs:label "BioSpherix | OxyCycler A44C Controller" ;
NIFRID:synonym "OxyCycler A44C",
"OxyCycler A44C Dynamic CO2 Animal Chamber Controller" ;
definition: "Provides either dynamic or static control of CO2 conditions for animal modeling when used in combination with one to four (1-4) A-Chamber Animal Chambers purposes." .
SCR:021185 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_A84XOV" ;
rdfs:label "BioSpherix | OxyCycler A84XOV Controller" ;
NIFRID:synonym "OxyCycler A84XOV Dynamic O2 Animal Chamber Controller" ;
NIFRID:abbrev "OxyCycler A84XOV" ;
definition: "Provides either dynamic or static control of O2 conditions for animal modeling when used in combination with the one to four (1-4) A-Chamber Animal Chambers." .
SCR:021186 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AT42CO" ;
rdfs:label "BioSpherix | OxyCycler AT42CO Controller" ;
NIFRID:synonym "OxyCycler AT42CO Carbon Monoxide Animal Chamber Controller" ;
NIFRID:abbrev "OxyCycler AT42CO" ;
definition: "Provides either dynamic or static control of parts per million levels of carbon monoxide (CO) conditions in animal models modeling when used in combination with either one or two (1 or 2) A-Chamber Animal Chambers." .
SCR:021187 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AT42N" ;
rdfs:label "BioSpherix | OxyCycler AT42N Controller" ;
NIFRID:synonym "OxyCycler AT42N Nitric Oxide Animal Chamber Controller" ;
NIFRID:abbrev "OxyCycler AT42N" ;
definition: "Provides either dynamic or static control of parts per million levels of nitric oxide (NO) in animal models modeling when used in combination with either one or two (1 or 2) A-Chamber Animal Chambers." .
SCR:021188 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AT82NN" ;
rdfs:label "BioSpherix | OxyCycler AT82NN Controller" ;
NIFRID:synonym "OxyCycler AT82NN Nitric Oxide Animal Chamber Controller with NO2 Limit Control" ;
NIFRID:abbrev "OxyCycler AT82NN" ;
definition: "Provides either dynamic or static control of parts per million levels of nitric oxide (NO) and limits the undesirable elevation NO2 in animal models when used in combination with either one or two (1 or 2) A-Chamber Animal Chambers." .
SCR:021189 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ARX Data Anonymization Tool" ;
NIFRID:abbrev "ARX" ;
definition: "Open source software for anonymizing sensitive personal data.Supports variety of privacy and risk models, methods for transforming data and methods for analyzing usefulness of output data." .
SCR:021190 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Easy Electrophysiology" ;
definition: "Open source software for analysis of patch-clamp electrophysiological data. Integrated analysis environment including routines for curve fitting, post-synaptic event and action potential analyses, data resampling, filtering, detrending and more." .
SCR:021192 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_379" ;
rdfs:label "Northwestern University Center for Advanced Molecular Imaging Core Facility" ;
NIFRID:synonym "Northwestern University Center for Advanced Molecular Imaging (CAMI)" ;
NIFRID:abbrev "CAMI" ;
definition: "Provides access to range of preclinical imaging modalities and support services. These include MRI, nuclear imaging (PET, SPECT, and CT), in vivo bioluminescence and fluorescence imaging, animal housing and prep spaces, and tissue culture. Image analysis services are available, as are software packages (JIM, Amira, Matlab) and a workstation for users to perform their own data analysis. Imaging services can be provided for investigators' own animal models, or animal models can be supplied by the Developmental Therapeutics Core." .
SCR:021193 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iScanVCFMerge" ;
definition: "Software Python package to merge cross species Illumina iScan genotype data with reference set of data from pre existing source." .
SCR:021194 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1175" ;
rdfs:label "Penn State Hershey College of Medicine Clinical Research Biospecimen Core Facility" ;
NIFRID:synonym "CSPC-Clinical Specimen Processing Core",
"Pathology and Specimen Processing" ;
definition: "Process, store and ship clinical trial samples from IRB approved studies. Collect remnant samples for outside company for instrument correlation, validation and specimen type verification with IRB approved protocol. CLIA Waver for urine pregnancy, urine dipstick results for participant study treatment." .
SCR:021195 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Jordan School of Nursing; Amman; Jordan" ;
definition: "Offers Baccalaureate Degree in Nursing and Ph.D. Nursing Program. Offers specialized and advanced graduate nursing education in Jordan." .
SCR:021196 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ABRF CoreMarketplace" ;
NIFRID:synonym "CoreMarketplace" ;
NIFRID:abbrev "ABRF CM" ;
definition: "ABRF CoreMarketplace project created for core facilities tracking. CoreMarketplace (CM) is searchable list of active core facilities that perform scientific research. The CM was initially created by Vermont IDeA Network of Biomedical Research Excellence (INBRE). CoreMarketplace is associated with Association of Biomolecular Research Facilities (ABRF) which is membership association to sponsor and help members to incorporate new biotechnology into their laboratories." .
SCR:021197 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Common Fund Data Ecosystem Portal" ;
NIFRID:abbrev "CFDE portal" ;
definition: "Portal allows researchers and clinicians to access and work across multiple Common Fund program data sets within digital cloud environment because biomedical research interaction with digital data is changing and no longer can large biomedical datasets be stored or analyzed using local computers and servers. Provides list of tutorials and resources to learn how to perform bioinformatic analyses and access data." .
SCR:021198 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1176" ;
rdfs:label "Penn State Hershey College of Medicine MRI Core Facility" ;
NIFRID:synonym "PSU COM-Center for Nuclear Magnetic Resonance Research (CNMRR) /MRI Core Facility" ;
definition: """MRI and NMR magnetic resonance imaging facility for animal and human research, providing MRI methodologies and expertise for in vivo studies Laboratory space includes biochemical, electronic and surgical suites, and fully equipped machine shop with (2) 3D printers. MRI Core facility has two MRI systems and EEG MRI-compatible system.3T Siemens PRISMA-Fit scanner equipped with True 2 Channel Tx and 64 Channel Rx. The latest RF coil set including a 64 Channel head coil and software packages with full clinical capability.7T Biospec 70/20 as small animal imaging system (Bruker Biospin, Ettlingen, Germany). Latest Hardware and Software. Avance NEO with Paravision 360. Full sensory fMRI stimulation systems:SenSaVue System for visual and auditory stimulation (Invivo Corp, FL, USA), which includes an LCD visual display, audio system, button response unit and software (E-Prime) for paradigm creation, patient management, protocol planning, precise delivery of brain stimulation, and behavioral analysis.ETT Olfactometer with full-programmable 6 independent channels for odor and trigeminal stimulation (ETT, LLC, Hershey, PA).Olfact Smell Test System (Osmic Enterprises, Inc., Cincinnati, OH) is a computerized instrument to test the smell functions of human subjects. The smell functions that can be tested are odor threshold, odor identification, and odor memory.ETT Gustatometer with full-programmable 7 independent channels for taste stimulation (ETT,LLC, Hershey, PA)
Eye Link 1000 Plus system via SR Research: The EyeLink 1000 Plus Host PC performs real-time eye tracking at 250, 500,1000, or 2000 samples per second while computing true gaze position on the display viewed by the participant. The Host PC also performs on-line detection and analysis of eye-motion events such as saccades, blinks, and fixations. In addition to the sample data, these events are stored in a data file on the Host PC. They can be sent through the Ethernet link to the Display PC with a minimal delay or output as analog signals (if the optional analog/digital I/O card is installed). From the Host PC, the operator performs participant setup, monitors their performance, and can communicate with applications running on a Display PC.""" .
SCR:021199 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1177" ;
rdfs:label "Penn State Hershey College of Medicine Zebrafish Functional Genomics Core Facility" ;
NIFRID:synonym "Penn State Zebrafish Functional Genomics Core" ;
definition: "Provides Penn State research community with modern, centralized facility for housing, breeding and performing experiments with zebrafish.Provides physical and intellectual infrastructure for investigators whose research can benefit from use of zebrafish as model system." .
SCR:021200 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1172" ;
rdfs:label "Penn State Hershey College of Medicine Transmission Electron Microscopy Core Facility" ;
NIFRID:synonym "TEM",
"TEM Facility at Penn State College of Medicine",
"Transmission Electron Microscopy Facility at Penn State College of Medicine" ;
definition: "Provides consultation and training in TEM imaging of biological, chemical, and materials science samples." .
SCR:021201 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1178" ;
rdfs:label "University of Massachusetts Medical School Biomedical Imaging Group Core Facility" ;
NIFRID:synonym "Biomedical Imaging Group" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 11, 2025. Interdisciplinary team of engineers and scientists, representing fields of physics, mathematics, and computer science, that combine their expertise in areas such as microscopy, lasers, optoelectronics, applied mathematics, image and signal processing, computer graphics, computer vision, statistics, software engineering, and biophysics, to develop imaging approaches for cell biology. Pioneers in high-resolution 3D imaging using wide-field fluorescence microscopy together with digital image deconvolution, and image visualization and quantitative analysis techniques, especially as applied to statistical analysis of images to determine co-localization of fluorescence markers inside cells.Research includes development and application of light microscopy and imaging in cell biology and biophysics.Developed TESM microscope that combines Total internal reflection fluorescence (TIRF) with Epi-fluorescence Structured illumination to provide new views of trafficking in near plasma membrane domain of cells.Provides custom-built, ultra-high-speed microscope system for imaging dynamics of intracellular calcium channel events, called calcium sparks, that are being found to regulate expanding array of cellular processes. Provides two photon fluorescence microscope for looking deep inside tissue, completing range from molecule to organism. Areas of ongoing technology research include high-speed, high-resolution imaging of live cells and tissues, novel image processing approaches, high-performance computing, and computer graphics." .
SCR:021202 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Illumina Experiment Manager" ;
NIFRID:synonym "Illumina Experiment Manager software",
"Illumina Experiment Manager v1.18.1",
"Illumina Experiment Manager v1.19.1" ;
NIFRID:abbrev "IEM" ;
definition: """Software to create and edit sample sheet in order to perform next generation sequencing on Illumina paltforms. Used for MiniSeq, MiSeq, NextSeq 500/550, HiSeq, and
NovaSeq 6000 Systems.""" .
SCR:021203 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_X2" ;
rdfs:label "BioSpherix | Xvivo System model X2" ;
NIFRID:abbrev "Xvivo",
"Xvivo System X2",
"Xvivo System X2 Research",
"Xvivo X2" ;
definition: "Isolator that provides physiologically relevant oxygen as well as low contamination risk cell incubation and handling. Subset of Cytocentric Platform designed for processing and producing cells in compliance with regulatory GMPs. Includes glovebox and tanked gases for atmosphere for controllable humidity and microbial risks. Modular and customizable." .
SCR:021204 a owl:NamedIndividual ;
rdfs:label "Analyze Spheroid Cell Invasion In 3D Matrix" ;
NIFRID:abbrev "ASCI" ;
definition: "Software tool to measure area of invading spheroid in 3D cell invasion assay. Can also count and measure area of nuclei within spheroid." .
SCR:021205 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_P120ppm" ;
rdfs:label "BioSpherix | ProCO2 120ppm Controller" ;
NIFRID:synonym "ProCO2 120ppm",
"ProCO2 120ppm Animal Chamber Off-Gas Limit Controller" ;
definition: "Parts per million limit controller primarily used for assuring consistent and acceptable off gas levels in variety of animal enclosures." .
SCR:021206 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioSpherix | Biological Safety Hood" ;
NIFRID:synonym "Safety Hood",
"Safety Hood for Animal Chambers" ;
definition: "Hood holds any animal lab chambers while continuously sweeping all experiment related off gases away.Used to capture and exhaust gases or vapors which escape from animal chamber and directs them to safe location.Helps to control animal odor in the lab. Available in standard and customized dimensions." .
SCR:021207 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of California at Santa Cruz CRISPR Core Facility" ;
NIFRID:abbrev "UCSC CRISPR Core" ;
definition: "Facility that provides CRISPR services and expertise to facilitate study of gene function. Services include project consultation, sgRNA design and cloning, lentivirus production, custom CRISPR cell line generation and genome wide CRISPR screen." .
SCR:021208 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ModelMatcher" ;
definition: "Matchmaking platform for clinicians and scientists to facilitate collaborative research on rare and undiagnosed diseases. Used for collaborative projects that advance scientific knowledge and patient care. Currently supports Mouse, Rat, Frog, Zebrafish, Fruit Fly, Nematode Worm, Budding Yeast, Fission Yeast, and E. coli. Used to identify human ortholog of genes in these model organisms and vice versa. Scientists who register in ModelMatcher are asked to classify their genes of interest into Public or Restricted categories.The Match feature will allow Clinicians to obtain information on genes that Scientists classify as both Public and Restricted." .
SCR:021209 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1181" ;
rdfs:label "Islamabad Health Services Academy Core Facility" ;
NIFRID:synonym "Health Services Academy",
"HSA",
"Institute for Research in Schools HSA" ;
definition: "Provides short training courses to in service public health practitioners and professionals.Offers teaching, research, and policy advice in public health in Pakistan." .
SCR:021210 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Snudda" ;
definition: "Software tool to create realistic networks of neurons, synapses placed using touch detection between axons and dendrites.Used to create detailed network of connected neurons, where connectivity is derived from reconstructed neuronal morphologies as well as from more qualitative experimental knowledge. Supports creation of network with connectivity based on touch detection." .
SCR:021211 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QIAGEN GeneGlobe Data Analysis Center" ;
NIFRID:synonym "GeneGlobe Data Analysis Center",
"QIAGEN GeneGlobe" ;
definition: "Web based portal using web based tools for analyzing real-time qPCR or next-generation sequencing data. NGS modules support analysis of QIAGEN's QIAseq NGS library kits and target enrichment panels." .
SCR:021212 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IRIS two photon acquisition package" ;
NIFRID:synonym "IRIS two-photon acquisition package" ;
definition: "Software LabView package for two-photon calcium imaging acquisition. Used for controlling two-photon microscope and preprocessing of calcium imaging data." .
SCR:021213 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Calliope calcium imaging processing package" ;
definition: "Software package for image processing for MATLAB. Used for processing of calcium imaging data." .
SCR:021214 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Friedrich Miescher Institute data repository" ;
NIFRID:synonym "FMI data repository" ;
definition: "Data repository for Friedrich Miescher Institute for Biomedical Research in areas of epigenetics, quantitative biology, and neurobiology." .
SCR:021215 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PROMIS 2 MY Health" ;
definition: "Portal for cross sectional study where population based sample of adult cancer patients were recruited for mailed survey (with telephone follow-up of non-responders) to evaluate equivalence of PROMIS measures across socio-demographic and clinical sub-groups." .
SCR:021216 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Platform agnostic networked display architecture 3D" .
SCR:021217 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Two photon Calcium Imaging in Mice Navigating Virtual Reality Environment" ;
NIFRID:synonym "Two-photon Calcium Imaging in Mice Navigating a Virtual Reality Environment" ;
definition: "Behavioral two photon imaging system. Includes two photon scanning microscope, software and virtual reality set up. Used for chronic two photon imaging in mice exploring virtual environment. Tool in neuroscience to allow for chronic measurement of activity of genetically identified cells during behavior." .
SCR:021218 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RNAProt" ;
definition: "Software tool for modelling RNA binding protein binding preferences. Used to predict RPB binding sites. Computational RBP binding site prediction framework based on recurrent neural networks. Includes functionalities from dataset generation over model training to evaluation of binding preferences and binding site prediction." .
SCR:021219 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CEMBA MethylC Seq Pipeline" ;
NIFRID:synonym "CEMBA",
"Center for Epigenomics of the Mouse Brain Atlas MethylC Seq Pipeline",
"MethylC-Seq Pipeline" ;
definition: "Software pipeline that supports processing of multiplexed single nuclei bisulfite sequencing data to detect methylated bases. Alignment and methylated base calling pipeline that trims adaptors, attaches cell barcodes, aligns reads to genome, filters reads based on quality and creates both VCF and ALLC file with Emethylation site coverage." .
SCR:021220 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FAIRSCAPE" ;
definition: "Software tool as reusable computational framework, enabling simplified access to modern scalable cloud based components. Implements FAIR data principles and extends them to provide fully FAIR Evidence, including machine interpretable provenance of datasets, software and computations, as metadata for all computed results.All objects are assigned persistent IDs, including software." .
SCR:021221 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Traefik" ;
definition: "Software tool based on open source solutions to make deploying microservices easy. Used for deployment of modern IT environments. Allows to expose applications to network in dynamic environment.Traefik Stack by Traefik Labs Inc. as cloud native stack to help enterprises manage their entire network across data centers, on-premises servers and public clouds.Tools options include Traefik Proxy,Traefik Enterprise,Traefik Mesh,Traefik Pilot." .
SCR:021222 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Keycloak" ;
definition: "Open source identity and access management solution written in Java. Offers features such as Single-Sign-On, Identity Brokering and Social Login, User Federation, Client Adapters, Admin Console, and Account Management Console by WildFly, a division of Red Hat." .
SCR:021223 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stardog" ;
NIFRID:synonym "Knowledge Graph platform",
"Stardog Enterprise Knowledge Graph platform" ;
definition: "Software tool as knowledge graph platform to create flexible, reusable data layer for answering complex queries across data silos. Used for organizing data to highlight relationships between data points. Unifies data based on its meaning, creating connected network of knowledge." .
SCR:021224 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MongoDB" ;
NIFRID:synonym "MongoDB 4.4" ;
definition: """General purpose, document based, distributed database built for modern application developers and for the cloud. Offers Community and Enterprise version of database.MongoDB Community is source available and free to use edition of MongoDB.
MongoDB Enterprise is available as part of MongoDB Enterprise Advanced subscription and includes comprehensive support for your MongoDB deployment. MongoDB Enterprise also adds enterprise-focused features such as LDAP and Kerberos support, on-disk encryption, and auditing.MongoDB also offers Atlas,hosted MongoDB Enterprise service option in cloud which requires no installation overhead and offers free tier to get started.""" .
SCR:021225 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Evidence Graph Ontology " ;
NIFRID:abbrev "EVI" ;
definition: "Evidence Graph Ontology extends core concepts from W3C Provenance Ontology PROV-O to describe evidence for correctness of findings in biomedical publications. Semantic data model in EVI is expressed using OWL2 Web Ontology Language." .
SCR:021226 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GMSH" ;
definition: "Open source software tool as 3D finite element grid generator with build in CAD engine and post processor. Provides meshing tool with parametric input and advanced visualization capabilities. Built around geometry, mesh, solver and post processing modules.Specification of any input to these modules is done either interactively using graphical user interface, in ASCII text files using Gmsh own scripting language (.geo files), or using C plus plus, C, Python or Julia Application Programming Interface." .
SCR:021227 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CytoMAP" ;
NIFRID:synonym "Histo-Cytometric Multidimensional Analysis Pipeline" ;
definition: "Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information." .
SCR:021228 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Smart-seq2 Single Sample Pipeline" ;
definition: "Software tool designed by Data Coordination Platform of Human Cell Atlas to process single-cell RNAseq data generated by Smart-seq2 assays.Processes stranded or unstranded, paired- or single-end, scRNA-seq data from an individual cell." .
SCR:021230 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Alzheimer Disease Preclinical Efficacy Database" ;
NIFRID:synonym "AlzPed" ;
definition: "Publicly available, searchable, data resource that aims to increase transparency, reproducibility and translatability of preclinical efficacy studies of candidate therapeutics for Alzheimer’s disease. Knowledge platform for dissemination of data and analysis to scientists, from academic centers, industry, disease focused foundations. Provides quick access and visibility to integrated preclinical efficacy data from published and unpublished studies." .
SCR:021231 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Diploidocus" ;
definition: "Software package for diploid genome assembly analysis. Sequence analysis toolkit for number of different analyses related to diploid genome assembly." .
SCR:021232 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DepthSizer" ;
definition: "Software tool for read-depth based genome size prediction. Wrapper for genome size estimate methods of Diploidocus.Uses long read depth of coverage and BUSCO single copy orthologue prediction to estimate genome size." .
SCR:021233 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BUSCOMP" ;
definition: "Software tool for BUSCO compilation and comparison. Used for assessing completeness in multiple genome assemblies.Used for assembly comparison designed to be robust to differences in assembly size and base calling quality." .
SCR:021234 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mechanical Finder " ;
definition: "Software tool to evaluate bone strength by considering entire bone as three dimensional structure and applying finite element analysis." .
SCR:021235 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_021251" ;
rdfs:label "ENVRI-KMS" ;
NIFRID:synonym "ENVironmental Research Infrastructures Knowledge Management System" ;
definition: "Web tool as cluster-level knowledge base that allows different ENVironmental Research Infrastructures (ENVRI) users, such as Research Infrastructures (RI) developers and data managers, to effectively share their technical practices, identify common data and service requirements and design patterns, and facilitate search and analysis of existing RI solutions for environmental RI interoperability challenges." .
SCR:021236 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Quant3p" ;
NIFRID:synonym "quant3p" ;
definition: "Software tool as set of scripts for 3' RNA-seq quantification." .
SCR:021237 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss | Lattice Lightsheet 7" ;
NIFRID:synonym "ZEISS Lattice Lightsheet 7 imaging system" ;
definition: "System for long term volumetric imaging of living cells. Makes light sheet fluorescence microscopy available for live cell imaging at subcellular resolution. Automated system for volumetric imaging of subcellular structures and dynamics over hours and days with protection from photo damage." .
SCR:021238 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "igraph for R" ;
NIFRID:synonym "R/igraph",
"rigraph" ;
definition: "Software R package of igraph network analysis library." .
SCR:021239 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggraph" ;
NIFRID:synonym "grammar of graphics for relational data" ;
definition: "Software tool as extension of ggplot2 aimed at supporting relational data structures such as networks, graphs, and trees. While it builds upon foundation of ggplot2 and its API it comes with its own self-contained set of geoms, facets, etc., as well as adding concept of layouts to grammar." .
SCR:021240 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rstatix" ;
definition: "Software R package for basic statistical tests including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. Output of each test is automatically transformed into data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate analysis of factorial experiments. Can compute several effect size metrics.Package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances." .
SCR:021242 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ti" ;
rdfs:label "Nikon | ECLIPSE Ti inverted microscope system" ;
NIFRID:synonym "Nikon ECLIPSE Ti inverted microscope" ;
definition: "ECLIPSE Ti Series of inverted microscopes combined with Nikon NIS-Elements imaging acquisition and analysis software, enables to generate data faster, more easily, and more accurately than ever before.Product Discontinued. Replaced by ECLIPSE Ti2 Series." .
SCR:021243 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Eclipse_E200" ;
rdfs:label "Nikon | Eclipse E200 microscope" ;
NIFRID:synonym "Eclipse E200",
"Eclipse E200 microscope" ;
definition: "Educational microscope. Designed as simple system that reduces fatigue from use over long periods. With structure and anti mold design, offers high quality and accuracy that can be retained for years even in hot and humid environments." .
SCR:021244 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ Stemi_DV4" ;
rdfs:label "Zeiss | Stemi DV4 Stereomicroscope" ;
NIFRID:synonym "Carl Zeiss Stemi DV4 Series Stereomicroscopes with LED Illumination",
"Stemi DV4 stereoscope" ;
definition: "Carl Zeiss Stemi DV4 series stereomicroscope." .
SCR:021245 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Appyters" ;
definition: "Collection of web-based software applications that enable users to execute bioinformatics workflows without coding. Turns Jupyter notebooks into fully functional standalone web-based bioinformatics applications. Each Appyter application introduces data entry form for uploading or fetching data, as well as for selecting options for various settings. Once user presses Submit, Appyter is executed in cloud and user is presented with Jupyter Notebook report that contain results. Report includes markdown text, interactive and static figures, and source code. Appyter users can share the link to the output report, as well as download the fully executable notebook for execution on other platforms." .
SCR:021247 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Wikidata_Q76693569" ;
rdfs:label "Author Disambiguator" ;
definition: "Wikidata metadata curation service. Wikidata service to help create or link author items to published articles." .
SCR:021248 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Wikidata_Q45340488" ;
rdfs:label "Scholia" ;
definition: "Software Python package and webapp for interaction with scholarly information in Wikidata. Wikidata profiling service.Wikidata service generating scholarly profiles, e.g. for authors, journals, topics, and organisations." .
SCR:021249 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pubchem Draw" ;
definition: "Web tool to draw chemical structure by PubChem." .
SCR:021250 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Minhee Analysis Package" ;
definition: "Software package for detection and measurement of spontaneous synaptic events. Integrated software package for detection and management of spontaneous synaptic events. Used in neurophysiology to detect spontaneous postsynaptic currents, search and visualize them in custom way, and perform hypothesis testing of retrieved data." .
SCR:021252 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TraNCE" ;
NIFRID:synonym "TRAnsforming Nested Collections Efficiently" ;
definition: "Software tool as framework for processing nested collection queries. Used to automate difficulties of designing distributed analyses with complex, biomedical data types. Uses query compilation and optimization techniques to ease difficulty of handling nested collections, and is designed for arbitrary, multi-modal analyses of complex data types." .
SCR:021253 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggalluvial" ;
definition: "Software tool as ggplot2 extension for alluvial plots. Used to visualize frequency distributions over time or frequency tables involving several categorical variables. Requires user to specify dimensions, either as separate aesthetics or as key-value pairs, relies on separate layers (stats and geoms) to produce strata, alluvia, and alluvial segments called lodes and flows." .
SCR:021254 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Roche | Ventana DISCOVERY Ultra" ;
NIFRID:synonym "DISCOVERY ULTRA",
"VENTANA DISCOVERY ULTRA AUTOMATED SLIDE PREPARATION SYSTEM",
"Ventana DISCOVERY Ultra IHC/ISH research platform" ;
definition: """Immunohistochemistry processor that can be used for immunohistochemistry and in situ hybridization slide preparation and processing. With 30 individual slide drawers, DISCOVERY ULTRA system enables to run both manual and fully automated experiments simultaneously with nosynchronization errors. Provides ability to fully automate broad range of IHC and ISH assays, including FISH, gene and protein IHC/ISH,
mRNA ISH and multiplex assays with any combination of IHC and ISH.""" .
SCR:021255 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Linear Analysis of Midgut" ;
NIFRID:synonym "Linear Analysis of Midgut (LAM)" ;
NIFRID:abbrev "LAM" ;
definition: "Software Python package for spatially defined cellular phenotyping using image segmentation data from linearizable tissue.Software quantitative phenotyping tool intended for regionally defined analysis of Drosophila midguts based on objects detected from microscopy images." .
SCR:021256 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Aperio_AT2" ;
rdfs:label "Leica | Aperio AT2 scanner" ;
NIFRID:synonym "Aperio AT2" ;
definition: "Digital whole slide scanner.400 slide capacity brightfield scanner. High throughput with small footprint. 2x3 slide option available.Aperio AT2 runs on Microsoft Windows 10 operating system." .
SCR:021257 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TMA_Grand_Master" ;
rdfs:label "3DHISTECH | TMA Grand Master" ;
NIFRID:synonym "TMA Grand Master" ;
definition: "Automated tissue microarrayer, allowing precise selection and extraction of specific regions of interest on donor blocks and their insertion in recipient blocks.Controlled by TMA Control software." .
SCR:021258 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QIIME2" ;
NIFRID:synonym "Quantitative Insights Into Microbial Ecology 2" ;
definition: """Software tool as next generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.Enables researchers to start analysis with raw DNA sequence data and finish with publication quality figures and statistical results.
Used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities.""" .
SCR:021259 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChronoRoot" ;
definition: "System which combines 3D printed open hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium. Deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process." .
SCR:021262 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Noldus | CatWalk XT" ;
NIFRID:synonym "CatWalk XT",
"Noldus" ;
definition: "Gait analysis system for quantitative assessment of footfalls and locomotion in rats and mice. System includes corridor that directs free movement in straight line, hardened glass walkway that enables CatWalk XT Illuminated Footprints technology,high speed color camera for spatial and temporal resolution, CatWalk XT software for recording and automated analysis of locomotor ability of rodents." .
SCR:021266 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "World Mortality Dataset" ;
definition: "International data on all cause mortality. Country level data on all cause mortality in 2015–2021 collected from various sources for 94 countries and territories." .
SCR:021267 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "purrr" ;
definition: "Software functional programming tools for R. Used for working with functions and vectors." .
SCR:021268 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bash" ;
NIFRID:synonym "Bourne Again SHell" ;
definition: """GNU Project shell. Sh-compatible shell that incorporates useful features from Korn shell (ksh) and the C shell (csh). Improvements offered by Bash include command-line editing,
unlimited size command history,job control,shell functions and aliases,indexed arrays of unlimited size,integer arithmetic in any base from two to sixty four.""" .
SCR:021269 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rcartocolor" ;
definition: "Software tool to provide color schemes for maps and other graphics designed by CARTO.Implementation of CARTOcolor palettes in R. It includes four types of palettes: aggregation, diverging, qualitative, and quantitative." .
SCR:021270 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "7-Zip" ;
definition: "Open source software tool as file archiver with high compression ratio." .
SCR:021272 a owl:NamedIndividual ;
rdfs:label "Software for generation of GB-speckles " ;
NIFRID:abbrev "GB-speckles" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 23, 2022." .
SCR:021273 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openSMILE" ;
NIFRID:synonym "open source Speech and Music Interpretation by Large-space Extraction" ;
definition: "Open source software toolkit for audio feature extraction and classification of speech and music signals. Used for audio analysis, processing and classification especially targeted at speech and music applications, e.g. automatic speech recognition, speaker identification, emotion recognition, or beat tracking and chord detection.Written in C plus plus and runs on desktop, mobile, and embedded platforms such as Linux, Windows, macOS, Android, iOS and Raspberry Pi." .
SCR:021274 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KinTek Explorer" ;
definition: "Software tool for fitting kinetic and equilibrium data based on numerical integration of rate equation from any model input user. Simulation and data-fitting software for research and education designed specifically for the field of chemical kinetics." .
SCR:021276 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AllFam" ;
NIFRID:synonym "AllFam database of allergen families" ;
definition: "Database for classifying allergenic proteins into protein families.You can browse lists of allergen families restricted by allergen source (plants, animals, fungi, bacteria) and route of exposure (inhalation, ingestion etc.) or search for specific allergens, sources or protein families. Every allergen family entry is linked to description of biochemical properties and allergological significance of family members as well as list of key references related to this family." .
SCR:021277 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TailTimer" ;
definition: "Device for automating tail immersion assay. Used for measuring acute thermal pain in rodents. Software recognizes several specific RFID keys as user interface commands, which allows TailTimer to be operated via RFID fobs." .
SCR:021281 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneCup" ;
definition: "Literature mining web service that searches all PubMed abstracts for user provided gene symbols in conjunction with set of custom keywords organized into customized ontology, as well as results from human genome wide association studies (GWAS). Searches gene symbols against list of keywords in PubMed to extract sentences that contain at least one gene and one keyword. Used to mine PubMed for gene relationships using custom ontology and deep learning." .
SCR:021282 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IDT custom DsiRNAs generator" ;
NIFRID:synonym "Custom Dicer-Substrate siRNA (DsiRNA) generator",
"Integrated DNA Technology custom DsiRNAs generator" ;
definition: "Web service to generate DsiRNAs for any sequence from any species by Integrated DNA Technologies." .
SCR:021283 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1184" ;
rdfs:label "University of California Santa Cruz Macromolecular Structure Function Core Facility" ;
NIFRID:synonym "Macromolecular Structure Function Core Facility-UCSC" ;
definition: "Provides instrumentation, supplies, and expertise to assist researchers in structural characterization of biological macromolecules. Resources are available for crystallization and structure determination as wells as biophysical characterization of macromolecular stability and interactions." .
SCR:021284 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_264" ;
rdfs:label "Dartmouth Geisel School of Medicine Mouse Modeling Core Facility" ;
NIFRID:synonym "Dartmouth Mouse Modeling Shared Resource",
"Mouse Modeling Shared Resource" ;
definition: "Supports generation and utilization of genetically modified mice, design and production of genetic constructs with methods including yeast and E.coli recombineering, ES cell targeting (transfection, drug selection, and expansion). Produces transgenic mice: DNA injections into oocytes, ES cell injections into blastocysts.Provides humanized immune system mouse models.Offers start to finish experiment services to assist your many needs, please ask for more info.Other services include animal husbandry, IP and IV injections, blood drawing, necropsy and surgeries- embryo transfers, ovariectomy, vasectomy, tumor removal." .
SCR:021285 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_811" ;
rdfs:label "University of Kentucky College of Medicine Genetic Technologies Core Facility" ;
NIFRID:synonym "Center for Molecular Medicine Genetic Technologies Core" ;
definition: "Core provides services related to manipulation and delivery of nucleic acids to biological systems. Services include Production and titering of recombinant viral vectors,including Lentiviruses, Adenoviruses, and Adeno associated viruses;Subcloning;Tagging of open reading frames;Development of plasmids and/or RNAs for CRISPR/Cas manipulation;piggyBac transposon delivery systems;Real-time PCR analysis;Recombineering;In vitro transcription; Core maintains stock of plasmids that provide components for building constructs envisioned by investigator and provides consultative services.Provides training opportunities in the technologies described above, either as a for-credit, one semester class or on a project-related, fee-based basis." .
SCR:021286 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_341" ;
rdfs:label "Frederick National Laboratory Protein Expression Laboratory Core Facility" ;
NIFRID:synonym "FNL Protein Expression Laboratory" ;
NIFRID:abbrev "PEL" ;
definition: "Comprises six service groups. Our services are available to all NIH intramural researchers, and by interagency agreements to FDA and US Army at Ft. Detrick. We are happy to consult and distribute materials to not-for-profit institutions.Clone Optimization service include DNA cloning for protein expression; Gateway-based; fluorescent, epitope, solubility, purification tags; mutagenesis; vectors for insect/ baculovirus, mammalian, E. coli, P. pastoris, K. lactis. Microbial Expression: E. coli, P. pastoris, K. lactis, 2 mL to 60 L, autoinduction and IPTG; fully instrumented fermenters.Eukaryotic Expression service include insect / baculovirus, mammalian transient and stable, monoclonal antibodies.Protein Purification service include parallel microscale for process development; affinity and native, tag and endotoxin removal; scale-up to low gram scale.Virus Technology service include custom and stock adenovirus and lentivirus production; titer determination; promoter and reporter panels in lentivirus ready to deliver.Molecular Detection: qPCR and ELISA assaysdeveloped and executed, focused on human viruses in human samples; qPCR assays for mycoplasma and human pathogenic viruses contaminating cell lines; cell line identity testing." .
SCR:021287 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1185" ;
rdfs:label "Cornell University BRC Epigenomics Core Facility" ;
NIFRID:synonym "Cornell University Epigenomics Core Facility",
"CU Epigenomics Core Facility" ;
definition: "Provides service that maps protein DNA interactions genome wide, tracks experimental metadata, and implements quality controlled data processing and research based analysis pipelines. Provides epigenomic and bioinformatic research resources and services that include sample preparation services and data generation. Open source platforms enable and reinforce FAIR data practices. Core is able to receive and process cell and tissue samples for various diagnostic epigenetic assays." .
SCR:021288 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_836" ;
rdfs:label "Northwestern University NUANCE BioCryo Core Facility" ;
NIFRID:synonym "BioCryo Facility - part of NUANCE" ;
definition: "Provides source for characterization of biological, soft matter, and hybrid samples with TEM (Transmission Electron Microscopy), SEM (Scanning Electron Microscopy), and STEM (Scanning Transmission Electron Microscopy) at cryogenic or at ambient temperature.Provide expertise and access to equipment for cryofixation and processing of frozen hydrated samples by high pressure freezing, plunge freezing, freeze fracturing, cryo ultramicrotomy, freeze substitution, and turbo freeze-drying. Conventional samples can be processed at ambient temperature with chemical fixation, dehydration, and resin embedding, or critical point drying. Offers EDX (Energy Dispersive X-ray Spectroscopy) for elemental analysis.Offers training on instruments and sample preparation techniques.BioCryo staff mentors new users, advises on experimental design, and collaborates with researchers in experiments with challenging and unconventional samples.BioCryo Facility participates in numerous educational and outreach events, e.g. workshops, seminars, demos, and facility tours." .
SCR:021289 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_216" ;
rdfs:label "University of Vermont Larner College of Medicine Microscopy Imaging Center Live Imaging and PhysiologyCore Facility" ;
NIFRID:synonym "MIC Live Imaging and Physiology Core" ;
definition: "The MIC Live Imaging and Physiology Core is a division of the Microscopy and Imaging Center of the UVM Larner College of Medicine. The Live Imaging and Physiology Core provides a wide range of imaging techniques mainly for live-cell, live-tissue and in-vivo preparations. We maintain a Noran/Prairie Technologies OZ LSCM (laser scanning confocal microscope), a DeltaVision RT restoration microscopy system, a Zeiss/BioRad 2100 dedicated multiphoton LSCM, a Zeiss LSM 7 MP dedicated multiphoton LSCM, a Nikon TIRF (total-internal reflection fluorescence) system, a Nikon/Yokogawa CSU-W1 spinning disk microscopy system, a PTI monochromator system, and a Nikon SMZ-1500 fluorescence stereoscope. Patch-clamp electronics are available for use on most microscope systems, and each system has an integrated perfusion setup." .
SCR:021290 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1186" ;
rdfs:label "University of North Carolina at Chapel Hill Biospecimen Processing Core Facility" ;
NIFRID:synonym "UNC Biospecimen Processing Facility" ;
NIFRID:abbrev "BSP",
"UNC BSP" ;
definition: "Centralized, quality controlled facility and biorepository for processing, storage and disbursement of human specimens.Offers high throughput processing of human biospecimens, with specific emphasis on DNA and RNA isolation and purification.Provides laboratory support for investigator initiated large scale clinical, epidemiologic, and other studies.Functions as human specimen biorepository resource for clinicians who wish to store and study samples from unusual or potentially important patients.Biorepository is managed by custom LIMS, with sample accessioning, tracking and audits at each step.Provides scientific resource for investigators seeking advice or consultation on study design including specimen collection and storage methods, and human subject issues. Core staff act as liaison to other UNC core facilities and outside collaborators." .
SCR:021291 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_228" ;
rdfs:label "University of Alaska Fairbanks Genomics Core Facility" ;
NIFRID:synonym "UAF-Genomics Core Laboratory" ;
definition: "Facility provides nucleic acid analysis in evolutionary biology, molecular biology, and wildlife and fisheries management. UAF has been the beneficiary of NSF EPSCoR, NIH BRIN (INBRE), and an NIH COBRE grants, parts of which have been designated for genomic instrumentation. Provides ABI 373 slab gel sequencer, Illumina MiSeq and Oxford NanoPore MinION sequencers. Other Equipment listing is on our website for more information on instruments. Services include nucleic acid sample analysis, and maintenance and support for molecular instruments, training workshops and seminars for instrumentation and techniques to help students, faculty, and staff learn to use available equipment. Provides tours to middle and high school students/teachers, undergraduate students, graduate students, research staff, faculty candidates, and local or out of state visitors. The Core Lab has also been involved in several undergraduate/graduate classes offered by the Biology Department and the Chemistry Department." .
SCR:021292 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_818" ;
rdfs:label "Harvard Medical School DNA Resource Core Facility" ;
NIFRID:synonym "DF/HCC DNA Resource Core",
"DF/HCC DNA Resource Core at Harvard Medical School",
"Harvard Medical School Dana Farber/Harvard Cancer Center DNA Resource Core" ;
definition: "Core offers high throughput Sanger sequencing for any number of samples with 24 hour turn around time,PCR cleanups and mini-preps as well as sample prep from colonies or pellets.Provides large plasmid repository with over 300,000 constructs.Provides ORFs from MGC, Yeast, Xenopus, Drosophila, mouse, as well as several many other organisms including bacterial species. Accept deposits." .
SCR:021293 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_995" ;
rdfs:label "Dartmouth Genomics and Molecular Biology Shared Resource (GMBSR)" ;
NIFRID:synonym "Molecular Biology Resource",
"Molecular Biology Shared Resource" ;
definition: "Genomics Section provides services and instrumentation that enable DNA/RNA extraction and quality control, next-generation Illumina and Nanopore sequencing, epigenetic profiling, and microarray analysis on a whole-genome scale, from the level organisms to single cells. Molecular Biology Section provides DNA fragment analysis qPCR, Sanger sequencing and NanoString Technology." .
SCR:021294 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1000" ;
rdfs:label "Ohio State University Center for Electron Microscopy and Analysis Core Facility" ;
NIFRID:synonym "Center for Electron Microscopy and Analysis" ;
NIFRID:abbrev "CEMAS" ;
definition: "Centralized, coordinated imaging facility.Provides electron and ion beam analytical microscopy instruments.Full service facility from extensive sample preparation laboratories to image processing tools and support." .
SCR:021296 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Wikidata_Q107068605" ;
rdfs:label "Clinical Trials Wiki Loader" ;
definition: "Software tool for importing clinical trials into Wikidata." .
SCR:021297 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Wikidata_Q96777166" ;
rdfs:label "ClinWiki" ;
definition: "Clinical trials database." .
SCR:021298 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_021306",
"Wikidata_Q107014192" ;
rdfs:label "VanderBot" ;
NIFRID:synonym "Vanderbot" ;
definition: "Software Python tool as Vanderbilt University curation tool.Used for exporting public profiles of university faculty from Vanderbilt University database into Wikidata.Used to create or update items in Wikidata using data from CSV spreadsheet data." .
SCR:021299 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Wikidata_Q26882268" ;
rdfs:label "TABernacle" ;
definition: "Web tool to edit property value of several items on one screen.Used to see and edit labels, descriptions, aliases, and properties for list of Wikidata items, in tabular form." .
SCR:021300 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Wikidata_Q20084080" ;
rdfs:label "QuickStatements" ;
NIFRID:synonym "QS" ;
definition: "Web tool used to batch edit Wikidata items, based on simple set of text commands. Can add and remove statements, labels, descriptions, and aliases.Can add statements with optional qualifiers and sources." .
SCR:021301 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Wikidata_Q20950365" ;
rdfs:label "Wikidata Query Service" ;
definition: "Web tool as official query tool for Wikidata." .
SCR:021302 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Wikidata_Q28054658" ;
rdfs:label "Mix n Match" ;
NIFRID:synonym "Mix'n'match",
"Mix-n-Match" ;
definition: "Software tool for importing data sets into Wikidata. Can list entries of some external databases, and allows users to match them against Wikidata items." .
SCR:021303 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hierarchical Data Modeling Framework" ;
NIFRID:abbrev "HDMF" ;
definition: "Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data." .
SCR:021304 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1190" ;
rdfs:label "University of British Columbia Vancouver Bioimaging Core Facility" ;
NIFRID:synonym "Bioimaging Facility",
"UBC Bioimaging Facility",
"University of British Columbia Bioimaging Facility" ;
NIFRID:abbrev "BIF" ;
definition: "Provides optical and electron microscope infrastructure for live cell imaging, multi photon imaging, advanced sample preparation including cryo-preparation for electron microscopy, routine SEM and TEM, Cryo-TEM, TEM tomography, and Correlative Light and Electron Microscopy (CLEM). Equipped with 4 electron microscopes (1 SEM and 3 TEMs), 2 advanced fluorescence microscopes (confocal/multi-photon and spinning disk), cryo-fixation (High pressure freezer, Vitrobot) and EM processing equipment (Microwave, critical point dryer, coaters).Provides microscopy access, training and service." .
SCR:021305 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Wikidata_Q5583871" ;
rdfs:label "OpenRefine" ;
NIFRID:synonym "Google Refine",
"openrefine" ;
definition: "Open source software Java tool for working with data. Used for loading data, cleaning up data, transforming data from one format into another and extending it with web services and external data." .
SCR:021307 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COVTree" ;
NIFRID:synonym "Coevolution in OVerlapped sequences by Tree" ;
definition: "Web server providing online analysis of coevolving amino acid pairs in overlapping genes, where residues might be located inside or outside overlapping region." .
SCR:021308 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GRADEpro" ;
NIFRID:synonym "G2DT",
"GDT",
"GRADE Guideline Development Tool",
"GRADEpro GDT",
"Guideline Development Tool" ;
definition: """Software tool used to create summary of findings tables for cochrane systematic reviews.
Web application to create, manage and share summaries of research evidence called Evidence Profiles and Summary of Findings Tables.""" .
SCR:021309 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Molecular Modeling Toolkit" ;
definition: "Open Source software library for molecular simulation applications. Provides ready-to-use implementations of standard algorithms.Serves as code basis that can be easily extended and modified to deal with standard and non standard problems in molecular simulations." .
SCR:021310 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GLOBE Observer Land Cover" ;
NIFRID:synonym "Land Cover" ;
definition: "Web app based tool as one of GLOBE Observer tools. Used to document what is on land. Once you have downloaded the app and created account, Land Cover tool will guide you through observation process. You will report on current surface conditions, then take photographs in all four cardinal directions, up and down. Optionally, you can classify land cover in your photographs, telling if it is grassland,forest or urban area, as well as compare your classification to satellite land cover observation and note any differences." .
SCR:021311 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Wikidata_Q21829773" ;
rdfs:label "WikiProject Clinical Trials" ;
definition: "Portal within Wikipedia platform for presenting content, tools, and discussion related to clinical trials.Anyone can join to express their interest in developing content in Wikidata related to clinical trials." .
SCR:021312 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Smart-seq2 Single Nucleus Multi Sample Pipeline" ;
NIFRID:synonym "Multi-snSS2",
"Smart-seq2 Single Nucleus Multi-Sample Pipeline" ;
definition: "Software pipeline for single-nucleus RNAseq data generated by Smart-seq2 assays.Used to simultaneously process multiple libraries of single nuclei Smart-seq2 and Smart-seq4 data. For each library (nucleus), the pipeline trims paired FASTQ files, aligns trimmed reads to the genome, counts intronic and exonic reads, and calculates quality control metrics. Counts and metrics for all libraries are combined into merged Loom formatted count matrix." .
SCR:021313 a owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_021690" ;
rdfs:label "Atria" ;
NIFRID:synonym "Atria Trimming Software v3.0.0" ;
definition: "Open source software tool as adapter and quality trimmer for Next-Generation Sequence data." .
SCR:021314 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1189" ;
rdfs:label "University of Nebraska Lincoln Nebraska Center for Biotechnology Proteomics and Metabolomics Core Facility" ;
NIFRID:synonym "UNL Proteomics and Metabolomics Facility" ;
NIFRID:abbrev "PMF" ;
definition: "Provides services using mass spectrometry, including identification and relative quantification of proteins and several advanced methods for profiling and quantitation of small molecules.Provides outreach and education program including workshops,seminars and courses.Proteomics services include Bottom-up Proteomics of whole organisms, organs, organelles, tissues, cell pellets, pulldowns, complex or single protein mixes from solutions or gels;Quantification by label-free or multiplexed labeling techniques with microscale subfractionation to increase coverage;Post Translational Modification Characterization especially phosphopeptide enrichment from whole organism digests, but also ubiquitylation, acetylation, etc.Metabolomics services include Untargeted Quantification of small molecules;Primary metabolism using GC-MS and NIST/Fiehn Libraries;Secondary metabolism using LC-MS and Progenesis QI, NIST Library, mzCloud;Targeted Quantification using HPLC or LCMS." .
SCR:021315 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adobe Premiere pro " ;
definition: "Software tool for video editing. Used for social sharing, TV, and film." .
SCR:021316 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_pT-100" ;
rdfs:label "CoolLED | pT-100" ;
NIFRID:synonym "pT-100" ;
definition: "LED illumination system for transmitted light applications, including brightfield, darkfield, DIC, Dodt gradient contrast and phase contrast. Includes LED illuminator and controller." .
SCR:021317 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:phenstat" ;
rdfs:label "PhenStat" ;
definition: "Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data." .
SCR:021318 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1191" ;
rdfs:label "University of California at Berkeley National Energy Research Scientific Computing Core Facility" ;
NIFRID:synonym "National Energy Research Scientific Computing" ;
NIFRID:abbrev "NERSC" ;
definition: "Supercomputer user facility operated by Lawrence Berkeley National Laboratory for the United States Department of Energy Office of Science.Houses high performance computing and data systems used by scientists at national laboratories and universities around the country." .
SCR:021319 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gtsummary" ;
definition: "Software R package creating customizable presentation ready tables, summarizing data sets, regression models, and more. Used for publication ready data summary and analytic result tables." .
SCR:021320 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ploidyNGS" ;
definition: "Open source software tool for visually exploring ploidy with Next Generation Sequencing data.Used to visualize and explore ploidy levels in newly sequenced genome, exploiting short read data. Allows identification of ploidy level of newly sequenced genome in visual way. Implemented in Python and R." .
SCR:021321 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1192" ;
rdfs:label "University of Colorado Anschutz Medical Campus ImmunoMicro Flow Cytometry Core Facility" ;
NIFRID:synonym "AMC ImmunoMicro Flow Cytometry Shared Resource",
"University of Colorado Anschutz Medical Campus ImmunoMicro Flow Cytometry Shared Resource" ;
definition: "Provides access to high parameter cell analysis and sorting instrumentation along with scientific expertise.Services provided include Cell Sorting,FACS Cell Sorting,Flow Cytometric Analysis,Multi-color Flow Cytometry,Spectral Flow Cytometry." .
SCR:021322 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChIPseeker" ;
definition: "Software package to retrieve nearest genes around peak, annotate genomic region of peak, implements statstical methods for estimate significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare own dataset with those deposited in database.Several visualization functions are implemented to summarize coverage of peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes." .
SCR:021323 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline" ;
definition: "Software tool as ChIP-seq pipeline for processing ChIP-seq reads, aligning to reference genome, peak calling, and IDR analysis of replicate data according to ENCODE standards." .
SCR:021324 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "plyranges" ;
definition: "Open source software R package for interacting with common Bioconductor classes Ranges and GenomicRanges. Grammar of genomic data transformation. Provides grammatical and consistent way of manipulating these classes to increase accessiblity for new Bioconductor users." .
SCR:021325 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rtracklayer" ;
definition: "Software R package for interfacing with genome browsers.Supports integration of existing genome browsers with experimental data analyses performed in R. R interface to genome annotation files and UCSC genome browser." .
SCR:021326 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genedata Analyst" ;
definition: "Analyst module for statistical analysis and interactive visualization of complex data such as genotype, phenotype, and omics data. Provides data mining solution that can be integrated into existing research IT environments with rich set of APIs. Supports integration of R scripts." .
SCR:021327 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AUCell" ;
NIFRID:synonym "Area Under the Curve" ;
definition: "Software R package to identify cells with active gene sets in single cell RNA-seq data. Used for analysis of gene set activity in single cell RNA-seq data.Used to calculate whether critical subset of input gene set is enriched within expressed genes for each cell." .
SCR:021328 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sp package" ;
NIFRID:synonym "sp Gallery",
"spatial Gallery" ;
definition: "Software R package that provides classes and methods for spatial data." .
SCR:021329 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Prokaryotic Genomes Automatic Annotation Pipeline" ;
NIFRID:synonym "Prokaryotic Genomes Automatic Annotation Pipeline (PGAP)" ;
NIFRID:abbrev "PGAP" ;
definition: "Software tool as NCBI prokaryotic genome annotation pipeline. Used to annotate both complete genomes and draft genomes comprising multiple contigs. Integrated into NCBI infrastructure and processes, and uses modular software framework, GPipe, developed at NCBI for execution of all annotation tasks, from fetching of raw and curated data from public repositories through sequence alignment and model based gene prediction, to submission of annotated genomic data to public NCBI databases." .
SCR:021330 a owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013727" ;
rdfs:label "ATCC Genome Portal" ;
definition: "Comprehensive collection of high quality microbial genomics reference data for bacteria, viruses, and fungi in holdings of American Type Culture Collection." .
SCR:021331 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "YCharOS" ;
NIFRID:synonym "Antibody Characterization through Open Science",
"YCharOS Inc." ;
definition: "Canadian, public interest, open science company with mission of characterizing commercially available antibody reagents for every human protein. Antibody characterization methodology and dataset. Gold standard genetic characterization process uses both cell line expressing adequate endogenous levels of target protein and CRISPR knockout version of same cell line as negative control. Antibody characterization methodology follows seminal methodology formalized at Montreal Neurological Institute." .
SCR:021338 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker ctAN software " ;
NIFRID:synonym "Bruker CTAN software",
"CTAN software" ;
definition: "Software tool for porosity analysis of tree slice. Used for 3D image analysis, density analysis, 3D distances and angles, thickness and separation, automated batch analysis." .
SCR:021340 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurodata Extensions Catalog" ;
NIFRID:abbrev "NDX Catalog" ;
definition: "Community led catalog of extensions to Neurodata Without Borders data standard." .
SCR:021341 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HDMF Documentation Utilities" ;
definition: "Software tool for generating documentation for data standard schema defined using HDMF specification language. Collection of CLIs, scripts and modules useful to generate NWB documentation." .
SCR:021342 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HDMF Common Schema" ;
NIFRID:synonym "hdmf common schema" ;
definition: "Software tool to define collection of common, reusable data structures that build foundation for modeling of advanced data formats and is integrated with HDMF.Provided data structures include DynamicTable, VectorData, VectorIndex, ElementIdentifiers, DynamicTableRegion, AlignedDynamicTable and CSRMatrix." .
SCR:021343 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1150" ;
rdfs:label "University of Michigan Ann Arbor Life Sciences Institute Cryo Electron Microscopy Core Facility" ;
NIFRID:synonym "UM - Cryo-EM Facility",
"University of Michigan Ann Arbor UM - Cryo-EM Facility" ;
definition: "Facility uses MiCores/iLab to schedule time on microscopes.Allows scientists to study form and function of biological machines that are too large to study using X-ray crystallography. Provides instruments and faculty expertise specializing in cryo electron microscopy." .
SCR:021344 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_272" ;
rdfs:label "University of Hawaii at Manoa Molecular and Cellular Immunology Core Facility" ;
NIFRID:synonym "Molecular & Cellular Immunology Core Facility" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2022. Provides services for flow cytometry, cell sorting and immunological services through COBRE support. Helps in developing new or customized immunological methods for COBRE Investigators and other Core users, regularly schedules training sessions are held for COBRE Investigators and other faculty and students across university and broader research community.Services include Flow Cytometry, Analysis and Sorting,Cell Counting, Size, and Viability,Multiplex Bead Assays including Luminex and CBA Platforms for DNA, Protein, and Antibodies Assays, Immunospot Plate Reading including ELISpot and FRNT, Cell Irradiation. Flow Cytometry Assays including Cell Phenotyping, Cell Cycle with Live or Fixed Cells, Apoptosis, FRET, Calcium Flux, Phosphorylation, Intracellular Cytokine and Protein Detection, Fluorescent Protein Expression,Cell Population Isolation, Single Cell Sorting, Dye Dilution Assays, Proliferation,Training opportunities.Experienced staff will provide hands-on training to investigators in conducting IBC/IACUC/CHS approved MCI research protocols. Please refer to MCI training document to help you get started on the process for obtaining clearance to work in the JABSOM Molecular and Cellular Immunology Core Facility." .
SCR:021345 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_164" ;
rdfs:label "University of Oklahoma Health Sciences Center Laboratory for Molecular Biology and Cytometry Research Core Facility" ;
NIFRID:synonym "Laboratory for Molecular Biology and Cytometry Research",
"University of Oklahoma Health Sciences Center Laboratory for Molecular Biology and Cytometry Research" ;
NIFRID:abbrev "LMBCR" ;
definition: "Core facility offering services involving DNA, protein, and whole cell analysis. Services include sequencing (custom PCR, plasmid and DNA, RNA, 16s, miRNA, ChIP ) and microsatellite detection via Illumina MiSeq or SeqStudio capillary sequencer. Expression analysis using Nanostring nCounter SPRINT platform, Mass Spectrometry and Proteomics using Waters Synapt with 2D UPLC. Provides qualitative and quantitative analysis of protein samples (cell lysate, IP, in solution) as well as simple protein identification from solution or gel slice. Flow and Imaging division offers BSL2 cell sorting, flow cytometry, Luminex, and confocal imaging." .
SCR:021346 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1195" ;
rdfs:label "American Type Culture Collection Sequencing and Bioinformatics Center Core Facility" ;
NIFRID:synonym "ATCC Sequencing & Bioinformatics Center",
"ATCC Sequencing and Bioinformatics Center Core Facility" ;
definition: "Core genomics and bioinformatics group at American Type Culture Collection.Offers whole genome sequencing and advanced bioinformatics analysis for wide range of biological materials ranging from viruses and bacteria, to fungi and human or animal cell lines, genome assembly, verified annotation, functional genomics analysis, transcriptomics analysis, cell line contamination assessments, microbiome profiling, and advanced cell line authentication services." .
SCR:021348 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_155" ;
rdfs:label "Brown Alpert Medical School Women and Infants Hospital of Rhode Island Kilguss Research Institute Molecular Biology and Imaging Core Facility" ;
NIFRID:synonym "Kilguss Research Core",
"Women and Infants Hospital of Rhode Island Kilguss Research Core" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2022. Core offers contemporary imaging, molecular biology, histology, flow cytometry, cell sorting, and real-time gene expression. Provides technologies and training including specialized microscope facility." .
SCR:021349 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Population cage modeling code for Arp53D gene" ;
NIFRID:synonym "Arp53D_popCage" ;
definition: "Population cage modeling code for Schroeder et al, 2021 eLife publication on Arp53D gene." .
SCR:021350 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SAGE Rejected Article Tracker" ;
NIFRID:synonym "rejected article tracker pkg" ;
definition: "Software package to take metadata for research articles and find published versions in CrossRef. Used to check if article has been published elsewhere." .
SCR:021351 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Axio Observer" ;
rdfs:label "Zeiss | Axio Observer" ;
definition: "Microscope with inverse platform for multimodal imaging of living and fixed specimens. Open and flexible inverted microscope platform with AI assisted experiment startup., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:021352 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lung Disease Knowledge Portal" ;
NIFRID:abbrev "LDKP" ;
definition: "Portal enables browsing, searching, and analysis of human genetic information linked to lung diseases and related traits, while protecting integrity and confidentiality of underlying data." .
SCR:021353 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1196" ;
rdfs:label "University of California at Santa Cruz Institute for Biology of Stem Cells Cell Culture Core Facility" ;
NIFRID:synonym "Cell Culture Facilities",
"IBSC Stem Cell Culture Facilities",
"IBSC Stem Cell Culture Resources",
"Institute for the Biology of Stem Cells (IBSC) Cell Culture Facility" ;
definition: "Provides services for culture and analysis of stem cells. Provides space for embryonic stem cell growth and manipulation. Facility staff offers expertise in experimental design, protocol development, and data analysis.Equipment including biosafety hoods, centrifuges, microscopes." .
SCR:021354 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1134" ;
rdfs:label "Max Planck Institute for Biology of Ageing - FACS & Imaging Core Facility" ;
NIFRID:synonym "MPI AGE_FACS & Imaging Core Facility" ;
definition: "Provides equipment including wide field and confocal microscopes, flow cytometry analyzers and sorters, shared histology equipment, and PC workstations for data analysis.Provides services such as software training, access to analysis software, and help with experimental planning and post acquisition analysis." .
SCR:021355 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1197" ;
rdfs:label "University of Vermont Innovate Model Fabricate Labs Core Facility" ;
NIFRID:synonym "UVM - IMF Labs" ;
NIFRID:abbrev "IMF Labs" ;
definition: "Core specializes in design and development of prototypes to advance research. Design engineers complete product development in Solidworks and testing in Labview. Machine shop exists to turn variety of materials into functional prototypes." .
SCR:021356 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1198" ;
rdfs:label "University of British Columbia Borgland Brain DNA and Tissue Bank Core Facility" ;
NIFRID:synonym "UBC-Borgland Brain DNA and Tissue Bank" ;
definition: "Centralized resource for collection, storage, and distribution of pre and post mortem biospecimen and tissue at Djavad Mowafaghian Centre for Brain Health.Biobank facility also provides vast range of specimen processing and storage services to other research groups." .
SCR:021357 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "three.js" ;
definition: "Software tool as JavaScript 3D Library.Used to create and display animated 3D computer graphics on Web browser. Three.js scripts may be used in conjunction with HTML5 canvas element, SVG or WebGL." .
SCR:021358 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gridrec" ;
definition: "Software tool for tomographic reconstruction." .
SCR:021359 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TomoPy" ;
NIFRID:synonym "Tomographic reconstruction in Python" ;
definition: "Open source software Python package for tomographic data processing and image reconstruction. Framework for analysis of synchrotron tomographic data." .
SCR:021360 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of California Santa Cruz Banana Slug Genomics Center Core Facility" ;
NIFRID:synonym "Banana Slug Genomics Center",
"University of California Santa Cruz Banana Slug Genomics Center" ;
definition: "Provides next generation sequencing data analysis through automated platform. Banana Slug Analytics Platform is intuitive, point-and-click system that leverages proven algorithms for next generation sequencing data analysis and helps researchers manage large volume studies without having bioinformatics expertise. Center also performs custom bioinformatics analysis and consultation as requested." .
SCR:021361 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XGBoost" ;
NIFRID:synonym "eXtreme Gradient Boosting" ;
definition: "Open source software tool as library for implementation of gradient boosting with various machine learning algorithms.Optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.Supports regression, classification, ranking and user defined objectives." .
SCR:021362 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SHapley Additive ExPlanations" ;
NIFRID:abbrev "SHAP" ;
definition: "Software tool as unified framework for interpreting predictions of machine learning models. Used to explain output of any machine learning model. Connects optimal credit allocation with local explanations using classic Shapley values from game theory and their related extensions." .
SCR:021363 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scikit posthocs" ;
NIFRID:synonym "scikit-posthocs" ;
definition: "Software Python package providing multiple comparison statistical tests for various parametric and nonparametric analyses. Pairwise multiple comparison tests in Python." .
SCR:021364 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EM900" ;
rdfs:label "Zeiss | Electron Microscope 900" ;
NIFRID:synonym "ZEISS 900",
"ZEISS EM900" ;
definition: "Research Transmission Electron Microscope with accelerating voltage of 80kV used to image low contrast biological samples." .
SCR:021365 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Tecnai_G2_20" ;
rdfs:label "Tecnai G2 20 Electron Microscope" ;
NIFRID:synonym "FEI Tecnai G2 20 Electron Microscope",
"Tecnai G2 20",
"TEM Tecnai G2 20" ;
definition: """Research transmission electron microscope with accelerating voltage of 80-200kV.
Transmission Electron Microscope from FEI (now Thermo Fisher Scientific) is equipped with LaB6 cathode. Enables both bright field EM and scanning transmission electron microscopy (STEM) at very high resolution (at 200kV: point resolution up to 0.27 nm).""" .
SCR:021366 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | EM HPM100 freezer" ;
NIFRID:synonym "HPM 100",
"Leica EM HPM100",
"Leica EM HPM100 Hight Pressure Freezer" ;
definition: "High pressure freezing device for cryofixing of biological and industrial samples. Samples that are cooled to temperature of liquid nitrogen at high pressure are vitrified and sub cellular organisation is preserved to close to native state without formation of ice crystal." .
SCR:021367 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | EM ICE High Pressure Freezer" ;
NIFRID:synonym "EM ICE",
"High Pressure Freezer Leica EM ICE" ;
definition: "High Pressure Freezing machine from Leica Microsystems to cryo fix biological samples for Electron Microscopy analysis.EM ICE machine allows light and electrical stimulation of samples prior to cryo fixation with millisecond time resolution." .
SCR:021368 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_687" ;
rdfs:label "University of Tennessee Knoxville Biological and Small Molecule Mass Spectrometry Core Facility" ;
NIFRID:synonym "UTK Biological and Small Molecule Mass Spectrometry Core" ;
NIFRID:abbrev "BSMMSC" ;
definition: "Mass Spectrometry Core provides metabolomics, lipidomics, and small molecule analyses to researchers both on campus and in our affiliated local and other institutions." .
SCR:021369 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PROCESS" ;
NIFRID:synonym "PROCESS v2",
"PROCESS v3" ;
definition: "Software tool as macro for SPSS, SAS, and R that conducts observed variable mediation, moderation, and conditional process analysis.Observed variable OLS and logistic regression path analysis modeling tool. Used for estimating direct and indirect effects in single and multiple mediator models parallel and serial, two and three way interactions in moderation models along with simple slopes and regions of significance for probing interactions, and conditional indirect effects in moderated mediation models with single or multiple mediators or moderators. Operates on Windows and Mac versions of SPSS and SAS." .
SCR:021370 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Certara" ;
NIFRID:synonym "Certara USA" ;
definition: "Provides drug development software and services. Company offers drug development and clinical pharmacology strategy, regulatory strategy, writing and submission, as well as HEOR and market access solutions. Certara serves biopharmaceutical and medical technology customers worldwide." .
SCR:021371 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "ARTTIC Innovation GmbH" ;
definition: "Consulting company in field of research and development.Supervises joint projects - from EU Research Framework Program 2 to Horizon 2020 funding program.Belongs to PNO Group , one of the largest consulting firms for publicly funded research and innovation projects." .
SCR:021372 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Takara Bio Inc." ;
definition: "Biotechnology company providing biotechnology products and services including kits, reagents, instruments, and services to help researchers explore questions about gene discovery, regulation, and function. Subsidiaries including Takara Bio USA, Inc., Takara Bio Europe AB, and more." .
SCR:021373 a NLX:152328,
owl:NamedIndividual ;
definition: "Japanese multinational pharmaceutical and biopharmaceutical company. It is the largest pharmaceutical company in Asia and one of the top 20 largest pharmaceutical companies in the world by revenue." .
SCR:021374 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LocusZoom.org" ;
NIFRID:synonym "LocusZoom.js" ;
definition: "Web tool to investigate genome wide association results in their local genomic context. Adds new features to LocusZoom such as Manhattan plots, annotation options, and calculations that put findings in context. Used for interactive and embeddable visualization of genetic association study results.Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources." .
SCR:021375 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Pfizer Inc." ;
definition: "American multinational pharmaceutical and biotechnology corporation. Develops and produces medicines and vaccines for immunology, oncology, cardiology, endocrinology, and neurology. Company has several blockbuster drugs or products that each generate more than US$1 billion in annual revenues." .
SCR:021376 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Protara Therapeutics" ;
NIFRID:synonym "ArTara Therapeutics" ;
definition: "Clinical stage company identifying and advancing transformative therapies for people with rare and specialty diseases. Former name was ArTara Therapeutics." .
SCR:021377 a NLX:152328,
owl:NamedIndividual ;
definition: "IQVIA, formerly Quintiles and IMS Health, Inc., is an American multinational company serving the combined industries of health information technology and clinical research." .
SCR:021378 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Public Health Alliance for Genomic Epidemiology SARS-CoV-2 Contextual Data Specification" ;
NIFRID:synonym "PHA4GE SARS-CoV-2 Contextual Data Specification" ;
definition: """Software package as collection template and associated materials for SARS-CoV-2 metadata.
Contains metadata collection template based on data standard designed to harmonize genomic surveillance contextual data (sample metadata, epidemiological/clinical/laboratory data, methods information) across datasets, laboratories and databases during pandemic, and beyond. Template contains standardized fields, terms and formats for structuring information, and is accompanied by field level reference guide which provides definitions, guidance and examples for populating fields. Fields have been prioritized using colour coding system as required (yellow), recommended (purple), and optional (white). Users can use as much or as little of specification as they wish, according to their needs, and need not share information unless permitted to do so. SOP and protocols for submitting to public repositories are also included.""" .
SCR:021379 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "questionr" ;
definition: "Software R package to make surveys processing and analysis easier. Set of functions include interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions." .
SCR:021380 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "svaRetro" ;
definition: "Software R package for retrotransposed transcript detection from structural variants." .
SCR:021381 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "svaNUMT" ;
definition: "Software R package for Nuclear Mitochondrial integration events NUMT detection using structural variant calls." .
SCR:021382 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Social LEAP" ;
NIFRID:synonym "Social LEAP Estimates Animal Pose" ;
NIFRID:abbrev "SLEAP" ;
definition: "Method for pose estimation that uses deep neural networks.Open source software tool as deep learning based framework for estimating positions of animal body parts.Supports multi animal pose estimation and tracking, and includes advanced labeling or training.SLEAP is next generation of LEAP and allows for tracking multiple animals." .
SCR:021383 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SLEAP, LEAP and MotionMapper project" ;
NIFRID:synonym "LEAP and MotionMapper",
"SLEAP" ;
definition: "Collection of tools to do video analysis in behavioral neuroscience applications.Offers open source software tools including SLEAP, LEAP and MotionMapper." .
SCR:021384 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MotionMapper" ;
definition: "Software tool to work on videos (not poses).Uses image analysis and multivariate statistical methods to find stereotyped behaviors in flies, mice, and other species." .
SCR:021385 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Behavioral Segmentation of Open-field in DeepLabCut" ;
NIFRID:synonym "B-SOiD v2.0" ;
NIFRID:abbrev "B-SOiD" ;
definition: "Software pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.Unsupervised learning algorithm that discovers and classifies actions based on inherent statistics of data points provided." .
SCR:021386 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Online Animal Tracker project" ;
NIFRID:synonym "Online Animal Tracker" ;
NIFRID:abbrev "OAT" ;
definition: "Project related to processing video, extracting object position information, and streaming data.Provides set of programs for processing video for behavioral research. Includes OAT software tool as real time position tracker which was developed by Massachusetts Institute of Technology scientists." .
SCR:021387 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepBehavior project" ;
NIFRID:synonym "DeepBehavior" ;
definition: "Project related to behavior tracking and analysis. Provides deep learning toolbox that automates taking high speed quality video to track behavior in rodents and humans." .
SCR:021388 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BonZeb project" ;
NIFRID:synonym "BonZeb" ;
definition: "Portal provides tools for investigating visuomotor integration specific to high speed kinematic tracking in small model organisms in closed loop experiments. University of Toronto scientists developed suite of Bonsai modules for specifically tracking and analyzing zebrafish movements and integrating these data with closed-loop experiments. BonZeb modules can also be used in an open-loop fashion for collecting, analyzing, and integrating data from multiple sources in real time, or from offline sources for batch processing of pre-recorded data." .
SCR:021389 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "D-Track project" ;
NIFRID:synonym "D-Track" ;
definition: "Project related to tracking animal behavior. Provided system includes two cameras and software package to track aquatic animals within captivity.Semi automatic 3D video tracking technique to analyse movements and routines of aquatic animals with application to captive dolphins." .
SCR:021390 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Locomouse project" ;
NIFRID:synonym "Locomouse" ;
definition: "Project related to study movement coordination in free walking mice. Provides noninvasive system consisting of cameras and machine learning algorithms that allow for three dimensional detection and tracking of mouse paws, tail, and nose." .
SCR:021391 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepLabCut" ;
definition: "Open source software package for markerless pose estimation. 2D keypoint detection in animals." .
SCR:021392 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BonZeb" ;
definition: "Open source, modular software tools for high resolution zebrafish tracking and analysis.Software suite of Bonsai modules for specifically tracking and analyzing zebrafish movements and integrating these data with closed loop experiments.Can be used in open loop fashion for collecting, analyzing, and integrating data from multiple sources in real time, or from offline sources for batch processing of pre-recorded data." .
SCR:021393 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FaceSync project" ;
definition: "Project related to emotions and facial expressions. Includes open source guide to building affordable head mount for camera to maintain high temporal and spatial resolution of face throughout duration of experiment. Device is paired with FaceSync, Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions." .
SCR:021394 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "D-Track" ;
definition: "Software package to track object in 3D based on 3D schematics of scene.Semi automatic 3D video tracking technique to analyse movements and routines of aquatic animals with application to captive dolphins." .
SCR:021395 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepPoseKit project" ;
NIFRID:synonym "DeepPoseKit" ;
definition: "Project related to pose estimation and tracking.Includes software toolkit for 2D pose estimation of user defined keypoints using deep learning.Method for pose estimation developed by behavioral scientists at the Max Planck Institute of Animal Behavior." .
SCR:021396 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:FaceSync" ;
rdfs:label "FaceSync" ;
definition: "Open source software Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.Framework for recording facial expressions with head mounted cameras." .
SCR:021397 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LocoMouse" ;
definition: "Software kinematics analysis tool used to study movement coordination and analyzing limb, head, and tail kinematics of freely walking mice." .
SCR:021398 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepLabCut Project" ;
definition: "Project for markerless pose estimation of user defined body parts with deep learning." .
SCR:021399 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openEyeTrack project" ;
NIFRID:synonym "openEyeTrack" ;
definition: "Project related to measurement of fast eye movement dynamics.Tracking eye position in head fixed applications system created by scientists from Boston University. Includes software tool as part of multithreaded eye tracker and Teledyne DALSA Camera with GigE-V framework APIs for Linux." .
SCR:021400 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepFly3D project" ;
NIFRID:synonym "DeepFly3D" ;
definition: "Project related to deep learning based pose estimator for studying how neural circuits control limbed behaviors in tethered Drosophila. Includes Deep Fly image annotation tool for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose." .
SCR:021401 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openEyeTrack" ;
definition: "Open source software tool used as part of multithreaded eye tracker.Video based eye tracker." .
SCR:021402 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepFly3D" ;
definition: "Software tool as PyTorch and PyQT5 implementation of 2D-3D tethered Drosophila pose estimation. Image annotation tool used for pose estimation and appendage tracking. Provides interface for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose." .
SCR:021403 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "neurotic project" ;
NIFRID:synonym "NEUROscience Tool for Interactive Characterization",
"NEUROTIC",
"neurotic" ;
definition: "Project about synchronizing video and neural signals. Provides software Python toolbox for interactive characterization in neuroscience.Software tool used to review and annotate signal data synchronized with video, performs simple initial analyses including signal filtering and spike detection, supports variety of file formats." .
SCR:021404 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Source Whisking Video Database portal" ;
definition: "Portal provides shared database of videos featuring juvenile and adult male rats and adult male mice exploring stationary objects.This dataset includes wide variety of experimental conditions including genetic, pharmacological, and sensory deprivation interventions to explore how active sensing behavior is modulated by different factors. Database of high speed videos of whisking behavior in freely moving rodents.Open source high speed infrared videography database to study principles of active sensing in freely navigating rodents." .
SCR:021405 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepPoseKit" ;
definition: "Software toolkit with high level API for 2D pose estimation of user defined keypoints using deep learning.Written in Python and built using Tensorflow and Keras.Method for pose estimation developed by behavioral scientists at the Max Planck Institute of Animal Behavior." .
SCR:021406 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "neurotic" ;
NIFRID:synonym "NEUROscience Tool for Interactive Characterization" ;
definition: "Software Python toolbox for interactive characterization in neuroscience.Users can read in variety of file formats for neural data and video, which they can then process, filter, analyze, annotate and plot.Used to review and annotate signal data synchronized with video, performs simple initial analyses including signal filtering and spike detection, supports variety of file formats.Facilitates collaborations by using portable specification for loading and processing data and retrieving data files from online sources.App for Windows, macOS, and Linux to review and annotate electrophysiology data and simultaneously captured video." .
SCR:021407 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Source Whisking Video Database" ;
definition: "Shared database of videos featuring juvenile and adult male rats and adult male mice exploring stationary objects.This dataset includes wide variety of experimental conditions including genetic, pharmacological, and sensory deprivation interventions to explore how active sensing behavior is modulated by different factors. Database of high speed videos of whisking behavior in freely moving rodents.Open source high speed infrared videography database to study principles of active sensing in freely navigating rodents." .
SCR:021408 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rodent Arena Tracker project" ;
NIFRID:synonym "Rodent Arena Tracker" ;
NIFRID:abbrev "RAT" ;
definition: "Project related to rodent tracking and task control.Provides closed loop system for machine vision rodent tracking and task control created by scientist from Washington University. System to track and report mouse activity while they are contained in simple arena. System uses OpenMV M7 microcontroller to acquire images of arena and process them in real-time to report mouse centroid data to text file. Wireless position tracker for automatically tracking mice in high contrast arenas." .
SCR:021409 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenMonkeyStudio project" ;
NIFRID:synonym "OpenMonkeyStudio" ;
definition: "Project for tracking interactions among freely moving monkeys.System includes integrated hardware and software for pose tracking in freely moving rhesus macaques." .
SCR:021410 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Behavioral Segmentation of Open-field in DeepLabCut project" ;
NIFRID:synonym "B-SOiD v2.0",
"Behavioral Segmentation of Open-field in DeepLabCut" ;
NIFRID:abbrev "B-SOiD" ;
definition: "Project related to unsupervised behavior analysis.Carnegie Mellon University has shared B-SOiD, open source unsupervised algorithm for discovery of spontaneous behaviors. Includes software pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users." .
SCR:021411 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Simple Behavior Analysis project" ;
NIFRID:synonym "SimBA",
"Simple Behavior Analysis" ;
definition: "University of Washington project SimBA for analysis of complex social behaviors.Used for automated behavioral scoring. Includes open source software toolkit for computer classification of complex social behaviors in experimental animals. Uses data from popular open source tracking tools in combination with small amount of behavioral annotations to create supervised machine learning classifiers that can then rapidly and accurately score behaviors across different background settings and lighting conditions." .
SCR:021412 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Online Animal Tracker" ;
NIFRID:abbrev "OAT" ;
definition: "Software tool as real time position tracker for behavioral research. Used for processing images, extracting object position information, and streaming data to disk and/or the network in real time." .
SCR:021413 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Simple Behavior Analysis" ;
NIFRID:synonym "SimBA" ;
definition: "Open source software toolkit for computer classification of complex social behaviors in experimental animals." .
SCR:021414 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepBehavior" ;
definition: "Software toolbox that automates taking high speed quality video to track behavior to analyze and track behavior in rodents and humans." .
SCR:021415 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Low Cost Open Source Eye Tracking project" ;
NIFRID:synonym "Low Cost Open Source Eye Tracking" ;
definition: "Project related to eye tracking system for human research.System includes open source software for accurate eye tracking. Can identify shapes such as circles, lines, and triangles.You can rotate and mirror images and also use variety of filters.Capable of processing video in real-time for optical flow. App for viewing multiple video streams from USB cameras." .
SCR:021416 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stytra project" ;
NIFRID:synonym "Stytra" ;
definition: "Project related to involvement in larval zebrafish behavioral experiments.Provides integrated system for stimulation, tracking and closed loop behavioral experiments. Provides timed stimulus presentation, interfacing with external devices and simultaneous real time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely swimming and head restrained preparations." .
SCR:021417 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "idtracker.ai project" ;
NIFRID:synonym "idtracker.ai" ;
definition: "Project related to tracking individual animals in large collective groups.Provides algorithm and software for tracking individuals in large collectives of unmarked animals.Tracks animal identification and tracks when animals touch or cross paths in front of one another." .
SCR:021418 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ezTrack project" ;
NIFRID:synonym "ezTrack" ;
definition: "Project related to behavior analysis.Mt.Sinai scientist developed open source video analysis pipeline for investigation of animal behavior.Used to track location, motion, and freezing of animal." .
SCR:021419 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Calcium ActiVity Explorer project" ;
NIFRID:synonym "Calcium ActiVity Explorer" ;
NIFRID:abbrev "CAVE" ;
definition: "Project related to calcium imaging.Provide open source tool for combined analysis of head mounted calcium imaging and behavior. Used to analyze imaging data from head mounted microscopes simultaneously with behavioral data." .
SCR:021420 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Worm Behavior Platform project" ;
NIFRID:synonym "Worm Behavior Platform" ;
definition: "Project related to sharing worm tracking data and analysis routines.Open access repository for storing, accessing, filtering data and analysis." .
SCR:021421 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Live Mouse Tracker project" ;
NIFRID:synonym "Live Mouse Tracker" ;
NIFRID:abbrev "LMT" ;
definition: "Project related to monitoring social interactions of mice. Provides real time behavioral analysis system for groups of mice.System includes random forest machine learning process, RFID sensors and infrared depth RGB-D camera.System includes software tool for Live Mouse Tracker analysis." .
SCR:021422 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mousecam project" ;
NIFRID:synonym "Mousecam" ;
definition: "Project related to capturing detailed behavior in freely moving mice. System combines lightweight head mounted camera and head movement sensors to detect behaviors in mice. Used to monitor behaviors including eye position, whisking, and ear movements in unrestrained animals.Can be mounted in combination with neural implants for recording brain activity.Provides software Python package with functions for extracting and analyzing data recorded using camera." .
SCR:021423 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Picamera project" ;
NIFRID:synonym "Picamera" ;
definition: "Project related to tracking animals in large spaces. Picamera system allows for tracking of animals in large behavioral arenas.Open source scalable multi camera tracking system that can be used to track behavior in combination with wireless recording systems.Design is comprised of 8 overhead Raspberry Pi cameras, capable of recording at high frame rate in large field of view, recording video independently in individual Raspberry Pi microcomputers and processed using Picamera Python library." .
SCR:021424 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ToxTrac project" ;
NIFRID:synonym "ToxTrac" ;
definition: "Project related to high speed tracking of animals.Provides software tool for tracking organisms.Can handle one or several animals in one or several environments.Used for fish, insects, rodents, etc." .
SCR:021425 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KineMouse Wheel project" ;
NIFRID:synonym "KineMouse Wheel" ;
definition: "Project is related to Columbia University designed KineMouse Wheel, light weight running wheel for head fixed locomotion that allows for 3D positioning of mice with single camera. System uses single camera and DeepLabCut (or similar) software." .
SCR:021426 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EthoScopes project" ;
NIFRID:synonym "EthoScopes" ;
definition: "Project related to analysis of behavior in Drosophila.Provides system capable of real time video tracking. System includes raspberry pi and R package for data analysis. Enables high throughput analysis of behavior in Drosophila and other animals." .
SCR:021427 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Head-Fixed Setup for Combined Behavior, Electrophysiology, and Optogenetics project" ;
NIFRID:synonym "and Optogenetics",
"Electrophysiology",
"Head-Fixed Setup for Combined Behavior" ;
definition: "Project related to temporally controlled rodent behavior. Provides system which utilizes optimal open source setup of hardware and software through behavioral setup for temporally controlled rodent behavior. Used for combined behavior, electrophysiology and optogenetics experiments. System allows for training of head fixed animals with calibrated sound stimuli, precisely timed fluid and air puff presentations as reinforcers.Combines microcontroller based behavior control with sound delivery system for acoustic stimuli, fast solenoid valves for reinforcement delivery and custom built sound attenuated chamber." .
SCR:021428 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FaceMap project" ;
NIFRID:synonym "FaceMap" ;
definition: "Project related to videographic processing of head fixed rodent behaviors. Provides software toolbox for unsupervised video analysis of rodent behavior." .
SCR:021429 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ZebraTrack project" ;
NIFRID:synonym "ZebraTrack" ;
definition: "Project related to distraction free behavioral acquisition. Provides imaging setup for distraction free behavioral acquisition with automated tracking using open source ImageJ software and workflow for extraction of behavioral endpoints of zebrafish. Used for online tracking of larval zebrafish at high framerates.Provides user interface to run experiments as well as flexible design to allow definition of arbitrary open- and closed- loop experiments." .
SCR:021430 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LocoWhisk project" ;
NIFRID:synonym "LocoWhisk" ;
definition: "Portable behavioural set up that incorporates both gait analysis (using pedobarograph) and whisker movements (using high speed video camera and infrared light source).Automatically records both whisker and gait information and provides added statistical tools to analyse data. LocoWhisk system includes ARTv2 software for simultaneous measurement of locomotion behaviours and whisker movements." .
SCR:021431 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pyper project" ;
NIFRID:synonym "Pyper" ;
definition: "Project related to motion tracking of specimen in open field. Provides software tool for motion tracking.Used to track path of object of interest in live feed from camera or recorded video. Used to track rodents in open field maze as well as retina of mice.New version of Pyper allows to customise image processing to track different kind of objects." .
SCR:021432 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automated Rodent Tracker project" ;
NIFRID:synonym "Automated Rodent Tracker" ;
NIFRID:abbrev "ART" ;
definition: "Project related to development of automated rodent tracking position and movement. Provides software tool to automatically track rodent.Used to track head movements, body movements and also aspects of body size.Identifies certain behaviours from video footage, such as rotations, moving forwards, interacting with objects and staying still." .
SCR:021433 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "M-Track project" ;
NIFRID:synonym "M-Track" ;
definition: "Project related to tracking movement of labelled paws in grooming and freely behaving mice. Provides software toolbox for automated detection of forepaw trajectories in mice." .
SCR:021434 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Behavioral Observation Research Interactive Software project" ;
NIFRID:synonym "Behavioral Observation Research Interactive Software" ;
NIFRID:abbrev "BORIS" ;
definition: "Project related to computer based review of previously recorded videos or live observations. Related to study of animal and human behavior. Provides open source, multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.Developed by scientists from University of Turin." .
SCR:021435 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EthoWatcher project" ;
NIFRID:synonym "EthoWatcher" ;
definition: "Project related to video tracking, detailed ethography, and extraction of kinematic variables from digital video files of laboratory animals.Provides computational tool developed at Federal University of Santa Catarina." .
SCR:021436 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Quantifying Animal Movement from Pre-recorded Videos project" ;
NIFRID:synonym "Quantifying Animal Movement from Pre-recorded Videos" ;
NIFRID:abbrev "STL" ;
definition: "Project related to visualizing and quantifying movement from pre-recorded videos. Provides software toolbox for visualizing and quantifying movement.Used for summarizing animal movement data as single image ( spectral time lapse algorithm) as well as automate analysis of animal movement data." .
SCR:021437 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Skinner Box project" ;
NIFRID:synonym "Skinner Box" ;
definition: "Project related to training animal behavior. Provides system which includes full behavioral apparatus and software platform. System includes software tool for data logging and analysis." .
SCR:021438 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LinCoM project" ;
NIFRID:synonym "LinCoM" ;
definition: "Project related to animal behavior in complex mazes.Provides software MATLAB package for linearization of place fields in complex mazes." .
SCR:021439 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Catalepsy Bar project" ;
NIFRID:synonym "Catalepsy Bar" ;
definition: "Project related to measuring of muscular rigidity that can result from several factors including Parkinsons disease, or pharmacological exposure to antipsychotics or cannabis. Provides automated apparatus for measuring catalepsy that increases measurement accuracy and reduces observer bias.Catalepsy bar test automatically measures and records time it takes for rat to remove its forelimbs from bar. 3D printed test apparatus used to make catalepsy measurements in rats more standardized and accurate." .
SCR:021440 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3DTracker project" ;
NIFRID:synonym "3DTracker" ;
definition: "Project related to markerless computerized behavioral analysis for laboratory animals.Provides open source 3D video based behavioral analysis system for neuroscience. System includes open source software tool for 3D-video based markerless computerized behavioral analysis." .
SCR:021441 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PiDose project" ;
NIFRID:synonym "PiDose" ;
definition: "Project related to oral drug administration to group housed mice. Provides open source system for oral drug administration to group housed mice. System includes home cage attached device that weighs individual animals and administers daily dosage of drug solution based on each animal bodyweight through their drinking water. Group housed mice are identified through use of RFID tagging and receive both regular water and drug solution drops by licking at spout within PiDose module." .
SCR:021442 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Joystick project" ;
NIFRID:synonym "Joystick" ;
definition: "Project related to studying motor behavior and decision making in mice. Open source behavior training platform for studying motor control, decision making, and reaching reaction time. Enables behavioral work to study unexplored features of action selection, motivation, and value based decisions." .
SCR:021443 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bonsai project" ;
NIFRID:synonym "Bonsai" ;
definition: "Project related to composing reactive and asynchronous data streams coming from video cameras, microphones, electrophysiology systems or data acquisition boards. Provides open source software tool as visual language for reactive programming." .
SCR:021444 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rigbox project" ;
NIFRID:synonym "Rigbox" ;
definition: "Project related to streamlining behavioral neuroscience experiments.Provides open source software MATLAB toolbox for running behavioral neuroscience experiments and managing data.Used for probing neurons and behavior." .
SCR:021445 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automated Home Cage Rodent Two bottle Choice Test project" ;
NIFRID:synonym "Automated Home Cage Rodent Two bottle Choice Test" ;
definition: "Project related to studies of liquid ingestive behaviors used in neuroscience to investigate reward related behavior, metabolism, and circadian biology. Provides automated home cage sipper device for monitoring liquid ingestive behavior in rodents developed by Washington University, St. Louis scientists. Homecage fitted apparatus for automated, photobeam based detection of licks in two bottle choice task." .
SCR:021446 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Platform for Acoustic STArtle project" ;
NIFRID:synonym "Platform for Acoustic STArtle" ;
NIFRID:abbrev "PASTA",
"ratPASTA" ;
definition: "Project related to multifunctional neurobehavioral system developed by scientists at University of Zagreb School of Medicine, Zagreb, Croatia.System includes hardware and software tools.Provides software package for processing and visualising data from startle experiments in rodents or experiments measuring grip strength in rodents." .
SCR:021447 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pathfinder project" ;
NIFRID:synonym "Pathfinder" ;
definition: "Project to detect spatial navigation behavior in animals.Provides open source software for analyzing spatial navigation search strategies developed by University of British Columbia scientists." .
SCR:021448 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoPilot project" ;
NIFRID:synonym "AutoPilot" ;
definition: "Project related to behavioral experiments.Provides software Python framework for running behavioral experiments designed by University of Oregon scientists." .
SCR:021449 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "flyPAD project" ;
NIFRID:synonym "flyPAD" ;
definition: "Project related to analysis of behavior and of neural activity. Provides FPGA code for running main board of flyPAD." .
SCR:021450 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepSqueak project" ;
NIFRID:synonym "DeepSqueak" ;
definition: "Project related to rodent social communication through repertoire of ultrasonic vocalizations. Provides deep learning based system for quantification of Ultrasonic Vocalizations.Includes software MATLAB package for high throughput USV detection, classification, and analysis." .
SCR:021451 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rodent Activity Detector project" ;
NIFRID:synonym "Rodent Activity Detector" ;
NIFRID:abbrev "RAD" ;
definition: "Project related to tracking and recording activity in rodent home cages.Provides device that utilizes passive infrared (PIR) sensor to detect movement in cages and logs data to microSD card. Device is wireless and battery powered, and can record data for about 3 weeks on charge." .
SCR:021452 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Actifield project" ;
NIFRID:synonym "Actifield" ;
definition: "Project related to measuring locomotor activity.System includes infrared motion detection and arduino to record activity in variety of chamber set ups. Provides actimeter and software tool to measure and record locomotor activity." .
SCR:021453 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "optoPAD project" ;
NIFRID:synonym "optoPAD" ;
definition: "Project related to analysis of behavior and of neural activity. Provides system which allows for specific perturbation of specific groups of neurons. Used as method to induce appetitive and aversive effects on feeding through activating or inhibiting gustatory neurons in closed loop manner." .
SCR:021454 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dual port Lick Detector project" ;
NIFRID:synonym "Dual port Lick Detector" ;
definition: "Project related to measuring licking behavior in mice.System includes device used for both real time measurement and manipulation of licking behavior in head fixed mice. System provides distribution package for Dual Port Lick Detector.Package includes files relevant to building lick detector." .
SCR:021455 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MedParse project" ;
NIFRID:synonym "MedParse" ;
definition: "Project related to saving precise times of behavioral events.Provides software tool to read MedPC data into Python and Matlab." .
SCR:021456 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mousetrap project" ;
NIFRID:synonym "Mousetrap" ;
definition: "Project related to mouse tracking and analysis of mouse movements during computerized lab experiments. Provides open source software plugin to record and analyze mouse movements." .
SCR:021457 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automated mouse homecage two bottle choice test project" ;
NIFRID:synonym "Automated mouse homecage two bottle choice test" ;
definition: "Project related to assessing preferences by mice among fluids in their homecages.Provided system includes homecage fitted apparatus for automated, photobeam based detection of licks in two bottle choice task. Used for automated mouse homecage two bottle choice test." .
SCR:021458 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Voluntary Access Static Incapacitance Chamber project" ;
NIFRID:synonym "Voluntary Access Static Incapacitance Chamber" ;
NIFRID:abbrev "VASIC" ;
definition: "Project related to assessment of pain in animal models.Provided system includes weight bearing device for high throughput and unbiased behavioral pain assessment in rodents.Includes custom printed circuit board, infrared sensor, Arduino microcontroller, 3D printed parts, and open source software for analysis." .
SCR:021459 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BPM Biosignals project" ;
NIFRID:synonym "BPM Biosignals" ;
definition: "Portal as educational resource regarding construction and implementation of bioamplifiers as well as interpretation of biosignals." .
SCR:021460 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Autoreward2 project" ;
NIFRID:synonym "Autoreward2" ;
definition: "Project related to detection and rewarding rodents in modified T-maze task. System designed to detect and reward rodents in modified T maze provided by Ruhr University Bochum, Germany scientists." .
SCR:021461 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Attys project" ;
NIFRID:synonym "Attys" ;
definition: "Portal related to biomedical signals.Provides wearable data acquisition device with special focus on biomedical signals such as heart activity (ECG), muscle activity (EMG) and brain activity (EEG).Open source high precision bluetooth data acquisition device." .
SCR:021462 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutonoMouse project" ;
NIFRID:synonym "AutonoMouse" ;
definition: "Project related to self initiated conditioning and behavior tracking in mice. Provides automated system that can track large numbers (over 25) of socially housed mice through implanted RFID chips on mice. With RFID trackers and other analyses, behavior of mice can be tracked as they train and are subsequently tested on (or self-initiate testing in) odor discrimination task over months with thousands of trials performed every day." .
SCR:021463 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Optimouse project" ;
NIFRID:synonym "Optimouse" ;
definition: "Project related to individual mice positions analysis, specifically their nose positions. Includes software tool for analysis of mouse position data designed by Hebrew University scientists. Provides open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error." .
SCR:021464 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Laubach Lab GitHub Repository project" ;
NIFRID:synonym "Laubach Lab GitHub Repository" ;
definition: "Portal related to control and decision making, focusing on role of prefrontal cortex. American University scientists through their GitHub repository provide 3D print files for many of behavioral devices used in their lab, including Nosepoke and Lickometer designed from rats." .
SCR:021465 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Oculomatic Eye Tracking project" ;
NIFRID:synonym "Oculomatic Eye Tracking" ;
definition: "Project related to investigate mechanisms of oculomotor behavior.Included system is provided by New York University scientists to track eye movement.System includes camera module, lens, IR-Light source, mounting solution, data acquisition device, and general purpose PC. System consists of open source software and modular hardware solution to eye tracking for use in humans and non-human primates." .
SCR:021466 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ArduiPod Box project" ;
NIFRID:synonym "ArduiPod Box" ;
definition: "Project related to presenting visual and auditory stimuli, recording behavior in form of nose pokes or screen touches, and delivering liquid rewards. ProvidesOperant chamber built with iPod Touch and Arduino microcontroller as main components." .
SCR:021467 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hao Chen Lab Repository project" ;
NIFRID:synonym "Hao Chen Lab Repository" ;
definition: "Project aims to establish computing platform for rodent behavior research using Raspberry Pi computer. They have built several devices for conducting operant conditioning and monitoring environmental data." .
SCR:021468 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Source platform for Sensory Tasks project" ;
NIFRID:synonym "Open Source platform for Sensory Tasks" ;
definition: "Project related to report animal decision in response to stimulus.Includes software tool as Arduino and Python based platform for Go or No Go sensory task to report animal decision in response to stimulus provided by University of Melbourne, Melbourne, VIC, Australia scientists." .
SCR:021469 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Feldman Lab Lickometer project" ;
NIFRID:synonym "Feldman Lab Lickometer" ;
definition: "Project related to function of cerebral cortex. Included model system for studying cortical function is provided by UC Berkeley scientists. System includes lickometer which employs infrared beam and sensor to minimize electrical noise artifacts during neurophysiology experiments and can be easily mounted in micromanipulator for precise and repeatable positioning.Open source lickometer was designed in conjunction with open source water delivery system.Together, these provide basic hardware for DIY behavioral assay and reward system for mice." .
SCR:021470 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MNE Scan project" ;
NIFRID:synonym "MNE Scan" ;
definition: "Project related to real time acquisition and processing of electrophysiological data.Provides software tool for acquisition and processing of electrophysiological data." .
SCR:021471 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ultrasonic Vocalizations Detector project" ;
NIFRID:synonym "Ultrasonic Vocalizations Detector" ;
definition: "Project related to ultrasonic vocalizations detection. Provides device designed for automatic detection of 50kHz ultrasonic vocalizations." .
SCR:021472 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spike Forest project" ;
NIFRID:synonym "Spike Forest" ;
definition: "Project related to neural data analysis. Provides open-source and reproducible software suite that benchmarks performance of automated spike sorting algorithms across extensive, curated database of ground truth electrophysiological recordings, displaying results interactively on continuously updating website." .
SCR:021473 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pypreclin project" ;
NIFRID:synonym "Pypreclin" ;
definition: "Project related to preprocessing of images. Provieds software Python tool to processes raw macaque fMRI images using algorithms embedded in automatic pipeline." .
SCR:021474 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cerebro Wireless Optogenetic System project" ;
NIFRID:synonym "Cerebro Wireless Optogenetic System" ;
definition: "Project related to wireless controlled optogenetic stimulation. Provides system for wireless optogenetic stimulation developed in Karpova Lab with ability to be customized.Features Cerebro,rechargeable, battery powered wireless receiver;head implant containing optical fibers and two independent laser diodes; base station for transmitting radio signals to Cerebro, controlled by Windows computer via USB or by TTL; charging dock; and Xavier, user friendly GUI for sending and logging base station commands." .
SCR:021475 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Closed Loop System project" ;
NIFRID:synonym "Closed Loop System" ;
definition: "Portal includes system for combined behavioral tracking, electrophysiology, and closed loop stimulation provided by University of Oslo scientists.Integrates Bonsai and Open Ephys with multiple modules.Provides guide for setting up this system." .
SCR:021476 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Wave Surfer project" ;
NIFRID:synonym "Wave Surfer" ;
definition: "Project related to neurophysiology data acquisition and analysis.Included open source software application for neurophysiology data acquisition and analysis is provided by Howard Hughes Medical Institute Janelia Research Campus scientists. Program is based in MatLab, and evolved from earlier open source software package called Ephus." .
SCR:021477 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Calcium Imaging data Analysis project" ;
NIFRID:synonym "Calcium Imaging data Analysis" ;
NIFRID:abbrev "CaImAn" ;
definition: "Project related to calcium imaging.Provides software library, CaImAn, for one and two-photon Calcium Imaging data Analysis." .
SCR:021478 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Toolboxes for Spike and LFP Analysis project" ;
NIFRID:synonym "Toolboxes for Spike and LFP Analysis" ;
definition: "Portal includes compared several toolboxes for spike and LFP analysis, connectivity analysis, dimensionality reduction, and generalized linear modeling. Discussion about major features of software available for Python and MATLAB including Brainstorm, Chronux, Elephant, FieldTrip, gramm, Spike Viewer, and SPIKY. They include succinct tables for assessing system and program requirements, quality of documentation and support, and data types accepted by each toolbox." .
SCR:021479 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scintillate project" ;
NIFRID:synonym "Scintillate" ;
definition: "Project related to time series calcium imaging evaluation and pre-processing. Included open source graphical viewer for time series calcium imaging evaluation and pre-processing is provided by Swedish University scientists ." .
SCR:021480 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCLA Miniscope project" ;
NIFRID:synonym "UCLA Miniscope" ;
definition: "Project related to fluorescence imaging to record neural activity in awake, freely behaving mice.Provided system is developed by UCLA scientists. Miniscope system includes Miniscope with single, flexible coaxial cable to carry power, control signals, and imaging data to open source Data Acquisition hardware and software. Open source miniature fluorescence microscope uses wide-field fluorescence imaging to record neural activity in awake, freely behaving mice." .
SCR:021481 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BrainGlobe project" ;
NIFRID:synonym "BrainGlobe" ;
definition: "Project is related to working with atlas data from multiple species on common platform.Provides collection of Python tools for working with atlas data from multiple species on common platform and for morphological analyses in systems neuroscience." .
SCR:021482 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "An open source motorized swivel for in vivo neural and behavioral recordings project" ;
NIFRID:synonym "An open source motorized swivel for in vivo neural and behavioral recordings" ;
definition: "Project related to neural recordings such as electrophysiology, calcium imaging, and optogenetics. Provides 3D-printed, motorized commutator for neural recordings of small animals in vivo.Open source motorized swivel for in vivo neural and behavioral recordings.Device operates independently of data acquisition system, and it can be controlled through any popular platform such as Arduino or Raspberry Pi." .
SCR:021483 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Two Armed Bandit Task project" ;
NIFRID:synonym "Two Armed Bandit Task" ;
NIFRID:abbrev "2ABT" ;
definition: "Project related to training mice on task that requires continued updating of action/outcome relationships. Behavioral project includes task protocol and corresponding build instructions.Open source behavioral box used to train mice on task that requires continued updating of action/outcome relationships. Permits investigation of motivated behavior that requires flexible relationships between sensory stimuli and motor action. Project provided by Harvard Medical School scientists." .
SCR:021484 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FinchScope project" ;
NIFRID:synonym "FinchScope" ;
definition: "Project related to fluorescent imaging. Provides single photon fluorescent imaging microscope systems. System includes modular in vivo all optical neurophysiology rigs with transparent hardware, and acquisition and analysis software.Provide designs for 3D printed, lightweight, wireless capable microscope and motorized commutator, designed for multi month monitoring neural activity of zebra finches while they sing their courtship songs. Adapted for rodents and birds such as canaries." .
SCR:021485 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenVape project" ;
NIFRID:synonym "OpenVape" ;
definition: "Project related to conducting research on effects of nicotine vapor. Provides open source chamber system for rodents to experience regulated nicotine vapor exposure from JUUL electronic cigarette.Vapor exposure apparatus comprised of Arduino Uno microcontroller that relays coded instructions to H-bridge motor controller.H-bridge then sends specific signals to motors that regulate produced vapor sent to exposure chambers." .
SCR:021486 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Capactive Touch Sensor project" ;
NIFRID:synonym "Capactive Touch Sensor" ;
definition: "Project related to accurately counting and monitoring the behavior of organisms.Provides open source capacitive touch sensing system.Capacitive sensors are positioned to readily detect direct physical touches from rodent under investigation. Device,designed around capacitive touch sensor MPR121,accurately counts and monitors behavior of organisms." .
SCR:021487 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open-tES project" ;
NIFRID:synonym "Open-tES" ;
definition: "Project is related to transcranial Electrical Stimulation.Included system contains aluminum box stimulator with banana connectors for both anode and cathode on front panel,power supply on rear, power switch and serial port, LCD screen and three buttons on top panel that are used to input settings for stimulator. Device for delivering non-invasive neuromodulation techniques such as transcranial direct current stimulation. If device is used for certain types of tDCS (otDCS and tPCs) or external triggering, computer control must be used. Microcontroller is used to regulate operating speed and pulse width modulation switching frequency administrated by device." .
SCR:021488 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CapTouch project" ;
NIFRID:synonym "CapTouch" ;
definition: "Project related to study learning and memory in preclinical research.Included tracking system for object recognition tasks provides standardization across experiments and labs.Automates scoring process using capacitive sensors, while providing validated 3D-printed objects in order to standardize object recognition to study learning and memory in preclinical research.Used for accurate measurement of interaction time during object recognition tasks." .
SCR:021489 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DIY-NAMIC project" ;
NIFRID:synonym "DIY-NAMIC" ;
definition: "Project is related to measurement of complex phenotypes in homecage. Homecage automated open source behavioral testing sytem to enable high throughput 24h testing of many standard operant paradigms. Using Arduino platform and easily sourced inexpensive components system can display light cues and dispense liquid rewards and has nosepoke receptacles with infrared detectors for operant responses, within homecage.Method provided by Dartmouth College scientists." .
SCR:021490 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pi Virtual Reality System project" ;
NIFRID:synonym "Pi Virtual Reality System" ;
NIFRID:abbrev "PiVR" ;
definition: "Project related to study of orientation behavior and neural circuit functions, through creation and analysis of small, freely moving animals in virtual realities. Provides virtual reality tool system for behavioral and neural circuit studies of small animals.Closed loop platform to study unrestrained sensorimotor behavior." .
SCR:021491 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BonVision project" ;
NIFRID:synonym "BonVision" ;
definition: "Project related to creating and controlling visual environments.Provided open source software package for creating and controlling visual environments was developed by University College London scientists." .
SCR:021492 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Home Cage Automated Skilled Reaching Apparatus project" ;
NIFRID:synonym "Home Cage Automated Skilled Reaching Apparatus" ;
NIFRID:abbrev "HASRA" ;
definition: "Project includes system for individualized training of group housed mice in single pellet reaching task.System allows user to host up to 5 mice in their home environment and automatically administer single pellet reaching test to those animals.Platform for training and assessing skilled reaching in mice with minimal need for experimenter handling." .
SCR:021493 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Precision Syringe Pump Controller project" ;
NIFRID:synonym "Precision Syringe Pump Controller" ;
definition: "Project related to dispensing precise volumes of fluid over precise timescales.System components include syringe holder and control board with syringe pump controller and programming library.Syringe pump controller was developed by American University scientists." .
SCR:021494 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ardbark project" ;
NIFRID:synonym "Ardbark" ;
definition: "Project related to fear conditioning studies.Includes hardware and software tools. Provides Arduino based device for producing naturalistic stimuli which can be integrated with existing commercial operant chambers with few modifications.. Stores custom made .wav files on SD card, interfaces with Med System and plays the .wav files through ceiling mounted speakers." .
SCR:021495 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Novel Gustometer for Human Taste Research project" ;
NIFRID:synonym "Novel Gustometer for Human Taste Research" ;
definition: "Project related to taste sensory system research in humans on behavioral, electrophysiological and hemodynamic activity levels.Provided system includes hardware and software tools." .
SCR:021496 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ezTrack" ;
definition: "Open source video analysis pipeline for investigation of animal behavior. Platform independent set of behavior analysis pipelines using interactive Python ( (iPython/Jupyter Notebook) that researchers with no prior programming experience can use." .
SCR:021497 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Low Cost Open Source Eye Tracking" ;
NIFRID:synonym "CameraMultiViewer" ;
definition: "Software tool as part of system designed to be easy to build and setup for real time eye tracking.Open source software provides accurate eye tracking. Can identify shapes such as circles, lines, and triangles.You can rotate and mirror images and also use variety of filters.Capable of processing video in real-time for optical flow. App for viewing multiple video streams from USB cameras." .
SCR:021498 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Calcium ActiVity Explorer" ;
NIFRID:abbrev "CAVE" ;
definition: "Open source tool for combined analysis of head mounted calcium imaging and behavior. Used to analyze imaging data from head mounted microscopes simultaneously with behavioral data." .
SCR:021499 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "idtracker.ai" ;
definition: "Software tool as Python Video Annotator software.Agorithm and tracking software that features two deep networks.Tracks animal identification and tracks when animals touch or cross paths in front of one another." .
SCR:021500 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stytra" ;
definition: "Open source software Python package to control stimulation and track behaviour.Provides timed stimulus presentation, interfacing with external devices and simultaneous real time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely swimming and head restrained preparations." .
SCR:021501 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Worm Behavior Platform" ;
NIFRID:synonym "Tracker Commons" ;
definition: "Software tool as repository of documentation, software, and discussions to share worm tracking data and analysis routines.Open access repository for storing, accessing, and filtering data; interchange format for notating single or multi worm behavior; and file formats written in Python for feature extraction, review, and analysis." .
SCR:021502 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ToxTrac" ;
definition: "Software tool for tracking organisms." .
SCR:021503 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mousecam" ;
definition: "Software Python package with functions for extracting and analyzing data recorded using camera system.Used to monitor behaviors including eye position, whisking, and ear movements in unrestrained animals.Can be mounted in combination with neural implants for recording brain activity." .
SCR:021504 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EthoWatcher" ;
NIFRID:synonym "ETHOWATCHER" ;
definition: "Software tool for behavioral and video tracking analysis in laboratory animals. Used to support detailed ethography, video tracking, and extraction of kinematic variables from digital video files of laboratory animals." .
SCR:021505 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Live Mouse Tracker analysis" ;
NIFRID:synonym "live mouse tracker analysis",
"LMT analysis",
"lmt-analysis" ;
definition: "Software package for Live Mouse Tracker analysis. lmt-analysis provides all analysis tools needed to extract information from tracking performed by live mouse tracker." .
SCR:021506 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3DTracker" ;
definition: "Open source software tool for 3D-video based markerless computerized behavioral analysis for laboratory animals.Used to reconstruct full 3D images of animals and fit skeletal models to 3D image to estimate 3D pose of animals.Open-source 3D video based behavioral analysis system for neuroscience." .
SCR:021507 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EthoScopes" ;
NIFRID:synonym "Ethoscope" ;
definition: "Software R package for data analysis.Enables high throughput analysis of behavior in Drosophila and other animals." .
SCR:021508 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "M-Track" ;
definition: "Software toolbox for automated detection of forepaw trajectories in mice.Open source code to simultaneously track movement of individual paws during spontaneous grooming episodes and walking in multiple freely behaving mice/rats." .
SCR:021509 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Behavioral Observation Research Interactive Software" ;
NIFRID:abbrev "BORIS" ;
definition: "Open source event logging software for video/audio coding and live observations.Multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations." .
SCR:021510 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automated Rodent Tracker" ;
NIFRID:abbrev "ART" ;
definition: "Software tool to automatically track rodent position and movement.Used to track head movements, body movements and also aspects of body size. It is able to identify certain behaviours from video footage too, such as rotations, moving forwards, interacting with objects and staying still." .
SCR:021511 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pyper" ;
NIFRID:synonym "Pyper v2" ;
definition: "Software tool for motion tracking.Provides real time or pre recorded motion tracking of specimen in open field. Used to track path of object of interest in live feed from camera or recorded video. Used to track rodents in open field maze as well as retina of mice.New version v2 of Pyper allows to customise image processing to track different kind of objects." .
SCR:021512 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bonsai" ;
definition: "Software tool as event based framework for processing and controlling data streams. Open source software tool as visual language for reactive programming.Used for composing reactive and asynchronous data streams coming from video cameras, microphones, electrophysiology systems or data acquisition boards." .
SCR:021513 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FaceMap" ;
definition: "Software toolbox for unsupervised video analysis of rodent behavior.Used for videographic processing of head fixed rodent behavior." .
SCR:021514 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Skinner Box" ;
definition: "Software tool for data logging and analysis." .
SCR:021515 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Quantifying Animal Movement from Pre-recorded Videos" ;
NIFRID:synonym "Spectral Time Lapse",
"STL Toolbox" ;
NIFRID:abbrev "STL" ;
definition: "Software toolbox for visualizing and quantifying movement from pre-recorded videos.Used for summarizing animal movement data as single image ( spectral time lapse algorithm) as well as automate analysis of animal movement data." .
SCR:021516 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Platform for Acoustic STArtle" ;
NIFRID:abbrev "ratPASTA" ;
definition: "Software package for processing and visualising data from startle experiments in rodents or experiments measuring grip strength in rodents." .
SCR:021517 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rigbox" ;
definition: "Open source software MATLAB toolbox for running behavioral neuroscience experiments and managing data.Used for probing neurons and behavior. Used for managing behavioral neuroscience experiments and acquiring experiment related data." .
SCR:021518 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoPilot" ;
NIFRID:synonym "Autopilot" ;
definition: "Software tool as open source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Toolkit of flexible modules to design experiments without rigid programming and API limitations." .
SCR:021519 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LinCoM" ;
NIFRID:synonym "Linear place fields in Complex Mazes" ;
definition: "Software MATLAB package for linearization of place fields in complex mazes.Graph theoretic approach for production of linear place fields in complex mazes. Used for producing linear place fields for hippocampal cells during behavior in complex mazes.Specifically designed to deal with mazes with one or more decision points (e.g., T-maze, W-maze, double T-maze, radial maze, plus maze, etc)." .
SCR:021520 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pathfinder" ;
definition: "Open source software for analyzing spatial navigation search strategies." .
SCR:021521 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dual Port Lick Detector" ;
NIFRID:synonym "DP-Lick-Detector" ;
definition: "Distribution package for Dual Port Lick Detector.Package includes files relevant to building lick detector." .
SCR:021522 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "flyPAD" ;
definition: "FPGA code for running main board of flyPAD. Code written in VHDL using Quartus 2 web edition software." .
SCR:021523 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mousetrap" ;
definition: "Integrated, open source mouse tracking software package.Software plugin to record and analyze mouse movements in computerized lab experiments.Software plugin provides two items that implement mouse tracking in OpenSesame." .
SCR:021524 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepSqueak" ;
definition: "Software MATLAB package for high throughput ultrasonic vocalizations detection, classification, and analysis." .
SCR:021525 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Oculomatic" ;
NIFRID:synonym "Oculomatic eye tracking" ;
definition: "Software tool for high speed eye tracking for Point Gray USB3.0 cameras.Oculomatic software tracks eye position within acquired image frame at frame rate dictated by image sensor." .
SCR:021526 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pypreclin" ;
definition: "Software Python tool to processes raw macaque fMRI images using algorithms embedded in automatic pipeline." .
SCR:021527 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Optimouse" ;
definition: "Software tool for analysis of mouse position data.Open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error." .
SCR:021528 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MedParse" ;
definition: "Software tool to read MedPC data into Python and Matlab. MedPC code for saving precise times of behavioral events and MatLab and Python functions to convert MedPC data into time event codes." .
SCR:021529 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Wave Surfer" ;
definition: "Open source software application for neurophysiology data acquisition and analysis. Program is based in MatLab, and evolved from earlier open source software package called Ephus." .
SCR:021530 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MNE Scan" ;
definition: "Software tool for real time processing of electrophysiological data." .
SCR:021531 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scintillate" ;
definition: "Open source graphical viewer for time series calcium imaging evaluation and pre-processing." .
SCR:021532 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spike Forest" ;
NIFRID:synonym "SpikeForest",
"SpikeForest v2" ;
definition: "Open source and reproducible software suite that benchmarks performance of automated spike sorting algorithms across extensive, curated database of ground truth electrophysiological recordings, displaying results interactively on continuously updating website." .
SCR:021533 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Calcium Imaging data Analysis" ;
NIFRID:abbrev "CaImAn" ;
definition: "Open source software tool for scalable calcium imaging data analysis. Used for large scale calcium imaging analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization." .
SCR:021534 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BonVision" ;
definition: "Open source software package for creating and controlling visual environments.Software package for Bonsai which allows for control of 2D and 3D environments." .
SCR:021535 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Federal University of Santa Catarina; Santa Catarina; Brazil" ;
definition: "Public university in Florianópolis, the capital city of Santa Catarina in southern Brazil." .
SCR:021536 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SMOG 2" ;
definition: "Software package for generating structure based models. SMOG 2 is complete rewrite of original SMOG software. SMOG 2 is standalone software package for generating SMOG models. Useful if you want to modify force field (e.g. include new residues, design new variant, etc)." .
SCR:021537 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SMOG" ;
definition: "Software package for generating structure based models." .
SCR:021538 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CRISPResso" ;
NIFRID:synonym "CRISPResso2" ;
definition: "Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments." .
SCR:021539 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scanorama" ;
definition: "Software tool for panoramic stitching of single cell data. Algorithm identifies and merges shared cell types among all pairs of datasets and accurately integrates heterogeneous collections of scRNA-seq data." .
SCR:021540 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ALRA" ;
NIFRID:synonym "Adaptively thresholded Low Rank Approximation" ;
definition: """Software tool for genotype imputation for scRNA-seq based on low rank approximation.
Used for imputation of missing values in single cell RNA-sequencing data.""" .
SCR:021541 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Single Cell Doublet Scoring" ;
NIFRID:abbrev "SCDS" ;
definition: "Software R package for computational doublet annotation of single cell RNA sequencing data. Software tool for in silico identification of doublets in scRNA-seq data." .
SCR:021542 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "STARsolo" ;
definition: "Software tool for accurate, fast and versatile mapping/quantification of single cell and single nucleus RNA-seq data. Used for mapping, demultiplexing and quantification for single cell RNA-seq. Comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR." .
SCR:021543 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chemical Probes Portal" ;
definition: "Portal to find and use small molecule reagents called chemical probes in biomedical research and drug discovery. Molecules are evaluated by recognized chemical probe experts (Scientific Expert Review Panel, SERP) and recommendations are provided how to best use these tools.Portal includes range of chemical tools, including small molecule inhibitors, agonists, PROTACs (proteolysis targeting chimeras) molecular glues, and molecular glue degraders.Portal also curates list of historical compounds, which have been used as inhibitors in the past but are no longer considered probes." .
SCR:021544 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mitochondrial Neuron Ubiquitin" ;
NIFRID:synonym "Mitochondrial Neuron Ubiquitin landscape" ;
NIFRID:abbrev "MitoNUb" ;
definition: "Shiny app for quick selection of ubiquitylation sites and proteins from diGly analysis of neurons stimulated with mitochondrial depolarisation.Used to visualise mitochondrial ubiquitin sites in neurons and search for ubiquitin components recruited to mitochondria upon mitochondrial depolarisation." .
SCR:021545 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Visual stimulator with customizable light spectra" ;
definition: "Project related to visual neuroscience.Provides spatial visual stimulator with arbitrary spectrum of light for visual neuroscientists.Open source, low cost visual stimulator which can be customized with up to 6 chromatic channels. Spectrum of light can be arbitrary and customizable to be adapted to different animal models based on their visual spectrum. Device details, including parts list and information for custom python library for generating visual stimuli (QDSpy), can be found in eLife publication." .
SCR:021546 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ACRoBaT" ;
NIFRID:synonym "Automated Center out Rodent Behavioral Trainer" ;
definition: "Project related to studying motor behavior. University of Washington in Seattle scientists have developed and published their device for training rats to perform modified center out task." .
SCR:021547 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3DOC" ;
definition: "Project related to animals learned perform action in order to achieve reward. Fully 3D printable chamber able to perform operant conditioning using off-the-shelf, low-cost optical and electronic components, that can be reproduced rigorously in any laboratory equipped with 3D printer." .
SCR:021548 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ToneBox" ;
definition: "Project related to auditory behavioral task data collection.Provided high throughput operant conditioning in mouse homecage system was developed by University of Maryland,College Park, scientists.Automated system for training up to hundreds of mice in auditory behavioral task features custom Matlab GUI running on desktop which connects to Raspberry Pi to administer auditory stimuli from USB soundcard and collects auditory data as well as licking data from water spout with commercially available capacitive sensors. Parts list and build instructions are readily available from paper and associated GitHub repository." .
SCR:021550 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Touchscreen Cognition" ;
definition: "Project related to cognitive testing method for rodents.Provides touchscreen operant platform for testing learning and memory in rats and mice.Includes device chambers that can be used to measure rodent behavior.Not open source device." .
SCR:021551 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FreemoVR project" ;
NIFRID:synonym "FreemoVR" ;
definition: "Portal related to virtual reality for freely moving animals.Provides virtual reality system set up for unrestrained animals.System developed by University of Frieburg scientists. This Virtual Reality system can be used with number of different species including mice, zebrafish, and Drosophila." .
SCR:021552 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenFeeder" ;
definition: "Project related to studying reward and feeding behavior. Provides open source automatic feeding system that can be customized for food types from seeds to pellets.System integrates plexiglass tubes, Arduino Uno, motor driver, and piezo sensor to reliably deliver accurate amounts of food, and can also be built using 3D printed parts." .
SCR:021553 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SignalBuddy" ;
definition: "Portal related to signal generation. Provided system was developed by Columbia University scientists. System includes signal generator for scientific applications which generates digital or true analog signals (sine waves, step functions, and pulse trains) and can be controlled with intuitive serial monitor interface." .
SCR:021554 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SnackClock" ;
definition: "Project related to feeding behavior.Provides device for dispensing pre-measured quantities of food at regular intervals throughout day. Device uses 24 hour clock movement to rotate dispenser wheel one revolution per day." .
SCR:021555 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ratcave project" ;
NIFRID:synonym "Ratcave" ;
definition: "Portal provides open source, cross platform Python library that adds 3D stimulus support to all OpenGL based 2D Python stimulus libraries. Ratcave comes with resources including basic 3D object primitives and wide range of 3D light effects. Intuitive object oriented interface allows for all objects, which include meshes, lights, and cameras, can be repositioned, rotated, and scaled." .
SCR:021556 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ArControl project" ;
NIFRID:synonym "Arduino Control Platform",
"ArtControl" ;
definition: "Portal related to delivering stimuli and monitoring responses. Provided behavioral platform was developed by scientists from Huazhong University of Science and Technology, Wuhan, China. System uses Arduino UNO board and simple drive circuit along with stand-along GUI application. Experimental data is automatically recorded with built-in data acquisition function and entire behavioral schedule is stored within Arduino chip." .
SCR:021557 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Modular Automated Platform for Large Scale Experiments project" ;
NIFRID:synonym "Modular Automated Platform for Large -Scale Experiments" ;
NIFRID:abbrev "MAPLE" ;
definition: "Portal related to measurement of fly social networks and behavior. Provides Drosophila handing robot that boasts modular design, allowing platform to both automate diverse phenotyping assays and aid with lab chores (e.g., collecting virgin female flies). MAPLE permits small part manipulator, USB digital camera, and fly manipulator to work simultaneously over platform of flies." .
SCR:021558 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DIY Rodent Running Disk" ;
definition: "Portal related to Rodent Running Disk. Provided Rodent Running Disk was developed by University of California, Berkeley scientist. Acrylic disk mounted to optical encoder to achieve fast locomotion decoding." .
SCR:021559 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Moving Wall Box" ;
definition: "Portal provides Moving Wall Box system used to testing strategy task where mouse is repeatedly forced to jump over small ice by slowly moving walls whereby presence of animal is automatically sensed via balances and analyzed by microcontroller board which in turn controls movements of walls. Device provided by Max Planck Institute of Psychiatry scientist. Used for repeated assessment of fear coping strategies." .
SCR:021560 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Teensy-Based Interface project" ;
NIFRID:synonym "Teensy-Based Interface" ;
definition: "Portal provides Teensy-Based Interface system. System includes Teensy 3.2 microcontroller based interface that is easily programmable, and offers high speed, precisely timed behavioral data acquisition and digital and analog outputs for controlling sCMOS cameras and other devices. Developed by Boston University scientists." .
SCR:021561 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Airtrack" ;
definition: "Portal provides head fixed behavioral environment that uses lightweight physical maze floating on air table that moves around animals body under direct control of animal itself." .
SCR:021562 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Autonomous Training of a Forelimb Motor Task project" ;
NIFRID:synonym "Autonomous Training of a Forelimb Motor Task" ;
definition: "Portal related to individualized tracking of self directed motor learning in group housed mice performing skilled lever positioning task in home cage. Provides system for fully autonomous training of group housed mice on forelimb motor task. Task is run and controlled by Raspberry Pi microcomputer, which allows for cages to be monitored remotely through active internet connection. System was developed by University of Ottawa scientists." .
SCR:021563 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FlyPi" ;
definition: "Portal provides open source and affordable microscope experimental setup device based on Raspberry Pi, Arduino microcontroller and off-the-shelf electronic components. System design is based on 3D-printed mainframe, Raspberry Pi computer, and high definition camera system as well as Arduino based optical and thermal control circuits. All functions of FlyPi can be controlled through custom written graphical user interface." .
SCR:021564 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Operant Box for Auditory Tasks project" ;
NIFRID:synonym "Operant Box for Auditory Tasks" ;
definition: "Portal provides operant box designed to train small primates in auditory tasks.Device is based on computer and Arduino Mega 2560 board, named OBAT (Operant Box for Auditory Tasks), designed to present two different auditory stimuli to small primates.All schematics and software source code are available." .
SCR:021565 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rodent Operant Bucket project" ;
NIFRID:synonym "ROBucket",
"Rodent Operant Bucket" ;
definition: "Portal for open source operant chamber, based on Arduino microcontroller platform, that can be used to train mice to respond for reward. Designed by NIDDK scientists.Apparatus contains two nose pokes, drinking well, and solenoid controlled sucrose delivery system. Chamber can run magazine training, fixed ratio and progressive ratio training schedules, and can be programmed to run more complicated behavioral paradigms." .
SCR:021566 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pearce Lab Syringe Pump project" ;
NIFRID:synonym "Pearce Lab Syringe Pump" ;
definition: "Open source syringe pump apparatus developed by scientists from Michigan Technological University. Syringe pump is designed using freely available open source computer aided design (CAD) software and manufactured using open source RepRap 3-D printer and readily available parts." .
SCR:021567 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automated Home-Cage Functional Imaging project" ;
NIFRID:synonym "Automated Home-Cage Functional Imaging system" ;
definition: "Portal provides automated system for mesoscopic functional imaging that allows subjects to self initiate head fixation and imaging within home cage. Developed by University of British Columbia scientists. System for automated head fixation within mouse home cages." .
SCR:021568 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nose Poke Device" ;
definition: "Portal provides arduino based, 3D-printed nose poke device for rats. Includes set of instructions on how to build this device using arduino, some 3D printed parts and some off-the-shelf electronic components." .
SCR:021569 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Camera Control project" ;
NIFRID:synonym "Camera Control" ;
definition: "Portal provides Python based camera software GUI developed by Harvard University scientists. Open source software package that allows video to be recorded in sync with behavior. Python API to record video system timestamps from Imaging Source USB cameras." .
SCR:021570 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CerebraLux" ;
definition: "Portal provides low cost, open source, wireless probe for optogenetic stimulation. This wireless system for optogenetic stimulation was developed by UCLA scientists. Device consists of two parts. Optical component is mounted on head permanently, whereas electronic component is removable and is applied for each experiment. Device is controlled via custom GUI (built with the TkInter Python 2.7 library) which sends pulses to device via Arduino Uno." .
SCR:021571 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhotometryBox" ;
definition: "Portal provides open source control system for in vivo fluorescence measurements from deep brain structures developed by University of California, San Francisco scientists. Microcontroller based solution for controlling optical components in intracranial photometry system and processing resulting signal." .
SCR:021572 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology project" ;
NIFRID:synonym "and Electrophysiology",
"Hybrid drive combining Optogenetics",
"Hybrid-drive combining Optogenetics",
"Pharmacology" ;
NIFRID:abbrev "HOPE" ;
definition: "Portal provides brain implant developed by MIT scientists. Implant carries 16 movable tetrodes along with two optic fibers or two injection cannulas. Designed with help of 3D CAD software, allowing modifications for various experimental needs, such as targeting different brain regions and use in other animal species (e.g., rats and non-human primates). Implant can be designed to shape of skull of individual monkeys based on pre-implantation magnetic resonance imaging, thus optimizing fit with skull surface and making recording from deep brain regions more reliable." .
SCR:021573 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Craniobot project" ;
NIFRID:synonym "Craniobot" ;
definition: "Portal provides computer numerical controlled robot for cranial microsurgeries developed by University of Minnesota scientist. Included cranial microsurgery platform combines automated skull surface profiling with computer numerical controlled milling machine to perform variety of cranial microsurgical procedures on mice." .
SCR:021574 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyControl project" ;
NIFRID:synonym "pyControl system" ;
definition: "Portal provides system that combines open source hardware and software for control of behavioral experiments. Open source framework, combines Python scripts and Micropython microcontroller. Framework can be run through command line interface, or in user friendly graphical user interface that allows users to manage variety of devices such as nose pokes, LED drivers, stepper motor controllers and more. Data collected using this system can then be imported into Python for data analysis." .
SCR:021575 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenSpritzer" ;
definition: "Portal provides open hardware used in labs for administering picoliters of liquid to biological samples. Pressure ejection system developed by University of Sussex scientist for reliably delivering picolitre volumes." .
SCR:021576 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pulse Pal project" ;
NIFRID:synonym "Pulse Pal generator",
"Pulse Pal system" ;
definition: "Portal provides open source, low cost, programmable pulse train generator for physiology and behavior. Device allows users to create and trigger software defined trains of voltage pulses with high temporal precision. Arduino powered device that generates precise sequences of voltage pulses for neural stimulation and stimulus control. Controlled either through its APIs in MATLAB, Python and C plus plus, or as stand-alone instrument using its oLED screen and clickable thumb joystick." .
SCR:021577 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NINscope" ;
definition: "Portal provides miniscope for fluorescence imaging and optogenetic stimulation. Used for monitoring of neural signals during unrestrained behavior." .
SCR:021578 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tetroplater" ;
definition: "Portal provides open source circuit for microwire tetrode gold plating. Circuit includes impedance meter and current generator for tetrode gold plating. Developed by University of Toyama scientist." .
SCR:021579 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenMV project" ;
NIFRID:synonym "OpenMV system" ;
definition: "Portal provides system capable of frame differencing, color tracking, marker tracking, face detection, eye tracking, person detection (with TensorFlow Lite), and more. Supports very easy to use GUI, the OpenMV IDE." .
SCR:021580 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Homecage Task Training and Mesoscale Imaging project" ;
NIFRID:synonym "Homecage Task Training and Mesoscale Imaging" ;
definition: "Project to build and use new generation of home cages with emphasis on training for simple headfixed tasks during simultaneous autonomous acquisition of mesoscale brain imaging data. Homecage platform for automated task training and mesoscale brain imaging for mice developed by University of British Columbia scientists." .
SCR:021581 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MouseMove project" ;
NIFRID:synonym "MouseMove system" ;
definition: "Portal provides MouseMove software system used to analyze Open Field behavior of mice after experimental stroke to show reduced locomotor activity and to quantify laterality deficits. System is used in combination with open source program ImageJ and MTrack2 plugin to analyze pre recorded Open Field test video. System has two downloadable components, ImageJ macro and separate program with custom built MouseMove GUI. ImageJ is used to subtract background video from experiment and create image of animals total trajectory. MouseMove GUI then completes detailed analysis of movement patterns, measuring fractional time spent stationary, distance traveled, speed mean and various details of laterality." .
SCR:021582 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeRD" ;
NIFRID:synonym "Neural Recording Device" ;
definition: "Portal provides open source neural recording device for wireless transmission of local field potential data in freely behaving animals. Used for electrophysiological recording of local field potentials in freely behaving animals." .
SCR:021583 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NINscope software" ;
definition: "Sofware tool for use with NINscope." .
SCR:021584 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Robotic Flower System for Bee Behavior project" ;
NIFRID:synonym "Robotic Flower System for Bee Behavior" ;
definition: "Portal provides system of robotic artificial flowers to study bumble bee behavior. System is designed to capture data when animal is feeding by placement of IR beams that are broken when engaged on flowers feeding mechanism and sends data to control unit.Developed by University of Oulu in Finland scientists. System includes control unit, separate artificial flowers, and personal computer. Control unit is to handle electronics of flowers, collect data from them, and to send data to computer. Flowers contain infrared sensor, their associated electronics, and electromechanical device that offers small, precise amount of sugar solution from reservoir. Computer runs software that controls refilling rate and data collection via the control unit. Circuit diagrams, parts list, and control software and source code are available in paper supplemental information." .
SCR:021585 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_021619" ;
rdfs:label "Argus" ;
definition: "Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior." .
SCR:021586 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRiED" ;
definition: "Portal provides open Source 3-D Printed Modular micro drive system for acute primate neurophysiology." .
SCR:021587 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CHEndoscope" ;
NIFRID:synonym "Compact Head Mounted Endoscope" ;
definition: "Portal provides open source Compact Head Mounted Endoscope for imaging in freely behaving mouse. Includes accessible and flexible set of calcium imaging tools for neuroscience research community." .
SCR:021588 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eco-HAB" ;
definition: "Portal provides open source, RFID-based system for automated measurement and analysis of social preference and in-cohort sociability in mice. System was developed by Nencki Institute of Experimental Biology scientists." .
SCR:021589 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "An Opensource lickometer and microstructure analysis program" ;
definition: "Portal provides open source lickometer that utilizes readily available or customizable components such as PC sound card and 3D printed drinking bottle holder. System consists of apparatus itself and open source software to collect and analyze data. Recording of raw data is handled by Audacity, open source audio program." .
SCR:021590 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microwave based Homecage Motion Detector project" ;
NIFRID:synonym "Microwave based Homecage Motion Detector" ;
definition: "Portal provides radar based motion detector for home cage activity monitoring in mice. System is used for motion detection without visual contact to animal and can be used with various cage types. Features custom printed circuit board and motion detector shield for Arduino, which saves raw activity and timestamped data in CSV files onto SD card.Developed by Max Planck Institute of Psychiatry scientists. Authors also provide Python script for data analysis and generation of actograms." .
SCR:021591 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "A Head Mounted Multi Camera System for Freely Moving Mice project" ;
NIFRID:synonym "A Head Mounted Multi Camera System for Freely Moving Mice" ;
definition: "Portal provides system of two multi camera head mounts for mice in order to record physiological changes in certain behaviors. System used for video tracking of rodents behavior." .
SCR:021592 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "4 Port Nose Poke" ;
definition: "Portal provides open source nose poke system utilizing Arduino microcontroller, several low cost electronic components, and PVC behavioral arena. System developed by University of Basel scientists for use in behavior experiments." .
SCR:021593 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Visual Discrimination with an iPad" ;
definition: "Portal provides touchscreen platform developed by Texas Christian University scientists. iPad apparatus set up consists of four wall operant chamber, remote desktop program, Visual Basic 6 software, and single wireless iPad. Wireless iPad allows for flexibility in setups during performing visual discrimination behavioral experiments." .
SCR:021594 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StimDuino" ;
definition: "Portal provides Arduino controlled stimulus isolator that allows for highly accurate, reproducible automated setting of stimulation currents. Automatic stimulation patterns are software controlled and parameters are set from Matlab coded simple, intuitive and user friendly graphical user interface." .
SCR:021595 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D Printed Headcap and Microdrive" ;
definition: "Portal provides novel head cap and microdrive design for chronic multi electrode recordings in rats through use of 3D printing technology. Head cap and microdrive designs can be fabricated at little cost using consumer grade 3D printers." .
SCR:021596 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TRIO Platform" ;
NIFRID:synonym "Three-In-One Platform" ;
definition: "Portal provides low profile in vivo imaging support and restraint system for mice. System is compact and provides sturdy head fixation, gas anesthesia mask, and warm water bed. Compact design allows to work with variety of microscope stages and use of 3D printed components makes this design customizable." .
SCR:021597 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automated Classification of Self-grooming in Mice project" ;
NIFRID:synonym "Automated Classification of Self-grooming in Mice" ;
definition: "Portal provides protocol that implements JAABA, open source machine learning based behavior detection system; motr, open-source mouse trajectory tracking software; and bonsai, open source system capable of streaming and recording video. Together they use these tools to process videos of mice performing grooming behaviors in variety of behavioral setups." .
SCR:021599 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ratcave" ;
definition: "Software 3D graphics python package for cognitive psychology experiments. Open source, cross platform Python library that adds 3D stimulus support to all OpenGL-based 2D Python stimulus libraries. These libraries include VisionEgg, Psychopy, Pyglet, and PyGam." .
SCR:021600 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Modular Automated Platform for Large Scale Experiments" ;
NIFRID:synonym "MAPLE v2 Control Software",
"MAPLEControlSoftware" ;
definition: "Software tool to automate various fly handling tasks.Control software for Drosophila handling robot MAPLE." .
SCR:021601 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FreemoVR" ;
NIFRID:synonym "freemovr_engine" ;
definition: "Software tool as virtual reality engine built on ROS and OpenSceneGraph.Perspective correct Virtual Reality for freely moving animals engine. Used for multicomputer realtime tracking and display with goal of being useful for scientific studies of vision and behavior.Part of FreemoVR system." .
SCR:021602 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Teensy-Based Interface" ;
definition: "Teensy microcontroller based interface for optical imaging camera control during behavioral experiments." .
SCR:021603 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Autonomous Training of a Forelimb Motor Task" ;
definition: "Software Python tool running on Raspberry Pi computer. Used for trial timing and data logging. Part of Autonomous Training of Forelimb Motor Task system." .
SCR:021604 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Operant Box for Auditory Tasks" ;
definition: "Software tool as part of Operant Box for Auditory Tasks system." .
SCR:021605 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ArControl" ;
definition: "Software tool as Arduino UNO/Mega based, visual programming and real-time behavioral platform for neuroscience. It can run Go/No-Go, 2AFPC and Optogenetic stimulation tasks. Stand alone and intuitive Gaphical User Interface application.Part of ArControl system." .
SCR:021606 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology" ;
NIFRID:synonym "hope" ;
definition: "Softwre tool as part of Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology project for brain implant." .
SCR:021607 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automated Home-Cage Functional Imaging" ;
definition: "Software tool as part of Automated Home Cage Functional Imaging system." .
SCR:021608 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "poke device arduino" ;
NIFRID:synonym "poke_device_arduino" ;
definition: "Software tool as script to test if IR led, IR photodiode, arduino and 3D printed nose poke device work properly. Part of Nose Poke Device system." .
SCR:021609 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "craniobot" ;
definition: "Software tool as part of Craniobot system.Generates, sends, and receives commands to communicate with the Craniobot." .
SCR:021610 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rodent Operant Bucket" ;
definition: "Software tool as ROBucket source code." .
SCR:021611 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pulse Pal" ;
definition: "Software tool as part of Pulse Pal system which allows users to create and trigger software defined trains of voltage pulses with high temporal precision." .
SCR:021612 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyControl" ;
definition: "Open source software Python tool for behavioural experiment control. Part of pyControl system." .
SCR:021613 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "linear actuator" ;
NIFRID:synonym "linear-actuator" ;
definition: "Code and model files for open source linear actuator. Part of Pearce Lab Syringe Pump system." .
SCR:021614 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Camera Control" ;
NIFRID:synonym "Camera_Control" ;
definition: "Open source software package that allows video to be recorded in sync with behavior. Python GUI and scripts allows investigators to record from multiple imaging source camera feeds with associated timestamps for each frame. Python API to record video system timestamps from Imaging Source USB cameras. Package requires Windows 10, Anaconda, and Git, and is compatible with Imaging Source USB3 cameras. Part of Camera Control project." .
SCR:021615 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenMV" ;
definition: "Software tool as part of OpenMV system." .
SCR:021616 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "chendoscope" ;
definition: "Software tool as part of CHEndoscope. Acquisition software that interfaces with CHEndoscope Ximea USB camera. This code is compatible with Linux and Windows systems." .
SCR:021617 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoHeadFix" ;
definition: "Software Python code for automated control of behavioural apparatus and imaging for mice in home cage environment.Part of Homecage Task Training and Mesoscale Imaging system." .
SCR:021618 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MouseMove" ;
definition: "Open source program for semi automated analysis of movement and cognitive testing in rodents. Accurately quantifies numerous parameters of movement including travel distance, speed, turning, stationary fraction and laterality. Part of MouseMove system." .
SCR:021620 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Boston University;Boston;Massachusetts;USA" ;
definition: "Private research institution with two primary campuses in heart of Boston and programs around the world." .
SCR:021621 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Michigan Technological University; Houghton; USA" ;
definition: "Public research university founded in 1885." .
SCR:021622 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Texas Christian University; Fort Worth; USA" ;
definition: "Private Christian university in Fort Worth, Texas. It was established in 1873 by brothers Addison and Randolph Clark as the Add Ran Male and Female College." .
SCR:021623 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "SpikeGadgets" ;
definition: "Company to design and sell powerful neuroscience hardware that interfaces with open source software platform supported by large community of scientists and developers. Support efforts of open source community in commercially sustainable way." .
SCR:021624 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Open Ephys" ;
definition: "Organization mission is to advance understanding of brain by promoting community ownership of neuroscience tools.Collaborative effort to develop, document, and distribute open source tools for systems neuroscience.Project aims to distribute reliable open source software as well as tools for extracellular recording and stimulation." .
SCR:021625 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneFriends" ;
definition: "Human RNA-seq-based gene and transcript co-expression database.Functional genomics tool based on gene co-expression map that describes which genes tend to be activated and deactivated simultaneously in large number of RNAseq data samples." .
SCR:021626 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kidney Tissue Atlas" ;
definition: "Atlas is set of interactive tools built to promote retrieval, exploration, discovery, and analysis of Kidney Precision Medicine Project data by greater research community. Datasets available in repository are combination of raw and processed data from KPMP participant biopsies and reference tissue samples." .
SCR:021627 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CNVpytor" ;
definition: "Software Python package and command line tool for CNV/CNA analysis from depth of coverage by mapped reads. Software tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing." .
SCR:021628 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_X4R _Pro_V100" ;
rdfs:label "Thermo Fisher | Sorvall X4R Pro 100V centrifuge" ;
NIFRID:synonym "100V",
"Thermo Scientific Sorvall X4R Pro" ;
definition: "Tissue culture Pro series touch screen centrifuge enables programming for quicker results plus easily access and track all runs, rotor life and centrifuge health. With capacity up to 4L, including 196 blood tubes and 96 15mL conical tubes, AutoLock for fast rotor exchange." .
SCR:021629 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kent Scientific | SomnoFlow Low Flow Electronic Vaporizer" ;
NIFRID:synonym "Kent Scientific SomnoFlow Electronic Vaporizer",
"SomnoFlow Electronic Vaporizer" ;
definition: "Compact, standalone vaporizer that uses either ambient air with internal air pump or compressed gas. It delivers only anesthetic required by animal according to its weight with flows down to 0.05 LPM. Low flow isoflurane anesthesia machine." .
SCR:021630 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1068" ;
rdfs:label "International Institute of Molecular and Cell Biology in Warsaw, Biophysics and Bioanalytics Facility" ;
NIFRID:synonym "IIMCB-Biophysics and Structural Biology Facility",
"International Institute of Molecular and Cell Biology IIMCB-Biophysics and Structural Biology Core Facility" ;
definition: "Offers comprehensive selection of molecular biophysics techniques such as SPR, SEC-MALS, AUC, ITC, CD, FT-IR useful in characterization of macromolecule size and intermolecular interactions." .
SCR:021631 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1087" ;
rdfs:label "Rutgers New Jersey Medical School Genomic Center Core Facility" ;
NIFRID:synonym "Genomic center",
"Rutgers",
"Rutgers New Jersey Medical School Genomic Center",
"The State University of New Jersey Genomic center" ;
definition: "Provides NGS services for research and clinical samples in CLIP and CAP accredited laboratory.Services include consultation, sample processing, sequencing and data analysis , as well as interpretation and reporting.Service support for genomics based applications including experimental design, bioinformatics, development of novel assays, grant writing and manuscript preparation. We are experienced in broad range of biological disciplines including basic biology, infectious diseases, cancer, neurobiology, immunology and clinical research. Clinical Genomics lab has extensive experience in molecular diagnostics and clinical research, and specializes in clinical biomarker discovery, validation and diagnostic test development." .
SCR:021632 a NLX:152328,
owl:NamedIndividual .
SCR:021633 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SourceMD" ;
NIFRID:synonym "Source M.D.",
"Source Metadata Tool" ;
definition: "Web tool as prototype service to automatically generate Wikidata items using metadata from scholarly publications. Citation lookup tool in Wikipedia platform. Takes persistent identifier for scholarly article and processes it by importing bibliographic metadata into Wikidata items. In August 2018, it was merged with ORCIDator into single tool that allows for fully automated batch processing based on ISBN-13, DOI, ORCID iD, PubMed ID, PMCID identifiers." .
SCR:021635 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ARGON" ;
definition: "Software tool as fast simulator of genetic data that samples from Discrete Time Wright Fisher process backwards in time. Used to simulate long chromosomes and large samples under DTWF, with computational time comparable to recent coalescent simulators." .
SCR:021636 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TreeMix" ;
definition: "Software tool for inferring patterns of population splits and mixtures in history of set of populations." .
SCR:021637 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1200" ;
rdfs:label "Texas A&M Health Science Center Integrated Microscopy and Imaging Laboratory Core Facility" ;
NIFRID:synonym "TAMHSC-IMIL-Integrated Microscopy and Imaging Laboratory",
"Texas A&M Health Science Center TAMHSC-IMIL-Integrated Microscopy and Imaging Laboratory" ;
NIFRID:abbrev "TAMHSC-IMIL" ;
definition: "Core supports research progress and grant development by encouraging researchers to explore advanced imaging modalities and to incorporate them into their existing research programs.Provides technical expertise and cutting edge microscope systems to support research of faculty and staff of Texas A&M University Health Science Center, Texas A&M University, and all other campuses.IMIL includes six microscopy rooms, supporting facilities, and image processing station.Technical staff is available to train and assist with design, implementation, and analysis of experiments as well as assist in troubleshooting." .
SCR:021638 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "neuronal reconstruction analysis project" ;
NIFRID:synonym "neuronal reconstruction analysis",
"zebrafish-analysis-protocol" ;
definition: "Project for quantitative neuronal morphometry by supervised and unsupervised learning. Includes protocol to quantify and interpret morphological properties of individual neurons reconstructed from microscopic imaging.Includes information about installation of analysis tools and downloading datasets and custom codes." .
SCR:021639 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneID" ;
NIFRID:synonym "geneid",
"geneid v1.2" ;
definition: "Software tool to predict genes in anonymous genomic sequences designed with hierarchical structure. Predicts genes, exons, splice sites and other signals along DNA sequence. Has been trained on several species." .
SCR:021640 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MEDITECH EHR" ;
NIFRID:synonym "MEDITECH",
"MEDITECH EHR system" ;
definition: "Software electronic health record system that provides clinical charting for health care professionals at midsized and community hospitals. Software solution for maintaining patient electronic health records and serving as laboratory information management system." .
SCR:021641 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "jcvi" ;
NIFRID:synonym "jcvi 1.1.17",
"jcvi_PyPI" ;
definition: "Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics." .
SCR:021642 a NLX:63400,
owl:NamedIndividual .
SCR:021643 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AstraZeneca PheWAS Portal" ;
definition: "Repository of gene phenotype associations for phenotypes derived from electronic health records, questionnaire data, and continuous traits computed on exomes released by UK Biobank. Repository was made available by AstraZeneca for public research." .
SCR:021644 a owl:NamedIndividual ;
rdfs:label "Cumulus" ;
definition: "Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data." .
SCR:021645 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pegasus" ;
NIFRID:synonym "Pegasus for Single Cell Analysis",
"Pegasus tool for massive single cell data processing" ;
definition: "Software package for massive single cell data processing. Enables analysis of million scale single cell RNA-seq data and is functionally comparable to Seurat and SCANPY. Command line tool, Python package and base for Cloud based analysis workflows. Supports variety of analysis tasks, such as cell and gene level quality control, highly variable gene selection, dimension reduction, kNN graph building, data integration, clustering, differential expression analysis and putative cell type annotation." .
SCR:021646 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cirrocumulus" ;
definition: "Web interactive visualization tool for large scale single cell genomics data.Interactive web application for exploring million scale single cell datasets. Can be hosted on Google App Engine application for collaborative use or can be run in standalone mode on personal computer. Consists of client side component implemented in JavaScript and server component implemented in Python. Client uses React to manage state and WebGL to visualize variables on 2D/3D embeddings in performant manner. Server component consists of functions to manage datasets, slice variables from dataset stored in PARQUET, Zarr or H5AD formats." .
SCR:021647 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BICCN Anatomy and Morphology Project" ;
NIFRID:synonym "Anatomy and Morphology Project",
"SCP - A&M" ;
definition: "Joint effort with Brain Architecture Portal and Single Cell Portal to visually combine anatomic and molecular brain data in. Users can search for neuroscience data using natural language and faceted search, and then this portal retrieves molecular data housed in the Single Cell Portal and anatomical data in the Brain Architecture Portal. Each study includes information on cell types, gene expression, related genes, and spatial transcriptomics. You can also download a study’s data to explore further and build on your science." .
SCR:021648 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Terra" ;
NIFRID:synonym "BCDC cloud computing environment",
"Terra Cloud Native Platform" ;
definition: "Open ecosystem of data repositories hosted by various partner organizations, who work together to ensure that their data can be federated across participating platforms. Open source platform for biomedical researchers to access data, run analysis tools, and collaborate. Terra powers important scientific projects including AnVIL, BioData Catalyst, Human Cell Atlas, BICCN, and many others. Easily access both open and access-controlled datasets hosted in cloud repositories. Explore, analyze, and visualize data using Jupyter Notebooks, RStudio, RShinyApps, and Galaxy." .
SCR:021649 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QTLbase" ;
definition: "Curates and compiles genome wide QTL summary statistics for many human molecular traits across tissues and cell types. Comprises tens of millions significant genotype molecular trait associations under different conditions. Users can visualize QTL results in phenome wide and tissue wide levels, and annotate their biological functions through comprehensive genomic features and functional evidence. QTLbase provides one stop shop of QTLs retrieval and comparison across multiple tissues and multiple layers of molecular complexity, and it will greatly help researchers interrogate biological mechanism of causal variants and guide direction of functional validation." .
SCR:021650 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lipid Droplet Knowledge Portal" ;
definition: "Interactive portal provides datasets, across variety of cell types, for LD biology, including transcriptional profiles of induced lipid storage, organellar proteomics, genome-wide screen phenotypes, and ties to human genetics. Provides comprehensive picture of genes and pathways affecting lipid droplet biology, including gene expression, proteomics, and LD morphology phenotypes, by integrating multiple relevant data types." .
SCR:021651 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NetMHC" ;
NIFRID:synonym "NetMHC-3.4",
"NetMHC- 1.0",
"NetMHC- 2.0",
"NetMHC- 2.1",
"NetMHC- 3.0",
"NetMHC- 3.2",
"NetMHC- 4.0" ;
definition: "Web tool for binding prediction of peptides to MHC class I molecules. The newest version NetMHC- 4.0 is used for prediction of peptide MHC class I binding affinity using gapped sequence alignment that allows insertions and deletions in alignment." .
SCR:021652 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Panorama" ;
NIFRID:synonym "Panorama: Repository Software for Targeted Mass Spectrometry Assays from Skyline" ;
definition: "Open source data management system for mass spectrometry data processed with Skyline targeted mass spectrometry environment. System includes Repository Server application for targeted mass spectrometry assays that integrates into Skyline mass spec workflow and has been implemented as module within LabKey Server data management platform; Panorama Web application facilitates viewing, sharing, and disseminating results contained in Skyline documents via web browser; Panorama Public repository employs full data visualization capabilities of Panorama which facilitates sharing results with reviewers during manuscript review." .
SCR:021653 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "powereQTL" ;
definition: "Software R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis." .
SCR:021655 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRI-stereoscope project" ;
definition: "Project provides miniature mirror stereoscope system for MRI-scanner. System takes advantage of commonly used display equipment, MRI head coil, and display screen. Miniature Wheatstone stereoscope is used for human neuroimaging." .
SCR:021656 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Auto_T4" ;
rdfs:label "McKinley | Cellometer Auto T4" ;
NIFRID:synonym "Auto T4",
"Cellometer Auto T4 Bright Field Cell Counter",
"Nexcellom Bioscience Cellometer Auto T4 Bright Field Cell Counter" ;
definition: "System includes automated cell counter for trypan blue viability for cell lines and bright field imaging and pattern recognition software to quickly and accurately identify and count individual cells. Cell count, concentration, diameter, and % viability are automatically calculated and reported." .
SCR:021657 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vulcan" ;
definition: "Software tool for improved long read mapping and structural variant calling via dual mode alignment." .
SCR:021658 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NanoZoomer_2.0-HT" ;
rdfs:label "Hamamatsu | NanoZoomer 2.0-HT" ;
NIFRID:synonym "Hamamatsu NanoZoomer 2.0-HT System" ;
definition: "High speed, high resolution digital scanner with network features. User friendly full slide scanner designed to process up to 210 slides automatically." .
SCR:021659 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ontquery" ;
definition: "Software tool as framework querying ontology terms within SciCrunch and SciCrunch SciGraph endpoints." .
SCR:021660 a owl:NamedIndividual ;
rdfs:label "NanoString | GeoMx Digital Spatial Profiler" ;
NIFRID:synonym "GeoMx Digital Spatial Profiler" ;
NIFRID:abbrev "GeoMx DSP" ;
definition: "Integrated commercial system comprising hardware, software and nCounter chemistry that enables simultaneous, highly multiplex spatial profiling of proteins or RNA in FFPE tissues. DSP platform quantifies abundance of protein or RNA by counting unique indexing oligonucleotides assigned to each target of interest. Used to rapidly and quantitatively assess biological implications of heterogeneity within tissue samples." .
SCR:021661 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CIRIquant" ;
definition: "Software Python package for accurate circRNA quantification and differential expression analysis. Comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data. Accurate quantification of circular RNAs identifies extensive circular isoform switching events." .
SCR:021662 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "find circ2" ;
NIFRID:synonym "find_circ2" ;
definition: "Software tool for circRNA detection from RNAseq reads. Python code to detect head-to-tail spliced (back-spliced) sequencing reads, indicative of circular RNA in RNA-seq data." .
SCR:021663 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CLEAR" ;
NIFRID:synonym "CIRCexplorer3-CLEAR",
"Circular and Linear RNA Expression Analysis from Ribosomal-RNA depleted (Ribo–) RNA-seq",
"CLEAR/circExplorer3" ;
definition: "Software tool as computational pipeline for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq. CIRCexplorer3-CLEAR is CLEAR pipeline for direct comparison of circular and linear RNA expression." .
SCR:021664 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CIRCexplorer2" ;
definition: "Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs." .
SCR:021666 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Julia Programming Language" ;
NIFRID:synonym "The Julia Programming Language" ;
definition: "High level, high performance, dynamic language for technical computing. It is a type system with parametric polymorphism in dynamc programming language." .
SCR:021667 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_021668" ;
rdfs:label "scEiaD" ;
NIFRID:synonym "single cell Eye in a Disk" ;
definition: "Software pipeline for creating harmonized single cell RNA-seq dataset for retina with publicly available data. Platform for analysis of single cell eye in disk. Snakefile based process to turn 1.4 million ocular cells into unified meta-atlas. Meta-atlas that compiles 1.2 million single-cell back of the eye transcriptomes across studies, publications, and species." .
SCR:021669 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1203" ;
rdfs:label "Cornell University Weill Medical College Human Immune Monitoring Core Facility" ;
NIFRID:synonym "WCM Human Immune Monitoring Core (HIMC) at Weill Cornell Medicine" ;
NIFRID:abbrev "HIMC" ;
definition: "Core provides technology platforms and services for single cell, in situ, and multiomic analysis for cutting edge immunology research and clinical studies to help make impactful discoveries and develop improved treatments for human diseases. Services include Spectral flow cytometry (Cytek Aurora), Imaging mass cytometry (Fluidigm Hyperion), CyTOF mass cytometry (Fluidigm Helios)." .
SCR:021670 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CIRIsimulator" ;
NIFRID:synonym "CIRI-simulator" ;
definition: "Software tool to make artificial RNAseq datasets with circRNA reads. Specific simulation tool for non-canonical transcripts. Takes FASTA-formatted reference file and GTF annotation file as input, and generates circular and linear RNA sequences." .
SCR:021671 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GPS-PAIL" ;
definition: "Software tool for prediction of lysine acetyltransferase specific modification sites from protein sequences." .
SCR:021673 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "epiR" ;
definition: "Software R package for analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on basis of single or multiple strata of count data presented in contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses." .
SCR:021674 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RSurveillance" ;
definition: "Software R package for design and analysis of disease surveillance activities. These functions were originally developed for animal health surveillance activities but can be equally applied to aquatic animal, wildlife, plant and human health surveillance activities. Utilities are included for sample size calculation and analysis of representative surveys for disease freedom, risk-based studies for disease freedom and for prevalence estimation." .
SCR:021675 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "freedom" ;
definition: "Software R package to calculate probability of freedom from disease in population based on surveillance data." .
SCR:021676 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StimGen" ;
definition: "Software tool as interface for designing and presenting visual stimuli." .
SCR:021677 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Pennsieve Data Management Platform" ;
definition: "Platform to manage and curate large scientific datasets. Used for scientific data management and analysis.Provides advanced functionality to organize files and complex metadata describing datasets and allows users to interact, search, and analyze these data through web application or programmatically using Python client. Provides end-to-end solution for publishing datasets through Blackfynn Discover, assigning DOIs and ensuring that published data becomes available to larger academic community in sustainable and FAIR manner." .
SCR:021678 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microns Explorer" ;
NIFRID:synonym "MICrONS Explorer" ;
definition: "Portal to release connectivity and functional imaging data collected by consortium of laboratories led by groups at Allen Institute for Brain Science, Princeton University, and Baylor College of Medicine, with support from broad array of teams, coordinated and funded by IARPA MICrONS program. Data include large scale electron microscopy based reconstructions of cortical circuitry from mouse visual cortex, with corresponding functional imaging data from those same neurons." .
SCR:021679 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Core Trust Seal" ;
NIFRID:synonym "CoreTrustSeal" ;
definition: "International, community based, nongovernmental, and nonprofit organization promoting sustainable and trustworthy data infrastructures governed by Standards and Certification Board. Offers to any data repository core level certification based on tDSA–WDS Core Trustworthy Data Repositories Requirements catalogue and procedures. CoreTrustSeal Data Repository certification replaces the DSA certification and WDS Regular Members certification." .
SCR:021680 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FlashPCA" ;
NIFRID:synonym "FlashPCA2" ;
definition: "Software tool as fast principal component analysis of large scale genome wide data. FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data. FlashPCA2 used for principal component analysis of biobank scale genotype datasets." .
SCR:021681 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Open Data Institute " ;
NIFRID:abbrev "ODI" ;
definition: "Nonprofit organization with mission to work with companies and governments to build open, trustworthy data ecosystem. They work with range of organisations, governments, public bodies and civil society to create world where data works for everyone." .
SCR:021682 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Epi Info" ;
NIFRID:synonym "Epi Info 6",
"Epi Info 7",
"Epi Info TM",
"Epi Info™" ;
definition: "Software suite of interoperable software tools designed for global community of public health practitioners and researchers. Provides easy data entry form and database construction, customized data entry experience, and data analysis with epidemiologic statistics, maps, and graphs for public health professionals who may lack information technology background.Statistical software for epidemiology developed by Centers for Disease Control and Prevention in Atlanta, Georgia. Available for Microsoft Windows, Android and iOS, along with web and cloud version." .
SCR:021683 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013571" ;
rdfs:label "NF Data Portal" ;
NIFRID:synonym "Neurofibromatosis Data Portal" ;
definition: "Portal created to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis and schwannomatosis.Public data repository that stores and shares data generated by multiple collaborative research programs focused on neurofibromatosis diseases." .
SCR:021691 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRAGUI Exploratory Analysis Tool" ;
NIFRID:abbrev "PEAT" ;
definition: "Software tool for PRAGUI pipeline exploratory analysis." .
SCR:021692 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRAGUI" ;
definition: "Software pipeline to process and analyse RNAseq data. Contains files needed to process and analyse RNAseq data." .
SCR:021693 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Rad | ChemiDoc Touch Imaging System" ;
definition: "System used for detection of chemiluminescence, fluorescence, colorimetry,densitometry, gel documentation. It has been replaced by ChemiDoc Imager. BioRad continues to provide support for customers with ChemiDoc Touch Systems." .
SCR:021694 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Catboost" ;
definition: "Software package for gradient boosting on decision trees library. Used for ranking, classification, regression and other ML tasks." .
SCR:021695 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyCaret" ;
NIFRID:synonym "PyCaret 2.3" ;
definition: "Open source, low code machine learning library in Python that allows you to go from preparing your data to deploying your model within minutes in your choice of notebook environment." .
SCR:021696 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BorutaShap" ;
definition: "Software tool as wrapper feature selection method which combines both Boruta feature selection algorithm with shapley values." .
SCR:021697 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LightGBM" ;
definition: """Software tool as gradient boosting framework that uses tree based learning algorithms.
Designed to be distributed and efficient with advantages:Faster training speed and higher efficiency;Lower memory usage;Better accuracy;Support of parallel, distributed, and GPU learning;Capable of handling large scale data.""" .
SCR:021698 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "imblearn" ;
NIFRID:synonym "Imbalanced-learn" ;
definition: "Software Python package to tackle curse of imbalanced datasets in machine learning.Offers number of re-sampling techniques commonly used in datasets showing strong between class imbalance." .
SCR:021699 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FuzzyWuzzy" ;
definition: "Software pacakge that uses Levenshtein Distance to calculate differences between sequences for string matching." .
SCR:021700 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eQTL Catalogue" ;
definition: "Catalog provides uniformly processed gene expression and splicing QTLs from all available public studies on human. Expression and splicing QTLs recomputed from public datasets." .
SCR:021701 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Targets Genetics Portal" ;
definition: "Portal offers features to help discover associations between genes, variants, and traits including Browse and rank gene and variant associations identified by Locus-to-Gene (L2G) scoring pipeline, Uncover credible sets for variant and trait associations based on mapping analyses pipeline, Explore and compare studies from UK Biobank, FinnGen, and GWAS Catalog using multi-trait comparison tool eQTL Catalogue." .
SCR:021702 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Targets Platform" ;
definition: "Platform for supporting systematic drug–target identification and prioritisation.Provides users with queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery based upon underlying evidence." .
SCR:021703 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013719" ;
rdfs:label "HuBMAP Data Portal" ;
definition: """Data portal as part of Human BioMolecular Atlas Program. Data available on HuBMAP Portal is open access data to be used for research of human biology. Certain data types with potential for re-identification are available in restricted access either directly through this portal by login-dependent permissions or through dbGAP. All data users are expected to respect privacy and confidentiality of donors who provided samples. Data are not to be used to re-identify donors or their family members without further approval from HuBMAP.
Data for single-cell, three-dimensional maps of various human tissues. Data include discrete, complex organs (kidney, ureter, bladder, lung, breast, small intestine and colon); distributed organ systems (vasculature); systems comprising dynamic or motile cell types with distinct microenvironments (lymphatic organs: spleen, thymus, and lymph nodes).""" .
SCR:021705 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ELAN" ;
definition: "Software annotation tool for audio and video recordings. Annotation can be sentence, word or gloss, comment, translation or description of any feature observed in media. Annotations can be created on multiple layers. Tiers can be hierarchically interconnected. Annotation can either be time-aligned to media or it can refer to other existing annotations. Content of annotations consists of Unicode text and annotation documents are stored in XML format (EAF)." .
SCR:021706 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Max Planck Institute for Psycholinguistics; Nijmegen; Netherlands" ;
definition: "Institute is entirely devoted to psycholinguistics – the study of how we produce and understand language, and how we acquire these skills as first or second language learners. The only institution in the world entirely dedicated to psycholinguistics, and is also one of only three among total of 90 within the Max Planck Society to be located outside Germany." .
SCR:021707 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "impuSARS" ;
definition: "Software tool for imputation of viral whole genome sequences from partially sequenced samples. Software tool for imputation of whole-genome SARS-CoV-2 sequences." .
SCR:021708 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VVD Viewer" ;
definition: "Open source application, built upon FluoRender, for visualization and analysis of 3D/4D datasets. Also supports advanced segmentation." .
SCR:021709 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vue.js" ;
definition: "Software JavaScript framework for building UI on the web. Used for building user interfaces and single-page applications." .
SCR:021710 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "YAML" ;
NIFRID:synonym "YAML 1.2" ;
definition: """YAML is a human friendly data serialization language for all programming languages.
Unicode based data serialization language designed around common native data types of agile programming languages. Useful for programming needs ranging from configuration files to Internet messaging to object persistence to data auditing.""" .
SCR:021711 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VIS Image Analysis Software" ;
NIFRID:synonym "Visiopharm image analysis software" ;
NIFRID:abbrev "VIS" ;
definition: "Software tool for image analysis. Used in Quantitative Digital Pathology. Compatible with leading slide scanner manufacturers, data management software, and wide variety of microscopes and cameras." .
SCR:021712 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoString | nCounter Analysis System" ;
NIFRID:synonym "Bruker nCounter Analysis System",
"nCounter Analysis System" ;
NIFRID:abbrev "nCounter" ;
definition: "System includes hardware and software. Options include nCounter SPRINT,nCounter MAX or nCounter FLEX. Platform used for multiplex analysis of up to 800 RNA, DNA, or protein targets. System can be combined with GeoMx Digital Spatial Profiler (DSP) to enable high-plex, spatially-resolved RNA, and protein quantification." .
SCR:021713 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1209" ;
rdfs:label "University of Texas at Austin Genomic Sequencing and Analysis Core Facility" ;
NIFRID:synonym "Genomic Sequencing and Analysis Facility",
"The University of Texas at Austin Genomic Sequencing and Analysis Facility" ;
NIFRID:abbrev "GSAF" ;
definition: "Full service sequencing core that provides both Sanger and Next Generation Sequencing services, in addition to library prep and quality check services, open access to equipment and training. Works directly with the bioinformatics core who can provide assist in any of your analysis needs to data storage solutions." .
SCR:021714 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1212" ;
rdfs:label "Gladstone Institutes Gladstone Flow Cytometry Core Facility" ;
NIFRID:synonym "Gladstone Flow Cytometry Core" ;
definition: "Core offers operation, training and consultation on both cell sorters and analyzers.Our core comprises BDFACsAria II, two BDFACSAria Fusions, Fortessa X-20 and Attune, with analyzing and sorting up to 18 colors possible. Core also offers antibody staining, protocol optimization and data analysis services." .
SCR:021716 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cellpose" ;
definition: "Software tool used to precisely segment cells from wide range of image types and does not require model retraining or parameter adjustments. Generalist algorithm for cellular segmentation. Anatomical segmentation algorithm written in Python 3." .
SCR:021717 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KymoButler" ;
definition: "Software tool as deep learning software for automated kymograph analysis. Uses artificial intelligence to trace lines in kymograph and extract information about particle movement. Speeds up analysis of kymographs by between 50 and 250 times, and comparisons show that it is as reliable as manual analysis." .
SCR:021718 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellTracker" ;
definition: "Software tool for image processing to perform automated, semi-automated, and manual cell migration detection. Open source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques. Written in MATLAB. Works with Windows, Macintosh and UNIX based systems." .
SCR:021719 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Flika" ;
definition: "Software tool as interactive image processing program for biologists written in Python. Used to write analyze images and movies of biological data." .
SCR:021720 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DiPer" ;
definition: "Software tool calculates direction autocorrelation, plots and calculates other essential parameters to analyze cell migration in two dimensions: it displays cell trajectories individually and collectively, and it calculates average speed and mean square displacements (MSDs) to assess the area explored by cells over time." .
SCR:021721 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VAMPIRE" ;
NIFRID:synonym "Visually Aided Morpho-Phenotyping Image Recognition" ;
definition: "Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity." .
SCR:021722 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ICGC Data Portal" ;
NIFRID:synonym "International Cancer Genome Consortium Data Portal" ;
definition: "Portal provides tools for visualizing, querying, and downloading cancer data, which is released on quarterly schedule." .
SCR:021723 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MutaRNA" ;
NIFRID:synonym "Mutational Analysis of RNAs" ;
definition: "Web server predicts and visualizes mutation induced structure changes of single nucleotide polymorphism in RNA sequence. This covers changes in accessibility (single strandedness) of molecule, its intra molecular base pairing potential and its base pairing probabilities. One of Freiburg RNA tools." .
SCR:021724 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Reference Free Sequence Classification" ;
NIFRID:synonym "Reference Free Sequence Classification Tool",
"Reference-Free Sequence Classification Tool" ;
NIFRID:abbrev "RFSC" ;
definition: "Software tool that using machine learning classifiers relies on ensemble of experts in order to provide efficient classification in metagenomic contexts. Used for DNA sequences in metagenomic samples." .
SCR:021725 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ZEN-ZEISS Efficient Navigation" ;
NIFRID:synonym "ZEISS Efficient Navigation",
"ZEN2010 B SP1 software",
"ZEN - ZEISS Efficient Navigation" ;
NIFRID:abbrev "ZEN" ;
definition: "Software package for ZEISS light microscopy systems. Universal user interface for every imaging system from ZEISS to assist to acquire images, process images, visualize big data by GPU powered 3D engine, analyze images via Machine Learning-based tools, correlate between light-light or light-electron microscopes, store raw data in secure format locally or in the cloud., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:021726 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "musicatk" ;
NIFRID:synonym "Mutational Signature Comprehensive Analysis Toolkit" ;
definition: "Software R package to discover and predict, visualize and analyze mutational signatures. Used to count and combine multiple mutation types, including SBS, DBS, and indels. Calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type." .
SCR:021727 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_74" ;
rdfs:label "Cornell University BRC Genomics Core Facility" ;
NIFRID:synonym "BRC Genomics Facility",
"Cornell University BRC Genomics Facility" ;
definition: "Full Service DNA Sequencing and Genotyping facility. Offers Sanger,Fragment Analysis, Illumina, RT and Digital PCR, Single Cell, large projects, sample/library prep and QC.Houses state of the art instruments for all your sequencing needs including, capillary DNA analysis, single cell applications, long read capabilities. We also provide many instruments that can be operated by you for sample preparation and quality control of all sample types." .
SCR:021728 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1215" ;
rdfs:label "University of Texas at Austin Biological Mass Spectrometry Proteomics Core Facility" ;
NIFRID:synonym "The University of Texas at Austin UTA CBRS Biological Mass Spectrometry Facility",
"UTA CBRS Biological Mass Spectrometry Facility" ;
definition: "Proteomics and Metabolomics services and collaborative efforts are provided at Biological Mass Spectrometry Facility. We use high resolution Orbitrap mass spectrometers with UPLC at high flow for metabolomics and nanoUPLC for proteomics work. We have Bruker Autoflex for self service MALDI. Our proteomics services are protein ID, quantitation, and modification analysis, with fractionation for deeper coverage and de novo sequencing of mAbs available. We collaborate for customized projects. We have untargeted metabolomics for quantitative or qualitative analysis of extracted metabolites using C18 column." .
SCR:021729 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1216" ;
rdfs:label "Stowers Institute for Medical Research Genome Engineering Core Facility" ;
NIFRID:synonym "SIMR Genome Engineering",
"Stowers Institute for Medical Research SIMR Genome Engineering" ;
definition: "Core supports genome engineering using CRISPR technology. Provide services to generate knockouts, insertions, deletions, and point mutations in various organisms. Services for genome engineering include guideRNA design, homology-directed repair template design, production of modified mammalian cell lines, preparation of reagents for delivery to embryos, and mutation detection by targeted deep sequencing. Pooled screening is also coordinated and supported by our team.We acquire, prepare, and validate pooled libraries as an Institute resource. In coordination of our pooled screen workflow, we work with other teams to track the progress of these projects. Once resulting cell populations from the screen are delivered, our team does genomic DNA purification, target amplification, and preparation for NGS. We now offer a TAIL-PCR service to identify the location of random integration events. We have successfully identified locations in killifish, fly, zebrafish, and sea anemone.Team is responsible for maintaining and distributing clone and vector collections for the Institute." .
SCR:021730 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iConnectome" ;
NIFRID:synonym "Center for Integrative Connectomics",
"integrative Connectome",
"Mouse Connectome Project" ;
NIFRID:abbrev "CIC" ;
definition: "Collaborative environment hosting scientists from backgrounds ranging from neuroanatomy, to microscopy and computer science, facilitating production, collection, and analysis of brain wide connectivity data. Home of Mouse Connectome Project seeks to develop multimodal multiscale connectome and cell-type map of mammalian brain using advanced tracing, imaging, and computational methods.Crossdisciplinary group develops neuroanatomic and neuroinformatic approaches to understand connectivity patterns in health and disease. Portal includes iConnectome Viewer, iConnectome Maps and Atlas Viewer." .
SCR:021731 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Million Veteran Program" ;
NIFRID:abbrev "MVP" ;
definition: "National research program to learn how genes, lifestyle, and military exposures affect health and illness." .
SCR:021732 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adult Zebrafish Brain Atlas" ;
NIFRID:abbrev "AZBA" ;
definition: "Software tool as 3D adult zebrafish brain atlas for digital age. Built by combining tissue clearing, light-sheet fluorescence microscopy, and three-dimensional image registration of nuclear and antibody stains." .
SCR:021733 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RepEnrich" ;
NIFRID:synonym "RepEnrich2" ;
definition: "Software tool to profile enrichment of next generation sequencing reads at transposable elements. Method to estimate repetitive element enrichment using high throughput sequencing data. Used to study genome wide transcriptional regulation of repetitive elements.RepEnrich2 is updated method to estimate repetitive element enrichment using high-throughput sequencing data." .
SCR:021735 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "avatarpy" ;
definition: "Software Python package.Python analysis module for AVATAR recording system. Uses three-dimentional coordinate data to produce motor coordination data from general information like velocity and total distance to behavior clustering based on python scripts." .
SCR:021736 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100014124" ;
rdfs:label "Open Data Commons for Traumatic Brain Injury" ;
NIFRID:abbrev "ODC-TBI" ;
definition: "Software as cloud based community driven repository to store, share, and publish traumatic brain injury research data. Aims to increase transparency with individual level data, enhance collaboration, facilitate advanced analytics, and conform to increasing mandates by funders and publishers to make data accessible. Members of ODC-TBI have access to private digital lab space managed by PI or multi-PIs for dataset storage and sharing. PIs can share their labs’ datasets with registered members of ODC-TBI community and make their datasets public and citable. ODC-TBI implements stewardship principles that scientific data be made FAIR (Findable, Accessible, Interoperable and Reusable)." .
SCR:021737 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1211" ;
rdfs:label "University of Ottawa Louise Pelletier Histology Core Facility" ;
NIFRID:synonym "Louise Pelletier Histology Core Facility" ;
NIFRID:abbrev "HCF" ;
definition: "Core is full service histology laboratory available to faculty, researchers, clinicians and students.Provides histological services for both animal and human tissue. Services include paraffin processing and embedding, paraffin and frozen sectioning as well as routine and special histological staining.Equippemnt includes:Leica Bond III Immunostainer to provide automated immunohistochemistry, in-situ hybridization and immunofluorescence staining;Automated tissue processors for paraffin processing; Automated microtomes for paraffin sectioning; Automated stainer that can be programmed to provide wide variety of routine and special stains;Cryostats for sectioning frozen tissue; Tissue Microarray machine.LPHCF can also perform manual chromogenic or fluorescent staining (single or multi-color labelling) on frozen and paraffin sections. We also provide full service slide scanning using Axio Scan.Z1 for Brightfield or Fluorescent stained slides at either 20X or 40X magnification.Personnel in the LPHCF are available for consultation on project/protocol design, technical assistance and training on facility instruments.Infinity software system is used for all of our histological services and instrument training." .
SCR:021738 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1217" ;
rdfs:label "Yale University Chemical and Biophysical Instrumentation Center Core Facility" ;
NIFRID:synonym "Yale Chemical and Biophysical Instrumentation Center" ;
NIFRID:abbrev "CBIC" ;
definition: "Core has range of instruments for characterization and structure elucidation of chemical and biophysical samples. Our staff maintains instruments and provides data collection services as well as training and support for self use of many of our instruments. We are most equipped in areas of NMR spectroscopy, Mass spectrometry and X-ray crystallography, but we also have optical and calorimetric instruments." .
SCR:021739 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:dr_disco" ;
rdfs:label "Dr. Disco" ;
definition: "Software tool fo detecting genomic breakpoints of fusion transcripts in random hexamer RNA-seq data. Used for detection of exonic, intronic and intergenic fusion transcripts and their genomic breakpoints in poly(A)+ and rRNA-minus RNA sequencing data." .
SCR:021740 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1218" ;
rdfs:label "Cornell University BRC Flow Cytometry Core Facility" ;
NIFRID:synonym "BRC Flow Cytometry Facility" ;
definition: "Facility provides training, consulting, assisted use and independent access for wide variety of cell sorting and analysis." .
SCR:021741 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_86" ;
rdfs:label "Cornell University BRC Imaging Core Facility" ;
NIFRID:synonym "BRC Imaging Facility" ;
definition: "Facility provides instrumentation and training in following areas of High resolution X-ray CT,Small animal X-ray CT,Flow cytometry and sorting,Confocal microscopy,Multiphoton microscopy,Super resolution microscopy,Laser capture microdissection,Light microscopy,Spectrofluorometry,Bioluminescence imaging,High resolution ultrasound imaging,Image visualization and analysis." .
SCR:021742 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_250" ;
rdfs:label "University of Kansas Lawrence Protein Structure and X-ray Crystallography Laboratory Core Facility" ;
NIFRID:synonym "Protein Structure and X-ray Crystallography Laboratory" ;
definition: "Core laboratory with infrastructure and expertise to perform all aspects of protein and small molecule structure determination using X-ray crystallography. For protein structure determination, high-throughput methods are utilized to move projects rapidly from gene-to-structure." .
SCR:021743 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1219" ;
rdfs:label "Cornell University BRC Proteomics and Metabolomics Core Facility" ;
NIFRID:synonym "BRC Proteomics and Metabolomics Facility" ;
definition: "Facility provides diverse range of Mass Spectrometry based proteomics and metabolomics services.Services include sample preparation, sample analysis, and data interpretation." .
SCR:021744 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "psych" ;
definition: "Software R package for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis.Procedures for Psychological, Psychometric, and Personality Research. Used for personality, psychometric theory and experimental psychology." .
SCR:021745 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CCP" ;
NIFRID:synonym "Canonical Correlation Analysis" ;
definition: "Software R package for significance tests for canonical correlation analysis, including asymptotic tests and Monte Carlo method." .
SCR:021746 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "yacca" ;
NIFRID:synonym "Yet Another Canonical Correlation Analysis" ;
definition: "Software R package provides alternative canonical correlation,redundancy analysis function, with associated print, plot, and summary methods." .
SCR:021747 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sample Size Shop" ;
definition: """Platform for multilevel and longitudinal data.Provide researchers such as behavioral and social scientists with tools and education related to study design including Calculating power and sample size for any univariate or multivariate test for general linear multivariate model, assuming fixed predictors;Producing confidence intervals on power estimates for designs with fixed predictors;Producing power calculations for designs with single Gaussian covariate;Supporting designs with unequal group sizes, and complicated covariance
structures;Creating basic power curves.""" .
SCR:021748 a NLX:63400,
owl:NamedIndividual .
SCR:021749 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Trialdesign" ;
NIFRID:synonym "Trialdesign.org" ;
definition: "Integrated platform for designing clinical trials." .
SCR:021750 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iSamples" ;
NIFRID:synonym "internet of Samples" ;
definition: "Project to align physical sample identifiers. Used to design, develop, and promote service infrastructure to uniquely, consistently, and conveniently identify material samples, record metadata about them, and persistently link them to other samples and derived digital content, including images, data, and publications." .
SCR:021751 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_37550" ;
rdfs:label "Ugo Basile | Dynamic Plantar Aesthesiometer" ;
NIFRID:synonym "Dynamic Plantar Aesthesiometer for mechanical stimulation Model 37550",
"Electronic Von Frey",
"Plantar Von Frey instrument",
"Ugo Basile Dynamic Plantar Aesthesiometer" ;
NIFRID:abbrev "DPA" ;
definition: "Aesthesiometer for mechanical stimulation Model 37550. Instrument designed to automate assessment of touch sensitivity on plantar surface of rats or mice and comes ready with all necessary accessories. At each paw withdrawal, automatically detects and records latency time, and actual force at time of paw withdrawal reflex. Movable force actuator is positioned below plantar surface of animal and desired force and force speed is applied, as preset by operator. Von Frey type 0.5mm rigid filament exerts increasing force, until animal twitches its paw." .
SCR:021752 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Seq-N-Slide" ;
definition: "Set of automated workflows for common sequencing based (Illumina) protocols, such as RNA-seq, ChIP-seq, ATAC-seq, WGBS/RRBS methylation, whole genome/exome/targeted variant detection, and contaminant screening. Sequencing data analysis pipelines." .
SCR:021753 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1220" ;
rdfs:label "University of Hawaii at Manoa Microscopy, Imaging, and Flow Cytometry Core Facility" ;
NIFRID:synonym "and Flow Cytometry Core",
"Imaging",
"UHCC Microscopy" ;
definition: "Core offers optical analysis instrumentation from specialized light microscopes to bioluminescence preclinical imagers to flow cytometers for multicolor cellular analysis. Services include high resolution optical sectioning of fixed cells and tissues, time lapse imaging of living cell cultures, non invasive monitoring of tumor formation in preclinical studies, and extracting specific cells of interest from tissue samples." .
SCR:021754 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1221" ;
rdfs:label "New York University School of Medicine IonLab Core Facility" ;
NIFRID:synonym "IonLab" ;
definition: "Electrophysiology core facility that is part of Ion Channels and Transporters in Immunity Research Program.Research area includes ion channel and transporter function and ionic signaling in immune cells.Users who are studying other cell types or organ systems are welcome.Provides assistance with experimental design, training, implementation, and data analysis." .
SCR:021755 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1223" ;
rdfs:label "University of California at Santa Cruz Biomolecular Cryo Electron Microscopy Core Facility" ;
NIFRID:synonym "Biomolecular Cryo Electron Microscopy Facility" ;
definition: "Biomolecular facility equipped with JEOL 120kV and Glacios 200 kV with K2 Summit direct detector. Provides insights and high throughput data collection and analysis,single particle analysis, sample screening, and high resolution reconstruction., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:021756 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1222" ;
rdfs:label "University of Texas at Austin Microscopy and Flow Cytometry Core Facility" ;
NIFRID:synonym "Center for Biomedical Research Support Microscopy and Imaging Core Facility",
"Center for Biomedical Research Support Microscopy and Imaging Facility at UT Austin",
"Microscopy and Flow Cytometry Facility University of Texas at Austin" ;
NIFRID:abbrev "CBRS MFC" ;
definition: "Provides light microscopy and flow cytometry equipment and services for ultra structural analysis of variety of sample types. Offers assisted use and training on its instrumentation and consultations on related research. Provides access to both standard and high-end imaging instrumentation to all levels of users." .
SCR:021757 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_109" ;
rdfs:label "Cornell University BRC Bioinformatics Core Facility" ;
NIFRID:synonym "BRC Bioinformatics Facility" ;
definition: "Facility provides access to high performance computing environment, BioHPC, which includes both hosted hardware and shared machines. Provides consulting and collaborations for Bioinformatics analysis and workflows." .
SCR:021758 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1206" ;
rdfs:label "Colorado State University Analytical Resources Core Facility" ;
NIFRID:synonym "Analytical Resources Core" ;
NIFRID:abbrev "ARC" ;
definition: "Core is comprised of Materials and Molecular Analysis (MMA), Imaging and Surface Science (ISS), and Bioanalysis and Omics (BIO) centers. MMA provides instrument capabilities and expertise in spectroscopic (optical, NMR, EPR), mass spectrometry, X-ray and materials (magnetic, thermal, physical) characterization of synthetic, environmental and biological materials, both at bulk and molecular scales; BIO provides analysis of complex biological samples using modern mass spectrometry based metabolomics and proteomics approaches, including supporting cheminformatics; ISS provides analysis of complex biological and inorganic samples using near and far field imaging methods, spectroscopy, and other surface analyses." .
SCR:021759 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Czech Centre for Phenogenomics" ;
definition: "Center for research infrastructure combining genetic engineering capabilities, advanced phenotyping and imaging modalities, specific pathogen free animal housing and husbandry, cryopreservation and archiving at BIOCEV campus. Center aims to analyze effect of loss of function gene mutations in mice with goal to produce catalog of gene function, that will help identify causative factors of human diseases as well as novel targets for therapeutic intervention. Through adoption of standardized procedures and pipelines, and usage of quality control measures and cross validation, shared goal is to produce high quality data. Center has phenotyping capabilities to accommodate both mouse and rat disease models." .
SCR:021760 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PsychENCODE" ;
definition: "Collaboration between research institutes working to provide framework of regulatory genomic elements in individuals with neuropsychiatric disorders.Collaboration has resulted in comprehensive set of manuscripts published in Science providing new insights into biology of developing, adult, and diseased human brain.Manuscripts are organized around three flagship articles, first analyzing human development, second studying disease transcriptomes, and third integrating tissue and single cell data with deep learning approaches." .
SCR:021761 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biomed Resource Watch" ;
definition: "Knowledgebase of biomedical research resources. Repository for storing validation and problematic information about variety of entities within biomedical domain, such as antibodies, cell lines, etc. Enables researchers to submit their own claims about specific entity to make validation/problematic information F.A.I.R. (Findable, Accessable, Interoperable, Reuseable)." .
SCR:021762 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FigsharePlus" ;
definition: "Web based interface designed for academic research data management and research data dissemination. Accepts all file types. Enables academics to upload, share, cite and discover all manner of research outputs with security of knowing our hosting options and platform support long term preservation of data.Used to share big datasets from 100GB up. Added features and expert guidance are also included for sharing your data FAIR-ly.During data deposit, personal email support is available and once submitted, Figshare data expert will conduct review of the metadata and spot check of your dataset files and offer guidance, with main aim of enhancing discoverability and reusability." .
SCR:021763 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MariaDB" ;
NIFRID:synonym "MariaDB Server",
"Relational DataBase Management System" ;
NIFRID:abbrev "RDBMS" ;
definition: "Open source relational database management system that is compatible drop in replacement for MySQL database technology. Includes selection of storage engines, including high performance storage engines, for working with other RDBMS data sources. Uses standard and popular querying language. Runs on number of operating systems and supports wide variety of programming languages.Modern Relational Database SQL on JSON support." .
SCR:021764 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IonWizard" ;
NIFRID:synonym "IonOptix IonWizard" ;
definition: "Software tool to perform rapid fluorescence and morphometric real time, synchronous data acquisition with IonOptix systems, as well as polynomial fitting and analysis for myocyte research. Features include data trace averaging and filtering,composite images, and transient analysis. Integrates presentation of fluorescence traces and images, analog voltages, and cell length data under intuitive interface. Analyzes raw data by performing ratio, ion, or linear calibration calculations." .
SCR:021765 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "BOC Sciences" ;
definition: "BOC Sciences provides wide range of research chemicals and biochemicals including inhibitors, building blocks, GMP Products, impurities and metabolites, APIs for Veterinary, Natural Compounds, ADCs, Stem Cell Molecule and chiral compounds." .
SCR:021766 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1226" ;
rdfs:label "University of Alabama at Birmingham Biological Data Science Core" ;
NIFRID:synonym "UAB Biological Data Science Core" ;
NIFRID:abbrev "U-BDS" ;
definition: "Core offers access to computational biology capabilities. Provide services, foster long term collaborations with UAB research community, and provide training for biomedical investigators on specific set of analysis tools and techniques.Places special emphasis in areas of genomics, transcriptomics, systems biology and translational medicine. Services include data analysis, biological interpretation, grant assistance, and training." .
SCR:021767 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1225" ;
rdfs:label "Creative Biolabs Core Facility" ;
NIFRID:synonym "CB-Creative Biolabs" ;
definition: "Custom service provider that has extensive experience in various antibody production and engineering fields.Services includes mouse and rat monoclonal antibody production using hybridoma technology, human, monkey, rabbit, chicken, dog, llama and camel monoclonal antibody production using various antibody library technologies (including phage display, bacterial display and yeast display).Conducting in depth antibody humanization and affinity maturation using phage display and DNA mutagenesis approaches.OEM services for bulk scale antibody manufacturing, including bacterial production of scFv, diabody, tandem scFv, miniantibody and Fab, and mammalian cell expression of minibody, chimeric IgG, and IgG, are also available at the most competitive price in industry." .
SCR:021768 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss LabScope" ;
NIFRID:synonym "Zeiss LabScope software" ;
definition: "Software tool for image acquisition using WiFi-enabled Zeiss microscopes. Compatible with Windows PCs and with Apple tablets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:021769 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atherosclerosis Risk in Communities" ;
NIFRID:synonym "The Atherosclerosis Risk in Communities (ARIC) Study" ;
NIFRID:abbrev "ARIC" ;
definition: "Platform for prospective epidemiologic study conducted in four U.S. communities. One of most significant and longest running heart health studies and is the largest study of heart health in African Americans. ARIC investigates risk factors for heart disease and stroke, and connections between cardiovascular and cognitive health. ARIC includes two parts: Cohort Component and Community Surveillance Component. Cohort Component began in 1987, and each ARIC field center randomly selected and recruited cohort sample of individuals aged 45-64 from defined population in their community, to receive extensive examinations, including medical, social, and demographic data. In Community Surveillance Component, four communities are investigated to determine long term trends in hospitalized myocardial infarction and coronary heart disease deaths in men and women aged 35-84 years." .
SCR:021770 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Online Kappa Calculator" ;
definition: "Software tool can be used to calculate kappa, chance adjusted measure of agreement, for any number of cases, categories, or raters." .
SCR:021771 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Halvade Somatic" ;
NIFRID:synonym "Halvade for Spark" ;
definition: "Software implements germline and somatic variant calling pipelines based on best practices pipelines from Broad Institute using Spark framework. Produces VCF output file which contains single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) when supported by used tools. Program requires Spark on either local cluster with one or more nodes, Amazon EMR cluster or Docker image to run." .
SCR:021772 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1228" ;
rdfs:label "SARS Creative Biolabs Core Facility" ;
NIFRID:synonym "SARS-Creative Biolabs" ;
definition: "Core helps to carry out analysis and research on SARS-COV2 virus. Provides COVID-19/ SARS-COV2/ 2019-nCoV Research Tools and Services.Team has developed related proteins, antibodies, nucleic acid extraction kits and other products to help researchers quickly develop effective anti-COVID-19 drugs and vaccines.Provides preclinical research services, various in vivo and in vivo research models, and in vivo diagnostic immunoassay services." .
SCR:021773 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FEI Helios G4 UX" ;
rdfs:label "FEI | Helios G4 UX" ;
NIFRID:synonym "Helios G4 UX" ;
definition: "Dual beam FIB/FESEM system, containing both focused Ga plus ion beam and ultra high resolution field emission scanning electron column and their combined use. Dual beam focused ion beam scanning electron microscope for nanofabrication." .
SCR:021774 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PF32" ;
rdfs:label "Photon Force | PF32 camera" ;
NIFRID:synonym "PF32",
"PF32 camera",
"Photon Force 32 camera",
"Photon Force PF32" ;
definition: "Single photon avalanche diodes camera for time correlated single photon counting imaging. Time resolved photon counting camera with in pixel timing electronics what enables time tagging of incoming photons with accuracy of 55ps." .
SCR:021775 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_245" ;
rdfs:label "University of Vermont Integrative Genomics Resource Core Facility" ;
NIFRID:synonym "Vermont Integrative Genomics Resource" ;
NIFRID:abbrev "VIGR" ;
definition: "Core provides services for Experimental Design, Metagenomics, Comparative Expression Analyses, Variant Analyses, and Systems Biology. Overarching umbrella encompassing four distinct shared resource facility arms: DNA Analysis,Microarray,Massively Parallel Sequencing Facilities,Bioinformatics Shared Resource." .
SCR:021776 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StrVCTVRE" ;
NIFRID:synonym "Structural Variant Classifier Trained on Variants Rare and Exonic" ;
definition: "Software tool as structural variant classifier for exonic deletions and duplications. Supervised learning method to predict pathogenicity of human genome structural variants.Used to distinguish pathogenic SVs from benign SVs that overlap exons." .
SCR:021777 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rpart" ;
NIFRID:synonym "Recursive Partitioning and Regression Trees" ;
definition: "Software R package as recursive partitioning for classification, regression and survival trees. Implementation of most of functionality of 1984 book by Breiman, Friedman, Olshen and Stone." .
SCR:021778 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GuideMaker" ;
definition: "Software to design gRNAs pools in non-model genomes and CRISPR-Cas systems. Used to design CRISPR-Cas guide RNA pools in non model genomes." .
SCR:021779 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1229" ;
rdfs:label "LFKRI New York Blood Center Flow Cytometry Core Facility" ;
NIFRID:synonym "LFKRI NYBC Flow Cytometry Core Facility",
"LFKRI NYBC-Flow Cytometry Core Facility" ;
definition: "Core provides in house investigators and external clients with equipment for multiparameter flow cytometric analysis and cell sorting, training and expert assistance with various techniques in flow cytometry,cell sorting as well as consultation in experimental design, data analysis, presentation, and publication." .
SCR:021780 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UMI4Cats" ;
NIFRID:synonym "Unique Molecular Identifiers combines chromosome conformation capture" ;
definition: "Software R package for analyzing UMI-4C chromatin contact data. Used to analyze chromatin contact profiles obtained by UMI-4C." .
SCR:021781 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Islet Regulome Browser" ;
definition: "Web visualization tool that provides access to interactive exploration of pancreatic islet genomic data. Allows access and exploration of pancreatic islet epigenomic and transcriptomic data produced by different labs worldwide." .
SCR:021783 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1232" ;
rdfs:label "Forsyth Institute Multiplex Core Facility" ;
NIFRID:synonym "Forsyth- Multiplex Core",
"Multiplex Core" ;
definition: "Core provides researchers access to multiplex analysis of any sample type using commercially available or in house developed assays.Includes simultaneous measurement of multiple biomarkers in single small sample volume. Offers expertise in sample preparation and handling and knowledge that comes with extensive experience." .
SCR:021786 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Idea Biomedical | WiScan Hermes High Content Imaging System" ;
NIFRID:synonym "HERMES imaging system",
"WiScan Hermes" ;
definition: "Microscopy imaging system. Easily generates publication quality images at high throughput speeds." .
SCR:021787 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LinuxCNC" ;
definition: "Software tool as open source controller for machine tools. Can drive milling machines, lathes, 3D printers, laser cutters, plasma cutters, robot arms, hexapods, and more." .
SCR:021788 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIDA center for genetic studies of drug abuse in outbred rats" ;
NIFRID:synonym "Genes and Addiction NIDA center for GWAS in outbred rats",
"NIDA center for GWAS in outbred rats" ;
definition: "Portal includes information about genetic studies of drug abuse in outbred rats. Data center created in 2014 to perform genome wide association studies on numerous behavioral traits that have well established relevance to drug abuse using outbred rats." .
SCR:021789 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colorado University at Boulder High Throughput Screening Core Facility" ;
definition: "Facility is equipped with instruments for both high throughput and high content biochemical and cell based assays, including live cell assays." .
SCR:021790 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Qiber3D" ;
definition: "Open source software package for morphometric quantification of networks from 3D image stacks. Combines required tools for complete analytical workflow, from raw image to final measured values." .
SCR:021791 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1237" ;
rdfs:label "Kings College London Microscopy Innovation Centre Core Facility" ;
NIFRID:synonym "KCL- Microscopy Innovation Centre",
"Kings College London Microscopy Innovation Centre" ;
definition: "Core works with academic and industrial partners to develop and house advanced microscopy instrumentation and analysis tools.Provides custom microscopes to support users in their advanced imaging needs." .
SCR:021792 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ImmGen" ;
NIFRID:synonym "Immunological Genome Project" ;
definition: """Project combines immunology and computational biology laboratories in effort to establish complete road map of gene-expression and regulatory networks in all immune cells.
Project will generate, with rigorously standardized conditions, complete compendium of genome-wide data sets showing expression of protein-coding genes for all defined cell populations of mouse immune system.""" .
SCR:021793 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "naturalsounds analysis" ;
NIFRID:synonym "naturalsounds_analysis" ;
definition: "Software tool as source code for analyzing functional ultrasound data." .
SCR:021794 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "network epistasis" ;
NIFRID:synonym "network_epistasis" ;
definition: "Software tool to detect epistasis between SNPs along edges of gene-gene interaction network." .
SCR:021795 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MLSBM" ;
NIFRID:synonym "Efficient Estimation of Bayesian SBMs and MLSBMs" ;
definition: "Software R package to Fit Bayesian stochastic block models and multi level stochastic block models using efficient Gibbs sampling implemented in Rcpp. Models assume symmetric, non reflexive graphs with unweighted, binary edges. Data are input as symmetric binary adjacency matrix, or list of such matrices." .
SCR:021796 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cocaine Biobank" ;
definition: "Repository of biological samples from genetically characterized outbred rats that exhibit compulsive like escalation of cocaine self administration. Biological tissue bank originating from outbred rats (Heterogenous Stock rats) that have been characterized as vulnerable or resistant to cocaine addiction. Samples are available under three different conditions to maximize compatibility with wide range of applications, including generation of iPSC lines (slow freezing/LN2), histology/neuroanatomy (perfused), and molecular biology (snap-frozen)." .
SCR:021797 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ScriptManager" ;
definition: "Interactive GUI Java software package for analysis of high throughput genomic sequencing data." .
SCR:021798 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TriKinetics | Drosophila Activity Monitoring System" ;
NIFRID:synonym "DAM",
"DAM System",
"Drosophila Activity Monitor",
"Drosophila Activity Monitoring System" ;
definition: "System from TriKinetics for monitoring Drosophila activity. Includes hardware and DAMSystem3 Software for data acquision and DAMFileScan Software for scanning data for errors. Applied to behavioral activity experiments, including sleep deprivation analyses and general studies of hypoactivity and hyperactivity." .
SCR:021799 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adobe InDesign" ;
definition: "Software tool for layout and page design software. Used for print and digital media to create graphic designs with typography from Adobe Stock. Publishing software, graph arrangement." .
SCR:021800 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Papers with Code" ;
definition: "Website devoted to papers that contain machine learning datasets, code, methods and evaluation tables. Done together with community, supported by NLP and ML.All content on this website is openly licenced under CC-BY-SA and everyone can contribute.Also operates specialized portals for papers with code in astronomy, physics, computer sciences, mathematics and statistics." .
SCR:021801 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1205" ;
rdfs:label "University of Kansas Microscopy and Analytical Imaging Research Resource Core Facility" ;
NIFRID:synonym "Microscopy and Analytical Imaging Research Resource Core Laboratory (MAI)",
"Microscopy and Analytical Imaging Shared Resource" ;
NIFRID:abbrev "MAI",
"MAISR" ;
definition: "Core laboratory in Room 1043 in Haworth Hall at the University of Kansas Lawrence campus.Provides life and physical sciences and engineering users with wide spectrum of sample preparation tools and techniques and imaging technologies.Provides training for undergraduate, graduate students, postdoctoral researchers, faculty, staff, and industry collaborators." .
SCR:021802 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:anvio" ;
rdfs:label "Anvi'o" ;
NIFRID:synonym "Anvi’o" ;
definition: "Open source software analysis and visualization platform for microbial omics including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in integrated fashion through extensive interactive visualization capabilities." .
SCR:021803 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LEON BIS" ;
NIFRID:synonym "LEON-BIS" ;
definition: "Software tool for sequence alignments evaluation. Multiple alignment evaluation of sequence neighbours using Bayesian inference system. Used to distinguish sections in multiple sequence alignments that are conserved across whole family or within subfamilies, and should be useful for automatic, high-throughput genome annotations, 2D/3D structure predictions, protein-protein interaction predictions etc." .
SCR:021804 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FAMSA" ;
definition: "Software tool as multiple sequence aligner. Algorithm for large scale multiple sequence alignments.Designed to produce rapid multiple sequence alignment of large protein families." .
SCR:021805 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PARASAIL" ;
NIFRID:synonym "Pairwise Sequence Alignment Library" ;
definition: "Software tool as multiple sequence alignement for global, local and semi global alignments." .
SCR:021806 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1239" ;
rdfs:label "University of Chicago Animal Resources Center Core Facility" ;
NIFRID:synonym "UChicago Animal Resources Center",
"University of Chicago UChicago Animal Resources Center" ;
definition: "Core assists investigators in performing their animal research while ensuring appropriate and humane care of all laboratory animals." .
SCR:021807 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clinica" ;
definition: "Open source software platform for reproducible clinical neuroscience.Set of automatic pipelines for processing and analysis of multimodal neuroimaging data, as well as tools for statistics, machine learning, and deep learning." .
SCR:021808 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mouse Developmental Anatomy Ontology Browser" ;
NIFRID:synonym "Mouse Developmental Anatomy Browser",
"Mouse Developmental Anatomy Ontology" ;
NIFRID:abbrev "EMAPA" ;
definition: "Browser for mouse developmental anatomy. Ontology of mouse developmental anatomy was originally developed by Jonathan Bard and his colleagues as part of Edinburgh Mouse Atlas Project (EMAP) in order to provide structured controlled vocabulary of stage specific anatomical structures for developing laboratory mouse." .
SCR:021809 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TriKinetics DAMSystem3 Software" ;
definition: "Software tool for data collection to upload output from set of activity monitors and periodically saves it in disk files on Macintosh or Windows PC. Part of TriKinetics Drosophila Activity Monitoring System." .
SCR:021810 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "REsearchFish" ;
definition: "Software tool to collect outcomes and outputs of research from web, external data sources and researchers themselves." .
SCR:021811 a owl:NamedIndividual ;
rdfs:label "SARS-CoV-2 network analysis" ;
NIFRID:synonym "SARS-CoV-2 Protein Interaction Network Analysis",
"SARS-CoV-2-network-analysis" ;
definition: "Software tool to predict human proteins that interact with SARS-CoV-2 proteins and trace provenance of predictions." .
SCR:021813 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NHP BIDS" ;
NIFRID:synonym "NHP-BIDS" ;
definition: "Code for NHP-MRI e.g., Retinotopy, Curve-tracing, Figure-ground. Pipeline for processing of NHP MRI data." .
SCR:021814 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NHP Freesurfer" ;
NIFRID:synonym "NHP-Freesurfer" ;
definition: "Software tool as guide to process NHP anatomical MRI data with adapted version of Freesurfer to generate surfaces and flatmaps." .
SCR:021815 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NHP pycortex" ;
NIFRID:synonym "NHP-pycortex" ;
definition: "Software tool as adaptation for NHP brains and pipelines. Pycortex python based toolkit for surface visualization of fMRI data." .
SCR:021816 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tracker MRI" ;
NIFRID:synonym "Tracker-MRI" ;
definition: "Software package for experimental control from Vision and Cognition Lab at Netherlands Institute for Neuroscience. Matlab based software for fMRI, Psychophysical experimentation and NHP training, with eye control using Measurement and Computing IO card. Interfaces with ISCAN eye tracker and communicates with the MRI console using trigger pulses. Uses Psychtoolbox3 graphics and control engine." .
SCR:021817 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Trikinetics DAM FileScan" ;
NIFRID:synonym "DAM FileScan" ;
definition: "Software tool used in Drosophila Activity Monitor system to scann data for errors. Also allows user to extract data from monitor files and bin data in different lengths." .
SCR:021819 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TractionsForAll" ;
definition: "Software tool to calculate 2D tractions exerted by adherent cell on its substrate. Used in field of mechanobiology to study contractile responses of variety of cell types." .
SCR:021821 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SqueezeMeta" ;
definition: "Software tool as fully automated pipeline for metagenomic analysis. Used for metagenomics covering all steps of analysis. Features several characteristics including co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of abundances of genes in each metagenome. Includes binning and bin checking for retrieving individual genomes." .
SCR:021822 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scMAPA" ;
definition: "Software tool to detect alternative polyadenylation and identify cell type specific APA in multi cluster setting." .
SCR:021823 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "randomForestExplainer" ;
definition: "Software R package to help explain which variables are most important in random forests. Various variable importance measures are calculated and visualized in different settings in order to get idea on how their importance changes classification or regression model accuracy." .
SCR:021824 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "karyoploteR" ;
definition: "Software R package used to karyoplots. Bioconductor package to plot customizable genomes displaying arbitrary data." .
SCR:021825 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "barcode splitter" ;
NIFRID:synonym "barcode-splitter" ;
definition: "Software tool used to separate or demultiplex pooled barcodes." .
SCR:021826 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenComet" ;
definition: "Software tool to quantify comet parameters while studying DNA strand breaks. Automated tool for comet assay image analysis." .
SCR:021827 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cellecta CloneTracker 50M Lentiviral Barcode Library" ;
NIFRID:synonym "CloneTracker 50M Lentiviral Barcode Library" ;
definition: "Software library used to tag or barcode individual cell population with unique 18 nucleotide barcodes." .
SCR:021828 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Circa" ;
NIFRID:synonym "circular plots",
"OMGenomics Circa",
"visualize genomic data" ;
definition: "Software tool used to plot circular plots and visualize genomic data along genomic locations." .
SCR:021829 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bayesian Analysis of Single Cell Sequencing" ;
NIFRID:synonym "BASiCS",
"Bayesian Analysis of Single-Cell Sequencing data" ;
definition: "Software tool for Bayesian analysis of single cell sequencing data. Used to perform statistical analyses of single cell RNA sequencing datasets in context of supervised experiments." .
SCR:021830 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ;
rdfs:label "Maxent" ;
definition: "Software tool for modeling species niches and distributions by applying machine learning technique called maximum entropy modeling. Used for maximum entropy modelling of species geographic distributions." .
SCR:021831 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QTRAP_6500plus" ;
rdfs:label "SCIEX | | AB SCIEX | QTRAP 6500 plus system" ;
NIFRID:synonym "AB SCIEX QTRAP 6500 plus mass spectrometer" ;
definition: "Used for performing applications requiring ultimate sensitivity for ultra low level quantitation of both small and large molecules." .
SCR:021832 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1241" ;
rdfs:label "University of Ottawa Preclinical Imaging Core Facility" ;
NIFRID:synonym "Pre-clinical Imaging Core" ;
NIFRID:abbrev "PCIC" ;
definition: "Facility offers internal and external clients experimental solutions to carry out animal studies requiring in vivo imaging, including consultations, research plan design, protocol development, data collection, analysis, and reporting. PCIC offers modalities like MRI and ultrasound enabling translational research." .
SCR:021833 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1248" ;
rdfs:label "University of Edinburgh Clinical Research Mass Spectrometry Core Facility" ;
NIFRID:synonym "Edinburgh Clinical Research Facility",
"Mass Spectrometry Core" ;
definition: "Core is part of Edinburgh Clinical Research Facility, situated in the Centre for Cardiovascular Sciences in the Queen's Medical Research Institute. We train and host undergraduate students, PhD and post-doctoral students in practical skills and mass spectrometry operation. We have expertise in sample preparation, separation and mass spectrometry analysis for targeted small molecule analysis in clinical and pre-clinical studies. We operate under Good Clinical Practice for laboratories for clinical studies. Steroids, drugs and endogenous molecules and metabolic pathways in plasma, serum, tissue. We also have Imaging Mass spectrometry capabilities with a Waters Synapt G2Si, MALDI and DESI." .
SCR:021834 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aquaria" ;
NIFRID:synonym "Aquaria.App" ;
definition: "Web application to help biologists use 3D structures to gain insight into protein function. Used in revealing novel insights into molecular mechanisms underlying protein function in health and disease. System for incorporating 3D structures into variant analysis." .
SCR:021835 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aquaria COVID Resource" ;
NIFRID:synonym "Aquaria-COVID Resource" ;
definition: "Web tool to visually summarise all available 3D structural information for all proteins comprising COVID-19 virus (SARS-CoV-2). Resource also gives access to structural models, generated by finding all sequence regions with detectable similarity to any currently published 3D structure. These structures are clustered into distinct states that provide insight into viral replication, mimicry, and hijacking." .
SCR:021836 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Meta-Prism" ;
NIFRID:synonym "Meta-Prism 2.0" ;
definition: "Software tool as microbial community sample search method based on smart pair wise sample comparison without compromising accuracy. Used as microbial communities similarites calculation and comparison tool." .
SCR:021837 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bam-lorenz-coverage" ;
definition: "Software package to generate Lorenz plots and Coverage plots, directly from BAM file. It can also output tables as text documents so you can generate custom plots. There is also support to only analyse specific regions." .
SCR:021838 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1250" ;
rdfs:label "University of Edinburgh EdinOmics Core Facility" ;
NIFRID:synonym "EdinOmics",
"University of Edinburgh EdinOmics" ;
definition: "Research facility based in the School of Biological Sciences and the UK Centre for Mammalian Synthetic and Systems Biology that provides proteomics and metabolomics services for qualitative and quantitative analysis." .
SCR:021839 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CMH Variant Warehouse" ;
NIFRID:synonym "Childrens Mercy Variant Warehouse Database" ;
definition: "Database of non identifiable, summary data on all variants identified in Childrens Mercy Genomic Medicine Center, including project data of Genomic Answers for Kids. Database can be searched and viewed with genomic annotations, population database cross references such as ClinVar, gnomAD and dbSNP, ACMG curations and local allele frequency. Variant data are available for bulk download as annotated VCF." .
SCR:021840 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genomic Answers for Kids" ;
NIFRID:abbrev "GA4K" ;
definition: "Flagship initiative of Childrens Mercy Research Institute and Genomic Medicine Center in Kansas City. This research program is building pediatric data repository to facilitate search for answers and novel treatments.Goal is to collect genomic data and health information for 30,000 children and their families to create a database of genomes." .
SCR:021841 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH NCI list of FDA approved cancer drugs" ;
definition: "Portal to find consumer friendly information about drugs for cancer and conditions related to cancer. The list is in alphabetical order by generic name and brand name." .
SCR:021842 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PassOnline" ;
NIFRID:synonym "Prediction of Activity Spectra for Substances Online" ;
definition: "Web tool to estimate biological activity profiles for compounds under study based on their structural formula presented in MOLfile or SDfile format. General list of predictable biological activities consists of terms including pharmacotherapeutic effects, biochemical mechanisms, toxicity, metabolism, gene expression regulation, transporter related activities. Prediction is based on knowledge base about structure activity relationships for compounds with known biological activities." .
SCR:021843 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_021851" ;
rdfs:label "NETMAGE" ;
definition: "Web tool for automated generation of interactive disease-disease network visualizations given input PheWAS summary data. Given genetic associations from Phenome-Wide Association Study, disease-disease network can be constructed where nodes represent phenotypes and edges represent shared genetic associations between phenotypes." .
SCR:021844 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1243" ;
rdfs:label "Cleveland Clinic Florida FRIC Flow Cytometry Core Facility" ;
NIFRID:synonym "Cleveland Clinic Florida FRIC Flow Cytometry Core",
"FRIC Flow Cytometry Core" ;
NIFRID:abbrev "FRIC" ;
definition: "Core offers cell sorting and high dimensional flow cytometric analysis as well as training, consultation and single cell partitioning for scRNA seq (10x)." .
SCR:021845 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1251" ;
rdfs:label "University of Ottawa Cell Biology and Image Acquisition Core Facility" ;
NIFRID:synonym "Cell Biology and Image Aquisition (CBIA) Core",
"University of Ottawa Cell Biology and Image Aquisition (CBIA) Core" ;
NIFRID:abbrev "CBIA" ;
definition: "Core provides advanced microscopes, image analysis tools, and technical support to facilitate your microscopy research. Offers consultations to determine appropriate microscope for your specific needs and proper design of your experimental set up." .
SCR:021846 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ExTaxsI" ;
NIFRID:synonym "Exploring Taxonomy Information" ;
definition: "Software Python tool to retrieve biodiversity data stored in NCBI databases and provide simple and explorable visualization. Used to elaborate and visualize molecular and taxonomic informations. Allows creation of interactive plots starting from NCBI search query or directly from offline taxonomic files." .
SCR:021847 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GESS" ;
NIFRID:synonym "Global Evaluation of SARS-CoV-2/hCoV-19 Sequences" ;
definition: "Database of global evaluation of SARS-CoV-2/hCoV-19 sequences.Provides comprehensive analysis results based on tens of thousands of high-coverage and high-quality SARS-CoV-2 complete genomes." .
SCR:021849 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DynaMut " ;
definition: "Web server for predicting impact of mutations on protein conformation, flexibility and stability." .
SCR:021850 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SIFT 4G" ;
NIFRID:synonym "SIFT4G",
"Sorting Intolerant From Tolerant For Genomes" ;
definition: "Software tool to predict whether amino acid substitution affects protein function. Faster version of SIFT that enables to scale up and provide SIFT predictions for more organisms." .
SCR:021852 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1252" ;
rdfs:label "Cleveland Clinic Florida Research and Innovation Center Imaging Core Facility" ;
NIFRID:synonym "Cleveland Clinic Florida JMH-Imaging Core",
"FRIC Imaging Core",
"JMH-Imaging Core" ;
definition: "Imaging Core at CCF FRIC provides access to advanced imaging technologies, including: Wide-field and confocal fluorescent microscopes, FLIM capability, Live cell imaging microscopes, Pre-clinical imaging microscopes, BSL-3 imaging platforms for pre-clinical and basic research microscopy projects.Provides consultation on experimental design and optimization, post-acquisition image processing, and support for analysis, visualization, and interpretation of data." .
SCR:021853 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GE | Amersham Imager 600" ;
NIFRID:synonym "Amersham Imager 600",
"GE Healthcare Amersham Imager 600" ;
definition: "Amersham Imager 600 is CCD camera system that produces digitial images of samples in gels or membranes in three different modes: chemiluminescence, colorimetric and fluorescent image capture. Provides imaging system to capture and analyze protein and DNA sample gels and membranes in high resolution." .
SCR:021854 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sustainable Grazing System Pasture Model" ;
NIFRID:synonym "SGS Pasture Model" ;
definition: "Software tool as biophysical simulation model for livestock systems. It has flexible interface for setting up and running simulations with extensive graphical and data output." .
SCR:021856 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:dentist" ;
rdfs:label "DENTIST" ;
definition: "Software as automated pipeline method to close gaps in assemblies with long reads. Used to close assembly gaps using long reads at high accuracy." .
SCR:021857 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1254" ;
rdfs:label "University of Kansas Mass Spectrometry and Analytical Proteomics Core Facility" ;
NIFRID:synonym "KU Mass Spec & Proteomics Core",
"Lawrence KU Mass Spec & Proteomics Core",
"University of Kansas Mass Spec and Proteomics Core Laboratory" ;
NIFRID:abbrev "MSAPL" ;
definition: "Provides range of mass spectrometry based services including small molecule analysis and quantitation, peptide and protein MW determination; MS based proteomics services and associated bioinformatics including: global proteome IDs and targeted proteomics, post-translational modification mapping, quantitative proteomics, consultation for designing proteomics experiments, thermal protein profiling and cellular thermal shift assay analysis." .
SCR:021858 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyxDamerauLevenshtein" ;
definition: "Software tool implements Damerau-Levenshtein (DL) edit distance algorithm for Python in Cython for high performance." .
SCR:021859 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PaintOmics" ;
NIFRID:synonym "Paintomics",
"PaintOmics 3" ;
definition: "Web tool for integrative visualization of multiple omic datasets onto KEGG pathways. Supports integrated visualization of multiple species of different biological kingdoms and offers user possibility to request any other organism present in KEGG database." .
SCR:021860 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PANC-DB" ;
definition: "Portal to make all Human Pancreas Analysis Program data available to anyone in research community and to interact with and connect scientific community. Stores clinical, molecular, cellular, immunology, imaging, and pathology data from pancreatic tissue and cell samples from organ donors with and without type 1 or type 2 diabetes." .
SCR:021861 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Platform for Epigenomic and Genomic Research" ;
NIFRID:abbrev "PEGR" ;
definition: "Web service platform logging metadata for genomic samples and high throughput sequencing, manages data processing workflows, and provides quality control reporting and visualization. PEGR links people, samples, protocols, sequencing and bioinformatics computation to comply with FAIR best practices for publications and data management plans.Tracks and quality controls experiments from conception to publication ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at wet bench, while continuing to fully support reproducibility and reliability for bioinformaticians through integration with Galaxy platform." .
SCR:021862 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Data independent acquisition proteomics workbench" ;
definition: "Software tools for analysis of data independent acqusition type proteomics data are implemented in Galaxy framework. Enables complete DIA data analysis including spectral library generation based on DDA type data, analysis of DIA data in raw or mzml format, and differntial statistical analysis. All tools are based on open-source software such as diypasef, OpenSwath, swath2stats and MSstats." .
SCR:021863 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allelic Dosage corrected Allele Specific human Transcription factor binding sites" ;
NIFRID:abbrev "ADASTRA" ;
definition: "Landscape of allele specific transcription factor binding in human genome. Creators conducted meta analysis of ChIP-Seq experiments and assembled database of allele specific binding events listing more than half million entries at nearly 270 thousand single nucleotide polymorphisms for several hundred human transcription factors and cell types." .
SCR:021864 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Arthropoda Assembly Assessment Catalog" ;
NIFRID:synonym "Arthropoda Assembly Assessment Catalogue" ;
NIFRID:abbrev "A3Cat",
"a3cat" ;
definition: "Database of metadata and assembly quality metrics for all Arthropod assemblies on NCBI." .
SCR:021865 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ANGSD" ;
NIFRID:synonym "Analysis of Next Generation Sequencing Data" ;
definition: "Software tool fo analysis of next generation sequencing data. Calculates various summary statistics, and performs association mapping and population genetic analyses utilizing full information in next generation sequencing data by working directly on raw sequencing data or by using genotype likelihoods." .
SCR:021866 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "C-GORD" ;
NIFRID:synonym "Center for GWAS in Outbred Rats Database",
"CGORD" ;
definition: "Center maintains database containing all phenotypical data collected by Research Projects and Ancillary collaborators, as well as RNAseq and genotype data.Provides access to data generated by NIDA center for genetic studies of drug abuse in outbred rats and additional research projects that use N/NIH heterogeneous stock (HS) outbred rats and Center’s core services that support genotyping and analysis.Alignes data generated in HS rats with FAIR (Findable, Accessible, Interoperative, Reusable) data management principles.Provides structured access to data associated with research papers produced by research projects that use HS rats." .
SCR:021867 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PI Motion Control Software" ;
NIFRID:synonym "Motion Control Software",
"Physik Instrumente Motion Control Software" ;
definition: "Software to control positioning systems without their own macro facility." .
SCR:021868 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JUMP Cell Painting Consortium" ;
NIFRID:synonym "JUMP-Cell Painting Consortium" ;
definition: "Consortium is creating new data driven approach to drug discovery based on cellular imaging, image analysis, and high dimensional data analytics. Creates public data set to validate and scale up this image based drug discovery strategy. By coordinating assay procedures across partners, future created data will be well matched. Aims to make cell images as computable as genomes and transcriptomes." .
SCR:021869 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cytoself" ;
definition: "Software tool for deep learning based approach for fully self supervised protein localization profiling and clustering. Leverages self supervised training scheme that does not require pre existing knowledge, categories, or annotations. Used for encoding protein localization patterns from microscopy images." .
SCR:021870 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenCell" ;
definition: "Proteome scale collection of protein localization and interaction measurements in human cells. Proteome scale endogenous tagging enables cartography of human cellular organization." .
SCR:021871 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "corticalmapping" ;
definition: "Software package for basic visual stimulation, imaging analysis, plotting, and cell visual response properties analysis functionality for calcium imaging." .
SCR:021872 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Igneous" ;
definition: "Python cloud pipeline for Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Remapping, and more. TaskQueue and CloudVolume based pipeline for producing and managing visualizable Neuroglancer Precomputed volumes.Uses CloudVolume for accessing data on AWS S3, Google Storage, or local filesystem." .
SCR:021873 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MeshParty" ;
definition: "Software package for working with neuronal meshes, skeletons, and annotations from electron microscopy data. Used to work with meshes, designed around use cases for analyzing neuronal morphology." .
SCR:021874 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rescognito" ;
definition: "Platform for recognizing and promoting Open Research. Open online service that aims to offer fairer and more democratic platform for recognizing researcher contributions.Allows researchers to openly acknowledge colleagues for meaningful contributions to research process, such as Publication, Mentoring,Teaching,Data sharing,Reproducibility practices, Sharing negative results, Participation in discussion groups,Software development, Clinical trials management, Leadership, Community outreach, Public engagement. ORCID iDs, DOIs, grant IDs and other persistent identifiers are used where available as links to appropriate contributions." .
SCR:021875 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multiple Bacteria Genome Compressor" ;
NIFRID:abbrev "MBGC" ;
definition: "Software tool for compressing genomes in FASTA or gzipped FASTA input format. Used for fast and efficient compression of bacteria species collections." .
SCR:021876 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TemplateFlow" ;
definition: "Software framework for human and nonhuman brain models.Combines open database with software for access, management, and vetting, allowing scientists to distribute their resources under FAIR principles. Supports multifaceted insight into brains across species, and enables multiverse analyses testing whether results generalize across standard references, scales.Community archive of imaging templates and atlases for improved consistency in neuroimaging R." .
SCR:021877 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DHM Utilities" ;
NIFRID:synonym "Digital Holographic Microscopy Utilities" ;
definition: "Software package as collection of plugins for use in Digital Holographic Microscopy. Used for digital holographic microscopy processing in ImageJ. Main plugins include DHM Utilities Reconstruction, for reconstructing and propagating holograms; DHM Utilities Phase Unwrapping, for phase unwrapping; DHM Utilities Multi Image Landmark Correspondences, for aligning images." .
SCR:021878 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "STENCIL" ;
definition: "Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise." .
SCR:021879 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProSA web" ;
NIFRID:synonym "ProSA-web" ;
definition: "Interactive web service for recognition of errors in three dimensional structures of proteins." .
SCR:021880 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProQ3" ;
NIFRID:synonym "Proq3" ;
definition: "Improved model quality assessments using Rosetta energy terms. Predictor combines training features from ProQRosCen, ProQRosFA and ProQ2." .
SCR:021881 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VoroMQA" ;
definition: "Web tool for assessment of protein structure quality using interatomic contact areas. Method for estimation of single protein structure quality." .
SCR:021882 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LOMETS" ;
NIFRID:synonym "Local Meta Threading Server",
"Local Meta-Threading Server",
"LOMETS2",
"LOMETS3" ;
definition: "Local threading meta server, for quick and automated predictions of protein tertiary structures and spatial constraints. New generation of meta server approach to template based protein structure prediction and structure based function annotation, which integrates multiple deep learning based threading methods and profile based programs (FFAS3D, HHpred, HHsearch, MRFsearch, MUSTER, SparksX)." .
SCR:021883 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3DRefine" ;
definition: "Interactive web server for efficient protein structure refinement with capability to perform web based statistical and visual analysis." .
SCR:021884 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CSpritz" ;
definition: "Web tool for prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs." .
SCR:021885 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MFDp2" ;
NIFRID:synonym "Multilayered Fusion based Disorder predictor v. 2.00" ;
definition: "Web tool for accurate prediction of disorder in proteins by fusion of disorder probabilities, content and profiles." .
SCR:021886 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PrDOS" ;
definition: "Web server to predict natively disordered regions of protein chain from its amino acid sequence. Returns disorder probability of each residue as prediction results." .
SCR:021887 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AI Researchers Portal" ;
definition: "Portal for connecting Artificial Intelligence researchers to Federal resources that can support their AI work from grant funding and datasets to computing and testbeds." .
SCR:021888 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NuCLS" ;
definition: "Software as scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation." .
SCR:021889 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurokit2" ;
definition: "Software Python package for neurophysiological signal processing. Used to analyze physiological data." .
SCR:021890 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "plusTipTracker" ;
definition: "Software package as quantitative image analysis software for measurement of microtubule dynamics. MATLAB software for tracking full dynamics of microtubules based on plusTIP marker live cell image sequences." .
SCR:021891 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Research Organization Registry" ;
NIFRID:abbrev "ROR" ;
definition: "Community led project to develop open, sustainable, usable, and unique identifier for every research organization in the world. Implementation of ROR IDs in scholarly infrastructure and metadata will enable more efficient discovery and tracking of research outputs across institutions and funding bodies." .
SCR:021892 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Resonance Technology | VisuaStimDigital" ;
definition: "Audio visual stimulation system for functional MRI (fMRI) applications." .
SCR:021893 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "jMRUI" ;
definition: "Software package for advanced time domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data." .
SCR:021894 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_021895",
"SCR_021896" ;
rdfs:label "DataJoint Elements" ;
NIFRID:synonym "DataJoint Elements for Neurophysiology" ;
definition: "Collection of curated modules for assembling workflows for major modalities of neurophysiology experiments, as well as related documentation, tools, and utilities." .
SCR:021897 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tecan | SPARK Multimode Microplate Reader" ;
NIFRID:synonym "acquipment",
"instrument",
"plate reader",
"SPARK",
"Spark",
"SPARK Multimode Microplate Reader",
"Spark multimode reader",
"SPARK plate reader",
"SPARK system",
"Tecan Trading AG",
"USEDit" ;
definition: "Multimode microplate reader as fully flexible detection platform with automation.Has four configurations to select from and then add or remove options.Optimised for genomics and proteomics, microbiology, cell based assays, and drug discovery areas. Performs measurements of fluorescent cell based assays. Has integrated, bright field cell imaging module. Enables label free cell counting, size distribution determination and trypan blue based cell viability analysis." .
SCR:021898 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1258" ;
rdfs:label "University of Texas at Austin Biomedical Imaging Center Core Facility" ;
NIFRID:synonym "Biomedical Imaging Center" ;
NIFRID:abbrev "bic" ;
definition: "Multimodal imaging facility that supports human and preclinical imaging research. Hosts range of systems for MRI, PET, CT and optical imaging and accommodates both independent and assisted use for human MRI and PET/CT on its instruments. Provides in house training in scanner safety and operation and supports range of task for functional MRI studies." .
SCR:021899 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Prism_7000" ;
rdfs:label "Thermo Fisher: Applied Biosystems | PRISM 7000 Sequence Detection System" ;
definition: "Real Time PCR system that detects and quantitates nucleic acid sequences. System components include 7000 Sequence Detector, Peltier based 96well block thermal cycling system,Tungsten halogen excitation source, Fluorescence detection via CCD camera, Sequence Detection software. Quantitative results are available immediately after PCR without additional purification or analysis." .
SCR:021900 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.5281/zenodo.4922800" ;
rdfs:label "SimulaBeta" ;
definition: "Software tool as simulation program for insulin glucose feedback control. Based on nonlinear MiMe-NoCoDI model." .
SCR:021901 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Applied Biosystems | 3500/3500xL Genetic Analyzer System" ;
NIFRID:synonym "Applied Biosystems 3500/3500xL Genetic Analyzer",
"Applied Biosystems 3500/3500xL Genetic Analyzer with 3500 Series Data Collection Software v 3.1",
"Applied Biosystems TM 3500/3500xL Genetic Analyzer" ;
definition: """System includes fluorescence based DNA analysis instrument using capillary electrophoresis technology with 8 or 24 capillaries, computer workstation and monitor,
and integrated 3500 Series Data Collection Software 3.1 for instrument control, data collection, quality control, base calling, and size calling of samples.""" .
SCR:021902 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Motif Mutation Analysis for Regulatory Genomic Elements" ;
NIFRID:abbrev "MMARGE" ;
definition: "Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation." .
SCR:021903 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Motif Alteration Genome wide to Globally Investigate Elements" ;
NIFRID:abbrev "MAGGIE" ;
definition: "Software Python package for identifying motifs mediating transcription factor binding and function. Links mutations of motif to changes of epigenomic feature without assuming linear relationship." .
SCR:021904 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1259" ;
rdfs:label "James Madison University Light Microscopy and Imaging Core Facility" ;
NIFRID:synonym "James Madison University JMU-Light Microscopy and Imaging Facility",
"JMU-Light Microscopy and Imaging Facility" ;
definition: "Core provides instrumentation, resources, training, and consultation. Facility offers access to diverse range of light microscope and imaging systems,image analysis software and solutions, practical and theoretical training for faculty, students and classes,consultation on data acquisition, analysis, and presentation." .
SCR:021905 a NLX:152328,
owl:NamedIndividual .
SCR:021906 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_021907" ;
rdfs:label "germline flow" ;
NIFRID:synonym "germline_flow" ;
definition: "High performance of GPU accelerated variant calling tool in genome data analysis." .
SCR:021908 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Turing Way handbook for reproducible data science" ;
definition: "Guide to reproducible data science to support students and academics as they develop their code, with aim of helping them produce work that will be regarded as gold standard examples of trustworthy and reusable research. Include training material on version control, analysis testing and open and transparent communication with future users." .
SCR:021909 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Princeton Handbook for Reproducible Neuroimaging" ;
NIFRID:synonym "The Princeton Handbook for Reproducible Neuroimaging" ;
definition: "Handbook provides reference for best practices in reproducible fMRI research.Many elements of handbook are specific to Princeton Neuroscience Institute computing infrastructure, but principles are widely applicable." .
SCR:021910 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "qPCRsoft" ;
definition: "Real Time PCR control and evaluation software, provides intuitive controls and automated evaluation. Part of Analytik Jena qTOWER3 system. Providies threshold calculation for determination of Ct values, standard curves, PCR efficiencies, and advanced evaluation methods." .
SCR:021911 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cytena | CELLCYTE X" ;
NIFRID:synonym "CELLCYTE X" ;
definition: "Live cell imaging system. Includes CELLCYTE Studio software." .
SCR:021912 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Creative Biogene" ;
definition: "Company provides mitochondrial research products. Has team of scientists and is equipped with variety of high end instruments to create comprehensive mitochondrial research service platform. Provides customers with customized mitochondrial research services." .
SCR:021913 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenEpi" ;
definition: "Web based, open source, operating system independent series of programs designed for use in public health and medicine for training or practice that provide number of epidemiologic and statistical tools for summary data. Developed in JavaScript and HTML, and can be run in modern web browsers. Program can be run from OpenEpi website or downloaded and run without web connection." .
SCR:021914 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1262" ;
rdfs:label "City University of New York Advanced Science Research Center Epigenetics Core Facility" ;
NIFRID:synonym "CUNY Advanced Science Research Center-Epigenetics Core" ;
definition: "Facility at Advanced Science Research Center of City University of New York provides research resources and services that include nucleic acid extraction and fragmentation, quantitative gene expression analysis, targeted DNA methylation analysis in specific genomic loci of interest, next generation sequencing RNA-seq and ChIP-seq, and single cell genomics.Provides advanced cell sorter with biosafety protection for flow cytometry service, services for RNAScope to allow for in situ hybridization detection of transcriptional targets with spatial resolution." .
SCR:021915 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HOBOware Pro" ;
NIFRID:synonym "Data loger HOBO" ;
definition: "Weather data logging software used for all HOBO data loggers and wireless data nodes. Used to read out and plot data, and export to spreadsheets for further analysis." .
SCR:021916 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "endoR" ;
definition: "Software R package to interpret fitted tree ensemble model.Used to extract and visualize how predictive variables contribute to tree ensemble model accuracy." .
SCR:021917 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CNVkit" ;
definition: "Software command line toolkit and Python library for detecting copy number variants and alterations genome wide from hight hroughput sequencing." .
SCR:021918 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciStat" ;
definition: "Software tool for statistical analyses on any device that has web browser and connection to internet." .
SCR:021919 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeoMapApp" ;
definition: "Web tool as map based application for browsing, visualizing and analyzing diverse suite of curated global and regional geoscience data sets. These cover geophysics, geology, geochemistry, physical oceanography, climatology, and more. Runs with Java under Windows, Mac OS X, Linux and Unix/Solaris operating systems." .
SCR:021920 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Puerto Rico Caribbean Primate Research Center" ;
NIFRID:synonym "University of Puerto Rico Caribbean Primate Research Center Resource Distribution Core" ;
NIFRID:abbrev "CPRC" ;
definition: "Facilitates supply of conventional and specific pathogen free nonhuman primates and biological samples. Priority is given to NIH-funded investigators in universities, NIH Intramural Program, and contractors working on behalf of researchers conducting experiments under NIH-funded programs. Non-NIH-funded investigators may still be considered depending on resource availability.To request for CPRC animals, authorized representative of institution will need to submit Animal Allocation Request form." .
SCR:021921 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_T100_Thermal_Cycler" ;
rdfs:label "Bio-Rad | T100 Thermal Cycler" ;
NIFRID:synonym "T100 Thermal Cycler" ;
definition: "Small compact 96well thermal cycler. PCR system features intuitive touch screen and thermal gradient technology to optimize reaction in single run." .
SCR:021922 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Izon Control Suite" ;
NIFRID:synonym "Izon Control Suite Software",
"Izon Control Suite Software V3.4",
"Izon qNano Control Suite Software",
"qNano Control Suite Software" ;
definition: "Data acquisition software. Allows raw or filtered measurement data to be viewed in real time. Part of qNano system. Izon Control Suite Software V3.4 is maintenance software release that updates Izon current software." .
SCR:021923 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Izon | qNano Gold" ;
NIFRID:synonym "qNano Gold" ;
definition: "Resource has been discontinued. Documented on January 13, 2022. Benchtop instrument for practical implementation of TRPS for fluid borne analysis of nano and micro scale particles by Izon Science Ltd. Single particle sizer. Directly measures particles using Tunable Resistive Pulse Sensing principle. Measures properties of individual nanoparticles in solution like particle diameter or volume, effective surface charge and zeta potential." .
SCR:021924 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "POPART" ;
NIFRID:synonym "Population Analysis with Reticulate Trees" ;
NIFRID:abbrev "PopART" ;
definition: "Software package that provides implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication ready figure production.Population genetics software. Used to understand evolutionary relationships among populations." .
SCR:021925 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1263" ;
rdfs:label "University of California at Santa Cruz Plasma Analytical Laboratory Core Facility" ;
NIFRID:synonym "UC Santa Cruz Plasma Analytical Laboratory" ;
definition: "Core facility provides Thermo Element XR high-resolution ICPMS,Thermo X-Series II quadrupole ICPMS,Thermo iCap 7400 ICP-OES, Photon Machines Analyte 193H excimer laser system, and Zygo NewView Element XR7200 Vertical Scanning Interferometer for depth profiling and analysis of laser pit morphology." .
SCR:021926 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1264" ;
rdfs:label "University of Freiburg Magnetic Resonance Development and Application Center Core Facility" ;
NIFRID:synonym "MRDAC - Magnetic Resonance Development and Application Center" ;
NIFRID:abbrev "MRDAC" ;
definition: "Core is registered in resources database of German Research Foundation under number RI_00444. Center origins in Medical Physics group, Dept. of Radiology, University Medical Center Freiburg, one of leading group in field of methodological developments in Magnetic Resonance Imaging and Spectroscopy and its application in clinics and research.Serves as platform for collaborations with partners in industry and research according to industrial quality and performance standards. Main branches of MRDAC include development of novel MR sequences and methods and design, implementation, and execution of pharmaceutical MR studies.Offers services such as teaching, training, and consulting." .
SCR:021927 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1265" ;
rdfs:label "University of Texas at Austin Mouse Genetic Engineering Core Facility" ;
NIFRID:synonym "Mouse Genetic Engineering Facility",
"University of Texas at Austin Mouse Genetic Engineering Facility" ;
NIFRID:abbrev "MGEF" ;
definition: "Provides services to generate, cryopreserve, and recover transgenic mice for modeling human disease.MGEF is fully equipped to make genetically engineered mice and is staffed with skilled personnel with decades of transgenic experience.Generates transgenic mice for studying mammalian gene function and modeling human disease, cryopreserves and archives transgenic mouse lines." .
SCR:021928 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HaploMaker" ;
definition: "Software pipeline for haplotype assembly of diploid genomes using paired end or PacBio reads." .
SCR:021929 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_021932" ;
rdfs:label "Diverse mating phenotypes impact the spread of wtf meiotic drivers in S pombe" ;
NIFRID:synonym "Diverse mating phenotypes impact the spread of wtf meiotic drivers in Schizosaccharomyces pombe",
"Diverse_mating_phenotypes_impact_the_spread_of_wtf_meiotic_drivers_in_S.-pombe" ;
definition: "Software used for flow cytometry analysis.Holds functions used to analyze cytometry data and to simulate spread of wtf meiotic drivers given initial experimental parameters." .
SCR:021930 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.5281/zenodo.5871355" ;
rdfs:label "alpha helix structural optimisation" ;
NIFRID:synonym "alpha-helix strutcural optimsation",
"alpha-helix-strutcural-optimsation",
"alpha-helix_strutcural_optimsation" ;
definition: "Source code for alpha helix structural optimisation written in MATLAB." .
SCR:021931 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_813" ;
rdfs:label "University of Luxembourg LCSB Genomics Platform Core Facility" ;
NIFRID:synonym "LCSB Sequencing Platform",
"LCSB Sequencing Platform Core Facility",
"University of Luxembourg LCSB Sequencing Platform Core Facility" ;
definition: "Core offers next generation sequencing services.Provided sequencers include NextSeq2000 and MiSeq from Illumina, and MinION nanopore sequencer from Oxford Nanopore Technologies. Illumina sequencers allow sequencing tunable read lengths up to 300 bases of single as well as paired end runs while MinION sequencer complements by ultra long read lengths up to several hundreds of kilobases. Together this offers high flexibility for the different sequencing needs. Platform offers full service, starting with advice in experimental design up to sequencing data generation. Receiving RNA or DNA samples, sample quality check, sample shearing, library preparation, sequencing run, raw data generation and preliminary data quality control report is performed. General applications include RNA sequencing, metagenomics, small genome sequencing, targeted gene sequencing, amplicon sequencing, and HLA typing. Upon user request, sequencing platform works closely with bioinformatics platform to offer downstream data analysis. Besides wide range of standard services, platform also offers new method development." .
SCR:021933 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genie 2000 Basic" ;
NIFRID:synonym "Genie 2000 Basic Spectroscopy Software",
"Marion Technologies Genie 2000 Basic",
"Marion Technologies Genie 2000 Basic Spectroscopy Software" ;
definition: "Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data." .
SCR:021935 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ABL835_FLEX" ;
rdfs:label "RADIOMETER | ABL835 FLEX blood gas analyzer" ;
NIFRID:synonym "Radiometer America ABL835 FLEX blood gas analyzer" ;
definition: "Analyzer to measure full panel of up to 18 STAT parameters on same blood sample to support fast diagnosis of critically ill patients. Arterial blood gas analyzer with capacity to measure glucose concentrations." .
SCR:021936 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NiemaGraphGen" ;
NIFRID:abbrev "NGG" ;
definition: "Software memory efficient global scale contact network simulation toolkit. Collection of C plus plus implementations of graph generators for use in sampling contact networks in global scale pandemic simulations." .
SCR:021937 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_655" ;
rdfs:label "University of North Carolina at Chapel Hill Department of Chemistry Mass Spectrometry Core Facility" ;
NIFRID:synonym "Department of Chemistry Mass Spectrometry Core Laboratory",
"University of North Carolina at Chapel Hill Department of Chemistry Mass Spectrometry Core Laboratory" ;
definition: "Core specializes in small molecule analysis. Services include, but are not limited to, quantitative mass spectrometry, liquid chromatography separations, fragmentation and structural elucidation mass spectrometry, complex mixture analysis, molecular formula confirmation, high resolution and accurate mass analysis.Provides individualized user training for undergraduate, graduate, and post-doctoral scholars of Department of Chemistry." .
SCR:021938 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Med Associates | Deluxe Behavioral Test Package with Rat Modular Chamber" ;
NIFRID:synonym "Deluxe Behavioral Test Package w/Rat Modular Chamber" ;
definition: "Operant behavior test package for rat built to meet needs of research studies requiring additional reward and stimulus flexibility. One of Med Associates, Inc. operant conditioning and general behavior product." .
SCR:021939 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1274" ;
rdfs:label "Vanderbilt University Mouse Metabolic Phenotyping Center Core Facility" ;
NIFRID:synonym "NIDDK - Vanderbilt Mouse Metabolic Phenotyping Center",
"Vanderbilt Mouse Metabolic Phenotyping Center" ;
NIFRID:abbrev "VMMPC" ;
definition: "Centralized resource for study of mouse models of diabetes, obesity, and related disease. Includes animal housing, energy balance, telemetry, and experiment rooms and surgical suites. Develops, standardizes, and provides surgical and experimental services for phenotyping mice. Surgical procedures include venous and arterial catheterizations, cannulation of brain regions, bariatric surgeries, and islet transplantations. VMMPC uses flexible platforms to study nutrient metabolism and energy balance that can be readily adapted for specific experimental requirements. Use of dual arterial and venous catheter implantation permit glucose clamps, treadmill exercise, metabolic flux analyses, and other procedures to be studied without the stress of handling mice. VMMPC offers courses annually to disseminate research laboratory practices for mouse." .
SCR:021940 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Alveole Leonardo" ;
NIFRID:synonym "Alvéole Leonardo software",
"Leonardo software" ;
definition: "Photopatterning software to control PRIMO system including UV illumination module, microscope, camera and stage, and to precisely define experimental conditions.Used to design your own micropatterning manipulations." .
SCR:021941 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Alveole | PRIMO photopatterning module" ;
NIFRID:synonym "Alveole PRIMO",
"Alvéole PRIMO" ;
NIFRID:abbrev "PRIMO" ;
definition: "Photopatterning device for performing micropatterning, microfabrication and hydrogel polymerization.Part of PRIMO system." .
SCR:021942 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PolySTest" ;
definition: "Web service for statistical testing, data browsing and interactive visualization. Contains multiple statistical tests and new method to incorporate missing values. Robust statistical testing of proteomics data with missing values to improve detection of biologically relevant features., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:021943 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Southern Denmark; Denmark" ;
NIFRID:abbrev "SDU" ;
definition: "University has campuses located in Southern Denmark and on Zealand with main campus in Odense and regional campuses in Slagelse, Kolding, Esbjerg and Sønderborg. University offers joint programes in co-operation with University of Flensburg and University of Kiel." .
SCR:021946 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellChat" ;
definition: "Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets." .
SCR:021947 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Atlas of Neonatal Development and Early Life Immunity" ;
NIFRID:synonym "Human Atlas of Neonatal Development and Early-Life Immunity" ;
NIFRID:abbrev "HANDEL-I" ;
definition: "HANDEL-1 program to better understand normal human immune development by acquiring stromal and mucosal tissues from infant and pediatric organ donors and to create novel and essential dataset informing immune system development in collaborative research project that leverages shared access to various tissues in conjunction with existing HANDEL-P program that seeks to understand development of pancreas and islet microenvironment in early life." .
SCR:021950 a owl:NamedIndividual ;
rdfs:label "PEPSI SANS" ;
NIFRID:synonym "PEPSI-SANS",
"Polynomial Expansions of Protein Structures and Interactions SANS" ;
definition: "Software tool as logical extension of Pepsi-SAXS method for small angle neutron scattering. Allows for explicit and implicit hydrogens, allows to specify deuteration level of sample and of buffer and exchange rate of labile hydrogens. Can also compute scattering intensity in absolute scale if sample concentration is provided. Can fit modelled profile on absolute scale within certain user specified margin. Instrumentation resolution is taken into account during processing of input data." .
SCR:021951 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Martini 3" ;
NIFRID:synonym "Matini3.0" ;
definition: "Software tool used for predictions of molecular packing and interactions. General purpose coarse grained force field for molecular dynamics simulations of biomolecular systems Martini 3 is refined model with improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability." .
SCR:021952 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PLUMED 2" ;
NIFRID:synonym "PLUgin for MolEcular Dynamics 2" ;
definition: "Open source, community developed library that provides range of different methods, which include enhanced sampling algorithms, free energy methods, tools to analyze vast amounts of data produced by molecular dynamics simulations. PLUMED 2 is complete rewrite of the code in object oriented programming language C plus plus. This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has simpler interface with the MD engines and provides single software library containing both tools and core facilities." .
SCR:021953 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Bayesian/Maximum Entropy" .
SCR:021954 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NOLB" ;
NIFRID:synonym "NOn-Linear rigid Block NMA",
"Nonlinear Rigid Block Normal-Mode Analysis Method" ;
definition: "Software tool for non-linear normal mode analysis." .
SCR:021956 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100006019",
"GRID grid.251017.0",
"ISNI 0000000404062057",
"Wikidata Q7913119" ;
rdfs:label "Van Andel Institute" ;
definition: "Independent biomedical research and science education organization in Grand Rapids, MI. Committed to improving health and changing lives of current and future generations through biomedical research and science education." .
SCR:021957 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "legacy STRAIGHT" ;
NIFRID:synonym "legacy_STRAIGHT" ;
definition: "Software as collection of speech analysis, modification and resynthesis tools." .
SCR:021958 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Heterogeneity through Discriminative Analysis" ;
NIFRID:synonym "HYDRA" ;
definition: "Software tool as novel non-linear learning algorithm for simultaneous binary classification and subtype identification. Can handle imaging and non-imaging data and can find applications in exploratory analyses other than clustering of brain images.Software performs clustering of heterogenous disease patterns within patient group." .
SCR:021959 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PombeX" ;
definition: "Software tool for robust cell segmentation for fission yeast transillumination images.Used for robust segmentation of fission yeast micrographs, especially those with quality challenged images." .
SCR:021960 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ExoCarta" ;
NIFRID:synonym "ExoCarta 2012" ;
definition: "Manually curated database of exosomal proteins, RNA and lipids. Web based compendium of exosomal cargo. Database catalogs information from both published and unpublished exosomal studies. Mode of exosomal purification and characterization, biophysical and molecular properties are listed." .
SCR:021961 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miRandola" ;
definition: "Manually curated database containing information on extracellular and circulating non-coding RNAs.You can search for RNAs typing in text area molecule of interest or you can browse database. Initially published in 2012, foreseeing relevance of ncRNAs as non-invasive biomarkers.miRandola 2017 is effort to update and collect accumulating information on extracellular ncRNAs that is spread across scientific publications and different databases with implemented new web interface." .
SCR:021963 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DRSC/TRiP Functional Genomics Resources and DRSC-BTRR" ;
definition: "Provides DRSC Drosophila cell-based screening, TRiP Drosophila fly stock production, Bioinformatics software tools and data access. Functional genomics platform for needs of Drosophila and broader community.Online tools include DIOPT for identification of orthologs (yeasts, worm, fly, frog, fish, mouse, rat, human),DIOPT-DIST for identification of human orthologs and links to disease, UP-TORR for RNAi reagent identification based on up-to-date gene annotations,DGET analysis of gene lists in the context of RNAseq data from modENCODE and others,Find CRISPRs and CRISPR efficiency evaluation online tools for CRISPR-Cas9 genome editing, FlyPrimerBank resource of pre-computed qPCR primers,RSVP RNAi fly stock validation database (data for TRiP, VDRC, NIG-Japan fly stocks), GeneLookup and Screen Summary views of DRSC cell screen data sets." .
SCR:021964 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1281" ;
rdfs:label "University of Southern California CHLA Cellular Imaging Core Facility" ;
NIFRID:synonym "CHLA Cellular Imaging Core",
"University of Southern California CHLA Cellular Imaging Core" ;
definition: "Core provides equipment in microscopy and digital imaging. Primary focus is technology transfer and provision of facilities for acquisition and analysis of histological and cytological preparations. Provides training in the use of imaging instrumentation and in the application of image analysis procedures for generation of quantitative data." .
SCR:021966 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IPA HiFi Genome Assembler" ;
NIFRID:synonym "IPA",
"Pacific Biosciences IPA",
"pbipa" ;
definition: "Software tool used for improved phased assembly.IPA assembly for Hifi PacBio reads. Official PacBio software for HiFi genome assembly." .
SCR:021967 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pb assembly" ;
NIFRID:synonym "pb-assembly" ;
definition: "Software tool as PacBio assembly tool suite." .
SCR:021968 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1280" ;
rdfs:label "Van Andel Institute Optical Imaging Core Facility" ;
NIFRID:synonym "VAI Optical Imaging Core" ;
definition: "Core helps investigators tackle wide range of research questions, from gene expression to cell motility, and is committed to providing training in microscopy best practices. Service requests are placed through CrossLab Solutions." .
SCR:021971 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ORCA _Flash4.0_LT" ;
rdfs:label "Hamamatsu | ORCA Flash4.0 LT plus digital sCMOS camera" ;
NIFRID:synonym "ORCA-Flash4.0 LT +",
"ORCA-Flash4.0 LT + CMOS camera",
"ORCA-Flash4.0 LT plus Digital CMOS camera",
"ORCA-Flash4.0 LT+ Digital CMOS camera" ;
definition: "Redesigned ORCA-Flash4.0 LT+ featuring 82 % peak quantum efficiency brings all advantages of sCMOS technology wide field of view, low light sensitivity, and large dynamic range increased flexibility and sensitivity of a scientific CMOS camera., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:021972 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_pE-300ultra" ;
rdfs:label "CoolLED | pE-300ultra" ;
definition: "Highly controllable fluorescence microscopy Illumination System which offers broad spectrum LED illumination for imaging most common fluorophores. System offers precise control over wavelength irradiance and shuttering. Used for LED microscope lighting." .
SCR:021975 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1282" ;
rdfs:label "Wake Forest University Microscopic Imaging Core Facility" ;
NIFRID:synonym "Wake Forest University WFU Microscopic Imaging Core",
"WFU Microscopic Imaging Core" ;
NIFRID:abbrev "WFU" ;
definition: "Light Microscopy and Scanning Electron Microscopy Facility managed by the Biology Department." .
SCR:021977 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dimensions" ;
definition: "Database that aggregates, harmonizes and links records of various publication types from diverse sources, including Crossref and PubMed Central using automated routines and artificial intelligence technologies. Publications, ranging from articles published in scholarly journals, books and book chapters, to preprints and conference proceedings. All publications are contextualized with linked data sets, funding, publications, patents, clinical trials, and policy documents. You can also view associated categories, funders, institutions, and researcher profiles." .
SCR:021978 a owl:NamedIndividual ;
rdfs:label "LogiXPro" ;
NIFRID:synonym "Resource" ;
definition: "Software tool for learning fundamentals of RSLogix ladder logic programming." .
SCR:021979 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1283" ;
rdfs:label "University of Texas at Austin Biomedical Research Computing Core Facility" ;
NIFRID:synonym "University of Texas at Austin UTA-Biomedical Research Computing Facility",
"UTA-Biomedical Research Computing Facility" ;
NIFRID:abbrev "BRCF" ;
definition: "Biomedical Research Computing Facility as core for Biomedical Research Support. Provides small, centrally managed compute clusters and storage, suitable for local, interactive computing, to biomedical research groups." .
SCR:021980 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1304" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Animal Imaging Shared Resource Core Facility" ;
NIFRID:synonym "Animal Imaging Shared Resource",
"University of Colorado Anschutz Medical Campus Cancer Center Animal Imaging Shared Resource" ;
NIFRID:abbrev "AISR" ;
definition: "Enables noninvasive imaging of animal models of human disease. Provides access and training on state-of-the-art animal scanners (MRI, CT, optical, PET/SPECT) for live imaging on rodents, perfoms all animal handling and assist with image analysis to establish imaging biomarkers." .
SCR:021981 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1306" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Biostatistics Core Facility" ;
NIFRID:synonym "Bioinformatics - Biostatistics and Bioinformatics Shared Resource" ;
NIFRID:abbrev "BiostatisticsBBSR" ;
definition: "Biostatistics provides quantitative support for planning, design, analysis, and presentation of basic science, clinical, and epidemiological investigations. We are dedicated to delivering high quality, methodically developed results to improve patient outcomes and clinical care." .
SCR:021982 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1307" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Cell Technologies Shared Resource Core Facility" ;
NIFRID:synonym "Cell Technologies Shared Resource" ;
NIFRID:abbrev "CTSR" ;
definition: "Supports basic and translational research projects in biomedical research. CTSR produces hybridomas/monoclonal antibodies to enhance basic research and preclinal studies and makes recombinant proteins for mechanistic and structural studies on proteins.Provides multiple platforms and analytic modules for real time live-cell imaging of cultured cells and organoids to enhance analysis of cancer cell biology. In addition, we maintain a collection of authenticated human cell lines for use in biomedical research. Sign in to iLab using University of Colorado credentials." .
SCR:021983 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1305" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics - Biostatistics and Bioinformatics Shared Resource" ;
NIFRID:abbrev "BioinformaticsBBSR" ;
definition: "Cancer focused bioinformatics group that assists in all needs related to omics and big data. We assist our collaborators with experimental design, data processing, interpretation, generating publication-quality figures, and preparing manuscripts and grants." .
SCR:021984 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1310" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Genomics Shared Resource Core Facility" ;
NIFRID:synonym "Genomics Shared Resource" ;
NIFRID:abbrev "GSR" ;
definition: "GSR provides genome-wide analyses of DNA sequence, transcriptomes, epigenetics and cytogenomics using next generation sequencing (NGS) and gene microarrays; and single cell genomic and transcriptomic analyses including single cell immune profiling and spatial gene expression." .
SCR:021985 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1311" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Human Immune Monitoring Shared Resource Core Facility" ;
NIFRID:synonym "Human Immune Monitoring Shared Resource" ;
NIFRID:abbrev "HIMSR" ;
definition: "Facilitates clinical and translational studies by dissecting immune based mechanisms with diagnostic and therapeutic applications. Offers assays including immunophenotyping and functional characterization, multicolor fluorescence tissue imaging, multiplex cytokine analysis, and cellular assays.Sign in to iLab using University of Colorado credentials." .
SCR:021986 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1308" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Drug Discovery and Development Shared Resource Core Facility" ;
NIFRID:synonym "Drug Discovery and Development Shared Resource" ;
NIFRID:abbrev "D3SR" ;
definition: "Provides expertise and infrastructure to facilitate drug discovery at different stages of development pipeline, including assay development and validation, high throughput screening and image based high content screening discovery, validation and optimization, and in vitro and in vivo pharmacology including pharmacokinetics and pharmacodynamics as well as toxicology.Sign in to iLab using University of Colorado credentials." .
SCR:021987 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1309" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Functional Genomics Core Facility" ;
NIFRID:synonym "Functional Genomics Shared Resource / Functional Genomics Facility" ;
NIFRID:abbrev "FGSR / FGF" ;
definition: "Core facilitates access to tools including shRNA, ORF, CRISPR to investigate gene function on genome wide scale. Provides protocols and expertise for use of these genomics tools. Serves as forum for scientific exchange and discussion in the field of functional genomics.Sign in to iLab using University of Colorado credentials." .
SCR:021988 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1312" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Mass Spectrometry Shared Resource Core Facility" ;
NIFRID:synonym "Mass Spectrometry Shared Resource" ;
NIFRID:abbrev "MSSR" ;
definition: "Provides investigators with capabilities to identify, characterize, and quantify biomolecules present in tissues, cells, and biological fluids. Facility houses both Proteomics and Metabolomics Cores, and aims to assist members with solving difficult or previously intractable problems in biomedical research. Methods for biomolecule isolation, separation, quantification, identification and bioinformatics analysis, together with expert guidance in study design, are integrated into expertise offered by the Facility." .
SCR:021989 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1316" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Pathology Shared Resource Biorepository Core Facility" ;
NIFRID:synonym "Biobanking Services",
"Pathology Shared Resource - Biorepository" ;
NIFRID:abbrev "PSR-BR" ;
definition: "Biorepository Section provides services to support biobanking, clinical trials, and research studies. Provides access to patient specimens collected from clinical and research procedures that are handled, processed, analyzed, and interpreted in uniform manner. Services include, collection, processing, storage, clinicopathological annotation, and distribution of biospecimens." .
SCR:021990 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1314" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center PreClinical Human Immune System Mice Shared Resource Core Facility" ;
NIFRID:synonym "PreClinical Human Immune System Mice Shared Resource" ;
NIFRID:abbrev "PHISM" ;
definition: "Core provides Human Immune System as preclinical in vivo model to study human immune system in experimental tractable animal model e.g. immune response to human tumors that readily grow in HIS-mice. Offers immune expertise, experimental procedures and data analysis of immune based assays, such as flow cytometry." .
SCR:021991 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1317" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Pathology Shared Resource Cytogenetics Core Facility" ;
NIFRID:synonym "Cytogenetics",
"Pathology Shared Resource - Cytogenetics" ;
NIFRID:abbrev "PSR-CG" ;
definition: "Core, in collaboration with Colorado Genetics Lab, provides cytogenetic and cytogenomic research services. Services include tissue culture, chromosome analysis, fluorescence in situ hybridization (FISH), and chromosomal microarray. Offers design and development of customized FISH probes.Available for consultation on study design and data analysis." .
SCR:021992 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1315" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Population Health Shared Resource Core Facility" ;
NIFRID:synonym "Population Health Shared Resource" ;
NIFRID:abbrev "PHSR" ;
definition: "Core supports access to and expertise in data management, analyses, and mapping and data visualization of population based databases. These databases are ideal for studies requiring access to large samples of patients and/or providers; examination of trends in treatment, screening, or other healthcare services; impact of policy changes or recommendations on healthcare services; investigating dissemination of evidence based technologies and interventions; disparities of treatment or other health care services between groups; geographic distributions of cancer patients and relationships with other geospatial data." .
SCR:021993 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1313" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Organoid and Tissue Modeling Shared Resource Core Facility" ;
NIFRID:synonym "Organoid and Tissue Modeling Shared Resource" ;
NIFRID:abbrev "OTMSR" ;
definition: "Core facilitates access, generation, and usage of novel in vitro mouse and human organoid systems to promote innovative basic and translational research and disease modeling. Provides expertise in genome editing technologies for targeted knock outs, point mutations, and reporter generation in organoid systems. Provides many specialized medias and reagents to support most common organoid culture systems." .
SCR:021994 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1319" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Pathology Shared Resource Research Histology Core Facility" ;
NIFRID:synonym "Pathology Shared Resource - Research Histology" ;
NIFRID:abbrev "PSR-RH" ;
definition: "Research Histology Section provides range of standardized paraffin histology procedures that can be tailored to specific research needs.Services include tissue grossing/cassetting, paraffin processing, sectioning, routine and special stains. We specialize in immunohistochemistry and antibody optimization procedures." .
SCR:021995 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1318" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Pathology Shared Resource Molecular Pathology Core Facility" ;
NIFRID:synonym "Molecular Pathology",
"Pathology Shared Resource - Molecular Pathology" ;
NIFRID:abbrev "PSR-MP" ;
definition: "Molecular Pathology Section offers clinical grade sample processing and molecular testing for research cases.All services are performed in CLIA certified environment and all molecular assays are accompanied by full data analysis including bioinformatics analysis for NGS data." .
SCR:021996 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1320" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Small Animal Image Guided Radiation Therapy Core Facility" ;
NIFRID:synonym "Small Animal Image-Guided Radiation Therapy" ;
NIFRID:abbrev "SAI-GRT" ;
definition: "Core specializes in targeted irradiation of small animals for use in preclinical trials of radiation therapy. Through use of XRAD-SmART Irradiator, core can use x-ray fluoroscopy and on board CBCT to accurately irradiate small lesion areas while protecting normal tissue. Provides experiment design, data analysis, and dosimetry calculations, as well as longitudinal acquisition of CBCT for temporal assessment of tumor growth kinetics." .
SCR:021997 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1322" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Structural Biology Shared Resource NMR Core Facility" ;
NIFRID:synonym "NMR Structural Biology Shared Resource Facility",
"Structural Biology Shared Resource - NMR Facility" ;
NIFRID:abbrev "SBSR-NMR" ;
definition: "Core enables study of biomolecular structure, dynamics and interactions in solution at atomic level. Provides NMR spectrometers from 600 MHz to 900 MHz equipped for biomolecular NMR studies. Equipment include 900 MHz Bruker Avance Neo with Oxford 21 T magnet - TCI Cryoprobe 600 MHz Bruker Avance Neo with Bruker Sample Jet (2024) - TCI Cryoprobe 600 MHz Varian Inova with HCN cryoprobe." .
SCR:021998 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1323" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Structural Biology Shared Resource X Ray Crystallography Core Facility" ;
NIFRID:synonym "Structural Biology and Biophysics Core Facilities X-ray Crystallography Core",
"Structural Biology X-ray Crystallography Core",
"Stuctural Biology Shared Resource - Xray Crystallography",
"Xray Crystallography Core" ;
NIFRID:abbrev "SBSR_XRAY" ;
definition: "Core performs all aspects of structure determination of large biomolecules such as proteins and nucleic acids including macromolecular crystallization, crystal screening, molecular structure and model building." .
SCR:021999 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1321" ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Structural Biology Shared Resource CryoEM Core Facility" ;
NIFRID:synonym "Structural Biology Shared Resource - CryoEM Facility" ;
NIFRID:abbrev "SBSR-CRYOEM" ;
definition: "Provides equipment, expert technical assistance and image analysis expertise to enable all aspects of macromolecular structure determination by single particle cryo-electron microscopy." .
SCR:022000 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1298" ;
rdfs:label "Colorado State University Flow cytometry, cell sorting, and single cell analysis Core Facility" ;
NIFRID:synonym "and single-cell analysis core",
"cell sorting",
"Flow cytometry" ;
NIFRID:abbrev "FCF" ;
definition: "Provides access to flow cytometry and cell sorting instrumentation, services, and expertise for all researchers at Colorado State University. FCF includes spectral flow cytometers Cytek Aurora which enables users to perform more than 25 markers in a sample. FCF also has 10X Genomics chromium controller used to barcode single cells to perform single cell sequencing. Offers data analysis of these complex flow cytmetry and single cell sequencing samples using R programming or bash shell based pipelines." .
SCR:022001 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1299" ;
rdfs:label "Colorado State University Geospatial Centroid Core Facility" ;
NIFRID:synonym "Geospatial Centroid" ;
NIFRID:abbrev "The Centroid" ;
definition: "Core facility that provides technical guidance, project support, and diverse training opportunities in geospatial sciences. With expertise in geographic information systems, spatial analysis, web mapping, and cartography, Centroid supports researchers in spatial data development, analysis, visualization, and publication ready maps." .
SCR:022002 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1302" ;
rdfs:label "Colorado State University School of Advanced Materials Discovery Core Facility" ;
NIFRID:synonym "School of Advanced Materials Discovery Core" ;
NIFRID:abbrev "SAMDCore" ;
definition: "Core facility that enables research and development programs by providing expertise and access to equipment for synthesis, processing and testing of materials. Support and enables materials research and education by offering range of materials synthesis, processing, and testing equipment, combined with individualized training and staff expertise." .
SCR:022003 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1300" ;
rdfs:label "Colorado State University Drone Center Core Facility" ;
NIFRID:synonym "Colorado State University Drone Center" ;
NIFRID:abbrev "CSU Drone Center" ;
definition: "Offers consultation on drone systems, UAS project guidance, UAS piloting, assistance with UAS pilot training, liaison and navigation of FAA regulations, and as point of contact for UAS inquiries from outside the University. Assists in authorizing flight requests at CSU and managing Christman Airfield use for drone flights. Maintains fleet of sUAS aircraft and air borne sensors." .
SCR:022004 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1303" ;
rdfs:label "Colorado State University Institute for Research in the Social Sciences Core Facility" ;
NIFRID:synonym "Institute for Research in the Social Sciences" ;
NIFRID:abbrev "IRISS" ;
definition: "Core facility that provides social science research expertise and resources for design, collection, management, analysis, and dissemination of original social science data, including interviews, focus groups, surveys, photo voice, social network analysis, program evaluation, team assessments, and mixed method studies." .
SCR:022005 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1301" ;
rdfs:label "Colorado State University Graybill Statistics and Data Science Laboratory Core Facility" ;
NIFRID:synonym "Graybill Statistics & Data Science Laboratory" ;
NIFRID:abbrev "Stat Lab" ;
definition: "Core facility that provides statistical expertise for benefit of advancing quality of scientific research and education at CSU and beyond, while educating next generation of applied statisticians." .
SCR:022006 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zentracker" ;
NIFRID:synonym "Wormtracker / Zentracker" ;
definition: "Software tool as multiworm tracker. Can be used as analysis toolkit for extracting morphological and behavioural data from videos of objects moving in 2D environment." .
SCR:022007 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuronanalyser" ;
definition: "Software analysis toolkit for tracking blobs and extracting intensity values from imaging data, designed for use with ratiometric fluorescent sensors." .
SCR:022008 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cross filter" ;
NIFRID:synonym "cross_filter" ;
definition: "Software pipeline to analyse genome data from forward genetic screen. Identification of causal variants for specific phenotype." .
SCR:022009 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Connect TBI" ;
NIFRID:synonym "Connect-TBI",
"THE COLLABORATIVE NEUROPATHOLOGY NETWORK CHARACTERIZING OUTCOMES OF TBI" ;
definition: """Portal for traumatic brain injury data. Common Data Elements (CDEs) and Unique Data Elements (UDEs) for digital neuropathological data and clinical data that will be collected in all CONNECT-TBI center projects. Goal is to establish multi-center, digital neuropathological data and clinical data reporting network with case accrual from each center project.
Collected neuropathological data and clinical data available by sharing with center site investigators approved by Administrative Core and by submitting into FITBIR. Central TBI data repository by collecting digital neuropathological data and clinical data from TBI cases and normal controls at each center and posting library of their holdings.""" .
SCR:022010 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ntCard" ;
definition: "Software tool for estimating k-mer coverage histogram of genomics data. Streaming algorithm for estimating frequencies of k-mers in genomics datasets." .
SCR:022011 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rcorrector" ;
NIFRID:synonym "RNA-seq error CORRECTOR" ;
definition: "Software tool as kmer based error correction method for RNAseq data. Can also be applied to other types of sequencing data where read coverage is nonuniform, such as single cell sequencing. Used for error correction for Illumina RNAseq reads." .
SCR:022012 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CoLoRMap" ;
NIFRID:synonym "Correcting Long Reads by Mapping" ;
definition: "Software tool as hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology. Used for correcting long reads by mapping short reads." .
SCR:022013 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SALSA" ;
NIFRID:synonym "SALSA2" ;
definition: "Software tool for scaffold long read assemblies with Hi-C data." .
SCR:022014 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rascaf" ;
definition: "Software tool for scaffolding with RNA-seq read alignments. Used for improving genome assembly with RNA sequencing data." .
SCR:022015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "calN50" ;
definition: "Software tool as simple script to calculate N50/NG50 and auN/auNG." .
SCR:022016 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ipyrad" ;
definition: "Software interactive toolkit for assembly and analysis of restriction site associated genomic data sets including RAD, ddRAD, GBS, for population genetic and phylogenetic studies. Used for interactive assembly and analysis of RADseq data sets." .
SCR:022017 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gFACs" ;
definition: "Software package provides comprehensive framework for evaluating, filtering, and analyzing gene models from range of input applications and preparing these annotations for formal publication or downstream analysis." .
SCR:022018 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BayeScan" ;
definition: "Software tool to identify candidate loci under natural selection from genetic data, using differences in allele frequencies between populations." .
SCR:022019 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pcadapt" ;
definition: "Software R package for fast Principal Component Analysis for outlier detection.Used to detect genetic markers involved in biological adaptation. Performs genome scans for selection based on principal component analysis." .
SCR:022020 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LEA" ;
NIFRID:synonym "Landscape and Ecological Associations" ;
definition: "Software R package for landscape and ecological associations studies.Dedicated to genomewide association tests in general, with emphasis on association with ecological gradients. Runs analyses of population structure and scans for genomic signatures of local adaptation." .
SCR:022021 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hierfstat" ;
definition: "Software R package for estimation and tests of hierarchical F statistics.Used to estimate hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in hierarchy.Intended for analysis of population structure using genetic markers." .
SCR:022022 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StAMPP" ;
definition: "Software R package for statistical analysis of mixed ploidy populations.Used for calculation of population structure and differentiation based on single nucleotide polymorphism genotype data from populations of any ploidy level, and/or mixed ploidy levels." .
SCR:022023 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PretextMap" ;
NIFRID:synonym "Paired REad TEXTure Mapper",
"Wellcome Sanger Institute's High Performance Assembly Group's Paired REad TEXTure Mapper" ;
definition: "Software tool to convert SAM formatted read pairs into genome contact maps. Prepares alignments for visualization with PretextView." .
SCR:022024 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PretextView" ;
NIFRID:synonym "REad TEXTure Viewer",
"Wellcome Sanger Institute's High-Performance Assembly Group's Paired REad TEXTure Viewer" ;
definition: "Software tool to enable visualization from PretextMap output. Desktop application for viewing pretext contact maps. OpenGL Powered Pretext Contact Map Viewer." .
SCR:022025 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Madena" ;
NIFRID:synonym "Madena Software" ;
definition: "Software package as medical image viewer and image processing tool. Can open all QuickTime compatible image file formats as well as import most Digital Imaging and Communications in Medicine (DICOM) and ACR/NEMA file formats. DICOM is industry standard for medical images and is used for CT, MR and US images. Madena can open image files found within folder and all enclosed subfolders in single command. QuickTime images are grouped into subsets according to folder in which they were found." .
SCR:022026 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AMR meta" ;
NIFRID:synonym "AMR-meta" ;
definition: "Software tool as k-mer and metafeature approach to classify antimicrobial resistance from high throughput short read metagenomics data. Kmer- and matrix factorization based classifier for metagenomics data." .
SCR:022027 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PlaForNEA" ;
NIFRID:synonym "PLAFORNEA" ;
definition: "Software allows estimating growth and production at stand level of main forest species implanted in Argentine Mesopotamia such as Pino taeda, Eucalyptus grandis, Pino elliottii and Araucaria angustifolia. Areas for which models were adjusted correspond to province of Misiones, northeast of Corrientes and Concordia in province of Entre Ríos." .
SCR:022028 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SparkAn" ;
definition: "Software tool for custom calcium imaging analysis." .
SCR:022029 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Blue Brain Nexus" ;
NIFRID:synonym "Nexus" ;
definition: "Software system for knowledge graph management and data driven science. Ecosystem allows to organize and better leverage data through use of Knowledge Graph." .
SCR:022030 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vector Generalized Linear and Additive Models" ;
NIFRID:abbrev "VGAM" ;
definition: "Software R package implementating multiple major classes of statistical regression models." .
SCR:022031 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Shahid Sadoughi University of Medical Sciences; Yazd; Iran" ;
NIFRID:synonym "Shahid Sadoughi University of Medical Sciences" ;
definition: "Public university located in center of Iran in World Heritage city of Yazd." .
SCR:022032 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neocortical Microcircuit Portal" ;
NIFRID:synonym "Blue Brain Neocortical Microcircuit Portal",
"NMC portal" ;
definition: """Neocortical microcircuit collaboration portal is resource for rat somatosensory cortex.
NMC portal allows users to access experimental data used in reconstruction process, download cellular and synaptic models, and analyze predicted properties of microcircuit.""" .
SCR:022033 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Polycystic Kidney Disease Research Resource Consortium" ;
NIFRID:abbrev "PKD RRC" ;
definition: "Consortium develops and shares investigative resources, reagents and expertise with broader research community to accelerate innovation and discovery in field of polycystic kidney disease.Provides assistance with protocols and trouble shooting. Provides funding opportunities." .
SCR:022034 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellScale | MicroTester G2 system" ;
NIFRID:synonym "SquisherJoy" ;
definition: "System includes MicroTester G2 device and software. MicroTester G2 is mechanical test device that can be used to test properties of variety of tissues and materials. Main components of device are load application microbeam, actuators, imaging system, and fluid bath/test chamber. MicroTester G2 software is divided into two modules: data collection module and review and analysis module." .
SCR:022035 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Colorado Anschutz Medical Campus Cancer Center Flow Cytometry Shared Resource Core Facility" ;
NIFRID:synonym "Flow Cytometry Shared Resource at the CU Cancer Center" ;
NIFRID:abbrev "FCSR" ;
definition: "Provides cytometry based services including cell sorting, flow cytometry and mass cytometry. Provides training, education, and experimental design assistance." .
SCR:022036 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TrainingSpace" ;
definition: "Portal that provides multimedia educational content from courses, conference lectures, and laboratory exercises from some of leading neuroscience institutes and societies to be more accessible to global neuroscience community." .
SCR:022037 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "MBF Bioscience\"s Neuromorphological file format",
"Neuromorphological File Format v 4.0" .
SCR:022038 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MDAR" ;
NIFRID:synonym "Materials Design Analysis Reporting" ;
definition: "MDAR Framework establishes minimum set of requirements in transparent reporting applicable to studies in life sciences. MDAR checklist is tool for authors, editors and others seeking to adopt MDAR framework for transparent reporting in manuscripts and other outputs and designed to provide harmonizing principle for reporting requirements currently in use at various journals." .
SCR:022039 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1324" ;
rdfs:label "University of California at San Diego Electron Microscopy Core Facility" ;
NIFRID:synonym "UCSD-CMM-Electron Microscopy Core" ;
NIFRID:abbrev "UCSD-CMM" ;
definition: "UCSD Cellular and Molecular Medicine Electron Microscopy core provides services in sample preparation and imaging by Transmission Electron Microscopy and Correlative Light and Electron Microscopy." .
SCR:022040 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SmartPLS" ;
definition: "Software with graphical user interface for variance based structural equation modeling using partial least squares path modeling method. Users can estimate models with their data by using basic PLS-SEM, weighted PLS-SEM, consistent PLS-SEM, and sumscores regression algorithms." .
SCR:022042 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sepsis3-amsterdamumcdb" ;
NIFRID:synonym "Sepsis-3 in AmsterdamUMCdb" ;
definition: "Repository contains files for implementing the Sepsis-3 definition in the freely-accessible Amsterdam University Medical Centers Database." .
SCR:022043 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Micro Meta App" ;
definition: "Software app for microscope metadata." .
SCR:022044 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dMod" ;
definition: "Software package for dynamic modeling and parameter estimation in R.Provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc." .
SCR:022045 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Heidelberg Eye Explorer" ;
NIFRID:synonym "HEYEX",
"HEYEX 2" ;
definition: "Platform that centralizes management of ophthalmic images. HEYEX interfaces with electronic medical record systems and third-party devices to allow exchange, storage, and dynamic review of diagnostic images. Heidelberg Engineering imaging products use Heidelberg Eye Explorer software platform and database to store patient information and images." .
SCR:022046 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Roland | RETI-port/scan 21" ;
definition: "System includes stimulator units and data recording and analyzing software. Electrophysiological Test Unit is usable for Pattern VEP + Pattern ERG + Flash VEP, for scotopic and photopic ERG, EOG fast and slow, mf ERG Flash stimulation and mf VEP Pattern stimulation." .
SCR:022047 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1325" ;
rdfs:label "Colorado School of Mines Shared Instrumentation Facility Surface Characterization and Thin Film Deposition Core Facility" ;
NIFRID:synonym "Colorado School of Mines Shared Instrumentation Facility Cleanroom and Thin Film Processing",
"Surface Characterization and Thin Film Processing" ;
definition: "Facility houses cleanrooms with processing equipment for making and characterizing electronic devices, thin film deposition tools for creation of metallic and ceramic thin film devices, and characterization lab with tools for surface, morphological, and optical characterization of materials." .
SCR:022048 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colorado School of Mines Shared Instrumentation Facility Electron and Scanning Probe Microscopy Core Facility" ;
NIFRID:synonym "Colorado School of Mines Shared Instrumentation Facility Electron and Scanning Probe Microscopy",
"Electron & Scanning Probe Microscopy" ;
definition: "Facility provides SEM, FIB, TEM, scanning probe, and optical techniques for analyzing materials." .
SCR:022049 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colorado School of Mines Shared Instrumentation Facility Time of Flight Secondary Ion Mass Spectrometry Core Facility" ;
NIFRID:synonym "Colorado School of Mines Shared Instrumentation Facility Time of Flight Secondary Ion Mass Spectrometry",
"Time of Flight - Secondary Ion Mass Spectrometry" ;
definition: "Core used to obtain elemental, isotopic, and molecular information from surface of solid materials and compacted powders." .
SCR:022050 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colorado School of Mines Shared Instrumentation Facility Rocky Mountain Environmental X-Ray Photoelectron Spectroscopy Core Facility" ;
NIFRID:synonym "Colorado School of Mines Shared Instrumentation Facility Rocky Mountain Environmental X-Ray Photoelectron Spectroscopy",
"Rocky Mountain Environmental X-Ray Photoelectron Spectroscopy" ;
definition: "Core to measure material surface compositions by measuring intensity of photoelectrons emitted as function of incident X-ray energy. Spectra features are used to identify surface species present and calculate fraction of surface occupied by each.Rocky Mountain E-XPS extends these traditional capabilities by enabling measurements in range of environmental conditions." .
SCR:022051 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colorado School of Mines Shared Instrumentation Facility Mechanical Testing Core Facility" ;
NIFRID:synonym "Colorado School of Mines Shared Instrumentation Facility Mechanical Testing",
"Mechanical Testing" ;
definition: "Provides variety of monotonic, fatigue, temperature, and strain measurement capabilities. These capabilities cover wide range of load capacities and resolutions, displacement rates, loading configurations, and custom fixturing." .
SCR:022052 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colorado School of Mines Shared Instrumentation Facility Liquid Chromotography Mass Spectrometry Core Facility" ;
NIFRID:synonym "Colorado School of Mines Shared Instrumentation Facility Liquid Chromotography Mass Spectrometry",
"Liquid Chromotography - Mass Spectrometry" ;
definition: "Liquid Chromatography Mass Spectrometry is analytical technique for determining ion mass-to-charge ratio by partitioning particles within liquid and measuring time it takes for each particle to travel through selected mobile phase. Ultimately this helps in determining contents of liquid sample and can be used to analyze biochemical, organic and inorganic compounds." .
SCR:022053 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colorado School of Mines Shared Instrumentation Facility X-ray Diffraction and Computed Tomography Core Facility" ;
NIFRID:synonym "Colorado School of Mines Shared Instrumentation Facility X-ray Diffraction and Computed Tomography",
"X-ray Diffraction and Computed Tomography" ;
definition: "Facility encompasses X-ray diffraction, providing crystallographic, structural, and compositional information, and X-ray tomography, enabling nondestructive tomographic imaging and grain reconstruction used to distinguish between phases, identify defects, and provide 3D crystallographic grain reconstructions." .
SCR:022054 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Colorado School of Mines; Golden; Colorado" ;
definition: "Public research university in Golden, Colorado, founded in 1874. School offers both undergraduate and graduate degrees in engineering, science, and mathematics, with focus on energy and environment." .
SCR:022055 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Narishige | MF 830 Microgrinder" ;
NIFRID:synonym "Narishige MF-830 Microgrinder" ;
definition: "Powerful microscope mounted to produce microelectrodes for patch clamping." .
SCR:022056 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeitz | DMZ Universal Electrode Puller" ;
NIFRID:synonym "DMZ Zeitz Puller" ;
definition: "Horizontal pipette puller to pull and polish microelectrodes from borosilicate capillaries." .
SCR:022057 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Narishige | PC 10 Puller" ;
NIFRID:synonym "Narishige PC-10 Puller" ;
definition: "Vertical pipette puller to create microelectrodes from borosilicate capillaries." .
SCR:022058 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MeDuSa" ;
NIFRID:synonym "Multi-Draft based Scaffolder" ;
definition: "Web server of multi draft based scaffolder.Exploits information obtained from set of genomes from related organisms to determine correct order and orientation of contigs." .
SCR:022059 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JSpeciesWS" ;
NIFRID:synonym "JSpecies Web Server" ;
definition: "Web server for prokaryotic species circumscription based on pairwise genome comparison. Service for in silico calculating extent of identity between two genomes, parameter routinely used in process of polyphasic microbial species circumscription. Service measures average nucleotide identity." .
SCR:022060 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "antiSMASH" ;
NIFRID:synonym "antiSMASH 6.0" ;
definition: "Web tool for detecting and characterising biosynthetic gene clusters in bacteria and fungi. AntiSMASH 6 increases number of supported cluster types from 58 to 71, displays modular structure of multi modular BGCs, adds new BGC comparison algorithm, allows for integration of results from other prediction tools, and detects tailoring enzymes in RiPP clusters." .
SCR:022061 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fastai" ;
definition: "Software python package simplifies training fast and accurate neural nets using modern best practices." .
SCR:022063 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EDTA" ;
NIFRID:synonym "Extensive de novo TE Annotator" ;
definition: "Software package to filter out false discoveries in raw TE candidates and generate high quality non redundant TE library for whole genome TE annotations.Produces filtered non redundant TE library for annotation of structurally intact and fragmented elements." .
SCR:022064 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TERL" ;
NIFRID:synonym "Transposable Elements Pepresentation Learner" ;
definition: """Software tool for classification of transposable elements by convolutional neural networks.
Preprocesses and transforms one dimensional sequences into two dimensional space data, image like data of sequences, and apply it to deep convolutional neural networks.""" .
SCR:022065 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tandem Repeats Finder" ;
definition: "Software tool to locate and display tandem repeats in DNA sequences. Used to analyze DNA sequences." .
SCR:022066 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RAxML Next Generation" ;
NIFRID:synonym "Randomized Axelerated Maximum Likelihood Next Generation" ;
NIFRID:abbrev "RAxML-NG" ;
definition: "Software phylogenetic tree inference tool which uses maximum likelihood optimality criterion. Used for maximum likelihood phylogenetic inference. Offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML." .
SCR:022067 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCScanX" ;
NIFRID:synonym "Multiple Collinearity Scan toolkit X version" ;
definition: "Software toolkit for detection and evolutionary analysis of gene synteny and collinearity." .
SCR:022068 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KaKs Calculator" ;
NIFRID:synonym "KaKs_Calculator",
"KaKs_Calculator2.0" ;
definition: """Software toolkit incorporating gamma series methods and sliding window strategies.
Used for calculating nonsynonymous (Ka) and synonymous (Ks) substitution rates for evaluating sequence variations for protein orthologs across different species or taxonomical lineages with unknown evolutionary status.""" .
SCR:022079 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WikiProject Zika Corpus" ;
definition: "Web portal related to Zika virus, including metadata collection for academic publications on the topic, structured data ontology of terms, and integrated resources in the Wikidata platform." .
SCR:022080 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Mitochondria Related Diseases" ;
NIFRID:synonym "Mitochondria Related Diseases" ;
definition: "Creative Biogene provides comprehensive range of services and products to assist researchers in mitochondrial assays and studies. Service to validate and explore pathogenesis of mitochondria associated diseases and possible interventions." .
SCR:022081 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Mitochondria Associated Syndromes" ;
definition: "Creative Biogene works with you to validate and explore pathogenesis of mitochondria associated syndromes and possible interventions, with professional services and products to support your research. Provides rapid mitochondrial function testing services, allowing clients to accurately analyze relationship between disease and mitochondria." .
SCR:022082 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Mitochondrial Gene Mutations" ;
definition: "Creative Biogene provides comprehensive range of services and products to assist researchers in cancer related mitochondria studies. Offers tests and services with advantage of cell based and animal based models." .
SCR:022083 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Mitochondria and Cardiac Diseases" ;
definition: "Creative Biogene provides range of services and products to assist researchers in cardiac disease related mitochondria studies. Offers comprehensive testing services for evaluation of variety of cardiac diseases. Mitochondria focused testings and services with advantage of animal based models." .
SCR:022084 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1332" ;
rdfs:label "University of Pittsburgh Microscopy and Imaging Suite Core Facility" ;
NIFRID:synonym "Microscopy and Imaging Suite",
"University of Pittsburgh Microscopy and Imaging Suite" ;
definition: "Facility equipped with instruments for optical and electron microscopy, and Flow Cytometry.Offers experimental design, equipment training, staff operated image acquisition, and image analysis. All users must be trained by Facility staff to access the equipment." .
SCR:022090 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CEU Mass Mediator" ;
NIFRID:synonym "CEU Mass Mediator 2.0",
"CEU Mass Mediator version 3.0",
"CMM 2.0",
"CMM 3.0" ;
NIFRID:abbrev "CMM" ;
definition: """Software tool for searching metabolites in different databases including Kegg, HMDB, LipidMaps, Metlin, NP Atlas, KNApSAcK, MINE and in house library. Designed for searches through experimental masses obtained from mass spectrometry techniques.
Metabolite annotation tool that uses expert system to score putative annotation based on analytical information acquired under different configurations.""" .
SCR:022091 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scRNAx" ;
definition: "Software pipeline to improve gene annotation for cross species analysis of single cell RNA-Seq. Cross-species transfer of high quality 3’UTR annotation for single cell RNA-Seq." .
SCR:022092 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CancerMIRNome" ;
definition: "Web server for cancer miRNome interactive analysis and visualization based on human miRNome data of cancer types from The Cancer Genome Atlas, and public cancer circulating miRNome profiling datasets from NCBI Gene Expression Omnibus and ArrayExpress. Comprehensive database for interactive analysis and visualization of miRNA expression profiles." .
SCR:022093 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Therapeutic Structural Antibody Database" ;
NIFRID:abbrev "Thera-SAbDab" ;
definition: "Tracks all antibody and nanobody related therapeutics recognized by World Health Organisation, and identifies any corresponding structures in Structural Antibody Database with near exact or exact variable domain sequence matches. Synchronized with SAbDab to update weekly, reflecting new Protein Data Bank entries and availability of new sequence data published by WHO." .
SCR:022094 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Antibody Prediction Toolbox" ;
NIFRID:synonym "The Antibody Prediction Toolbox" ;
NIFRID:abbrev "SAbPred" ;
definition: "Web tool as structure based antibody prediction server. Collection of computational tools that make predictions about properties of antibodies, focusing on their structures. Single platform containing multiple applications which can: number and align sequences; automatically generate antibody variable fragment homology models; annotate such models with estimated accuracy alongside sequence and structural properties including potential developability issues; predict paratope residues; and predict epitope patches on protein antigens." .
SCR:022095 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AHo’s Amazing Atlas of Antibody Anatomy" ;
NIFRID:abbrev "AAAAA" ;
definition: "AAAAA aims to become the ultimate tool for antibody structural analysis, modelling and engineering." .
SCR:022096 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Structural Antibody Database " ;
NIFRID:abbrev "SAbDab" ;
definition: "Database containing all antibody structures available in the PDB, annotated and presented in consistent fashion.Each structure is annotated with number of properties including experimental details, antibody nomenclature (e.g. heavy-light pairings), curated affinity data and sequence annotations. You can use the database to inspect individual structures, create and download datasets for analysis, search the database for structures with similar sequences to your query, monitor the known structural repetoire of antibodies." .
SCR:022097 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Strain Anaerobic Culture Service Resource" ;
definition: "Service for anaerobic bacteria cultivation and culture using variety of culture media and culture conditions. Includes collection, strain cultivation, isolation, identification and strain preservation." .
SCR:022098 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Isolation and Cultivation of Specific Bacteria Service Resource" ;
NIFRID:synonym "Isolation & Cultivation of Specific Bacteria" ;
definition: "Provides service for isolation and cultivation of specific bacteria connected with sequencing technology. Services include high throughput sequencing, determination of culture conditions, isolation, cultivation, purification and identification of target strain." .
SCR:022099 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Aerobic Cultivation Service Resource" ;
definition: "Aerobic cultivation services to culture various microorganisms that can be isolated from readily available sources." .
SCR:022100 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Facultative Anaerobes Cultivation Service Resource" ;
definition: "Service to culture various microorganisms that can be isolated from readily available sources. Assists with investigation of anaerobic processes such as glycolysis and lactic acid fermentation." .
SCR:022101 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Microbial Strains Preservation Service Resource" ;
NIFRID:synonym "Microbial Strains Preservation" ;
definition: "Provides service to culture and preserve various microorganisms that can be isolated from readily available sources. Microbiologists develop and optimize preservation methods to ensure long term viability of different microorganisms." .
SCR:022102 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Creative Biogene" ;
definition: "Service company that specializes in microbiological research related issues including sample collection, preservation methods, preliminary experiments and effect evaluation, experiments and data analysis. Simultaneously carries out Illumina MiSeq, Ion PGM, Roche 454 high-throughput sequencing analysis, PacBio third-generation high-throughput sequencing analysis, PCR-DGGE denature-gradient gel analysis, real-time quantitative PCR (Real-time qPCR), cloning library and other microbial analysis methods, to solve your problem from many aspects. Cooperates with many institutions and markets its products and services in various countries." .
SCR:022103 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1334" ;
rdfs:label "Howard Hughes Medical Institute at Janelia Research Campus Light Microscopy Core Facility" ;
NIFRID:synonym "Howard Hughes Medical Institute at Janelia Research Campus Light Microscopy",
"Light Microscopy" ;
definition: "Facility is open to Janelia scientists. Houses microscopes and multiple workstations dedicated to image processing." .
SCR:022104 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Photometry analyser" ;
definition: "Software tool for fibre photometry recordings analysis developed by Metofico LTD." .
SCR:022105 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Antibody Protein Bacteria Interactions Service Resource" ;
NIFRID:synonym "Antibody (Protein)-Bacteria Interactions",
"Creative Peptides Antibody (Protein)-Bacteria Interactions" ;
definition: "Provides Creative Peptides customers with experts and advanced surface plasmon resonance instruments. Provides high precision antibody bacterial interaction analysis services. Helps with projects, including methods development, validation, analysis of delivered samples and transfer to the client upon request. Provides ready to publish or ready to file data in any format required." .
SCR:022106 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Backbone Cyclized Peptides Service Resource" ;
NIFRID:synonym "Backbone-Cyclized Peptides" ;
definition: "Service for chemical synthesis and biosynthesis. Scientists will tailor the most appropriate methods. Every step of peptide synthesis is subject to quality control. Typical delivery specifications include HPLC chromatogram, Mass spec analysis, Synthesis report, Certificate of Analyses." .
SCR:022107 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Cell Penetrating Peptide Design and Synthesis Service Resource" ;
NIFRID:synonym "Cell Penetrating Peptide Design and Synthesis Services" ;
definition: "Provides GMP grade cell penetrating peptide synthesis services such as HIV-TAT and Oligo-Arg, etc. Can also design new cell penetrating peptides with unsuitable or non-natural amino acids, peptide branches, and other modifications according to customer needs. Offers comprehensive series of cell penetrating peptides complying with specific purities, scales, and modifications for pharmaceutical and biochemical applications." .
SCR:022108 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Cosmetic Peptides Service Resource" ;
definition: "Service to synthesize cosmetic peptides. Provides any level of cosmetic peptides, including GMP grades, using advanced peptide synthesis equipment. Used for development and production of cosmetic peptides." .
SCR:022109 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Design Platform Service Resource" ;
NIFRID:synonym "Creative Peptides Design Platform" ;
NIFRID:abbrev "CPDP" .
SCR:022110 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EndHiC" ;
definition: "Software Hi-C scaffolding tool, using Hi-C links from contig end regions instead of whole contig regions to assemble large contigs into chromosomal level scaffolds." .
SCR:022111 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HiCExplorer" ;
definition: "Software tool to analyse Hi-C and capture Hi-C data. Command line suite of tools to process, normalize and visualize Hi-C data." .
SCR:022112 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Creative Peptides" ;
definition: "Creative peptides is specialized in process development and manufacturing of bioactive peptides.Offers custom peptide synthesis, process development, manufacturing as well as catalog products for customers in industry and research area. Creative Peptides is staffed by scientific teams with experts in the fields of peptide technology, antibodies and synthetic chemistry." .
SCR:022113 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Near Infrared Camera" ;
NIFRID:abbrev "NIRCam" ;
definition: """Instrument aboard the James Webb Space Telescope. It has two major tasks, as imager from 0.6 to 5 micron wavelength, and as wavefront sensor to keep 18-section mirrors functioning as one.
Imager covers infrared wavelength range 0.6 to 5 microns. NIRCam detects light from the earliest stars and galaxies in process of formation, population of stars in nearby galaxies, as well as young stars in Milky Way and Kuiper Belt objects. NIRCam is equipped with coronagraphs, instruments that allow astronomers to take pictures of very faint objects around central bright object, like stellar systems.""" .
SCR:022114 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "qudi-HiM" ;
definition: "Software package for control of optical microscope setups with different hardware components optimized to perform multiplexed imaging experiments. Modular laboratory experiment management suite." .
SCR:022115 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Least Bridges Graphs Mathematica package" ;
definition: "Software tool as freely distributed computational method for analyzing distance relationships." .
SCR:022117 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pisces " ;
definition: "Software tool as somatic and germline variant caller for amplicon data. Calls low frequency variants, on linux or windows.Runs on tumor only samples, and search for SNVs, MNVs, and small indels. It takes in .bams and generates .vcf or .gvcf files. It is included with Illumina MiSeqReporter pipeline and various BaseSpace workflows. Can also be run as standalone program." .
SCR:022118 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_022220" ;
rdfs:label "Creative Peptides Peptide Drug Discovery Service Resource" ;
NIFRID:synonym "Creative Peptides Peptide Drug Discovery",
"Peptide Drug Discovery" ;
definition: """Services include Structure Based Drug Discovery to design and optimize hits compounds using structural information obtained from X-ray crystallography, cryo-EM or NMR; Cell Based Drug Discovery
by selecting correct cell models and culture to study pharmacological and biochemical properties; Ligand Based Drug Discovery.""" .
SCR:022119 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Target Validation in Peptide Drug Discovery Service Resource" ;
NIFRID:synonym "Creative Peptides Target Validation in Peptide Drug Discovery",
"Target Validation in Peptide Drug Discovery" ;
definition: """Services include Target analysis in silico, Protein sequence analysis and Homology modeling for targets;
Target analysis in bioscience, Cell based models.""" .
SCR:022120 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Target Analysis In Silico Service Resource" ;
NIFRID:synonym "Creative Peptides Target Analysis In Silico",
"Target Analysis In Silico" ;
definition: """Services include Binding site identification and druggability assessment, Protein sequence analysis,
Protein multiple sequences alignments and selectivity analysis,Analysis of available structural data and protein structure,Homology modeling for targets lacking crystal structures,Design appropriate peptides against specific targets,Water assessment.""" .
SCR:022121 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Target Analysis in Bioscience Service Resource" ;
NIFRID:synonym "Creative Peptides Target Analysis in Bioscience",
"Target Analysis in Bioscience" ;
definition: """Services include Value adding in vitro assays to measure biological activity of target, Characterize pharmacology and assess effects of modulating function, Synthesis of your peptide drug with reactive groups,Design experiments based on your objectives,Custom assay development,Protein expression,
Cellular assays, Build cell based models,Peptide binding assays.""" .
SCR:022122 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Hit Identification in Peptide Drug Discovery Service Resource" ;
NIFRID:synonym "Creative Peptides Hit Identification in Peptide Drug Discovery",
"Hit Identification in Peptide Drug Discovery" ;
definition: "Provides Medium or high-throughput screening to perform rapid screening thousands of samples with biological activities at model organism, cell, pathway, or molecular levels, accelerating target analysis procedure; High content screening to analyze the way peptide compound interacts with target at subcellular level; Fragment screening to obtain higher affinity lead ligands by growing low molecular weight chemical fragments into larger drug like molecules;Virtual screening to automatically evaluate large databases with known 3D structures; Artificial Intelligence for difficult targets to support discovering and developing more drug candidates; Knowledge based design in hit identification;Hits identified by NMR screening." .
SCR:022123 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "BOC Sciences PROTAC Target Protein Services",
"BOC Sciences Target Protein Services",
"Target Protein Services" ;
definition: "Service provider in drug discovery and research. Provides one stop proteolysis targeting molecular drug discovery based on chimeric. Provides target protein services to customers to meet new drug discovery goals." .
SCR:022124 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BOC Sciences Ligand Design for Target Protein Service Resource" ;
NIFRID:synonym "BOC Sciences Ligand Design for Target Protein",
"BOC Sciences PROTAC Ligand Design for Target Protein" ;
definition: "Service provider in drug discovery and development. Provides one stop development, which has become strategy in field of small molecular drug discovery. Provides ligand design for target protein to customers to meet new drug discovery goals." .
SCR:022125 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BOC Sciences Peptide ligand for target protein Service Resource" ;
definition: "Service provider in drug discovery and development. Provides one stop PROTA development, which has become strategy in field of small molecular drug discovery. Provides peptide ligand design for target protein to customers to meet new drug discovery goals." .
SCR:022126 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BOC Sciences Small molecule target protein ligand Service Resource" ;
NIFRID:synonym "BOC Sciences PROTAC Small molecule target protein ligand",
"BOC Sciences Small molecule target protein ligand",
"Small molecule target protein ligand" ;
definition: "Provides small molecule target protein ligand service to customers to meet new drug discovery goals." .
SCR:022127 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BOC Sciences Protein Ubiquitination Service Resource" ;
NIFRID:synonym "BOC Sciences PROTAC Protein Ubiquitination Service",
"BOC Sciences Protein Ubiquitination Services",
"Protein Ubiquitination Services" ;
definition: "Service in field of drug discovery and research. BOC Sciences service in one stop Proteolysis Targeting Chimeric based molecular drug discovery which has become strategy in area of drug discovery." .
SCR:022128 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1123" ;
rdfs:label "Texas A and M University Microscopy and Imaging Center Core Facility" ;
NIFRID:synonym "TAMU-Microscopy and Imaging Center",
"Texas A&M University TAMU-Microscopy and Imaging Center" ;
NIFRID:abbrev "MIC" ;
definition: "Core with expertise in Transmission Electron Microscopy, Scanning Electron Microscopy, Light Microscopy, and supporting instruments. Staff members provide quality training and education through sessions, short courses, formal courses, open house seminars, and more." .
SCR:022129 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ;
rdfs:label "Ruby on Rails" ;
NIFRID:abbrev "RoR" ;
definition: "Open source web application development framework. Model View Controller framework, providing default structures for database, web service, and web pages." .
SCR:022130 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides PNA Synthesis Service Resource" ;
NIFRID:synonym "Creative Peptides PNA Synthesis",
"PNA Synthesis" ;
definition: "Provides various types of PNA conjugates and tailor made PNA products." .
SCR:022131 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides PNA Oligomer Synthesis Service Resource" ;
NIFRID:synonym "Creative Peptides PNA Oligomer Synthesis",
"PNA Oligomer Synthesis" ;
definition: "Provides two chemical synthesis methods to synthesize Peptide Nucleic Acid oligomers, including Boc chemistry and Fmoc chemistry." .
SCR:022132 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Chemical Synthesis of PNA Oligomers with Fmoc Service Resource" ;
NIFRID:synonym "Chemical Synthesis of PNA Oligomers with Fmoc",
"Creative Peptides Chemical Synthesis of PNA Oligomers with Fmoc" ;
definition: "Provides Fmoc based PNA synthesis. Route consists of repeated cycles of deprotection, activation, coupling and capping.Synthesis of small scale PNA oligomers, which can be performed on common DNA synthesis platforms." .
SCR:022133 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Synthesis by Mmt Chemistry Service Resource" ;
NIFRID:synonym "Creative Peptides Synthesis by Mmt Chemistry",
"Synthesis by Mmt Chemistry" ;
definition: "Provides service with chemical method to synthesized any new PNA/DNA chimera where only Mmt/acetyl protected monomers can not damage the DNA part, and can synthesize any desired sequence." .
SCR:022134 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides PNA/DNA Chimera Synthesis Service Resource" ;
NIFRID:synonym "Creative Peptides PNA/DNA Chimera Synthesis",
"PNA/DNA Chimera Synthesis" ;
definition: "Provides multiple types of PNA/DNA chimera related services. Uses HPLC analysis and mass spectrometry to ensure purity and confirm identity." .
SCR:022135 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ansys Fluent" ;
NIFRID:synonym "ANSYS-FLUENT" ;
definition: "Software for advanced physics modeling capabilities and accuracy. Used to create advanced physics models and analyze variety of fluids phenomena. Fluent is software edited by Ansys in order to make computational fluid dynamics calculations." .
SCR:022136 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DHARMa" ;
NIFRID:synonym "Diagnostics for HierArchical Regession Models" ;
definition: "Software R package to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Package also provides number of plot and test functions for typical model misspecification problems." .
SCR:022137 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Companion to Applied Regression" ;
NIFRID:abbrev "car" ;
definition: "Software R package as functions to accompany J. Fox and S. Weisberg R companion to applied regression." .
SCR:022138 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LeTRS" ;
NIFRID:synonym "leader TRS" ;
definition: "Software Perl tool for identification of leader TRS junctions and plotting graphs of results. Accepts fastq files derived from Illumina paired-end and Nanopore cDNA/direct RNA sequencing, and bam files produced by splicing alignment method with SARS-CoV-2 genome." .
SCR:022139 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stitchr" ;
definition: "Software Python tool for stitching coding T cell receptors nucleotide sequences from V,J,CDR3 information. Produces complete coding sequences representing fully spliced TCR cDNA given minimal V,J,CDR3 information." .
SCR:022140 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "App for searching human and mimivirus homologous proteins" ;
definition: "Web interactive and searchable genome wide comparison tool for browsing human and mimivirus homologous proteins. User friendly Shinny app helps users browse protein sequence homology between humans and mimivirus at genome wide level for querying new homologs and generating new hypotheses." .
SCR:022141 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Anatomy Project" ;
NIFRID:synonym "The Open Anatomy Project" ;
definition: "Project aims to change anatomy atlas by building atlases through open data, community based collaborative development, and free distribution of medical knowledge. Provides access to several 2D and 3D browser based tools." .
SCR:022143 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1337" ;
rdfs:label "University of Southern California CHLA Extracellular Vesicle Core Facility" ;
NIFRID:synonym "CHLA Extracellular Vesicle Core",
"Saban Research Institute at Children\"s Hospital Los Angeles Extracellular Vesicle Core",
"University of Southern California CHLA Extracellular Vesicle Core" ;
definition: "Core provides isolation, characterization, and analysis of extracellular vesicles and other nano sized particles." .
SCR:022144 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Exicycler_96_v4" ;
rdfs:label "Bioneer | Exicycler 96" ;
NIFRID:synonym "Bioneer Exicycler 96 RealTime Quantitative Thermal Block",
"Bioneer Exicycler 96 TM Version 4",
"Exicycler™ 96 (Ver.4)" ;
definition: "Real Time quantitative thermal block. 96-well PCR system designed for real time qPCR application." .
SCR:022145 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RatGTEx Portal" ;
definition: "Portal to download and visualize rat gene expression and associations between genotypes and molecular phenotypes, uniformly processed across tissues." .
SCR:022146 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sctransform" ;
definition: "Software R package for normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression." .
SCR:022147 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_16" ;
rdfs:label "University of Vermont Larner College of Medicine Flow Cytometry and Cell Sorting Core Facility" ;
NIFRID:synonym "Flow Cytometry and Cell Sorting Facility",
"Harry Hood Bassett FCCS Facility",
"University of Vermont Larner College of Medicine Flow Cytometry and Cell Sorting Facility" ;
NIFRID:abbrev "FCCS" ;
definition: "Harry Hood Bassett FCCS Facility is located in Given Medical Research Building Room C316-UVM. Facility provides flow cytometers and personnel provide scientific and technical consultation to faculty and staff in design of flow cytometric experiments, and assistance in data analysis and interpretation." .
SCR:022148 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pipsqueak Pro" ;
definition: "Image analysis software. Used for custom cell detection and colocalization analysis. Pipsqueak Pro takes moves Pipsqueak out of ImageJ/FIJI and into integrated interface." .
SCR:022149 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pipsqueak AI" ;
definition: "Software image analysis tool as older ImageJ/Fiji plugin version." .
SCR:022150 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Castor Electronic Data Capture System" ;
NIFRID:abbrev "Castor EDC" ;
definition: "Cloud based Electronic Data Capture system or clinical data management platform used to store quantitative data." .
SCR:022151 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Inquisit LAB" ;
NIFRID:synonym "Inquisit 5 LAB",
"Inquisit 6 LAB" ;
definition: "Software tool for designing and administering psychological tests and experiments on computers." .
SCR:022152 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fujifilm | Vevo 3100 Imaging System" ;
NIFRID:synonym "Vevo 3100 micro ultrasound imaging system" ;
NIFRID:abbrev "Vevo 3100" ;
definition: "Vevo 3100 micro ultrasound imaging system reduces speckle noise and artifacts while preserving and enhancing critical information for small animal in vivo studies. System helps you visualize your data at high resolution." .
SCR:022153 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Brand:NexION" ;
rdfs:label "Perkin Elmer | NexION 2000B ICP Mass Spectrometer" ;
NIFRID:synonym "NexION 2000 ICP-MS",
"NexION 2000B ICP Mass Spectrometer",
"Perkin-Elmer NexION 2000 ICP-MS" ;
NIFRID:abbrev "ICP-MS" ;
definition: "Allows to adjust signal transmission to measure elements with low and high concentrations in the same sample in the same run. This extends dynamic range up to 12 orders of magnitude and optimizes productivity while preserving lifetime of detector." .
SCR:022154 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nutritics" ;
definition: "Software for recipe and menu management, food labels, diet and activity analysis, meal planning. Nutrition management software for healthcare, elite sport, food industry and education." .
SCR:022155 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Health For All Children " ;
NIFRID:synonym "Harlow Healthcare Health For All Children" ;
definition: "Portal for joint working party on child health surveillance." .
SCR:022156 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mRnd" ;
definition: "Web tool for calculations for Mendelian Randomization. Power calculations for Mendelian Randomization. Used to calculate statistical power for Mendelian Randomization study, using Non Centrality Parameter based approach." .
SCR:022157 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colorado State University Laboratory Animal Resources Core Facility" ;
NIFRID:synonym "Colorado State University Laboratory Animal Resources" ;
NIFRID:abbrev "LAR" ;
definition: "LAR provides care for laboratory animals in support of Colorado State University research community. Oversees care and management of animals in animal holding space facility for small and large animals including animal biosafety level 3." .
SCR:022158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "granulator" ;
definition: "Software R package for cell type deconvolution of heterogeneous tissues based on bulk RNAseq data or single cell RNAseq expression profiles.Provides unified testing interface to rapidly run and benchmark multiple deconvolution methods." .
SCR:022159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EL MAVEN" ;
NIFRID:synonym "EL-MAVEN" ;
definition: "Open source LC-MS data processing engine for simplifying metabolomics analysis. Mass spectrometry data processing engine that is optimal for isotopomer labeling and global metabolomic profiling experiments. Interactive software platform that accelerates analysis of LC-MS, GC-MS, and LC-MS/MS datasets." .
SCR:022160 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KM Cyberary" ;
definition: "Portal designed for Library and KM Professionals to locate internet resources related to their profession. Not for profit service to knowledge resources. Platform with links to e-resources on Knowledge Management, Librarianship, Philosophy, Health, Technology, ITES/BPO/ ITIL, Call Centers, Business Information etc." .
SCR:022161 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Microbiome Data Collaborative" ;
NIFRID:abbrev "NMDC" ;
definition: "Platform facilitates comprehensive discovery of and access to multidisciplinary microbiome data in order to unlock new possibilities with microbiome data science. Multi organizational effort to integrate microbiome data across diverse areas in medicine, agriculture, bioenergy, and environment. Founded to support long term advancement of microbiome science." .
SCR:022162 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KBase" ;
NIFRID:synonym "Department of Energy Systems Biology Knowledgebase",
"DOE Systems Biology Knowledgebase",
"The Department of Energy Systems Biology Knowledgebase" ;
definition: "Data science platform for predicting and designing biological function. Platform to model plant and microbial physiology and community dynamics. Knowledge creation and discovery environment for biologists and bioinformaticians. Integrates variety of data and analysis tools from US Department of Energy and other public services into platform that leverages scalable computing infrastructure and performs systems biology analyses. Enables scientists to analyze their own data within context of public data and share findings across system." .
SCR:022163 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Labome" ;
definition: "Validated Antibody Database and Reagents. Platform to search antibodies, siRNA/shRNA, ELISA, cDNA clones, proteins/peptides, assays, and biochemicals." .
SCR:022164 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1336" ;
rdfs:label "Cold Spring Harbor Laboratory Flow Cytometry Shared Resource Core Facility" ;
NIFRID:synonym "Cold Spring Harbor Laboratory Flow Cytometry Shared Resource",
"CSHL - Flow Cytometry Shared Resource" ;
NIFRID:abbrev "CSHL" ;
definition: "Resource provides equipment, training, and operating assistance for cell sorting and analysis. Facility staff oversees equipment maintenance, trains new users, and assists with assay development and operation of equipment." .
SCR:022165 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1340" ;
rdfs:label "Forsyth Institute Histology Core Facility" ;
NIFRID:synonym "Forsyth Histology Core",
"The Forsyth Institute Forsyth Histology Core" ;
definition: "Core offers consulting and support services for both soft tissue and precise hard tissue analysis. Services include: tissue processing, embedding, sectioning, staining, and guidance on protocols. Can embed samples in standard molds or custom molds in paraffin, resin, or as frozen tissue for routine histology. Provides special stains and immunohistological studies." .
SCR:022166 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1341" ;
rdfs:label "Forsyth Institute Oral Microbiome Core Facility" ;
NIFRID:synonym "Forsyth Oral Microbiome Core" ;
NIFRID:abbrev "FOMC" ;
definition: "Offers Next Generation Sequencing (NGS) and comprehensive data analyses and interpretation for 16S rRNA gene amplicon sequences and other big data sequence applications. Offers analyses of previously obtained sequences. Many investigators are familiar with Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) as well as its predecessor the Human Oral Microbe Identification Microarray (HOMIM) for rapid 16S rDNA analyses of oral clinical samples. We continue in that tradition using bioinformatic methodology, which will provide the best possible taxa identification." .
SCR:022167 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R31NJMM8",
"DOI:10.25504/FAIRsharing.2VADoR",
"DOI:10.34711",
"r3d100013120" ;
rdfs:label "INPTDAT" ;
definition: "Interdisciplinary data platform provides access to research data and information from all fields of applied plasma physics and plasma medicine. Aims at distributing, publishing and archiving of data and information, supporting findability, accessibility, interoperability and re-use of data, for low temperature plasma physics community.Most of data are freely available and can be used under terms of license listed on dataset description page. Each dataset can be identified, cited and shared by using Digital Object Identifier." .
SCR:022168 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1344" ;
rdfs:label "North Carolina State University High Performance Computing Services Core Facility" ;
NIFRID:synonym "NCSU High Performance Computing",
"North Carolina State University NCSU High Performance Computing" ;
definition: "Core, available through NC State Office of Information Technology, provides entry and intermediate level computing resources and consulting support for research and instruction." .
SCR:022169 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1338" ;
rdfs:label "Texas A and M University College of Veterinary Medicine and Biomedical Sciences Flow Cytometry Core Facility" ;
NIFRID:synonym "TAMU Flow Cytometry Facility",
"Texas A&M University TAMU Flow Cytometry Facility" ;
definition: "Provides flow cytometry experimental design, data collection, data analysis and cell sorting services; training for flow cytometers, imaging flow cytometer, and data analysis using IDEAS and FlowJo software;staff assisted flow cytometry and imaging flow cytometry data acquisition, cell sorting, and data analysis, experimental design and consultation services. FCF currently has Beckman Coulter Moflo Astrios cell sorter, Luminex/Amnis Image Stream X Mark II, Luminex/Amnis Cell Stream, and Becton Dickinson Accuri C6 flow cytometer. Astrios cell sorter is housed in ClassII BSC and has 3 lasers (405nm, 488nm, 642nm) and 11 detectors and can sort up to 6 populations simultaneously. Image Stream X Mark II is equipped with 20x, 40x, 60x objectives, 4 lasers (405nm, 488nm, 561nm, 642nm), 10 detection channels, EV mode for small particle detection, and an autosampler.Cell Stream is equipped with 3 lasers (405nm, 488nm, 642nm), 13 detection channels, EV mode for small particle detection, and autosampler. Accuri C6 is equipped with 2 lasers (488nm, 642nm), and 4 detection channels." .
SCR:022170 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1346" ;
rdfs:label "University of California at Berkeley QB3 Genomics Core Facility" ;
NIFRID:synonym "UCB-QB3 Genomics",
"University of California at Berkeley UCB-QB3 Genomics" ;
definition: "Partnership between Vincent J. Coates Genomics Sequencing Laboratory,Functional Genomics Laboratory, and Computational Genomics Resource Laboratory. Offers consultation on experimental design and data analysis, full suite of technical services related to high throughput sequencing and genomics experiments, and access to high performance computational infrastructure." .
SCR:022171 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spectrum Mill" ;
NIFRID:synonym "Agilent Spectrum Mill MS Proteomics Workbench",
"Spectrum Mill v7.11" ;
definition: "Software tool for high throughput processing of MS/MS and MS spectra to provide protein and peptide identifications and relative quantitation." .
SCR:022172 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Amsterdam Decoding And Modeling" ;
NIFRID:synonym "ADAM toolbox" ;
NIFRID:abbrev "ADAM" ;
definition: "Software Matlab based MVPA toolbox for EEG analyses. Allows direct comparison of ERP/ERF results to MVPA results using any dataset in standard EEGLAB or Fieldtrip format. Performs and visualizes multiple comparison corrected group decoding and forward encoding results in variety of ways, such as classifier performance across time, temporal generalization (time-by-time) matrices of classifier performance, channel tuning functions (CTFs) and topographical maps of (forward-transformed) classifier weights." .
SCR:022173 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MVPA Light" ;
NIFRID:synonym "MVPA-Light" ;
definition: "Software Matlab based MVPA toolbox for EEG and MEG analyses. Classification and regression toolbox for multi dimensional data. Performs cross validation, hyperparameter tuning, and nested preprocessing. Computes various classification and regression metrics and establishes their statistical significance." .
SCR:022174 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Residue Iteration Decomposition" ;
NIFRID:synonym "Residue Iteration DEcomposition" ;
NIFRID:abbrev "RIDE" ;
definition: "Software Matlab based toolbox for temporal decomposition of EEG signal. Used for decomposition, reconstruction, and single trial analysis of event related potentials." .
SCR:022175 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "System for Omics Data Access and Retrieval" ;
NIFRID:abbrev "SODAR" ;
definition: "Software package for managing data in omics research projects. Integrates with iRODS (integrated rules oriented data system) software for mass data management." .
SCR:022176 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DCBC toolbox" ;
NIFRID:synonym "DCBC" ;
definition: "Software Python toolbox for brain parcellation evaluation." .
SCR:022177 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biolabs Model Organism Antibodies Service Resource" ;
definition: "Antibody group provides researchers with functional proteomics research platform. Antibody customization service provider. Custom antibody development team can work with you to create customized antibody solution to meet your specific research needs. Provides monoclonal antibody screening. Prepares monoclonal antibody library to screen monoclonal antibodies for appropriate peptide epitope of each protein." .
SCR:022178 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProteinPlus" ;
definition: "Web portal for structure analysis of macromolecules." .
SCR:022179 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PDBrenum" ;
definition: "Webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences.Fixes PDB sequence numbering problem by replacing author numbering with numbering derived from corresponding UniProt sequences." .
SCR:022180 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rascore" ;
definition: "Web tool for analyzing RAS protein structures.Used to build updatable database of all available RAS structures in Protein Data Bank (PDB) with their catalytic switch 1 (SW1) and switch 2 (SW2) loopsconformationally classified and their molecular contents annotated. Database presenting updated and searchable dataset of human KRAS, NRAS, and HRAS structures in PDB, and which includes page for analyzing user uploaded RAS structures." .
SCR:022181 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PISCES" ;
definition: "Software tool as protein sequence culling server. Used for culling sets of protein sequences from Protein Data Bank (PDB) by sequence identity and structural quality criteria. Can provide lists culled from entire PDB or from lists of PDB entries or chains provided by user." .
SCR:022182 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WordNet" ;
definition: "Lexical database of English. Nouns, verbs, adjectives and adverbs are grouped into sets of cognitive synonyms (synsets), each expressing distinct concept. Synsets are interlinked by means of conceptual-semantic and lexical relations. Resulting network of meaningfully related words and concepts can be navigated with browser." .
SCR:022183 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mondo" ;
NIFRID:synonym "Mondo Disease Ontology" ;
definition: "Open, community-driven ontology that integrates key medical and biomedical terminologies, supporting disease data integration to improve diagnosis, treatment, and translational research. Mondo records sources of all data and is continually updated, making it suitable for research and clinical applications that require up-to-date disease knowledge." .
SCR:022184 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3DHISTECH | Pannoramic 250 Flash III slide scanner" ;
NIFRID:synonym "Pannoramic 250 Flash III",
"Pannoramic 250 Flash III digital slide scanner" ;
definition: "Scanner for digital pathology for scanning in brightfield and fluorescence. Offers fast scanning (35 sec/slide) and high throughput (60 slides/hour) (brightfield scanning, 41x optical magnification, 15mm x 15mm area, 15 FOVs Focus Distance, JPG compression, MRXS file format).Offers slide loading capacity 300 and continuous loading with vertical slide arrangement." .
SCR:022185 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IX71" ;
rdfs:label "Olympus | IX71 Microscope" ;
NIFRID:synonym "Olympus IX71" ;
definition: "Research inverted system microscope. Olympus IX2 inverted microscope combined with UIS2 optical system. Used for live cell experiments." .
SCR:022186 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Visualising Longitudinal and Cross-sectional Variant Effects" ;
NIFRID:synonym "GP2-visualise-longitudinal-variant-effects" ;
definition: "Software for visualising longitudinal and cross-sectional variant effects." .
SCR:022187 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GP2 Data Visualization Tool" ;
definition: "Software tool for GP2 data visualization." .
SCR:022188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PD GWAS Locus Browser" ;
NIFRID:synonym "Parkinson's Disease Genome-Wide Association Study Locus Browser" ;
definition: "Web platform that aims to collect as much data as possible (including genetic, genomic and functional). to identify and characterize potential causal genes and underlying molecular mechanisms that contribute to PD risk and pathogenesis. Web tool provides users with method of identifying potential causal genes at all known PD risk loci from large‐scale PD genome‐wide association studies." .
SCR:022189 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Euclidean Distance Matrix Analysis" ;
NIFRID:synonym "EDMAinR",
"Euclidean Distance Matrix Analysis in R" ;
NIFRID:abbrev "EDMA" ;
definition: "Software tool as coordinate free approach for comparing biological shapes using landmark data." .
SCR:022190 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | EVOS XL Core Imaging System" ;
definition: "Designed to eliminate complexities of microscopy, EVOS XL Core system captures high-quality brightfield cell images right at your benchtop within minute. Instrument for monitoring cell cultures, either within hood or in cell culture room." .
SCR:022191 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aperio | ScanScope FL System" ;
NIFRID:synonym "Aperio ScanScope FL Slide Scanner" ;
definition: "Aperio slide scanner for fluorescent images. Used for whole slide scanning of slides stained with multiple fluorochromes. With quad multi-bandpass filter set, up to four color channels can be acquired; users can add other filters for greater flexibility. Advanced illumination, autoexposure, and autofocus capabilities eliminate need for trial-and-error scanning, reducing problem of photobleaching." .
SCR:022192 a owl:NamedIndividual ;
rdfs:label "BWA-MEM2" ;
NIFRID:synonym "BWA-MEM" ;
definition: "Software tool for sequence mapping.The next version of BWA-MEM. Used for aligning sequencing reads against large reference genome." .
SCR:022193 a owl:NamedIndividual ;
rdfs:label "Tandem Repeats Finder" ;
NIFRID:abbrev "TRF" ;
definition: "Software tool to locate and display tandem repeats in DNA sequences. Program to analyze DNA sequences." .
SCR:022194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MashMap" ;
definition: "Software tool as fast approximate aligner for long DNA sequences. Used for computing local alignment boundaries between long DNA sequences." .
SCR:022195 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChrOrthLink" ;
NIFRID:synonym "Chromosomal Orthologous Link" ;
definition: "Software tool for chromosomal orthologous link analysis." .
SCR:022196 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ruffus" ;
definition: "Software lightweight Python library for computational pipelines. Reproducible pipeline framework." .
SCR:022197 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepCell" ;
NIFRID:synonym "Deepcell" ;
definition: "Software for segmenting individual cells in microscopy images using deep learning. Cell segmentation software." .
SCR:022198 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SomaDataIO" ;
definition: "Software R package which loads SomaLogic, Inc. proprietary data file, called an ADAT file ('*.adat'). Provides auxiliary functions for extracting and manipulating relevant information from ADAT, as well as exporting modified ADAT to file." .
SCR:022199 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SAS JMP Pro" ;
NIFRID:synonym "JMP Pro from SAS" ;
NIFRID:abbrev "JMP Pro" ;
definition: "Statistical software tool. Predictive analytics software. Offers all tools in JMP plus advanced features for more sophisticated analyses." .
SCR:022200 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1347" ;
rdfs:label "Texas A and M Health Science Center IBT Protein Production, Characterization and Molecular Interaction Core Facility" ;
NIFRID:synonym "Characterization and Molecular Interaction (PPCMI)",
"IBT-Protein Production",
"Texas A&M Health Science Center IBT-Protein Production" ;
NIFRID:abbrev "PPCMI" ;
definition: "Core provides cloning, expression and purification services of functional proteins at scale that meets the quantity and purity benchmarks for structural, biophysical, biochemical, and therapeutics studies; characterizes macromolecular biophysics and interaction energetics using instrumentation and techniques that can analyze association and kinetic binding constants by surface plasmon resonance, enthalpies and entropies of binding by isothermal titration calorimetry, as well as determination of stoichiometry, stability, and homogeneity by both techniques." .
SCR:022201 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1348" ;
rdfs:label "Texas A and M University Veterinary Medicine and Biomedical Sciences Research Histology Unit Core Facility" ;
NIFRID:synonym "TAMU-CVMBS Core Histology Laboratory",
"Texas A and M University Veterinary Medicine and Biomedical Sciences Core Histology Laboratory Research Histology Unit Core Facility",
"Texas A&M University TAMU-CVMBS Core Histology Laboratory" ;
definition: "Provides histology (including cryosectioning, IHC and IFC) digital pathology and veterinary pathology (board certified veterinary pathologist on staff) services." .
SCR:022202 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1349" ;
rdfs:label "Texas A and M University Materials Characterization Core Facility" ;
NIFRID:synonym "TAMU-Materials Characterization Facility (MCF)",
"Texas A&M University TAMU-Materials Characterization Facility (MCF)" ;
NIFRID:abbrev "MCF" ;
definition: "Core provides access to instrumentation essential for studies of surface and interfacial properties of materials, such as ion and electron based spectroscopies, electron, optical and scanning probe microscopies. Core provides training to students and faculty on instrumentation as well as consolation of measurements needs and data interpretation, supports educational activities involving lab tours, workshops, hands on demonstrations, outreach and broader impact related activities through our open house and lunchtime seminar series.Supports collaborative research projects with outside industrial users." .
SCR:022203 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1352" ;
rdfs:label "State University of Campinas Multidisciplinary Center for Biological Investigantion on Laboratory Animals Science Core Facility" ;
NIFRID:synonym "CEMIB" ;
definition: "Core produces mice and rats for biomedical research. Provides services for customers are researchers from Unicamp and other Institutions from Brazil." .
SCR:022204 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1350" ;
rdfs:label "National Autonomous University of Mexico Microscopy Core Facility" ;
NIFRID:synonym "Unidad de Microscopia IIBO-UNAM" ;
definition: "Core is specialized in stereology techniques, live cell imaging, CLSM (confocal microscopy), and STORM. Provided instruments include CONFOCAL microscopes Zeiss LSM 5 Pascal, Olympus BX51-WI,Olympus IX71 inverted microscope, Nikon Labophot-2 microscope,Nikon Optiphot 2 microscope." .
SCR:022205 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 501100006416",
"GRID grid.411087.b",
"ISNI 0000 0001 0723 2494",
"Wikidata Q2060678" ;
rdfs:label "State University of Campinas; São Paulo; Brazil" ;
NIFRID:synonym "Universidade Estadual de Campinas (UNICAMP)" ;
definition: "Public research university in Brazil commonly called Unicamp. Recognized as one of the best universities in Latin America." .
SCR:022206 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harmony" ;
NIFRID:synonym "Harmony for immunogenomics" ;
definition: "Software R package to project cells into shared embedding in which cells group by cell type rather than dataset specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. Used for integration of single cell data." .
SCR:022207 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spacemake" ;
NIFRID:synonym "spacemake" ;
definition: "Software pipeline for processing and analysis of large scale spatial transcriptomics data. Enables reproducible data processing from raw sequencing data to automatically generated downstream analysis reports." .
SCR:022208 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChemChaste" ;
definition: "Software tool for simulating spatially inhomogenous biochemical reaction diffusion systems for modelling cell environment feedbacks. Simulation software for spatially organised biochemical systems." .
SCR:022209 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1353" ;
rdfs:label "Harvard Medical School Microscopy Resources On the North Quad Core Facility" ;
NIFRID:synonym "Harvard Medical School HMS-MicRoN",
"HMS-MicRoN" ;
NIFRID:abbrev "MicRoN" ;
definition: "Light microscopy core is open to HMS researchers, including Affiliated hospitals. Supports imaging modalities ranging from wide field, TIRF, spinning disk and single point scanning confocal, multiphoton, FLIM and supper resolution. Microscopes are embedded within Departments of Microbiology, Immunology, and Genetics, housed in five microscope rooms on five floors of NRB and HIM." .
SCR:022210 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_610" ;
rdfs:label "University of Toronto Advanced Instrumentation for Molecular Structure Mass Spectrometry Laboratory Core Facility" ;
NIFRID:synonym "AIMS Mass Spectrometry Laboratory",
"University of Toronto AIMS Mass Spectrometry Laboratory" ;
definition: "Core mass spectrometry facility located in Department of Chemistry, University of Toronto, which houses several mass spectrometers. Services include:High resolution, accurate mass determinations of small molecules via EI, ESI and DART ionization;Mass determinations of intact peptides and proteins via ESI-QTOF-MS and MALDI-MS; HPLC-MS/MS analysis of protein digests via ESI-QTOF-MS; Quantitative analysis via HPLC-MS/MS using QqQ instrumentation." .
SCR:022211 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_234" ;
rdfs:label "University of South Carolina at Columbia College of Pharmacy Microarray Core Facility" ;
NIFRID:synonym "SCCC DNA Microarray Facility",
"South Carolina College of Pharmacy Microarray Core Facility",
"University of South Carolina at Columbia South Carolina College of Pharmacy Microarray Core Facility",
"USC Microarray Core Facility" ;
definition: "Services include RNA quality control, amplification and labeling, array hybridization, scanning and data analysis, assisting customers in design and performance of microarray experiments, using Agilent (pre-made and custom) and Affymetrix arrays. Provides support for quantitation and quality assessment of DNA, RNA and protein on Agilent 2100 Bioanalyzer. Provides training and support for Agilent and Affymetrix Hybridization oven users. Provides support for microarray scanning and for data analysis with variety of software packages for both Agilent and Affymetrix platforms.Quantity and quality of your RNA, DNA, proteins and cells are determined with help of Agilent 2100 Bioanalyzer." .
SCR:022212 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Orbitrap Eclipse nanoLC/MS system" ;
NIFRID:synonym "Orbitrap Eclipse nanoLC/MS",
"Thermo Orbitrap Eclipse nanoLC/MS" ;
definition: "System includes Thermo Orbitrap Eclipse Tribid mass spectrometer and Waters M-Class Acquity nanoUPLC. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments." .
SCR:022214 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1354" ;
rdfs:label "Texas A and M University Institute of Biosciences and Technology High Throughput Research and Screening Center Combinatorial Drug Discovery Core Facility" ;
NIFRID:synonym "TAMU - Combinatorial Drug Discovery Program (CDDP)",
"TAMU IBT High Throughput Research and Screening Center CDDP",
"Texas A&M Health Science Center TAMU - Combinatorial Drug Discovery Program (CDDP)",
"Texas A&M University Houston IBT High Throughput Research and Screening Center CDDP" ;
NIFRID:abbrev "CDDP" ;
definition: "Core provides industry standard high throughput screening and automated microscopy capabilities to scientists performing drug discovery research. Provides access to automated infrastructure to support phenotypic and biochemical targets. Provides ready access to collections of current FDA approved drugs and clinical candidates exhibiting drug like qualities of acceptable solubility, desirable ADME/toxicology properties and adequate bioavailability. Has collections of mechanistically annotated informer sets that are pathway specific modulators for studying mechanism of action or target identification, collections of natural products and diverse sets of small molecules that can be interrogated for new target discovery. Each project is individually evaluated and team of scientists from CDDP is created to fit specific needs of project from assay design and development through primary, secondary and orthogonal screening." .
SCR:022215 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Exploris 480 nanoLC/MS system" ;
NIFRID:synonym "Exploris 480 system" ;
definition: "Exploris 480 system is hybrid quadrupole Orbitrap mass spectrometer with Waters M-Class Acquity. Proteomics system for hands on use by highly trained users." .
SCR:022216 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Exploris 240 LC/MS system" ;
NIFRID:synonym "Exploris 240 system" ;
definition: "Exploris 240 system is hybrid quadrupole Orbitrap mass spectrometer with Waters H-Class Acquity, ZipChip, and DART front ends. Flexible platform for wide range of small molecule and intact protein analyses." .
SCR:022217 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Waters | SQD2 LC/MS system" ;
NIFRID:synonym "Stanford Waters SQD2 LC/MS system" ;
definition: "System includes SQD2 as single quadrupole MS with Waters H-Class Acquity UPLC, operated as open access platform for trained users. SQ Detector2 is single quadrupole mass detector for chromatography compatible with range of chromatography platforms and ionization sources." .
SCR:022218 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Waters | Andrew Pipetting Robot" ;
NIFRID:synonym "Waters Andrew+ Pipetting Robot" ;
definition: "Pipetting Robot offers repeatable, traceable pipetting with connected single and multichannel electronic pipettes. Enables automation of many routine sample preparation workflows." .
SCR:022219 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Total Peptide Library Construction Service Resource" ;
NIFRID:synonym "Total Peptide Library Construction Technology" ;
definition: "Service uses bioinformatics methods to compress peptide information, which can integrate information of multiple peptide into one peptide. Provides collection of small peptide of specific length and different sequences, which includes permutation and combination of various amino acid sequences in short peptide of this length.Total peptide library for new drug research and development." .
SCR:022221 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Peptide Drug Bioconjugations Service Resource" ;
NIFRID:synonym "Peptide Drug Bioconjugations" ;
definition: "Custom peptide synthesis, modification, and conjugation services involve chemical modification of peptide at highly specific sites. This allows for attachment of drugs or bioactive molecules though variety of coupling techniques." .
SCR:022222 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides | Peptide Lead Optimization Service Resource" ;
NIFRID:synonym "Peptide Lead Optimization" ;
definition: "Provides optimized one stop solution for peptide lead drugs. Used to improve upon lead molecule that demonstrates activity at target of interest by optimizing its potency or selectivity at target and its absorption, distribution, metabolism and elimination properties." .
SCR:022223 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides | Formulation Development Service Resource" ;
NIFRID:synonym "Formulation Development" ;
definition: "Service to determine optimal dosage form, composition and manufacturing route for pharmaceutical products." .
SCR:022224 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "napari-kics" ;
definition: "Software plugin to estimate chromosome sizes from karyotype images." .
SCR:022225 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_449" ;
rdfs:label "Sanford Burnham Prebys Medical Discovery Institute Proteomics Core Facility" ;
NIFRID:synonym "Proteomics",
"Sanford Burnham Medical Research Institute Proteomics" ;
definition: "Facility provides mass spectrometry based proteomics services with methods tailored to needs of scientific investigators for routine mass spectrometric analysis of peptides and proteins, identification of novel proteins, characterization of post translational modifications, and quantitative proteomics analysis of simple to complex biological samples. Core identifies, validates and develops new methods designed for characterization and identification of biologically important proteins. Supports users with software applications and development, data analysis and experimental design of proteomics studies. Expands its capabilities in large scale differential proteomics analysis and phosphoproteomics for unbiased discovery of potential biomarkers and mapping protein profiles." .
SCR:022226 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides PNA Modification Service Resource" ;
NIFRID:synonym "PNA Modification" ;
definition: "Peptide nucleic acid modification includes modification of backbone and base. Service provides Backbone modification, Nucleobase modification, Modification of connection between nucleobase and backbone." .
SCR:022227 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides PNA Modification of Connection between Nucleobase and Backbone Service Resource" ;
NIFRID:synonym "Modification of Connection between Nucleobase and Backbone",
"PNA Modification of Connection between Nucleobase and Backbone" ;
definition: "Peptide nucleic acid modification service includes cooperation with customers at each stage of PNA development, providing complete test plan, selection of appropriate program and process, and monitoring entire test process.Provides modification strategies based on product diversity and inherent biological characteristics.Provides series of quality assurance studies, such as GC-MS, HPLC analysis, to achieve quality monitoring and understanding of effects of finished products." .
SCR:022228 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides PNA Backbone Modification Service Resource" ;
NIFRID:synonym "PNA Backbone Modification" ;
definition: "Peptide nucleic acid backbone modification service includes backbone modification of N-(2-aminoethyl) glycine unit structure of PNA to increase water solubility and enhancing hybridization performance." .
SCR:022229 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides PNA N/C Terminal Modification Service Resource" ;
NIFRID:synonym "N/C Terminal Modification" ;
definition: """Service to modify monomer backbone, including chemically active sites at both ends. Monomer
N-terminal and C-terminal modification.""" .
SCR:022230 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides PNA Modification by C Replacement Service Resource" ;
NIFRID:synonym "Modification by C Replacement" ;
definition: "PNA modification service provides replacement of backbone C." .
SCR:022231 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides | Peptide Synthesis Service Resource" ;
NIFRID:synonym "Peptide Synthesis" ;
definition: "Provides peptide drug synthesis services, allowing researchers to synthesize peptide drug that is integral to drug discovery and development. Offers services in chemical synthesis of variety of peptide compounds." .
SCR:022232 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Active Peptide Ingredients from Natural Products Service Resource" ;
NIFRID:synonym "Active Peptide Ingredients from Natural Products" ;
definition: "Provides peptide drug extracting from natural products. Extracted peptides evaluated as possible therapeutic agents for various diseases." .
SCR:022233 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Peptide Drug Biosynthesis Service Resource" ;
NIFRID:synonym "Peptide Drug Biosynthesis" ;
definition: "Services include Enzyme decomposition synthesis, Fermentation method, Genetic engineering method, Peptide design coupled with computational design, Peptide drug design and stabilization." .
SCR:022234 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Peptide Drug Chemical Synthesis Service Resource" ;
NIFRID:synonym "Peptide Drug Chemical Synthesis" ;
definition: "Chemical synthesis service for peptide production by coupling carboxyl group of incoming amino acid to N-terminus of growing peptide chain." .
SCR:022235 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Peptides Custom Peptide Synthesis Service Resource" ;
NIFRID:synonym "Custom Peptide Synthesis" ;
definition: "Custom peptide synthesis service. Provides solid phase peptide synthesis, liquid phase peptide synthesis, glycochemistry, small molecule synthesis and high throughput synthesis." .
SCR:022236 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Mitochondrial Genomics Service Resource" ;
NIFRID:synonym "Mitochondrial Genomics" ;
definition: "Office service platforms for mitochondrial genome monitoring and analysis." .
SCR:022237 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Mitoepigenetics Service Resource" ;
NIFRID:synonym "Mitoepigenetics" ;
definition: "Provides mitoepigenetics analysis platform to help carry out mitochondrial research. Services include mitochondrial DNA methylation and hydroxymethylation, physiological and pathological modification of mitochondrial epigenetics, interaction between mitochondria and nuclei, use of mitochondrial epigenetic products as biomarkers, and effects of environment and nutritious diet on mitochondrial epigenetics." .
SCR:022238 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Methylation and Hydroxymethylation Service Resource" ;
NIFRID:synonym "Methylation and Hydroxymethylation" ;
definition: "Creative Biogene services for mitochondrial methylation and hydroxymethylation." .
SCR:022239 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Mitochondrial Physiological and Pathological Modifications Service Resource" ;
NIFRID:synonym "Mitochondrial Physiological and Pathological Modifications" ;
definition: "Provides multi species mitochondrial epigenetic analysis and customizes appropriate research route. Providies services on epigenetic characteristics of mitochondria under different physiological and pathological conditions." .
SCR:022240 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Mitochondrial Biomarkers and Therapeutic Targets Service Resource" ;
NIFRID:synonym "Mitochondrial Biomarkers and Therapeutic Targets" ;
definition: "Creative Biogene service for discovery of disease specific proteins associated with mitochondrial epigenetic products, which can be used as molecular targets for new drug design and provide molecular markers for early diagnosis of diseases." .
SCR:022241 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Autotrophic Bacteria Cultivation Service Resource" ;
NIFRID:synonym "Autotrophic Bacteria Cultivation" ;
definition: "Provides service for autotrophic bacteria cultivation." .
SCR:022242 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Prosthecochloris Cultivation Service Resource" ;
NIFRID:synonym "Prosthecochloris Cultivation" ;
definition: "Service offers culture of Prosthecochloris bacteria with specific formulations of growth media for use in cloning, plasmid DNA preparation, and protein expression." .
SCR:022243 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Chlorobium Cultivation Service Resource" ;
NIFRID:synonym "Chlorobium Cultivation" ;
definition: "Service for Chlorobium cultivation." .
SCR:022244 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Pelodictyon Cultivation Service Resource" ;
NIFRID:synonym "Pelodictyon Cultivation" ;
definition: "Service for Pelodictyon cultivation." .
SCR:022245 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Creative Biogene Clathrochloris Cultivation Service Resource" ;
NIFRID:synonym "Clathrochloris Cultivation" ;
definition: "Service for Clathrochloris cultivation." .
SCR:022246 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BOC Sciences PROTAC Design Services Service Resource" ;
NIFRID:synonym "PROTAC Design Services" ;
definition: "Provides service for one stop proteolysis targeting molecular drug discovery based on chimeric PROTAC." .
SCR:022247 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BOC Sciences Linker Design and Optimization Services Service Resource" ;
NIFRID:synonym "Linker Design and Optimization" ;
definition: "Provides Linker Design and Optimization services to meet new drug discovery goals." .
SCR:022248 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BOC Sciences PROTAC Design based on Bioinformatics" ;
NIFRID:synonym "PROTAC Design based on Bioinformatics" ;
definition: "Provides PROTAC design based on bioinformatics services to customers to meet new drug discovery goals. Used for analysis of large scale multi group data to discover potential drug targets based on biological network characteristics, multi gene chip, proteome, metabolome data." .
SCR:022249 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BOC Sciences PROTAC diastereomer Design negative control Service Resource" ;
NIFRID:synonym "PROTAC diastereomer Design negative control" ;
definition: "Service to design PROTAC diastereomer to meet new drug discovery goals." .
SCR:022250 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BOC Sciences PROTAC GMP Services Service Resource" ;
NIFRID:synonym "PROTAC GMP Services" ;
definition: "Specializes in development and GMP manufacture of pharmaceutical grade products. Provides pharmaceutical discovery services to assist clients in reaching their R&D goals." .
SCR:022251 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LMAS" ;
NIFRID:synonym "Last (Meta)Genomic Assembler Standing" ;
definition: "Automated workflow enabling benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. Results are presented in interactive HTML report where selected global and reference specific performance metrics can be explored." .
SCR:022252 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRE Clinical Interagency Research Resource TBI" ;
NIFRID:synonym "PRE-Clinical Interagency Research Resource-TBI" ;
NIFRID:abbrev "PRECISE-TBI" ;
definition: "Resource to accelerate development of therapies for traumatic brain injury by elevating rigor, reproducibility, and transparency in preclinical research." .
SCR:022253 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MotionWare" ;
definition: "Software provides analysis functions for sleep, circadian rhythm and physical activity alongside device and data management tools within one integrated solution. Accelerometer data from MotionWatch or PRO-Diary is interpreted by software algorithms to provide the end points. Intuitive graphical user interface provides valuable insights into subject behaviour while providing flexible data selection and reporting tools." .
SCR:022254 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FinnGen" ;
definition: "Public private partnership combining genotype data from Finnish biobanks and digital health record data from Finnish health registries. Provides opportunity to study genetic variation in relation to disease trajectories in isolated population." .
SCR:022255 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OSTI ID:1812943; re3data DOI:10.17616/R31NJN56; FAIRsharing DOI:10.25504/FAIRsharing.45bf5b",
"r3d100013802" ;
rdfs:label "Pacific Northwest National Laboratory DataHub: Scientific Data Repository" ;
NIFRID:synonym "pnnl2",
"PNNL DataHub",
"PNNL.Data" ;
definition: "Provides tools and services to meet scientific data challenges at Pacific Northwest National Laboratory . DataHub helps researchers address the full data life cycle for their institutional projects and provides path to creating findable, accessible, interoperable, and reusable data products. Although open science data is crucial focus of DataHub’s core services, we are interested in working with evidence based data throughout PNNL research community." .
SCR:022256 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CoffeeProt" ;
definition: "Open source software tool for correlation and functional enrichment of proteome wide systems genetics. Analyzes genetic variants associated to protein networks and phenotypic traits. Uses proteomics data to perform correlation network analysis and annotates protein-protein interactions, subcellular localizations and drug associations." .
SCR:022257 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xlrd" ;
definition: "Software library for reading data and formatting information from Excel files in .xls format." .
SCR:022258 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openpyxl" ;
definition: "Software Python library to read and write Excel 2010 xlsx/xlsm/xltx/xltm files." .
SCR:022259 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cmocean" ;
definition: "Software package contains colormaps for commonly used oceanographic variables." .
SCR:022260 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "adjustText" ;
definition: "Software library for automatically adjustment of text position in matplotlib plots to remove or minimize overlaps with labels and data points." .
SCR:022261 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pingouin" ;
definition: "Open source statistical package written in Python 3 and based mostly on Pandas and NumPy. Designed for users who want simple yet exhaustive stats functions." .
SCR:022262 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lonza | Nucleofector 2b Device" ;
NIFRID:synonym "Nucleofector 2b Device" ;
definition: "System for efficient transfection of a variety of hard-to transfect cell lines and primary cells. Using certified aluminium electrode cuvettes this single cuvette system is capable of transfecting various substrates in a low throughput format." .
SCR:022263 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LSM _900" ;
rdfs:label "Zeiss | LSM 900 with Airyscan 2" ;
definition: "Laser scanning confocal microscope for multiplex imaging and analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:022264 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PLR-GEN" ;
definition: "Software package for generation of pseudo long reads by using short reads of metagenomic sample and microbial reference genome sequences as input." .
SCR:022265 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ;
rdfs:label "SNP-sites" ;
NIFRID:synonym "Single Nucleotide Polymorphisms-sites" ;
definition: "Software tool to find SNP sites from multi-FASTA alignment file. Can output results in multiple formats for downstream analysis." .
SCR:022266 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COVID CG" ;
NIFRID:synonym "COVID-19 CG",
"COVID-19 CoV Genetics",
"COVID-19 CoV Genetics (CG)",
"covidcg.org" ;
definition: "Open browser to inform therapeutics development for tracking SARS-CoV-2 single nucleotide variations, lineages, and clades using virus genomes on GISAID database while filtering by location, date, gene, and mutation of interest. can Provides information on which virus mutations are present in area during specific period by processing data on mutations found in viral genetic material collected worldwide from hundreds of thousands of people with COVID-19, which are hosted in existing online database." .
SCR:022267 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AL2CO" ;
definition: "Software tool to calculate positional conservation for multiple sequence alignment. Used for calculation of positional conservation in protein sequence alignment." .
SCR:022268 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "%MinMax" ;
definition: "Software tool for calculating and comparing synonymous codon usage and its impact on protein folding. Used to harmonize codon usage frequencies for heterologous gene expression. Codon usage calculator that evaluates relative usage frequencies of synonymous codons used to encode protein sequence of interest and compares these results to rigorous null mode.Evaluates synonymous codon usage patterns for any coding sequence from any fully sequenced genome." .
SCR:022269 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HEXplorer score" ;
definition: "Web tool for genomic HEXploring allows landscaping of novel potential splicing regulatory elements. Allows landscaping of splicing regulatory regions, provides quantitative measure of mutation effects on splice enhancing and silencing properties and permitts calculation of mutationally most effective nucleotide." .
SCR:022270 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ESRseq score" ;
definition: "Software for comprehensive quantitative measure of splicing impact of complete set of RNA 6-mer sequences by deep sequencing successfully spliced transcripts." .
SCR:022271 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Coarse grained co-translational folding analysis" ;
NIFRID:synonym "Coarse-grained co-translational folding analysis" ;
definition: "Software for statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved, and also co-translational protein folding model." .
SCR:022272 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COVID-19 Host Genetics Initiative" ;
definition: "Platform for global network of researchers to investigate role of human genetics in SARS-CoV-2 infection and COVID-19 severity. Provides results of three genome-wide association meta analyses that consist of patients with COVID-19 from studies across countries." .
SCR:022273 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KineFold" ;
definition: "Web service for RNA/DNA folding predictions including pseudoknots and entangled helices.Used for prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations." .
SCR:022274 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NUPACK" ;
NIFRID:synonym "Nucleic Acid Package" ;
definition: "Web server for analysis and design of nucleic acid systems. Enables thermodynamic analysis of dilute solutions of interacting nucleic acid strands. Analysis and design of nucleic acid secondary structure for systems involving one or more species of interacting strands." .
SCR:022275 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SigCom LINCS" ;
NIFRID:synonym "SigCom Library of Integrated Network-based Cellular Signatures" ;
definition: "Web server that serves over million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. Data and metadata search engine for gene expression signatures." .
SCR:022276 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Plant Cataloging Workflow" ;
definition: "Software workflow for automatized spatio temporal plant positioning based on UAV images." .
SCR:022277 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xHLA" ;
definition: "Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer." .
SCR:022278 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Polysolver" ;
NIFRID:synonym "POLYmorphic loci reSOLVER",
"POLYSOLVER" ;
definition: "Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference." .
SCR:022279 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_05461" ;
rdfs:label "OptiType" ;
definition: "Software tool for precision HLA typing from next generation sequencing data." .
SCR:022280 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kourami" ;
definition: "Software graph guided assembly for novel human leukocyte antigen allele discovery. Graph guided assembly for HLA haplotypes covering typing exons using high coverage whole genome sequencing data.Implemented in Java and supported on Linux and Mac OS X." .
SCR:022281 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HLAscan" ;
definition: "Software tool for genotyping of HLA region using next generation sequencing data. Performs alignment of reads to HLA sequences from international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database." .
SCR:022282 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HLAminer" ;
definition: "Software for HLA predictions from next generation shotgun sequence read data and supports direct read alignment and targeted de novo assembly of sequence reads. Used for identifying HLA alleles directly from shotgun sequence datasets.Supports predictions from variety of DNA sequencing technologies including those from Illumina, MGI, PacBio and Oxford Nanopore." .
SCR:022283 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HLA-LA" ;
NIFRID:synonym "HLA*LA" ;
definition: "Software implements new graph alignment model for human leukocyte antigen, based on projection of linear alignments onto variation graph. Enables accurate HLA type inference from whole genome and whole exome Illumina data; from long-read Oxford Nanopore and Pacific Biosciences data and from genome assemblies." .
SCR:022284 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HLA-VBSeq" ;
definition: "Software for accurate HLA typing at full resolution from whole genome sequencing data. Used to estimate the most likely HLA types from high throughput sequencing data." .
SCR:022285 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HLA-HD" ;
NIFRID:synonym "HLA typing from High-quality Dictionary" ;
definition: "Software HLA typing algorithm for next generation sequencing data.Can accurately determine HLA alleles with 6 digit precision from NGS data (fastq format). RNA-Seq data can also be applied." .
SCR:022286 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "arcasHLA" ;
definition: "Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq." .
SCR:022287 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1358" ;
rdfs:label "Texas A and M University Laboratory for Synthetic Biologic Interactions Core Facility" ;
NIFRID:synonym "Laboratory for Synthetic-Biologic Interactions",
"Texas A&M University Laboratory for Synthetic-Biologic Interactions" ;
NIFRID:abbrev "LSBI" ;
definition: "Facility housed in Department of Chemistry.Designed to be multi user laboratory supporting major research initiatives. Instruments are currently available on fee for use basis, and others may be made available on case by case considerations." .
SCR:022288 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1360" ;
rdfs:label "University of Colorado Boulder Polymeric and Optical Materials Characterization Shared Core Facility" ;
NIFRID:synonym "Polymeric and Optical Materials Characterization (POM-C) Shared Facility",
"University of Colorado Boulder Polymeric and Optical Materials Characterization" ;
NIFRID:abbrev "POM-C" ;
definition: "Facility specializes in material characterization of polymers, hydrogels, liquid crystals, and composites." .
SCR:022289 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1361" ;
rdfs:label "Harvard Medical School Research Computing Core Facility" ;
NIFRID:synonym "Harvard Medical School HMS Research Computing Core",
"HMS Research Computing Core" ;
definition: "Promotes deeper collaboration across Harvard biomedical research ecosystem.This includes improved capabilities and performance by establishing more transparent and sustainable IT services for our research community." .
SCR:022290 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1362" ;
rdfs:label "Montpellier Imagining Resources MRI Core Facility" ;
NIFRID:synonym "Montpellier Ressources en Imagerie" ;
definition: "Cell imaging facility of Montpellier area, France.Offers access to cutting edge instruments for optical and electron microscopy, flow cytometry, and X-ray micro tomography. Instruments are housed in seven sites that mirror distribution of Life Science research campuses of the region. Mission is to support research by offering imaging instruments and image analysis solutions." .
SCR:022291 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Akern Bodygram Dashboard" ;
definition: "Software valifìdated for evaluation of body composition using Body Impedance Assessment." .
SCR:022292 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BIDS-Matlab" ;
NIFRID:synonym "Brain Imaging Data Structure - Matlab" ;
definition: "Software MATLAB/Octave tools to interact with datasets conforming to Brain Imaging Data Structure format." .
SCR:022293 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lens" ;
definition: "Portal to search, analyze and manage patent and scholarly data. Serves global patent and scholarly knowledge as public good to inform science and technology enabled problem solving." .
SCR:022294 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iReceptor" ;
definition: "Data discovery platform that facilitates curation, analysis and sharing of antibody/B-cell and T-cell receptor repertoires from multiple labs and institutions. Used to increase value of data through sharing with community. Platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories." .
SCR:022300 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutomaticSleepScoringTool" ;
definition: "Software pipeline for sleep researchers to perform automatic sleep scoring for rodents. Artificial neural network for automated behavioral state classification in rats." .
SCR:022301 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fastText" ;
definition: "Software library for efficient text classification and representation learning." .
SCR:022302 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PreprintMatch" ;
definition: "Software tool to match bioRxiv preprints with their corresponding PubMed paper." .
SCR:022303 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1363" ;
rdfs:label "University of Montreal Structural Biology Platform Core Facility" ;
NIFRID:synonym "Structural Biology Platform at the Universit� de Montr�a",
"UdeM-Structural biology platform" ;
definition: "Offers access to several scientific instruments intended to answer structural biological questions for scientific community.Consists of high field nuclear magnetic resonance spectrometers (500 MHz, 600 MHz with cryo-probe and 700 MHz) controlled with recent NEO consoles from Bruker, small angle X-rays scattering (SAXS) instrument, with high throughput robotics. SAXS can be coupled to liquid chromatography system for SEC-SAXS applications.Other instruments include size exclusion chromatography system coupled to multi angle light scattering detector (SEC-MALS), isothermal titration calorimetry (ITC) instrument as well as several liquid handling robots for rapid bio molecular crystal preparation and screening. Users have also access to bio-informatics room with several Linux computers for data analysis.Personnel is available and will teach and support users on instruments, research consultation and turn key services are also available upon request." .
SCR:022304 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1364" ;
rdfs:label "University of California at Berkeley QB3 High Throughput Screening CoreFacility" ;
NIFRID:synonym "QB3 High-Throughput Screening Facility",
"University of California at Berkeley QB3 High Throughput Screening Facility" ;
definition: "Facility provides expert staff for training, services, and cell culturing space for HT automated cell seeding, liquid handling equipment, multi label plate reader and high content automated confocal imaging for any type of multi well, multi conditional mammalian cell experiments." .
SCR:022309 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1365" ;
rdfs:label "University of Cape Town Institute of Infectious Disease and Molecular Medicine Confocal and Light Microscope Imaging Core Facility" ;
NIFRID:synonym "Confocal and Light Microscope Imaging Facility",
"Institute of Infectious Disease and Molecular Medicine Microscopy Unit" ;
definition: "Light and fluorescence microscopy core facility with focus on applications in infectious disease, pathogen and human health research." .
SCR:022310 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1369" ;
rdfs:label "University of Pennsylvania School of Veterinary Medicine Center for Host Microbial Interactions Core Facility" ;
NIFRID:synonym "Center for Host-Microbial Interactions" ;
NIFRID:abbrev "CHMI" ;
definition: "Provides services in disciplines of genomics, microbiology and immunology. We engage in collaborative projects that benefit from close interactions with veterinarians and human clinicians alike." .
SCR:022311 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1366" ;
rdfs:label "University of Montreal BioImaging Platform Core Facility" ;
NIFRID:synonym "University of Montreal Bio-Imaging Platform" ;
definition: "Offers instruments and services to support research in microscopy." .
SCR:022312 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1368" ;
rdfs:label "McMaster University Centre for Advanced Light Microscopy Core Facility" ;
NIFRID:synonym "Centre for Advanced Light Microscopy (CALM)" ;
NIFRID:abbrev "CALM" ;
definition: "Provides access to light microscopy, photo-patterning, and light-assisted 3D printing techniques to help researchers in science, engineering and life sciences as well as our industrial partners achieve their scientific goals." .
SCR:022313 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1367" ;
rdfs:label "Roswell Park Cancer Institute Flow and Image Cytometry Shared Resource Core Facility" ;
NIFRID:synonym "Flow and Image Cytometry Shared Resource",
"Roswell Park Cancer Institute Flow and Image Cytometry Shared Resource" ;
NIFRID:abbrev "FICSR" ;
definition: "Provides advanced flow cytometric and morphology services at cellular and subcellular levels of resolution.Services include investigator access to equipment, education and consultation, comprehensive sample processing, data acquisition and data analysis, luminex cytokine, chemokine and growth factor quantification, and core flow cytometry services for investigator and biotech sponsored clinical trials." .
SCR:022314 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tabula Sapiens" ;
definition: "Single cell transcriptomic atlas of multiple organs from individual human donors. Multiple organ, single cell transcriptomic atlas of humans. Molecular reference atlas for cell types of human body. Provides molecular definition of these cell types and reveals many other aspects of human biology, including how same gene can be spliced differently in different cell types, how shared cell types in different tissues can have subtle differences in their identities, and how clones of immune system can be shared across tissues." .
SCR:022315 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Aberdeen Iain Fraser Cytometry Centre Core Facility" ;
NIFRID:abbrev "IFCC" ;
definition: "Provides services and expertise in flow cytometry to government agencies, industry, educational and private individuals." .
SCR:022316 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Aberdeen;Aberdeen;Scotland" ;
definition: "Public research university in Aberdeen, Scotland." .
SCR:022317 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "insane.py" ;
definition: "Software tool for generating custom membranes for molecular simulations. Software Python script to setup Martini bilayer systems." .
SCR:022318 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "martinize.py" ;
definition: "Software python script to generate Martini protein topology and structure files based on atomistic structure file. Used to convert (atomistic) protein structures to Martini coarse grain structures and topologies. Replaces old seq2itp, atom2cg and ElNeDyn scripts." .
SCR:022319 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HiCRes" ;
definition: "Software pipeline to estimate and predict genomic resolution of Hi-C libraries. Used for estimating and predicting HiC library resolution." .
SCR:022320 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gplates" ;
definition: "Software tool to manipulate reconstructions of geological and paleogeographic features through geological time. Interactively visualize vector, raster and volume data. Desktop software for interactive visualisation of plate tectonics." .
SCR:022321 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FoxDen Data Exploration Network" ;
NIFRID:synonym "Fox DEN tool",
"Michael J Fox Data Exploration Network" ;
definition: "Provides software tool to explore, download and apply statistical models on aggregated data collected for Fox Insight online clinical study. Study collects patient reported outcomes and genetic data from people with Parkinson's disease and their loved ones." .
SCR:022323 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1370" ;
rdfs:label "Aarhus University Fluorescence Activated Cell Sorting Core Facility" ;
NIFRID:synonym "Aarhus University AU-FACS Core Facility",
"AU-FACS Core Facility" ;
definition: "Facility is equipped with cell sorters, analyzers, ImageStream and full spectrum flow cytometer. Staff provides training and maintenance." .
SCR:022324 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1371" ;
rdfs:label "Emory University and Pediatric Winship Flow Cytometry Core Facility" ;
NIFRID:synonym "Emory and Pediatric Winship Flow Cytometry Core" ;
definition: "Core provides cytometry services for analysis and sorting of cells as well as expert consultation for experimental design and planning. Offers access to several analytical flow cytometers as well as high speed cell sorting. Training and technical expertise is available." .
SCR:022325 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pi-based Remote Acquisition Technology for Motion Capture project" ;
NIFRID:synonym "Pi-based Remote Acquisition Technology for Motion Capture" ;
NIFRID:abbrev "PiRATeMC" ;
definition: "Open source video recording system for acquiring video data that is scalable, flexible, and affordable.Utilizes Raspberry Pi (RPi) miniature computer and 8-megapixel Camera Board that allows for greater manipulation of recording parameters. System may be accessed on GitHub." .
SCR:022326 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TetrODrive" ;
definition: "3D printed microdrive for electrophysiology and optophysiology. Consists of main body and head. Used for in vivo tetrode recording, optical imaging, and optogenetic manipulation in freely moving mice.Design files and build instructions for this device can be found on TetrODrive GitHub.Microdrive can be assembled in 15 min and price for all materials, including 3D printer, is lower than single commercial microdrive." .
SCR:022327 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pi-based Remote Acquisition Technology for Motion Capture" ;
NIFRID:abbrev "PiRATeMC" ;
definition: "Software data management pipeline for camera synchronization and combined data directories." .
SCR:022328 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brainrender" ;
definition: "Software Python package for visualizing and interacting with datasets registered to brain atlases. Used for visualization of neuroanatomical and morphological data." .
SCR:022329 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COMPASS" ;
NIFRID:synonym "Continuous Open Mouse Phenotyping of Activity and Sleep Status" ;
definition: "Non invasive, infrared activity and sleep measurement system that uses passive infrared sensors and Arduino microprocessor. Publication provides protocol for assembling COMPASS as well as provides support protocols and python scripts for data analysis, best practices for optimum results, troubleshooting, and alternative protocols for different use scenarios." .
SCR:022330 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoStereota" ;
definition: "Automated surgical instrument for brain tissue aspiration.Instrument for microendoscope implantation. Utilizes robotic control of needle connected to vacuum pump to aspirate brain tissue. System consists of robotic surgical instrument built around commercially available stereotaxic instrument and open source MATLAB-based GUI for control." .
SCR:022331 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OORTT" ;
NIFRID:synonym "Open source Open access Reaction Time Test" ;
definition: "Software Pyton scripts to run computerised task of Reaction Time. Scripts, together with their instructions and scoresheets.Used for assessment of RTs that is freely available, compatible with all operating systems, without license and activation costs, and based on open source software platform." .
SCR:022332 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cellpose" ;
definition: "Software tool as generalist algorithm for cell and nucleus segmentation." .
SCR:022333 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pyneal" ;
definition: "Open source software package to support rt-fMRI via data in formats generated by Siemens, Philips, and GE. Used to support real time functional magnetic resonance imaging." .
SCR:022334 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DBscorer" ;
definition: "Open source, MATLAB based software for forced swim test and tail suspension test video analysis." .
SCR:022335 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyOS-5 project" ;
NIFRID:synonym "pyOS-5",
"Python based operant box system in 5-choice design" ;
definition: "Open source operant box system optimized for use with tethered animals. System includes hardware and software. Control electronics are build on pyControl, controlling custom PCB integrating 5 infra-red break-beam sensors and 5 stimulus LEDs, single nose-poke for reward receptacle, stepper motor for control of custom peristaltic pump for reward delivery, audio board for tone generation through attached speaker, house light and fan, LED driver for optogenetic stimulation, and bidirectional communication with external devices via TTL pulses." .
SCR:022336 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyOS-5" ;
definition: "Operant Box code" .
SCR:022337 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FlyBrainLab" ;
definition: "Interactive software for visualizing and uncovering function of circuits created from large scale fruit fly brain data. Interactive computing platform for studying function of executable circuits constructed from fruit fly brain data." .
SCR:022338 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GazeMetrics" ;
definition: "Software tool for data extraction and computation of spatial accuracy and precision of head mounted display based eye trackers. Allows for significant customization without altering source code but changes to the code allow for further alteration." .
SCR:022339 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atlas Based Analysis" ;
NIFRID:synonym "ABA project" ;
NIFRID:abbrev "ABA" ;
definition: "Software semi automated brain atlas based analysis pipeline for c-Fos immunohistochemical data. Used to analyze c-Fos in multiple brain regions simultaneously." .
SCR:022340 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DABEST" ;
NIFRID:synonym "Data Analysis with Bootstrapped ESTimation" ;
definition: "Software package for data analysis using bootstrap coupled estimation. Library combining Python, R, and MATLAB for estimation statistics." .
SCR:022341 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Permuco" ;
definition: "Software R package for permutation test in linear model with nuisances variables.Used for permutation testing in regression, ANOVA, and comparison of signals." .
SCR:022342 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VocalMat" ;
definition: "Software MATLAB based toolbox for automated quantitative analysis of ultrasonic vocalizations. Utilizes image processing libraries to detect USVs and computational vision and machine learning algorithms to classify detected USVs. Used for analysis of ultrasonic vocalizations from mice using computer vision and machine learning." .
SCR:022343 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Raspberry Pi based auditory stimulus generator" ;
NIFRID:synonym "Raspberry Pi based auditory stimulus generator project" ;
definition: "Stimulation system for auditory EEG experiments using Raspberry Pi3 B+ board, HiFiBerry audio card to enhance sound quality and trigger tone latency, and custom Python library to generate auditory stimuli." .
SCR:022344 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Florida research open source synchronization tool" ;
NIFRID:synonym "FROST project" ;
NIFRID:abbrev "FROST" ;
definition: "Open source system built around Arduino based microcontroller for analog and digital input and synchronization combined with custom printed circuit board. Hardware and Arduino-based firmware used to synchronize experimental and electrophysiological data." .
SCR:022345 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LED Matrix Stimuli" ;
definition: "Open source device consists of three LED matrices that can be independently controlled via open source Arduino Uno microcontroller. Matrices of LEDs are mounted above nose pokes to examine perceptual decision making in rats. Highly modifiable LED matrices for visual stimulus presentation in behavioral studies.Designs for printing these accessory devices are available in GitHub account for the project." .
SCR:022346 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MARS Developer" ;
definition: "Software MARS based Python pipeline used for detection, pose estimation and behavior classification in experiments of any format. Repository contains all the code you'll need to train your own version of MARS." .
SCR:022347 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mouse Action Recognition System" ;
NIFRID:abbrev "MARS" ;
definition: "Software Python pipeline for automated detection, pose estimation, and behavior classification in socially interacting mice.Used for pose estimation and behavior quantification in pairs of freely behaving mice." .
SCR:022348 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Behavior Ensemble and Neural Trajectory Observatory" ;
NIFRID:abbrev "BENTO" ;
definition: "Software Matlab based tool to visualize and analyze multimodal datasets." .
SCR:022349 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neonatal Stereotaxic Mouse Adaptor" ;
definition: "3D printed device for stereotaxic viral delivery into brains of neonatal mice.Used for stable and precise stereotaxic surgery in neonatal mice." .
SCR:022350 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pain Assessment at Withdrawal Speeds" ;
NIFRID:abbrev "PAWS" ;
definition: "Statistical software platform for automated scoring of pain in mice.Software R package takes paw trajectory data in response to stimulus and provides automated scoring of pain." .
SCR:022351 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepBhvTracking" ;
definition: "Software tool as novel tracking algorithm that combines deep learning and background subtraction." .
SCR:022352 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRI Compatible Microdrive" ;
definition: "MRI compatible microdrive that can precisely position electrodes without causing significant imaging artifacts." .
SCR:022353 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GuPPy" ;
NIFRID:synonym "Guided Photometry Analysis in Python" ;
definition: "Software Python toolbox that makes fiber photometry data analysis intuitive and light on programming.Used to measure neural activity of freely behaving animals." .
SCR:022354 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EZcalcium" ;
definition: "Software package for MATLAB that makes motion correction, segmentation, signal extraction and dimension reduction, analysis, and visualization of calcium imaging data easy to implement. Open source toolbox for analysis of calcium imaging data." .
SCR:022355 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepEthogram" ;
NIFRID:abbrev "DEG" ;
definition: "Software tool to extract relevant features from images and use time series of these features to classify whether given behavior is present in each frame of video recording.machine learning pipeline for supervised behavior classification from raw pixels. Performs action recognition ,automated behavior classification, over frames. Used for automated behavior classification to detect and track behavior over time." .
SCR:022356 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pycro Manager" ;
definition: "Open source software for customized and reproducible microscope control. Software Python package that enables control of micro-manager as well as development of customized experiments integrated with real-time image processing." .
SCR:022357 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1372" ;
rdfs:label "University of Massachusetts Amherst Biophysical Characterization Core Facility" ;
NIFRID:synonym "UMass Amherst Biophysical Characterization Core Facility",
"University of Massachusetts Amherst UMass Amherst Biophysical Characterization Core Facility" ;
definition: "Provides expertise and access to instruments for study of structures and interactions of biological macromolecules such as proteins, nucleic acids, lipids, and complexes. Facility supports both discovery based research and assay development for translational applications. Offers to use equipment independently or with the help of faculty who have expertise in each method." .
SCR:022358 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellExplorer" ;
definition: "Open source framework for single cell characterization and visualization.Graphical user interface, standardized processing module and data structure for exploring and classifying single cells acquired using extracellular electrodes." .
SCR:022359 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DLStream" ;
NIFRID:synonym "DeepLabStream" ;
definition: "Software tool enables closed loop behavioral experiments using deep learning based markerless, real time posture detection.Closed loop behavioral experiment toolkit using pose estimation of body parts." .
SCR:022360 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TweetyNet" ;
NIFRID:synonym "TweetyNet project" ;
definition: "Software tool as single neural network model that learns how to segment spectrograms of birdsong into annotated syllables." .
SCR:022361 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TRex" ;
definition: "Open source animal tracking software tool. Used to visually track movement of multiple animals at once." .
SCR:022362 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenPose" ;
definition: "Software tool as multi subject keypoint detection library for real time pose estimation.Used to track behavior of monkeys in natural environments, without disrupting their typical pattern of behavior. Deep learning software system for body, face, hands, and foot estimation in monkeys." .
SCR:022363 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Timed pressure control hardware and software for delivery of air mediated distensions in animal models" ;
NIFRID:synonym "Timed pressure control hardware and software for delivery of air mediated distensions in animal models project" ;
definition: "System uses Arduino microcontroller to control relay module that operates solenoid valve which all sit in 3D printed housing. Solenoid works in conjunction with flowmeter regulator to allow for controlled flow of pressurized air into target. Timing of distensions is controlled via either custom Python based UI, or by triggered TTL pulse.Timed pressure control hardware and software used for delivery of air mediated distensions in animal models." .
SCR:022364 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SIPEC" ;
NIFRID:synonym "SIPEC project" ;
definition: "Software pipeline for video analysis. Deep learning Swiss knife for behavioral data analysis.Performs segmentation, identification, pose-estimation and classification of complex behaviour. Used for analysis of behavior of multiple animals in complex environments." .
SCR:022365 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Closed Loop Automated Reaching Apparatus" ;
NIFRID:synonym "Closed Loop Automated Reaching Apparatus Project" ;
NIFRID:abbrev "CLARA" ;
definition: "Closed loop automated reaching apparatus for interrogating complex motor behaviors.Mechanical components include behavior box, series of cameras, and food pellet dispenser. Single workstation computer manages cameras, communicates with microcontroller, and analyzes mouse behavior in real time using modules extracted from DeepLabCut. Integrates fully automated, markerless kinematic tracking of multiple features to classify animal behavior and delivers neural stimulation based on behavioral outcomes. CLARA is compatible with advanced neurophysiological tools, enabling testing of neurostimulation devices and identification of novel neurological biomarkers.System fully automates trial initiation and pellet delivery and is capable of accurately delivering stimulation in response to trial outcome with short latency." .
SCR:022366 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1201" ;
rdfs:label "Vanderbilt University Creative Data Solutions Core Facility" ;
NIFRID:synonym "Creative Data Solutions" ;
definition: "Shared Resource that offers bioinformatics and informatics services for basic research and clinical projects." .
SCR:022367 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "shinyCircoss" ;
definition: "Software R/Shiny application for interactive creation of Circos plot. Used for creation of Circos plot interactively." .
SCR:022368 a NLX:63400,
owl:NamedIndividual .
SCR:022369 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pediatric Cancer Data Commons" ;
NIFRID:abbrev "PCDC" ;
definition: "PCDC brings together clinical, genomic, and imaging data from institutions around the world to transform pediatric cancer research and outcomes. Headquartered at University of Chicago, PCDC works with international leaders in pediatric cancers and National Cancer Institute to develop and apply uniform data standards that facilitate collection, combination, and analysis of data from many different sources. PCDC Consortium developes common core data dictionary and common governance structure spanning pediatric cancers neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, and Hodgkin lymphoma to enable innovative cross disease research as well as set standard for future cancer data commons endeavors." .
SCR:022370 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Knowledge based Identification of Pathway Enzymes" ;
NIFRID:abbrev "KIPEs" ;
definition: "Software tool as automatic approach for identification of players in biosynthesis pathway. Used for automatic annotation of flavonoid biosynthesis steps in new transcriptome of genome sequence assembly. Various enzymes of entire metabolic networks can be identified if sufficient knowledge about functionally relevant amino acids is available.Combines comprehensive sequence similarity analyses with inspection of functionally relevant amino acid residues and domains in subjected peptide sequences." .
SCR:022371 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Markov Affinity based Graph Imputation of Cells" ;
NIFRID:abbrev "MAGIC" ;
definition: "Software tool for imputing missing values restoring structure of large biological datasets.Method that shares information across similar cells, via data diffusion, to denoise cell count matrix and fill in missing transcripts." .
SCR:022372 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1385" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Animal Biosafety Level 3 Core Facility" ;
NIFRID:synonym "University of Pennsylvania Perelman School of Medicine Animal Biosafety Level 3 Core Facility (ABSL-3)" ;
definition: "Facility offers procedural and animal housing to perform in vivo research with biosafety level 3 pathogens, such as SARS-CoV-2. Services include consultation, specialized training, and basic/advanced technical services. Provides equipment to longitudinally monitor mice over course of infection. Animal housing space includes three ABSL-3 separate housing cubicles with Allentown BCU-2 animal cages. Animals will be housed under pathogen free conditions at AAALAC accredited University Laboratory Animal Resources facilities within Vernon and Shirley Hill Pavilion using animal protocols approved by Institutional Animal Care and Use Committee." .
SCR:022373 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1387" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Cell and Developmental Biology Microscopy Core Facility" ;
NIFRID:synonym "CDB Microscopy Core",
"Cell & Developmental Biology Microscopy Core",
"University of Pennsylvania Perelman School of Medicine CDB Microscopy Core" ;
definition: "Core provides personalized assistance on all aspects of imaging, from tips on sample preparation to training on one of our microscopes to assistance with image data analysis. Facility houses confocal microscopes, Bruker Vutara 352 super resolution system, Zeiss Z.1 Lightsheet system, three widefield light microscopes, and several computers dedicated to image processing and analysis. Offers scanning electron microscope sample preparation and imaging." .
SCR:022374 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1386" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Bioinformatics Core Facility" ;
NIFRID:synonym "University of Pennsylvania Perelman School of Medicine Bioinformatics Core" ;
definition: "Core provides bioinformatics services that include data analysis and consultation and building of efficient pipelines that handle various biomedical data including Next-Generation Sequencing (NGS) data." .
SCR:022375 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1390" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Electron Microscopy Resource Lab Core Facility" ;
NIFRID:synonym "Electron Microscopy Resource Lab",
"University of Pennsylvania Perelman School of Medicine Electron Microscopy Resource Lab" ;
NIFRID:abbrev "EMRL" ;
definition: "Training and service facility dedicated to providing both conventional transmission electron microscopy of cells and tissues and state of the art cryo-electron microscopy and cryo-electron tomography for structural investigation of macromolecules and cells." .
SCR:022376 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1389" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Cytomics and Cell Sorting Resource Laboratory Core Facility" ;
NIFRID:synonym "Cytomics and Cell Sorting Resource Laboratory",
"Penn Cytomics",
"University of Pennsylvania Perelman School of Medicine Cytomics and Cell Sorting Resource Laboratory" ;
definition: "Flow cytometry shared resource laboratory at the University of Pennsylvania. Facility has instruments, which include analyzers, cell sorters, small particle detectors, dual fluorescence cell counter/viability instrument, tissue dissociator for cell preparation. Provides on-site and off-site support to instrument users, including analyzer and cell sorter training. Core's Research and Development team collaborates/consults with principal investigators in developing high-dimensional panels, as well as staining, acquisition, and analysis." .
SCR:022377 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1378" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Cell and Animal Radiation Core Facility" ;
NIFRID:synonym "Cell and Animal Radiation Core",
"University of Pennsylvania Perelman School of Medicine Cell and Animal Radiation Core" ;
NIFRID:abbrev "CARC" ;
definition: "Core provides services to users for performing precision, image guided radiotherapy with both Photons and Protons (including FLASH proton radiotherapy) on cells, rodents and larger animals. Physicists will provide expert dosimetry and treatment planning capabilities. Instrumentation consists of two image guided SARRP 200 Small Animal Radiation Research Platforms (Xstrahl) capable of irradiating rodent tissues from 1 mm-20 mm in diameter; research proton beamline (IBA, Roberts Proton Center); one X-RAD 320ix cabinet x-ray irradiator (Precision X-Ray); and two Cs gamma-ray irradiators (Shepherd Mark I), suitable for whole body radiation of rodents." .
SCR:022378 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1388" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine CRISPR Cas9 Mouse Targeting Core Facility" ;
NIFRID:synonym "CRISPR Cas9 Mouse Targeting Core",
"University of Pennsylvania Perelman School of Medicine CRISPR Cas9 Mouse Targeting Core" ;
definition: "Core facilitates use of CRISPR/Cas9 genome editing technology to generate novel mouse genetic tools." .
SCR:022379 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1391" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine High Throughput Screening Core Facility" ;
NIFRID:synonym "High-Throughput Screening Core (HTSC)",
"University of Pennsylvania Perelman School of Medicine High-Throughput Screening Core (HTSC)" ;
NIFRID:abbrev "HTSC" ;
definition: "Core provides distribution of lentivirus based shRNA and cDNA plasmid DNA clones; technical expertise in developing biological assays (i.e. biochemical-, cell-, and high-content) in miniaturized, multiwell microtiter plates that are laboratory automation compatible; high-throughput chemical and functional genomic screening, including data analysis and interpretation. Our goal is to use cutting biological models to discover genes and small molecules that enable scientists to further study functions of poorly understood proteins, signaling pathways, and cells in complex biological process relevant to human physiology and disease." .
SCR:022380 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1383" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Human Immunology Core Facility" ;
NIFRID:synonym "Human Immunology Core (HIC)",
"University of Pennsylvania Perelman School of Medicine Human Immunology Core (HIC)" ;
NIFRID:abbrev "HIC" ;
definition: "Core provides wet bench expertise and infrastructure support for early phase�clinical trials and other investigations. Offers purified cell subsets from healthy human apheresis donors. �HIC staff are qualified to�perform blood (PBMC)�and tissue processing for viable cryopreservation following validated�standard operating procedures. Offers�range of immunological assays including digital ELISA, ELISA, ELISPOT, Luminex, flow cytometry and immune repertoire profiling (NGS of BCR and TCR rearrangements in bulk and single cell formats).Offers investigators expertise and guidance in clinical trial sample processing, regulatory compliance, immunology assay design and validation, data analysis and grant writing support." .
SCR:022381 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1392" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Metabolomics Core Facility" ;
NIFRID:synonym "Metabolomics Core",
"University of Pennsylvania Perelman School of Medicine Metabolomics Core" ;
definition: "Core is overseen by Cardiovascular Institute and is partnership with the Abramson Cancer Center and the Institute for Diabetes, Obesity and Metabolism at Penn. Provides expertise in targeted and untargeted metabolomics of biological samples using liquid chromatography/mass spectrometry. Performs assays and assists in interpretation of results." .
SCR:022382 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1394" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Next Generation Sequencing Core Facility" ;
NIFRID:synonym "Next Generation Sequencing Core (NGSC)",
"University of Pennsylvania Perelman School of Medicine Next Generation Sequencing Core (NGSC)" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 10,2025. Core provides services related to single cell and bulk whole genome, RNA-Seq, ATAC-Seq, BIS-Seq, Exome-Seq, ChIP-Seq, CLIP-Seq, etc.Provides Illumina NovaSeq 6000 in addition to NextSeq and MiSeq sequencers - which all feature self-service as well as full-service operation. Offers experience with difficult, low input samples as well as sequencing and analyzing novel library types. Small Oxford Nanopore sequencer allows for full-length RNA or cDNA sequencing as well as very long read (100KB) sequencing from genomes. Offers experimental design services prior to starting your experiment." .
SCR:022383 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1457" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Penn Genomic Analysis DNA Sequencing Core Facility" ;
NIFRID:synonym "Penn Genomic Analysis Core: DNA Sequencing Facility",
"University of Pennsylvania Perelman School of Medicine Penn Genomic Analysis Core: DNA Sequencing Facility" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 8th,2024. Facility offers sequencing services on three platforms, gold standard Sanger sequencing on ABI capillary sequencers, next generation sequencing (NGS) on Ion Torrent PGM and S5 and, Illumina MiSeq along with experimental design and data analysis.NGS service includes library preparation for multiple applications including targeted sequencing, RNA-Seq and Exome-Seq. Capillary sequencers also enable microsatellite genotyping and fragment analysis for VNTR, SNaPshot and Human Cell Line Authentication. Molecular biological services include PCR, cloning, subcloning, mutagenesis, construct preparation and, plasmid DNA preps at different scales." .
SCR:022384 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1395" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Penn Gnotobiotic Mouse Core Facility" ;
NIFRID:synonym "Penn Gnotobiotic Mouse Facility",
"University of Pennsylvania Perelman School of Medicine Penn Gnotobiotic Mouse Facility" ;
definition: "Our core, which is part of the PennCHOP Microbiome Program, provides access for researchers to small experimental isolators for variety of in vivo studies using germ free mice. Core personnel provide technical support for germ-free experiments. New addition to core is state-of-the-art Isocage system." .
SCR:022385 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1396" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Small Animal Imaging Core Facility" ;
NIFRID:synonym "Small Animal Imaging Facility (SAIF)",
"University of Pennsylvania Perelman School of Medicine Small Animal Imaging Facility (SAIF)" ;
NIFRID:abbrev "SAIF" ;
definition: "Core provides comprehensive suite of imaging modalities including magnetic resonance imaging (MRI), spectroscopy (MRS), optical imaging (including bioluminescence, fluorescence, and near-infrared imaging), computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), and ultrasound (US). In addition, dedicated housing is available for mice and rats undergoing longitudinal imaging studies. Ancillary facilities and resources of SAIF are devoted to radiochemistry and image analysis." .
SCR:022386 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1393" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Neurobehavior Testing Core Facility" ;
NIFRID:synonym "Neurobehavior Testing Core (NTC)",
"University of Pennsylvania Perelman School of Medicine Neurobehavior Testing Core (NTC)" ;
NIFRID:abbrev "NTC" ;
definition: "Core provides equipment and services to investigate behavior phenotypes of models related to neurological and other disorders. Core is utilized by scientists across disciplines that are interested in behavioral consequences of unique physiological disruptions (e.g., metabolic, drugs etc.). Provides assessment of many domains of behavior including sensory, motor, social, communication, affect related behaviors and learning and memory. NTC was established in 2012 through generous startup funds from the Penn School of Medicine, the Institute for Translational Medicine and Therapeutics (ITMAT), Center for Sleep and Circadian Neurobiology (CSCN) and Penn Medicine Neuroscience Center (PMNC)." .
SCR:022387 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1379" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Ovarian Cancer Research Center Tumor BioTrust Collection Core Facility" ;
NIFRID:synonym "OCRC Tumor BioTrust Collection",
"University of Pennsylvania Perelman School of Medicine OCRC Tumor BioTrust Collection" ;
NIFRID:abbrev "OCRC TBC" ;
definition: "Provides specimens including gynecologic cancer specimens such as fresh and frozen tissues, plasma, serum, peripheral blood mononuclear cells, blood, formalin fixed paraffin embedded (FFPE) samples, and Tissue Microarrays (TMAs). All samples collected have clinical annotation including demographic patient profiles, pathological and clinical notations, treatment history, and detail disease information, etc. We are building and maintaining centralized research database according to HIPPA specifications and Penn IRB standards." .
SCR:022388 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1397" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Transgenic and Chimeric Mouse Core Facility" ;
NIFRID:synonym "Transgenic and Chimeric Mouse Facility",
"University of Pennsylvania Perelman School of Medicine Transgenic and Chimeric Mouse Facility" ;
definition: "Facility provides centralized service to efficiently produce genetically altered mice for basic research.� They include transgenic, chimeric and genome edited mice carrying transgenes or gene knockout and Knockin of specific interest.�Core also provides embryo and sperm cryopreservation as well as in vitro fertilization and re-derivation of live and cryopreserved lines, along with long-term storage of cryopreserved samples." .
SCR:022389 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1458" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Penn Genomic Analysis Molecular Profiling Core Facility" ;
NIFRID:synonym "Penn Genomic Analysis Core: Molecular Profiling Facility",
"University of Pennsylvania Perelman School of Medicine Penn Genomic Analysis Core: Molecular Profiling Core" ;
definition: "Facility provides full service whole genome and targeted molecular profiling of DNA and RNA on multiple platforms. Core supports quantitative RNA profiling (gene expression) on Affymetrix GeneChips and high-throughput Gene Titan instruments, Fluidigm BioMark HD and, ABI QS 12K real-time PCR machine. DNA profiling (genotyping) is offered on Affymetrix SNP GeneChip and high-throughput Gene Titan instruments, Fluidigm BioMark HD and, ABI QS 12K. Agilent aCGH platform provides genome-wide chromosomal analysis.Users benefit from consultation and training available throughout their projects, including during experimental design and budget development, sample accrual, data management and analyses and, manuscript preparation." .
SCR:022390 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1398" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Chemical and Nanoparticle Synthesis Core Facility" ;
NIFRID:synonym "Chemical and Nanoparticle Synthesis Core (CNSC)",
"University of Pennsylvania Perelman School of Medicine Chemical and Nanoparticle Synthesis Core (CNSC)" ;
NIFRID:abbrev "CNSC" ;
definition: "Provides expertise in medicinal chemistry, metal chelate chemistry, polymer synthesis, nanoparticle production and surface functionalization, and site-specific antibody labeling. Our chemists provide custom, problem specific support for researchers in medical, chemical, and materials science fields. Specific services include consultation and assistance with the design of chemical/medicinal compounds, in house synthesis of chemical/medicinal compounds, custom nanoparticle design and synthesis, custom nanoparticle surface functionalization, polymer and dendrimer synthesis, and site specific antibody labeling." .
SCR:022391 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1401" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Cell Center Services Core Facility" ;
NIFRID:synonym "Cell Center Services Facility",
"University of Pennsylvania Perelman School of Medicine Cell Center Services Facility" ;
definition: "Facility provides basic cell culture training and services in various cell culture and related procedures e.g. Mycoplasma and Endotoxin testing. Services include cell culture at various scales, expansion of primary cells, seed cell cultures from on site cell bank, cell storage; large scale growth of hybridoma and other cell lines followed by antibody purification by protein G column or recombinant protein production; EBV induced transformation of lymphocytes.Offers hybridoma generation by cell fusion and screening and, transfection of mammalian cells. Facility prepares specialized cell culture media, Drosophila media and, various tissue culture and molecular biological reagents." .
SCR:022392 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1399" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Acute Care Biobanking Core Facility" ;
NIFRID:synonym "Acute Care Biobanking Core",
"University of Pennsylvania Perelman School of Medicine Acute Care Biobanking Core" ;
definition: "Core encourages and facilitates microbiome focused research in pathogenesis, diagnosis and treatment of patients with critical illness. Core assists in research by providing de-identified samples with linked clinical metadata to support research in this area, collect specimens as needed in support of microbiome research, and offer support for development of such research in the critical care setting." .
SCR:022393 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1400" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Biostatistics Analysis Center Core Facility" ;
NIFRID:synonym "Biostatistics Analysis Center",
"University of Pennsylvania Perelman School of Medicine Biostatistics Analysis Center" ;
definition: "Provides wide range of biostatistical and epidemiological consulting services." .
SCR:022394 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1380" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Brain Science Service Center Core Facility" ;
NIFRID:synonym "Brain Science Service Center",
"University of Pennsylvania Perelman School of Medicine Brain Science Service Center" ;
definition: "Provides infrastructure support for research on human cognition, perception, affect, disordered cognition, and extension to preclinical models. By consolidating methodological expertise in these domain areas as services, center seeks to facilitate cutting edge research using largely shared set of methods and tools for elucidating brain behavior relationships in health and disease." .
SCR:022395 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1403" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Center for Advanced Computer Tomography Imaging Services Core Facility" ;
NIFRID:synonym "Center for Advanced Computer Tomography Imaging Services (CACTIS)",
"University of Pennsylvania Perelman School of Medicine Center for Advanced Computer Tomography Imaging Services (CACTIS)" ;
NIFRID:abbrev "CACTIS" ;
definition: "CACTIS mission is to oversee proposed research protocols that involve human, animal, phantom or specimen studies in an effort to achieve two goals, to ensure that all research performed on CT scanners comply with CACTIS and University policy, and Federal Regulations, and to determine if CACTIS can maintain the resources required to carry out each research protocol, including personnel, software, hardware and scan time. Additionally, CACTIS oversees the day-to-day operations of all CT procedures associated with research protocols, provides information regarding the use of CT facilities to the research community at the University of Pennsylvania, provides CACTIS users with all of the policies of the institution governing research, and ensures that CACTIS is in compliance with these policies. The service center strives to support the Perelman School of Medicine�s research endeavors by providing CT research services for a fee designed only to cover actual costs." .
SCR:022396 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1404" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Center for Advanced Metabolic Imaging in Precision Medicine Core Facility" ;
NIFRID:synonym "University of Pennsylvania Perelman School of Medicine Center for Advanced Metabolic Imaging in Precision Medicine (CAMIPM)" ;
NIFRID:abbrev "CAMIPM" ;
definition: "Core dedicated to development and application of innovative, novel magnetic resonance and optical imaging techniques. Provides research and computing resources for projects with focus on developing instrumentation, methodologies, and data analysis techniques for quantitative assessment of functional, structural, and metabolic parameters in humans with use of multinuclear magnetic resonance, novel spectral, perfusion, functional, and optical imaging techniques." .
SCR:022397 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1406" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Center for Biomedical Image Computing and Analytics Core Facility" ;
NIFRID:synonym "Center for Biomedical Image Computing & Analytics (CBICA)",
"University of Pennsylvania Perelman School of Medicine Center for Biomedical Image Computing & Analytics (CBICA)" ;
NIFRID:abbrev "CBICA" ;
definition: "Offers development and application of advanced computational and analytical techniques that quantify morphology and function from biomedical images, as well as on relating imaging phenotypes to genetic and molecular characterizations, and on integrating this information into diagnostic and predictive tools in era of personalized medicine. Computational methods can contribute significantly to automated, reproducible and quantitative interpretations of biomedical images. Translates advanced computational and analytical imaging methods to clinic, by providing forum in which interactions between researchers and clinicians facilitate bidirectional flow of ideas, algorithms and data between laboratory and clinic." .
SCR:022398 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1405" ;
rdfs:label "University of Pennsylvania Center for Advanced Magnetic Resonance Imaging and Spectroscopy Core Facility" ;
NIFRID:synonym "Center for Advanced Magnetic Resonance Imaging and Spectroscopy",
"Center for Advanced Magnetic Resonance Imaging and Spectroscopy Core Facility",
"Center for Advanced MRI and Spectroscopy (CAMRIS)",
"University of Pennsylvania Perelman School of Medicine Center for Advanced MRI and Spectrometry (CAMRIS)" ;
NIFRID:abbrev "CAMRIS" ;
definition: "Center for Advanced Magnetic Resonance Imaging and Spectroscopy (CAMRIS) is a Radiology research core at the University of Pennsylvania’s Perelman School of Medicine providing oversight in the responsible use and application of Magnetic Resonance (MR) in research at Penn. CAMRIS oversees eight state-of-the-art whole-body MR scanners and provides scanning services by experienced technologists to a diverse community of investigators conducting innovative human and animal research." .
SCR:022399 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1402" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Cell Center Stockroom Core Facility" ;
definition: "Core is division of Genetics Core Facilities, University service center to provide consultation, training, and services in areas of cell culture and hybridomas. Stockroom serves University of Pennsylvania investigators and affiliate institutions by coordinating relations with various suppliers of molecular biological research materials. This involves not only bulk purchasing of these products, but negotiation of discounts and convenient delivery arrangements. Special ordering of non regularly stocked products is available from 28 bioreagent vendors with discounted pricing and overnight delivery." .
SCR:022400 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1409" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Center for Preventive Ophthalmology and Biostatistics Biostatistical Consulting Core Facility" ;
NIFRID:synonym "Center for Preventive Ophthalmology and Biostatistics (CPOB) Biostatistical Consulting",
"University of Pennsylvania Perelman School of Medicine Center for Preventive Ophthalmology and Biostatistics (CPOB) Biostatistical Consulting" ;
definition: "Service supports consultation and collaboration in areas of biostatistics and epidemiology to Penn vision scientists. Biostatisticians and data management experts provide advice on study design, and offer services in sample size determinations, data management, data analysis, data interpretation, and data presentation. They are active participants in the development and writing of grant applications and manuscripts.Consulting personnel are CPOB members. In addition to their methodological and technical expertise, consultants are knowledgeable about ocular conditions under study in Penn vision community, about commonly used measures that are unique to vision research (visual acuity, refractive error, visual field indices, etc) and specialized statistical analysis techniques required for many experimental designs used in vision research (correlated data techniques to handle appropriately data from two eyes of same subject). Majority of projects are patient oriented researchers,however, CPOB Consulting Service also works on data analysis with bench laboratory scientists." .
SCR:022401 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1407" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Center for BioMedical Informatics Core Facility" ;
NIFRID:synonym "Center for BioMedical Informatics Core (BMIC)",
"University of Pennsylvania Perelman School of Medicine Center for BioMedical Informatics Core (BMIC)" ;
NIFRID:abbrev "BMIC" ;
definition: "Supports next generation infrastructure for clinical data storage and management, next generation analytics, next generation infrastructure for support of clinical research including new clinical trials management system and software, next generation infrastructure for centralizing and integrating external sources of data such as genomics data. Enables future clinical and translational research through biomedical informatics education and training targeted at graduate students, postdoctoral students, residents, fellows, as well as faculty across the biomedical research spectrum." .
SCR:022402 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1408" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Center for Human Phenomic Science (CHPS)" ;
NIFRID:synonym "Center for Human Phenomic Science (CHPS)" ;
NIFRID:abbrev "CHPS" ;
definition: "CHPS is comprised of several Clinical Research Cores designed to facilitate research process. Provides resources, environment, operations, and training to support and promote high quality clinical and translational research by qualified investigators." .
SCR:022403 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1410" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Center for AIDS Research Virus and Reservoirs Core Facility" ;
NIFRID:synonym "CFAR Virus & Reservoirs Core",
"University of Pennsylvania Perelman School of Medicine CFAR Virus & Reservoirs Core" ;
definition: "Facility provides comprehensive viral and molecular support in area of basic, translational and clinical HIV research, consultation, training, and mentoring.Is available to develop customized viral and molecular support services as needed. Offers deep sequencing support and single genome amplification services. " .
SCR:022404 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1411" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Clinical Research Collaboration Unit Core Facility" ;
NIFRID:synonym "Clinical Research Collaboration Unit (CRCU)",
"University of Pennsylvania Perelman School of Medicine",
"University of Pennsylvania Perelman School of Medicine Clinical Research Collaboration Unit (CRCU) Core Facility" ;
NIFRID:abbrev "CRCU" ;
definition: """Provides comprehensive services essential to the conduct of clinical research projects, including Phase I-IV, multi-center, randomized, clinical trials, registry, and cohort studies. Offers expert staff who maintain a strong focus on data integrity and quality and offers support in optimizing process tracking and management to enhance operational efficiency.
Core specializes in the following: Study design and development; Site management and training; Data collection, processing, and quality control; Regulatory requirements and reporting; Database development, storage, and security; System integration (e.g., EPIC data); 21CFR Part 11 Compliance; Proposal development and administration; REDCap development; Honest Broker services.""" .
SCR:022405 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1415" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Radioimmunoassay and Biomarkers Core Facility" ;
NIFRID:synonym "Radioimmunoassay and Biomarkers Core Facility",
"RIA/Biomarkers Core" ;
definition: "Core offers immunoassay, metabolite, and HPLC services to basic, translational, and clinical investigators performing diabetes and related metabolic disease research.RIA /Biomarkers Core is located on the 12th floor of Smilow Center for Translational Research.Approximately 100 different diabetes, obesity and metabolism-related biomarkers from multiple species including human can be assayed using radioimmunoassay (RIA), enzyme-linked immunosorbent assay (ELISA, both absorbance and fluorometric), multiplex ELISA on the Luminex platform, and enzymatic and HPLC methods for an expanding variety of diabetes and metabolism related metabolites, hormones, catecholamines and cytokines derived from blood, urine, and tissue samples." .
SCR:022406 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1412" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine CUBIC (HPC Cluster)" ;
NIFRID:synonym "CUBIC (HPC Cluster)" ;
definition: "Linux based High Performance Computing resource available to faculty conducting research related to medical imaging and informatics. There are over 150 compute nodes with more than 5000 Intel Xeon CPUs and 58TB of RAM, over 100 GPUs, and 600TB of storage in the cluster. Facility management structure is designed to encourage data sharing and use of common software on this powerful resource, particularly in development of new software and application of imaging to new domains." .
SCR:022407 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1414" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Cooperative Human Tissue Network Core Facility" ;
NIFRID:synonym "Cooperative Human Tissue Network (CHTN)",
"University of Pennsylvania Perelman School of Medicine Cooperative Human Tissue Network (CHTN)" ;
NIFRID:abbrev "CHTN" ;
definition: "Human tissue procurement service within Department of Pathology at HUP, that assists investigators with collection, processing and preservation of research samples. Our staff will personalize sample acquisition and processing to meet project requirements. Samples (malignant, normal, diseased, etc.) and biofluids can be preserved in a range of methods (fresh, frozen, fixed, etc.)." .
SCR:022408 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1413" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Community Engagement and Research Core Facility" ;
NIFRID:synonym "Community Engagement & Research (CEAR)",
"University of Pennsylvania Perelman School of Medicine Community Engagement & Research (CEAR)" ;
NIFRID:abbrev "CEAR" ;
definition: "Core aims to facilitate and build capacity for community based research and community engagement, while enhancing translation of research and technological developments to key public health and community stakeholders. Offers consultation on community engagement, training in participatory research methods, and assistance with development, implementation, and evaluation of community translation activities. Core is part of the Penn Institute for Translational Medicine and Therapeutics (ITMAT)." .
SCR:022409 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1418" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine IBI Clinical Research Informatics Core Facility" ;
NIFRID:synonym "IBI Clinical Research Informatics Core",
"University of Pennsylvania Perelman School of Medicine IBI Clinical Research Informatics Core" ;
NIFRID:abbrev "CIC" ;
definition: "Core assists faculty, staff, and students with conducting research projects using electronic health record data.Facilitates access to clinical data and performs data analysis using artificial intelligence, ontologies, natural language processing, machine learning, and visual analytics. Provides innovative research services by applying data science to clinical data in order to learn actionable healthcare knowledge and develop impactful solutions for improving patient care. Services include facilitating access to Penn Medicine clinical data resources, performing data analysis using diverse computational methods, and providing tools for exploratory data analysis/visualize with priority access to the IBI Idea Factory for immersive display of data and research results. �" .
SCR:022410 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1419" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center Core Facility" ;
NIFRID:synonym "IFI CyTOF Service Center",
"University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center" ;
NIFRID:abbrev "CyTOF" ;
definition: "CyTOF�enables multi-parametric high-dimensional single�cell analysis�of more than 40 markers per cell, with�minimal background and compensation�issues.�Core�offers variety of�CyTOF-related services including�reagent distribution, consultation,�antibody conjugation, and data acquisition.�" .
SCR:022411 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1420" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Pancreatic Islet Cell Biology Core Facility" ;
NIFRID:synonym "Pancreatic Islet Cell Biology Core",
"University of Pennsylvania Perelman School of Medicine Pancreatic Islet Cell Biology Core" ;
definition: "Provides support including experimental design, islet isolation, and performance of and/or training in range of assays for physiological, metabolic, and morphometric assessment of pancreatic islets as wells as many other tissues and cell types. Offers islet isolation and culture, free intracellular calcium ion measurements, quantitative oxygen consumption of pancreatic islets, electrode based closed cell respirometry, and access to Agilent�s� Seahorse Extracellular Flux Analyzer XFe96." .
SCR:022412 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1417" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Human Intervention Core Facility" ;
NIFRID:synonym "Penn Microbiome Human Intervention Core",
"University of Pennsylvania Perelman School of Medicine Human Intervention Core" ;
definition: "Offers services to assist with design and implementation of microbiome studies.Assist with longitudinal studies as well as pilot studies.� Pilot studies can be rapidly implemented with human intervention core staff, project managers and research coordinators." .
SCR:022413 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1422" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine ITMAT Study Design and Biostatistics Core Facility" ;
NIFRID:synonym "ITMAT Study Design and Biostatistics Core (SDAB)",
"University of Pennsylvania Perelman School of Medicine ITMAT Study Design & Biostatistics Core (SDAB)" ;
NIFRID:abbrev "SDAB" ;
definition: "Core works with existing resources to provide targeted study design and biostatistics support to ITMAT/CTSA investigators.Services include protocol review, study design, proposal development, and performance of simple to potentially substantial complex analyses. SDAB integrates support available with HUP and CHOP Center for Human Phenomic Science (CHPSs), expertise and resources of faculty in Center for Clinical Epidemiology and Biostatistics / Department of Biostatistics and Epidemiology (CCEB/DBE), Biostatistics Analysis Center (BAC), and Biostatistics and Data Management Core (BDMC) at CHOP." .
SCR:022414 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1423" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Johnson Foundation Biophysical and Structural Biology Core Facility" ;
NIFRID:synonym "Johnson Foundation Biophysical and Structural Biology Core (JFBSB)",
"University of Pennsylvania Perelman School of Medicine Johnson Foundation Biophysical and Structural Biology Core (JFBSB)" ;
NIFRID:abbrev "JFBSB" ;
definition: "Provides unique equipment and expertise to facilitate modern biophysical characterization and structural analysis of proteins and other biomolecules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:022415 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1421" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank Core Facility" ;
NIFRID:synonym "University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank" ;
NIFRID:abbrev "PMBB" ;
definition: "BioBank supports researchers by providing centralized access to large number of annotated blood and tissue samples." .
SCR:022416 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1416" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Host-Microbial Analytic and Repository Core Facility" ;
NIFRID:synonym "Host Microbial Analytic and Repository Core (H-MARC)",
"University of Pennsylvania Perelman School of Medicine Host-Microbial Analytic and Repository Core (H-MARC)" ;
NIFRID:abbrev "H-MARC" ;
definition: "Core within Division of Gastroenterology provides services which�represents intersection between host and their microbes in both�preclinical and clinical human subject research.Offers human biospecimen repository with associated clinical metadata, instrumentation/access to critical analytic services to characterize expression (i.e. genomics, transcriptomics, metabolomics, microbial culture, etc.) in both microbes and�their mammalian hosts, as well as expertise to extend pre-clinical in vitro and animal model research into human clinical domain. �" .
SCR:022417 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1381" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Microbial Culture and Metabolomics Core Facility" ;
NIFRID:synonym "Microbial Culture & Metabolomics Core",
"University of Pennsylvania Perelman School of Medicine Microbial Culture & Metabolomics Core" ;
definition: "Provides equipment for aerobic and anaerobic culture of microbial species in both batch and continuous systems, as well as targeted metabolomic services of amino, bile, and short chain fatty acids. Offers training and usage for culture equipment; consultation regarding experimental design, and; anaerobic culture services. Examples of culture studies include isolation of microbial taxa from mammalian samples; interrogation of the physiology of microbial strains under different conditions (e.g., anaerobic/microaerobic/aerobic, differing nutrient limitations) using isolated strains or strains obtained from culture collections (another service offered by the core); co-culturing of defined microbial consortia to investigate microbe-microbe interactions, and; preparation of microbial products (live bacteria, heat-killed bacteria, bacterial supernatants) from single or defined-mixed microbial cultures for use in mammalian cell culture and/or animal model systems." .
SCR:022418 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1425" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Mixed Methods Research Lab Core Facility" ;
NIFRID:synonym "Mixed Methods Research Lab (MMRL)",
"University of Pennsylvania Perelman School of Medicine Mixed Methods Research Lab (MMRL)" ;
NIFRID:abbrev "MMRL" ;
definition: "Fosters the use of qualitative and mixed methods research methodologies with focus on integrating key stakeholder perspectives and goals into research designs. Collaborates with investigators to address timely, pressing questions across diverse disciplines and works with investigators to provide conceptual as well as technical support for broad research programs, including clinical, community based, and implementation science research questions." .
SCR:022419 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1377" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Mouse Cardiovascular Phenotyping Core Facility" ;
NIFRID:synonym "Mouse Cardiovascular Phenotyping Core",
"University of Pennsylvania Perelman School of Medicine Mouse Cardiovascular Phenotyping Core" ;
definition: "Core provides services to assess cardiovascular function in mouse models and to provide validated surgical models of heart and vascular disease in mice to assess genetic or therapeutic interventions. Works with investigators to design and implement study along with any associated grant applications, animal protocol submissions and manuscript preparation. While central focus of facility is cardiovascular research, techniques employed are often useful to investigators in other fields. Helps to assess your needs and provide necessary technical training and scientific assistance in animal protocol preparation. Core runs on a fee for service model.�Accordingly, investigators will be responsible for costs incurred for their projects and prior animal protocol approval by Penn IACUC., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:022420 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1426" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Molecular Pathology and Imaging Core (MPIC)" ;
NIFRID:synonym "Molecular Pathology and Imaging Core (MPIC)" ;
NIFRID:abbrev "MPIC" ;
definition: "Provides histological services, equipment, and technical expertise for processing and analyses of digestive, pancreatic, and liver tissues as well as three dimensional tissue culture models.�Part of the Center for Molecular Studies in Digestive and Liver Diseases" .
SCR:022421 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1428" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Neurons R Us Core Facility" ;
NIFRID:synonym "Neurons R Us (NRU)",
"University of Pennsylvania Perelman School of Medicine Neurons R Us (NRU)" ;
NIFRID:abbrev "NRU" ;
definition: "Core supplies suspensions of neuronal cells prepared from rodent brain for various downstream applications, including primary cell culture. Supplies rat or mouse cells isolated from cortex or hippocampus either in suspension or plates. Custom dissection services are available for other brain regions or for user supplied genetically modified mice." .
SCR:022422 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1427" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Muscle Physiology Assessment Core Facility" ;
NIFRID:synonym "Muscle Physiology Assessment Core",
"University of Pennsylvania Perelman School of Medicine Muscle Physiology Assessment Core" ;
definition: "Core provides investigators with customizable tools and methodolgies to assess in vivo exercise performance, metabolism and respiratory function, as well as in vivo and ex vivo muscle contractility. Provides guidance and training to investigators who want to learn how to collect and process muscle samples for specific uses." .
SCR:022423 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1429" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Nuclear Medicine Physics and Instrumentation Group Core Facility" ;
NIFRID:synonym "Nuclear Medicine Physics & Instrumentation Group",
"University of Pennsylvania Perelman School of Medicine Nuclear Medicine Physics & Instrumentation Group" ;
definition: "Core focuses on imaging in nuclear medicine, and engages in collaboration with clinicians and research investigators to optimize new instruments for applications in both clinical and pre clinical (animal) imaging scenarios. Offers equipment to build, test and characterize detectors for PET imaging, operates cluster of high powered Linux computers, which reconstruct, process, and analyze imaging data. Focuses on technology, which increases signal to noise of reconstructed images for whole body studies. Conducts research on SPECT imaging with emphasis on applications to small animal and brain imaging, oversees operation of cyclotron and imaging probe synthesis facilities." .
SCR:022424 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1432" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Research Instrumentation Shop Core Facility" ;
NIFRID:synonym "Research Instrumentation Shop (RIS)",
"University of Pennsylvania Perelman School of Medicine Research Instrumentation Shop (RIS)" ;
NIFRID:abbrev "RIS" ;
definition: "Shared resource machine shop serving various University of Pennsylvania Schools and Departments. Assists researchers to design and construct both laboratory and clinical instruments." .
SCR:022425 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1424" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine MINS Machine Shop Core Facility" ;
NIFRID:synonym "MINS Machine Shop",
"University of Pennsylvania Perelman School of Medicine MINS Machine Shop" ;
definition: "Designes and buildes novel instruments and apparatus for research to user specifications. Works with users to develop initial project drawing, and will explore alternate designs to insure desired functionality. Fabricates user devices to high tolerance, using machine tools and materials, and can repair laboratory devices even if devices were constructed elsewhere." .
SCR:022426 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1430" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Induced Pluripotent Stem Cell Core Facility" ;
NIFRID:synonym "Induced Pluripotent Stem Cell Facility",
"University of Pennsylvania Perelman School of Medicine Induced Pluripotent Stem Cell Facility" ;
NIFRID:abbrev "iPSC" ;
definition: "Provides resources for disseminating human pluripotent stem cell technology within UPenn and surrounding research communities. �Our services include derivation of patient specific iPSCs, genome engineering of stem cell lines using CRISPR/Cas9 technology, and lineage specific differentiation of iPSCs/hESCs in 2D and 3D organoid culture.�Core has large collection of patient derived iPSC lines and cell lines of gastrointestinal tract (esophageal, pancreatic and intestinal) available to users.�Committed to training investigators in stem cell culture techniques and providing quality tested stem cell reagents to users." .
SCR:022427 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1433" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Rodent Metabolic Phenotyping Core Facility" ;
NIFRID:synonym "Rodent Metabolic Phenotyping Core (RMPC)",
"University of Pennsylvania Perelman School of Medicine Rodent Metabolic Phenotyping Core (RMPC)" ;
NIFRID:abbrev "RMPC" ;
definition: "Core (RMPC, formerly MPPMC) is metabolic core. Offers technology and phenotyping services to allow investigators to study metabolism in pre-clinical rodent models. Services include measurements of body composition (fat and lean mass) using NMR and DEXA, energy balance (food intake, locomotor activity, energy expenditure) using indirect calorimetry in either Columbus Instruments CLAMS system or Sable Systems Promethion System (with optional gas analyzer), and other in vivo metabolic phenotyping services (glucose clamps, insulin and glucose tolerance tests, telemetric monitoring of blood glucose or blood pressure, bomb calorimetry)." .
SCR:022428 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1434" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Translational Bio-Imaging Center Core Facility" ;
NIFRID:synonym "Translational Bio-Imaging Center (TBIC)",
"University of Pennsylvania Perelman School of Medicine Translational Bio-Imaging Center (TBIC)" ;
NIFRID:abbrev "TBIC" ;
definition: "Mission is to act as portal for research community into Bio-medical imaging resources of University of Pennsylvania. Goals include creating and maintaining access for research community to Bio-medical imaging technologies, enabling research investigators to benefit from Bio-imaging expertise and experience, and educating researchers about Bio-medical imaging options through targeted seminars, research fellowships, and established training programs." .
SCR:022429 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1431" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Positron Emission Tomography Center Core Facility" ;
NIFRID:synonym "PET Center",
"University of Pennsylvania Perelman School of Medicine PET Center" ;
definition: "Dedicated to continuing advancement of molecular imaging and seeks to build network of collaborators to conduct translational research using existing and new radiotracers to help better understand the diagnosis, physiology and treatment of multiple diseases. Educates referring clinicians and their patients about emerging benefits of PET/CT diagnostic procedures, other radiotracer imaging methods and radionuclide therapies as tools in their research and clinical practice.Provides opportunities and mentoring for individuals interested in pursuing work or collaborations within molecular imaging field. Provides scanners as well as cyclotron facility." .
SCR:022430 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1435" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Tumor Tissue Biospecimen Bank Core Facility" ;
NIFRID:synonym "Tumor Tissue/Biospecimen Bank (TTAB)",
"University of Pennsylvania Perelman School of Medicine Tumor Tissue/Biospecimen Bank (TTAB)" ;
NIFRID:abbrev "TTAB" ;
definition: "Centralized biorepository of human biosamples. TTAB is responsible for the collection, processing, and storage of human blood, fluid, and tissue at the University of Pennsylvania Health System. TTAB has a collection bench within Surgical Pathology Suite at Hospital of University of Pennsylvania (HUP).� Our collection bench sits adjacent to frozen section teams managing clinical sample collection and allowing for tight integration of tissue sample collection with clinical pathology teams." .
SCR:022431 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1436" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Ultrasound Research Laboratory Core Facility" ;
NIFRID:synonym "Ultrasound Research Laboratory",
"University of Pennsylvania Perelman School of Medicine Ultrasound Research Laboratory" ;
definition: "Develops new ultrasound technologies and clinical applications, to bridge gap between technology and clinical applications, and to provide ultrasound imaging resources to other research. Consists of core group of scientists, sonographers and technicians with expertise in ultrasound technology and computer programming. This group works with clinicians in multiple specialties; including radiologists, cardiologists and surgeons. Core provides ultrasound scanner, sonographer and part-time radiologist on staff to conduct clinical and pre-clinical imaging.Helps with studies involving measurement of angiogenesis, vascularity, tissue elasticity, contrast agents, and effects of various physical and pharmaceutical agents on blood flow and tissue vascularity. Studies include research on cancer, cardiovascular disease and musculoskeletal disease." .
SCR:022432 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1437" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Vector Core Facility" ;
NIFRID:synonym "University of Pennsylvania Perelman School of Medicine Vector Core",
"Vector Core" ;
definition: "Resource for investigators requiring viral vectors for preclinical studies and other basic research applications such as gene therapies for acquired and inherited diseases.Provides production of high quality vectors and distribution of improved vector technologies services." .
SCR:022433 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1438" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Viral Molecular High Density Sequencing Core Facility" ;
NIFRID:synonym "Viral Molecular High Density Sequencing Core Facility" ;
definition: "Offers Illumina sequencing and bioinformatic expertise to assist researchers�with gene therapy trial evaluations, viral integration profiling,�CRISPR off-target�analyses. Assists with bioinformatic analyses including RNAseq transcription profiling�and 16S taxonomic assignments.�" .
SCR:022434 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1440" ;
rdfs:label "University of Pennsylvania Penn Vet Center for Host Microbial Interactions Core Facility" ;
NIFRID:synonym "Penn Vet Center for Host Microbial Interactions",
"University of Pennsylvania Penn Vet Center for Host Microbial Interactions" ;
NIFRID:abbrev "CHMI" ;
definition: "Offers consultation and laboratory services for high-throughput sequencing (HTS) experiments, with particular expertise and interest in microbiome/metagenome and RNA-seq applications. Provides instrumentation, including Illumina NextSeq 2000 and single cell platforms from 10X genomics and 1CellBio. Offers full service options, as well as hands on instruction for trainees who want to learn best practices for wet lab aspects of genomics experiments. Offers consultation services for all phases of HTS studies, from study design to bioinformatics analysis." .
SCR:022435 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1439" ;
rdfs:label "University of Pennsylvania Animal Model Core Facility" ;
NIFRID:synonym "Animal Model Core",
"University of Pennsylvania Perelman School of Medicine Animal Model Core" ;
definition: "Supports discovery to invention to innovation in medical translation.Provides animal model development to enhance scientific rigor during in vivo studies in experimental or naturally occurring disease models. Studies can start on small scale leading towards pivotal non-clinical IND/IDE-enabling trials in support of FDA or OUS-FDA submissions. Core hosts PIs, trainees and sponsors during clinical procedures to support and enrich their experience in cross functional team setting." .
SCR:022436 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1443" ;
rdfs:label "University of Pennsylvania Penn Vet Imaging Core Facility" ;
NIFRID:synonym "Penn Vet Imaging Core",
"University of Pennsylvania Penn Vet Imaging Core" ;
NIFRID:abbrev "PVIC" ;
definition: "Provides access to optical imaging capabilities for researchers at the University of Pennsylvania, Perelman School of Medicine, Children's Hospital of Philadelphia, and Wistar Institute. Provides instruments and expertise to perform widefield, confocal, multiphoton/intravital imaging, fluorescence lifetime imaging, high content live cell screening, long term single cell imaging, second harmonic imaging, structured illumination super resolution, and total internal reflection fluorescence microscopy, as well as software tools for image analysis. Core has adjacent (in and out) ULAR approved facility to house animals for long term live animal studies." .
SCR:022437 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1444" ;
rdfs:label "University of Pennsylvania Leonard Davis Institute of Health Economics Data Analyst Pool Core Facility" ;
NIFRID:synonym "LDI Health Economics Data Analyst Pool (HEDAP)",
"University of Pennsylvania Leonard Davis Institute of Health Economics LDI Health Economics Data Analyst Pool (HEDAP)" ;
NIFRID:abbrev "HEDAP" ;
definition: "Provides LDI affiliated investigators access to high quality, skilled data analysts. HEDAP recruits, trains, and manages group of masters level and PhD level statistical analysts. These analysts work with multi disciplinary investigators across funded projects using statistical software packages such as SAS, Stata, and R to manipulate and analyze health care data under guidance of investigators and other collaborators." .
SCR:022438 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1382" ;
rdfs:label "University of Pennsylvania Penn Vet Comparative Pathology Core Facility" ;
NIFRID:synonym "Penn Vet Comparative Pathology Core",
"University of Pennsylvania Penn Vet Comparative Pathology Core" ;
NIFRID:abbrev "CPC" ;
definition: "Provides support to investigators utilizing animal models to study disease. Comparative Pathology Core, Abramson Cancer Center shared resource, provides expert pathological characterization and validation of mouse and other animal models used in biomedical research by offering expertise of board certified veterinary pathologists and access to histology, immunohistochemistry, and digital pathology services." .
SCR:022439 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1445" ;
rdfs:label "University of Pennsylvania Leonard Davis Institute of Health Economics Health Services Research Data Center Core Facility" ;
NIFRID:synonym "LDI Health Services Research Data Center (HSRDC)",
"University of Pennsylvania Leonard Davis Institute of Health Economics LDI Health Services Research Data Center (HSRDC)" ;
NIFRID:abbrev "HSRDC" ;
definition: "Provides secure environment for investigators analyzing protected health information. �It coordinates acquisition, storage, and analysis of data from private and government sources (e.g., Medicare, Medicaid, and others) and facilitates their use by researchers who seek to answer important questions regarding health policy and health care.�" .
SCR:022440 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1447" ;
rdfs:label "University of Pennsylvania Penn Vet Referral Center for Animal Models of Human Genetic Disease Core Facility" ;
NIFRID:synonym "Penn Vet Referral Center for Animal Models of Human Genetic Disease",
"University of Pennsylvania Penn Vet Referral Center for Animal Models of Human Genetic Disease" ;
definition: "Core mission is to discover, create, characterize, treat, and share naturally occurring hereditary disorders in dogs and cats that are orthologous to those found in human patients.�Provides expertise in discovering, characterizing, and developing therapies for genetic disease in dogs and cats, which serve as models of same diseases that occur in children.�Specializes in molecular discovery of mutations, clinical phenotyping, biochemical and histological characterization, development of therapies which are translatable to human patients and preclinical trials in animal models of human disease.�" .
SCR:022441 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1448" ;
rdfs:label "University of Pennsylvania Penn Vet Transgenic Mouse Core Facility" ;
NIFRID:synonym "Penn Vet Transgenic Mouse Core",
"University of Pennsylvania Penn Vet Transgenic Mouse Core" ;
definition: "Offers embryological manipulation services, focused on, but not limited to, murine model systems. These services primarily enable generation of genetically modified murine models, as well as experimental research in germ cell function and early embryonic development." .
SCR:022442 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1442" ;
rdfs:label "University of Pennsylvania Penn Dental Medicine Live Cell Imaging Core Facility" ;
NIFRID:synonym "Penn Dental Medicine Live Cell Imaging Core",
"University of Pennsylvania Penn Dental Medicine Live Cell Imaging Core" ;
definition: "Offers wide array of live cell imaging applications.Provides Nikon A1R Laser Scanning Confocal Microscopy system equipped with 4 laser lines to provide 6 different excitation/emission configurations; multiple photomultiplier tubes (PMTs), 32-channel spectral detector, full complement of microscope objectives, high speed image scanner, fully motorized stage and completely controllable environmental chamber. Users have access to NIS Elements AR software and 2D/3D deconvolution module offering sophisticated image analysis and processing features." .
SCR:022443 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1446" ;
rdfs:label "University of Pennsylvania Penn Dental Medicine Flow Cytometry Core Facility" ;
NIFRID:synonym "Penn Dental Medicine Flow Cytometry Core",
"University of Pennsylvania Penn Dental Medicine Flow Cytometry Core" ;
definition: "Provides Becton Dickinson LSR II flow cytometer equipped with four lasers.Blue laser can be used to detect forward and side scatter and 4 colors (eg., FITC/Alexa 488, PE, PerCP-CY55, PE-CY7), red laser can be used to detect 2 colors (e.g., APC and APC-CY7), violet laser can be used to detect 2 colors (e.g., Pacific blue, Am cyan) and a UV laser which can also be used to detect 2 colors (e.g., INDO1 blue, Indo1-violet/DAPI). The instrument is located in Room 330 in the Levy Building (240 South 40th Street)." .
SCR:022444 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1441" ;
rdfs:label "University of Pennsylvania Penn Vet Extracellular Vesicle Core Facility" ;
NIFRID:synonym "Penn Vet Extracellular Vesicle (EV) Core Facility",
"University of Pennsylvania Penn Vet Extracellular Vesicle (EV) Core Facility" ;
definition: "Provides comprehensive or selected services in necessary isolation, quantification and characterization of EVs. Isolation of EV is based on size exclusion using high-performance (SEC-HPLC) or gravity fed (e.g. iZon column) liquid chromatography, ultracentrifugation, and/or density gradient ultracentrifugation. Accurately characterizes EV particle size distribution and concentration using resistive pulse sensing techniques (nCS1, Spectradyne, LLC). Immunophenotype can be accomplished using nanoscale flow cytometry and/or chip array (ExoViewTM) techniques. Provides services in training and education for individuals and lab groups in all methods above and study design consultation." .
SCR:022463 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SipperViz" ;
definition: "Software Python GUI for graphing measures of liquid ingestion in rodents from Sippers. Python GUI for visualizing Sipper data." .
SCR:022464 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Meta Essentials" ;
NIFRID:synonym "Meta-Essentials" ;
definition: "Software tool for meta analysis. Facilitates integration and synthesis of effect sizes from different studies. Consists of set of workbooks designed for Microsoft Excel that automatically produces all required statistics, tables, figures, and more." .
SCR:022465 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tourmaline" ;
definition: "Software tool as amplicon sequence processing workflow using QIIME 2 and Snakemake management system.Enables rapid analysis of environmental and biomedical amplicon data, decreasing time from data generation to actionable results." .
SCR:022466 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1356" ;
rdfs:label "University of Ottawa Bioinformatics Core Facility" ;
NIFRID:synonym "Ottawa Bioinformatics Core Facility",
"uOttawa - Bioinformatics Core Facility" ;
definition: "Core of University of Ottawa and Ottawa Hospital Research Institute. Provides advice on bioinformatics research design, conduct bioinformatics analysis, and provide support for grant proposals that involve bioinformatics (including conducting pilot studies, support/collaboration letters and methodological text). Areas of expertise include:Analysis of high throughput sequencing data; single cell (Chromium 10x), RNA-seq (including small RNA), ChIP-seq, ATAC-seq, Hi-C.Large scale analysis integrating multiple data types.Helps to arrange for analysis of your biological samples with local core facilities such as StemCore, Proteomics Resource Center, or OHRI Mass Spectrometry Core Facility. Provides yearly training courses in RNA-seq analysis and Bioinformatics analysis using R as well as individual training and analysis support on request." .
SCR:022467 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1375" ;
rdfs:label "University of Nebraska Medical Center Advanced Microscopy Core Facility" ;
NIFRID:synonym "UNMC Advanced Microscopy Core Facility" ;
definition: "Facility houses imaging technologies ranging from super resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across imaging instrumentation. Instrumentation includes Zeiss ELYRA PS.1 is inverted microscope for super resolution (SR) structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM);Zeiss 800 CLSM with Airyscan is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology; Zeiss 710 LSM is inverted microscope supporting most basic imaging applications, multi channel and spectral, co localization, live cell, 3D, and time series imaging; Zeiss Celldiscoverer 7 is widefield imaging system for automated, time lapse imaging of live samples; Zeiss Axioscan 7 is high performance whole slide scanning system for fluorescence, brightfield, and polarization imaging;Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (LSFM) extends fluorescent imaging into true 3D, large scale volumetric imaging of intact tissues, organs, and small organisms. AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Indica Labs) and IMARIS (Oxford Instruments) facilitating data rendering, analyses, and presentation options." .
SCR:022468 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1374" ;
rdfs:label "University of Nebraska Medical Center Advanced Magnetic Resonance Imaging Core Facility" ;
NIFRID:synonym "UNMC Core for Advanced Magnetic Resonance Imaging" ;
NIFRID:abbrev "CAMRI" ;
definition: "Provides research MRI capabilities for investigators at UNMC and across greater Omaha area. Housed in Hixson-Lied Center, CAMRI operates Siemens 3T Prisma MRI instrument that can collect high quality data of any MR modality using advanced gradients and research grade pulse sequences. Variety of head coils (20-, 32-, and 64-channel) are available to optimize data collection for needs of specific studies. Studies incorporating functional MRI can take advantage of CAMRI�s suite of MRI-compatible response devices, mirrored 32-inch LCD screen, and integrated stimulus display computer." .
SCR:022474 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeePVP" ;
definition: "Software tool for identification and classification of phage virion proteins using deep learning." .
SCR:022475 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fast Healthcare Interoperability Resources" ;
NIFRID:synonym "FHIR" ;
definition: "Standard for health care data exchange, published by HL7. Platform provides healthcare information exchange standard that makes use of HL7-defined set of “resources” to support information sharing by variety of means, including documents, messages, services and RESTful interfaces. FHIR defines resources for clinical and administrative content (e.g. Observation, Patient, etc.) as well as resources for “infrastructure” purposes. Some of these infrastructure resources are used to define standard itself – i.e. what the characteristics of resources are, what codes can be used in them, etc." .
SCR:022476 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DUB Portal" ;
definition: "Provides integration and analysis of publicly available resources as well as newly collected transcriptomic data following deubiquitinating enzyme (DUB) knockout or inhibition to facilitate exploration of DUB function in oncology." .
SCR:022477 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Variational Embedding of Animal Motion" ;
NIFRID:synonym "VAME: Variational Embedding of Animal Motion",
"Variational Animal Motion Embedding" ;
NIFRID:abbrev "VAME" ;
definition: "Software Python tool to cluster behavioral signals obtained from pose estimation tools. Unsupervised probabilistic deep learning framework capable of finding behavioral motifs in pose estimation data. Capable of augmenting quantitative behavioral analyses of data derived from standard pose-estimation software packages. Written based on core functions from DeepLabCut, and readily works with pose data from that package. Can also work with data from other pose estimation packages such as SLEAP." .
SCR:022478 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1376" ;
rdfs:label "University of Nebraska Medical Center Multiphoton Intravital and Tissue Imaging Core Facility" ;
NIFRID:synonym "University of Nebraska Medical Center UNMC Multiphoton Intravital & Tissue Imaging (MITI) Core",
"UNMC Multiphoton Intravital & Tissue Imaging (MITI) Core" ;
NIFRID:abbrev "MITI" ;
definition: "Core provides intravital imaging equipment to acquire advanced descriptive and quantitative data for imaging studies. Includes Olympus FVMPE-RS advanced multiphoton microscope, multichannel, multiphoton excitation system specifically tailored for intravital and deep tissue imaging.System is additionally equipped with 458 and 588 nm stimulation laser lines for photobleaching, light stimulation and/or photoactivation of various fluorescent or caged constructs. Uses Spectra-Physics InSight X3 dual-line, tunable multiphoton laser for ultrafast, multichannel imaging.Available Neurotar Mobile Home Cage allows researchers to integrate real-time imaging with behavioral/locomotion tracking. Offers training and access to imaging system, support in design of experimental procedures, acquisition of image data, and analysis of acquired images." .
SCR:022479 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1451" ;
rdfs:label "Texas A and M University Image Analysis Laboratory Core Facility" ;
NIFRID:synonym "TAMU - Image Analysis Laboratory",
"Texas A&M University TAMU - Image Analysis Laboratory" ;
definition: "Provides advanced imaging technologies and image analysis tools including vital imaging of cellular processes within cells, tissue explants, and organoids.Supports services for transmission electron microscopy of biological samples.Imaging capabilities include fluorescence imaging of samples;Transmitted light imaging; Live cell imaging;FRAP, FLIP, Photoactivation/conversion;FRET, FLIM; Image processing, analysis, quantification; Transmission electron microscopy.Microscopes and Equipment include:Zeiss Axio Imager M2 Motorized Upright Microscope;Zeiss Cell Discoverer 7; Zeiss ELYRA S.1 Superresolution Microscope; Zeiss LSM 780 NLO Multiphoton Microscope;Zeiss TIRF3;Zeiss Stallion Digital Imaging Workstation;FEI Morgagni Transmission Electron Microscope;Leica UC6 Ultramicrotome;ImageXpress Pico & BioTek Cytation 7;Cryostar NX70 Cryostat." .
SCR:022480 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1453" ;
rdfs:label "University of California at Santa Cruz Marine Analytical Laboratory Core Facility" ;
NIFRID:synonym "Marine Analytical Laboratory",
"University of California at Santa Cruz Marine Analytical Laboratory" ;
definition: "Operated by Institute of Marine Sciences with support from UCSC Division of Physical and Biological Sciences. Available to UCSC and University of California marine and coastal research community.Provides equipment including Shimadzu TOC-VCPH TC/TN analyzer,Dionex ICS-2000 Ion Chromatograph,UIC Carbon Coulometer Analyzer, Perkin-Elmer AAnalyst 100 Atomic Absorption Spectrophotometer, Thermo Genesys 10S UV-Visible Spectrophotometer, Turner Designs 10-AU Field Fluorometer, Turner Designs TD-700 Lab Fluorometer, Turner Designs TD-20/20 Luminometer,Lachat QuikChem 8000 Flow Injection Analyzer, Guildline 8410 PortaSal Salinometer, Labconco Freeze Dryer." .
SCR:022481 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1452" ;
rdfs:label "University of Nebraska Medical Center Bioimaging Core Facility" ;
NIFRID:synonym "University of Nebraska Medical Center UNMC-Bioimaging Core Facility",
"UNMC-Bioimaging Core Facility" ;
definition: "Provides infrastructure for imaging based small animal research.Includes noninvasive anatomy, physiology, and biochemistry assessment for disease detection and therapeutic monitoring." .
SCR:022482 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1455" ;
rdfs:label "Texas A and M University Soft Matter Core Facility" ;
NIFRID:synonym "Soft Matter Facility",
"Texas A&M University Soft Matter Facility" ;
NIFRID:abbrev "SoMF" ;
definition: "Facility is focused on characterization of multifunctional soft materials. Includes four instrumentation suites based on soft matter centered research areas which will be unified by general theme of characterization of hierarchically structured multicomponent, multifunctional soft materials: Molecular Characterization, Processing and Mechanics, Thin Films and Interfacial Analysis, and Nanostructure Characterization." .
SCR:022483 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Alignstein" ;
definition: "Software package for liquid chromatography mass spectrometry retention time alignment." .
SCR:022484 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellEngine" ;
NIFRID:synonym "CellCarta CellEngine" ;
definition: "Flow cytometry analysis software for fast analysis, easy collaborative access to data, and tailored data visualization." .
SCR:022485 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1459" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Biomedical Data Science Core Facility" ;
NIFRID:synonym "Biomedical Data Science Core",
"University of Pennsylvania Perelman School of Medicine Biomedical Data Science Core" ;
NIFRID:abbrev "BDSC" ;
definition: "Core provides consultations and fee for service support in big data analyses using methods of data science in biomedical and health research related to digestive disease and liver research." .
SCR:022486 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1460" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine ITMAT Bioinformatics Laboratory Core Facility" ;
NIFRID:synonym "ITMAT Bioinformatics Laboratory",
"University of Pennsylvania Perelman School of Medicine ITMAT Bioinformatics Laboratory" ;
definition: "Provides project based bioinformatics support for ITMAT translational researchers. Provides computational infrastructure and programming support needed to conduct high-throughput proteomics experiments. We also support other genomics high-throughput technologies to a lesser extent. The projects range from building Web applications for data analysis pipelines, scripting, clinical and basic science research support, and database and algorithm development. Recent efforts have focused on explorations of new models of computation, specifically cloud computing and GPUs, for use in genomic scale research." .
SCR:022487 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ARBF_1461" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Clinical Imaging Service Center Core Facility" ;
NIFRID:synonym "Clinical Imaging Core Service Center",
"RADCORE Clinical Research Core Facility (Clinical Imaging Core)",
"University of Pennsylvania Perelman School of Medicine Clinical Imaging Core Service Center" ;
NIFRID:abbrev "RADCORE" ;
definition: "Clinical Imaging Core Service Center includes RADCORE, Tumor Response Assessment (TRAC) and Research imaging guided biopsies cores. Supports cancer clinical trials. RADCORE staff include clinical research professionals with range of expertise in imaging based clinical research protocols and offers services in consultation, management of research protocols and Radiology IND/IDE support office. Tumor Response Assessment Core (TRAC) team of Radiologist is skilled in evaluating tumor response imaging assessments for patients enrolled in cancer clinical trials being conducted at UPHS. Research imaging guided biopsies Interventional Radiology and technical staff provides consultation to define biopsy protocol and pathology tissue collection." .
SCR:022489 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyMARE" ;
NIFRID:synonym "Python Meta Analysis and Regression Engine",
"Python Meta-Analysis and Regression Engine" ;
definition: "Software Python library for mixed effects meta regression including meta analysis." .
SCR:022490 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TTRUST" ;
NIFRID:synonym "Transcriptional Regulatory Relationships Unraveled by Sentence based Text mining" ;
definition: "Reference database of human transcriptional regulatory interactions. Manually curated database of human and mouse transcriptional regulatory networks." .
SCR:022491 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MAVEN" ;
NIFRID:synonym "Metabolomic Analysis and Visualization ENgine" ;
definition: "Software program for interactive processing of LC-MS-based metabolomics data. Open source cross platform metabolomics data analyser. Used to reduce complexity of metabolomics analysis by developing highly intitute interface for exploring and validating metabolomics data. Program features multi-file chromatographic aligner, peak-feature detector, isotope and adduct calculator, formula predictor, pathway visualizer, and isotopic flux animator. Data from both triple quadropole and full spectrum instruments is supported." .
SCR:022492 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1456" ;
rdfs:label "Simon Fraser University Flow Cytometry Lab Core Facility" ;
NIFRID:synonym "SFU-Flow Cyt Lab",
"Simon Fraser University SFU-Flow Cyt Lab" ;
definition: """Offers high speed cell sorting and bench top flow cytometric analysis services as well as training and support to research community.Instruments include BD FACSAria Fusion Cell Sorter,4-Laser | 16-Colour (2B/3R/5YG/6V) within Class II Type A2 BioSafety Cabinet and BD LSRFortessa X-20 Cell Analyzer
4-laser | 16-Colour (2B/3R/5YG/6V).""" .
SCR:022493 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tidySingleCellExperiment " ;
definition: "Software tool as adapter that abstracts SingleCellExperiment container in form of tibble and allows data manipulation, plotting and nesting." .
SCR:022494 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Betareg " ;
definition: "Software R package for modeling beta distributed dependent variables, e.g., rates and proportions. In addition to maximum likelihood regression (for both mean and precision of beta distributed response), bias corrected and bias reduced estimation as well as finite mixture models and recursive partitioning for beta regressions are provided." .
SCR:022495 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Marker Enrichment Modeling" ;
NIFRID:abbrev "MEM" ;
definition: "Software tool to calculate enrichment scores. Generates human and machine readable labels that quantify features enriched in sample. Used to identify multiple populations of cells and to compare each population to all of other remaining cells from original sample." .
SCR:022496 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggeffects" ;
definition: """Software R package to create tidy data frames of marginal effects for ggplot from model outputs.
Used to compute marginal effects and adjusted predictions from statistical models and returns result as tidy data frames.""" .
SCR:022497 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harrell Miscellaneous" ;
NIFRID:abbrev "Hmisc" ;
definition: "Software R package for data analysis, graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, and recoding variables." .
SCR:022498 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SHARCQ" ;
NIFRID:synonym "and Cell Quantification",
"Registration",
"Slice Histology Alignment" ;
definition: "Software tools to register histological section images and cell count locations to mouse brain atlas. Semi automated workflow and GUI for automated brain slice histology alignment, registration, and cell quantification. Used to explore Allen Mouse Brain Atlas, register asymmetric slice images to atlas using manual input, and analyze region of interest data by registering locations of fluorescently labeled cells to standardized regions of Atlas." .
SCR:022501 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1224" ;
rdfs:label "University of Miami Sylvester Flow Cytometry Shared Resource Core Facility" ;
NIFRID:synonym "UM Sylvester Flow Cytometry Shared Resource",
"University of Miami UM Sylvester Flow Cytometry Shared Resource" ;
NIFRID:abbrev "FCSR" ;
definition: "Provides researchers with sophisticated methods for analysis and preparative sorting of both normal and tumor cells. Helps researchers to measure parameters including apoptosis, gene expression, drug metabolism, immune responses and pathways of cellular activation, both normal and tumor related. Provides access to high parameter cytometry instrumentation including spectral cytometry, mass cytometry and imaging mass cytometry." .
SCR:022502 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1463" ;
rdfs:label "University of Miami Sylvester Onco Genomics Shared Resource Core Facility" ;
NIFRID:synonym "UM Sylvester Onco-Genomics Shared Resource",
"University of Miami UM Sylvester Onco-Genomics Shared Resource" ;
NIFRID:abbrev "OGSR" ;
definition: "Provides access to technologies and services for study of genomics and epigenomics of cancer, in addition to providing technical expertise for project design, trouble shooting and pre and post award support. Services include next generation sequencing, single cell genomics, spatial genomics, gene expression assays and molecular quantitation, services for sample extraction and QC." .
SCR:022503 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SurvBenchmark" ;
definition: "Software package for comprehensive benchmarking study of survival analysis methods using both omics data and clinical data. Evaluates diverse collection of survival models for both clinical and omics datasets." .
SCR:022504 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OrthoVenn2" ;
definition: "Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences." .
SCR:022505 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneTools" ;
definition: "Software package includes comprehensive tools to provide full range of analysis for applications including chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging and colony counting." .
SCR:022506 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genedata Screener" ;
definition: "Software for data processing and analysis, automated reporting and data management, data normalisation, generation of dose response curves, generation of IC50. Captures data from all assays, regardless of therapeutic modality or area." .
SCR:022507 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Genetics Amplifier" ;
NIFRID:abbrev "HuGeAMP" ;
definition: "Software platform and infrastructure that aggregates, integrates, and analyzes human genetic and genomic data to spark insights into complex diseases. Data and software platform for storing, processing, and presenting genetic and genomic data." .
SCR:022508 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PavCA project" ;
NIFRID:synonym "PavCA",
"Pavlovian Conditioned Approach" ;
definition: "Project related to tracking behavior. Used to identify subgroups of individuals that differentially attribute incentive value to food cue. Includes apparatus for studying Pavlovian conditioned approach behavior. Customized rat PavCA chambers are constructed based on modular devices purchased from Med-Associates. Code used to operate equipment and collect data was written using Med-Associates’ MEDSTATE programming language. This program is then loaded into Med-PC V operating program, also created by Med-Associates." .
SCR:022509 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PopLDdecay " ;
definition: "Software tool for linkage disequilibrium decay analysis based on variant call format files." .
SCR:022510 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LI-COR | Odyssey XF Imaging System" ;
NIFRID:synonym "Li-Cor Odyssey XF Imaging System",
"Odyssey XF",
"Odyssey XF Imaging System" ;
definition: "System includes Odyssey XF Imager and Empiria Studio Software for streamlined image acquisition, organization, and analysis of Western blots. Used for imaging near infrared and enhanced chemiluminescent Western blots, to detect multiple targets on same blot with two channel multiplex fluorescence, and document DNA gels." .
SCR:022511 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GoFish Ajuwon etal 2022" ;
NIFRID:synonym "GoFish_Ajuwon_etal_2022" ;
definition: "Bonsai code for running GOFish platform for behavioural experiments in fish." .
SCR:022512 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Empiria Studio" ;
NIFRID:synonym "Empiria Studio Software",
"Li-Cor Empiria Studio Software" ;
definition: "Software is post processing, data integrity software for quantitative protein expression analysis including In-Cell Western Assays, Western blots, membranes, slides, and gels." .
SCR:022513 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VCF2Dis" ;
definition: "Software to calculate p-distance matrix based Variant Call Format." .
SCR:022514 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stardust" ;
definition: "Software tool for integration of spatial information in spatial transcriptomics data clustering." .
SCR:022515 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "autoreject" ;
definition: "Software library to automatically reject bad trials and repair bad sensors in magneto/electroencephalography data." .
SCR:022516 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ExonScan Web Server" ;
NIFRID:synonym "ExonScan" ;
definition: "Software framework for modeling sequence motifs based on maximum entropy principle." .
SCR:022517 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FAS ESS web server" ;
NIFRID:synonym "FAS-ESS web server" ;
definition: "Web tool to predict and analyze exonic splicing silencers." .
SCR:022518 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ZDOCK Server" ;
definition: "Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers." .
SCR:022519 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ridge regression Best Linear Unbiased Prediction" ;
NIFRID:abbrev "rrBLUP" ;
definition: "Software R package for mixed models with single variance component besides residual error, which allows for efficient prediction with unreplicated training data. Makes ridge regression and other kernel methods accessible to plant breeders interested in genomic selection." .
SCR:022520 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "h2o4gpu" ;
NIFRID:abbrev "H2o4GPU" ;
definition: "Interface to H2O4GPU, collection of GPU solvers for machine learning algorithms." .
SCR:022521 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ranger" ;
definition: "Software R package as fast implementation of Random Forests for high dimentional data." .
SCR:022522 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bayesian Generalized Linear Regression" ;
NIFRID:abbrev "BGLR" ;
definition: "Software R package implements large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures." .
SCR:022523 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "simplePHENOTYPES" ;
NIFRID:synonym "Linked and Epistatic Phenotypes",
"Simulation of Pleiotropic" ;
definition: "Software R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in wide range of genetic architectures, including additive, dominance and epistatic models. Used to simulate multiple traits controlled by loci with varying degrees of pleiotropy." .
SCR:022524 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Classification And Regression Training" ;
NIFRID:synonym "Classification And REgression Training" ;
NIFRID:abbrev "caret" ;
definition: "Software R package that contains functions for training and plotting classification and regression models. Includes methods for pre-processing training data, calculating variable importance, and model visualizations." .
SCR:022525 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tinglab ureter analysis" ;
NIFRID:synonym "tinglab_ureter_analysis" ;
definition: "Analysis code relevant to scRNA sequencing analysis. Code for Fink and Sona et.al. (2022) publication." .
SCR:022526 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1454" ;
rdfs:label "Penn State Hershey College of Medicine Light Microscopy Imaging Core Facility" ;
NIFRID:synonym "The Light Microscopy Imaging Core (Penn State COM)" ;
NIFRID:abbrev "Penn State COM" ;
definition: "Provides consultation and training in ultra high resolution imaging of cells and tissues in fixed or live states. Provides expertise in quantitative image analysis and consultations on microscopy related research projects." .
SCR:022527 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Heartbeat Medical Solutions GmbH" ;
definition: "Provider of measurement and analysis of Patient Reported Outcomes and their linkage to clinical data. By embedding resulting insights into individual treatments and care management, enables Value based Healthcare initiatives. Software company works from Berlin, Cologne and London on product development and supports centers, registries and research projects. Patient-Reported Outcomes are collected directly from patients in form of standardized questionnaires and provide insights into treatment effects and health related quality of life. Automatically linked with clinical observations, data based decision making basis is created for medical, therapeutic, and economic issues." .
SCR:022528 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ESHA Food Processor Nutrition Analysis" ;
NIFRID:synonym "Food Processor",
"Food Processor Nutrition Analysis",
"Food Processor Nutrition Analysis Software" ;
definition: "Software tool for nutrition analysis, diet and exercise tracking, and menu planning. Combines researched food and ingredient database with interface for accurate and comprehensive nutrition analysis." .
SCR:022529 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1470" ;
rdfs:label "University of Texas Southwestern Medical Center Neuro Models Core Facility" ;
NIFRID:synonym "University of Texas Southwestern Medical Center UTSW-Neuro-models Facility",
"UTSW-Neuro-models Facility" ;
NIFRID:abbrev "NMF" ;
definition: "Facilitates scientific research of nervous system function to enhance development and testing of novel therapeutic strategies for treatment of nervous system disorders. Provides resource capacity typically unavailable or impractical in individual laboratory. Major areas of specialization include surgical approaches to model production and assessment, behavior testing of sensorimotor functions, in vivo electrophysiological recording (EEG, EMG, ERP). Procedures are intended for mice and rats. Procedures can be developed based on client interests." .
SCR:022530 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioKB" ;
NIFRID:synonym "Biomedical Knowledge Base" ;
definition: "Web tool for text mining and semantic technologies for biomedical content discovery. Knowledge base of biomedical text mining results. Used to discover cause-effect relations between multiple entity types and deliver standardized representation of knowledge." .
SCR:022531 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AxonDeepSeg" ;
definition: "Open source software tool for automatic axon and myelin segmentation from microscopy data using convolutional neural networks." .
SCR:022532 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1471" ;
rdfs:label "Cornell University Biotechnology Resource Center Transcriptional Regulation and Expression Core Facility" ;
NIFRID:synonym "BRC Transcriptional Regulation and Expression Facility",
"Transcriptional Regulation and Expression Facility" ;
NIFRID:abbrev "TREx" ;
definition: "Facility offers genomics profiling services including RNAseq, small RNA sequencing, and ATACseq." .
SCR:022533 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1472" ;
rdfs:label "Texas A and M University AgriGenomics Laboratory Core Facility" ;
NIFRID:synonym "TAMU-AgriGenomics Laboratory",
"Texas A&M University TAMU-AgriGenomics Laboratory" ;
NIFRID:abbrev "AGL" ;
definition: "Assists graduate students, staff and faculty launch, economize and expedite their research, especially when it involves DNA extraction and quality checks, targeted genotyping and DNA content analysis. Facilitates usage of complementary cores and assists with research planning and data analysis.AGL members have free lab access and reduced costs for services as well as one-on-one training and advising with AGL staff." .
SCR:022534 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "d-StructMAn" ;
NIFRID:synonym "d-Structural Mutation Annotation" ;
definition: "Software tool provides annotation of non-synonymous single nucleotide variants in context of structural properties of resulting amino acid changes in corresponding proteins. Improved implementation of StructMAn, shipped in container form and extended to annotation of short in-frame indels and alterations arising as consequence of alternative splicing events. Produces range of structural features by combining information from experimentally resolved structures of many related proteins, which is unique feature of StructMAn family tools. Can also harness all protein structure models stored in AlphaFold Protein Structure Database." .
SCR:022535 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FreeCAD" ;
definition: "Open source parametric 3D modeler to design real life objects of any size. Parametric modeling allows modify your design by going back into your model history and changing its parameters." .
SCR:022536 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OHAUS | CS200P Portable Balance" ;
definition: "OHAUS CS lightweight, portable, compact balance for use in laboratory, industrial, education and home use applications. CS offers great value without sacrificing accuracy for weighing jobs of 200g to 5000g." .
SCR:022537 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NanoZoomer_S60" ;
rdfs:label "Hamamatsu | NanoZoomer S60 Digital slide scanner" ;
NIFRID:synonym "NanoZoomer S60 Digital slide scanner" ;
definition: "Whole slide scanner that scan glass slides to convert them to digital data. NanoZoomer S60 supports both brightfield imaging, fluorescence imaging and double size slides." .
SCR:022538 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FACSymphony_A5" ;
rdfs:label "BD Biosciences | FACSymphony A5 Cell Analyzer" ;
NIFRID:synonym "BD FACSymphony A5" ;
definition: "Flow cytometer as novel cell analyzer that leverages inherent benefits of flow cytometry and enables simultaneous measurement of up to 50 different characteristics of single cell." .
SCR:022539 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nextpnr" ;
definition: "Open Source portable FPGA place and route tool." .
SCR:022540 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FlowSorted.Blood.EPIC" ;
definition: "Software package includes new cell reference for adult peripheral blood deconvolution arrayed using Illumina HumanMethylationEPIC.Optimized library for reference based deconvolution of whole blood biospecimens assayed using Illumina HumanMethylationEPIC BeadArray." .
SCR:022541 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:emerald_metagenomics_annotations_pipeline" ;
rdfs:label "EMERALD METAGENOMICS ANNOTATIONS PIPELINE" ;
definition: "Software metagenomics annotations pipeline that regularly enrich up-to-date ENA and MGnify metagenomics studies with metadata extracted from research articles in EuropePMC." .
SCR:022542 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_592" ;
rdfs:label "Drug Discovery Core Facility" ;
NIFRID:synonym "Drug Discovery Core",
"Miami Project To Cure Paralysis Drug Discovery Core" ;
NIFRID:abbrev "DDC" ;
definition: "Core at Miami Project to Cure Paralysis leverages PerkinElmer Opera Phenix Plus high content screening system to provide assay development and phenotypic screening. Facility is also equipped with PerkinElmer Janus G3 liquid handler, featuring modular and variable dispense heads, to automate screening workflows and enhance throughput. Core supports phenotypic and target-based assays. Phenotypic assays range from 2D to 3D, widefield to confocal, and antibody to dye based. It collaborates with users to develop customized assays and analytical pipelines tailored to their specific needs. Current specializations include neurite tracing, lipid droplet quantification, cell viability, morphological and kinetic analyses, phagocytosis, cell marker detection, cell adhesion, among others." .
SCR:022543 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ANTS marking and analysis tools" ;
NIFRID:synonym "ANTS_marking_and_analysis_tools" ;
definition: "Software tool for marking ant motion trajectories dataset from video. Provided marking software, three data quality analysis scripts, and tracking performance evaluation tool." .
SCR:022544 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Karyon" ;
definition: "Software pipeline for assembly and analysis of highly heterozygous genomes. Used for diagnosis of hybrids, aneuploids, and other non standard architectures in genome assemblies." .
SCR:022545 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mlconfound" ;
definition: "Software tools for analyzing and quantifying effects of confounder variables on machine learning model predictions." .
SCR:022546 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VisiView" ;
NIFRID:synonym "Visitron Systems GmbH VisiView" ;
definition: "Software to control automated microscopes and microscope equipment in combination with multidimensional acquisition and analysis. Used for high speed image acquisition and processing." .
SCR:022547 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1207" ;
rdfs:label "Cornell University BRC Genomics Innovation Hub Core Facility" ;
NIFRID:synonym "BRC Genomics Innovation Hub",
"Cornell University BRC Genomics Innovation Hub" ;
definition: "Core complements services provided by BRC Genomics Facility.Working on collaborative model, protocol and method development by early adopters pave the way for larger scale production services." .
SCR:022548 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "neuro python plotting" ;
NIFRID:synonym "neuro-python-plotting" ;
definition: "Software Python scripts to plot neuroimaging results especially functional connectivity results." .
SCR:022549 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "yosys" ;
definition: "Software tool interprets Verilog descriptions of programmable hardware and transforms these into combinations of small look-up tables as provided on FPGAs from Xilinx or Lattice." .
SCR:022550 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ribosome Angle Decomposition tool" ;
NIFRID:abbrev "RADtool" ;
definition: "Software tool for analysis, visualization and animation of ribosome structures. Plugin for use with VMD that can automate download, structure alignment, analysis, visualization and animation of ribosome structures." .
SCR:022551 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenSMOG" ;
definition: "Software library that enables use of structure based SMOG models of biopolymers with OpenMM." .
SCR:022552 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_022553" ;
rdfs:label "CANVAS" ;
NIFRID:synonym "Complexity Analysis Viral Sequences" ;
definition: "Software tool for complexity analysis viral sequences." .
SCR:022554 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Transcriptional Regulatory Relationships Unrevealed by Sentence based Text mining database" ;
NIFRID:synonym "TRRUST database",
"TRRUSTv2" ;
NIFRID:abbrev "TRRUST" ;
definition: "TRUSST is reference database of human transcriptional regulatory interactions.TRRUST v2 is manually curated expanded reference database of human and mouse transcriptional regulatory interactions." .
SCR:022555 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SeuratWrappers" ;
definition: "Software R package that helps format Seurat objects into objects that can be used for trajectory analysis in other packages such as Monocle" .
SCR:022556 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cardiff University Bioimaging Hub Core Facility" ;
definition: "Provides advanced light microscopy imaging modalities and histological services. Offers training and application support in experimental design, sample preparation, data generation and analysis through to scientific publication and grant assistance." .
SCR:022557 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ipknot" ;
rdfs:label "IPknot plus plus" ;
NIFRID:synonym "IP based prediction of RNA pseudoKNOTs plus plus",
"IPknot",
"IPknot++" ;
definition: "Web server is an improved version of IPknot web server, which provides services for predicting RNA secondary structures including wide class of pseudoknots. Can perform RNA secondary structure prediction including pseudoknots for very long sequences. Can predict consensus secondary structure when multiple alignment of RNA sequences is given." .
SCR:022558 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MXfold2" ;
definition: "Web server predicts RNA secondary structures using deep learning. RNA secondary structure prediction using deep learning with thermodynamic integration." .
SCR:022559 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scopus" ;
definition: "Abstract and indexing database with full text links that is produced by Elsevier Co. Combines expertly curated abstract and citation database with enriched data and linked scholarly literature across wide variety of disciplines." .
SCR:022560 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LED Zappelin’" ;
definition: "Open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2 photon imaging. Device that rapidly time interleaves stimulation and detection epochs during two photon imaging." .
SCR:022561 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BiG-SCAPE " ;
NIFRID:synonym "Biosynthetic Gene Similarity Clustering and Prospecting Engine" ;
definition: "Software tool that calculates distances between BGCs in order to map BGC diversity onto sequence similarity networks, which are then processed for automated reconstruction of Gene Cluster Families, groups of gene clusters that encode biosynthesis of highly similar or identical molecules." .
SCR:022562 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OrthoANIu" ;
NIFRID:synonym "Average Nucleotide Identity" ;
definition: "Software tool for calculating average nucleotide identity." .
SCR:022563 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Intego" ;
definition: "Computerized morbidity registration network in Belgium based on general practice data.Contains demographic, clinical, biomedical, and prescription data, registered with computer generated keywords in electronic health record." .
SCR:022564 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SwissDock" ;
definition: "Web service to predict molecular interactions that may occur between target protein and small molecule. Protein small molecule docking web service based on EADock DSS." .
SCR:022565 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Penn State College of Medicine Metabolic Phenotyping Core Facility" ;
NIFRID:synonym "Metabolic Phenotyping Core",
"Penn State College of Medicine Rodent Metabolic Phenotyping Core" ;
definition: "Supports research that requires comprehensive assessment of energy balance and body composition in experimental rodents by providing necessary equipment and expertise. Services include training in the use of equipment, consultation on experiment design, and help with data analysis. Instrumentation includes Bruker TD-NMR LF100 Minispec and TSE Phenomaster System with Integrated Stellar Telemetry." .
SCR:022566 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LINCS Data Portal 2.0" ;
NIFRID:synonym "Library of Integrated Network Based Cellular Signatures 2.0" ;
NIFRID:abbrev "LDP v2" ;
definition: "Primary access point for compendium of LINCS data with substantial changes in data architecture and APIs, completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. LINCS datasets are accessible at data point level enabling users to directly access and download any subset of signatures across entire library independent from originating source, project or assay. Newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures." .
SCR:022567 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "zmax_edf_merge_converter" ;
definition: "Software tool for comprehensive conversion of folder with Hypnodyne zmax EDF files into merged European Data Format." .
SCR:022568 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BX53" ;
rdfs:label "Olympus | BX53 Upright Microscope" ;
definition: "LED illuminator for BX53 is equivalent to or better than 100 W halogen lamp, delivering brightness appropriate for teaching or contrast methods. Can be customized for different observation methods, such as phase contrast and fluorescence, with modular components." .
SCR:022569 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCBI Datasets" ;
definition: "Platform to let you gather data from across NCBI databases. Allows to find and download gene, transcript, protein and genome sequences, annotation and metadata." .
SCR:022570 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pMAT" ;
NIFRID:synonym "Photometry Modular Analysis Tool" ;
definition: "Open source software suite for analysis of fiber photometry data." .
SCR:022571 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sei" ;
definition: "Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types." .
SCR:022572 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "learnMSA" ;
definition: "Software tool as multiple sequence alignment formulated as statistical machine learning problem, where optimal profile hidden Markov model for potentially very large family of protein sequences is searched and alignment is decoded." .
SCR:022573 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Deep cryo-EM Map Enhancer " ;
definition: "Software Python package to perform post-processing of cryo-EM maps. Deep learning model trained on pairs of experimental volumes and atomic model corrected volumes that is able to obtain post-processed maps using as input raw volumes, preferably half maps." .
SCR:022574 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "janitor" ;
definition: "Software R package to format data, frame column names, provide quick counts of variable combinations and isolate duplicate records, format tabulation results." .
SCR:022575 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggforce" ;
definition: "Software R package providing missing functionality to ggplot2 through extension system introduced with ggplot2 v2.0.0." .
SCR:022576 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VirtualPlant" ;
NIFRID:synonym "VirtualPlant 1.3" ;
definition: "Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses." .
SCR:022577 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ConnecTF" ;
definition: "Software platform to integrate transcription factor gene interactions and validate regulatory networks. Gene regulatory network validation." .
SCR:022578 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Coselens" ;
NIFRID:synonym "COnditional SELection on the Excess of NonSynonymous Substitutions" ;
definition: "Software R package to detect gene level differential selection between two groups of samples.Used for calculation of excess of non synonymous mutations between two groups." .
SCR:022579 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "richR" ;
definition: "Software package to provide functions richGO, richKEGG,and enrich to do functional enrichment analysis. Used for function enrichment analysis and network construction." .
SCR:022580 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PanglaoDB" ;
definition: "Database for exploration of single cell RNA sequencing experiments from mouse and human. Collects and integrate data from multiple studies and present them through unified framework." .
SCR:022581 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hexamer Additive Linear" ;
NIFRID:abbrev "HAL" ;
definition: "Web tool to predict effects of sequence variants on alternative splicing. Predicts changes in alternative 5' splice events as well as skipped exon events." .
SCR:022582 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GE | Phoenix Nanotom S system" ;
NIFRID:synonym "Phoenix Nanotome S" ;
definition: "Nanofocus computed tomography system for applications in material science, precision injection moulding, micromechanics, electronics geology and biology. System includes nanofocus X-ray tube, precision mechanics and advanced software modules. Used for range of 3D CT applications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:022585 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MfN Berlin Micro-CT Laboratory Core Facility" ;
NIFRID:synonym "MfN Berlin Micro-CT Laboratory",
"Museum fuer Naturkunde Berlin Micro-CT Laboratory" ;
definition: "Provides analysis of biological, palaeontological and geological objects using computer assisted methods. Center for research at museum and for digitisation of scientific collections. Open to external users. In addition to various devices for three dimensional scanning, laboratory has workstations for processing and analysing raw data using 3D volume processing software." .
SCR:022586 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bioregistry" ;
definition: "Open source, community curated registry, meta-registry, and compact identifier resolver. Used for unifying identification of biomedical entities through integrative, open,community driven metaregistry. The registry contains metadata about ontologies, controlled vocabularies, and resources including their preferred prefix, name, description, homepage, mappings to other registries, and more." .
SCR:022587 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Artec 3D | Leo" ;
definition: "Wireless and fully standalone professional 3D scanner with new NVIDIA Jetson TX2 processor onboard. 3D scanning solution for data capture." .
SCR:022588 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Artec 3D | Space Spider" ;
definition: "3D scanner based on blue light technology. Precision instrument for CAD users and engineers. Used for capturing small objects or intricate details of large industrial objects in high resolution, with accuracy and brilliant color." .
SCR:022589 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Artec 3D | Eva Fast 3D scanner" ;
definition: "3D scanner for making quick, textured, and accurate 3D models of medium sized objects such as human bust, alloy wheel, or motorcycle exhaust system. Used for capturing objects of almost any kind, including objects with black and shiny surfaces." .
SCR:022590 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Secrepedia" ;
definition: "Encyclopedia of white and brown adipocyte secretome in mouse models and humans as key prerequisite to elucidating role of these mediators in normal physiology and disease." .
SCR:022591 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adaptive Immune Receptor Repertoire Data Commons API Specification" ;
definition: "Provides programmatic access to query and download AIRR-seq data. ADC API uses JSON as its communication format, and standard HTTP methods like GET and POST. ADC API is read only and mechanism of inclusion of AIRR-seq studies into data repository is left up to repository. ADC API Specification explains how to construct and execute API requests and interpret API responses." .
SCR:022592 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adaptive Immune Receptor Repertoire Rearrangement Schema" ;
definition: "Part of AIRR Data Model, defines annotations needed for rearrangements, which are sequences describing rearranged adaptive immune receptor chain (e.g., antibody heavy chain or TCR beta chain). Data for Rearrangement objects are stored as rows in tab delimited file and should be compatible with any TSV reader. Dataset is defined in this context as: TSV file, TSV with companion YAML file containing metadata, or directory containing multiple TSV files and YAML files." .
SCR:022593 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adaptive Immune Receptor Repertoire: Repertoire Schema" ;
definition: "Part of AIRR Data Model, describes abstract organizational unit of analysis that is defined by researcher and consists of study metadata, subject metadata, sample metadata, cell processing metadata, nucleic acid processing metadata, sequencing run metadata, set of raw sequence files, data processing metadata, and set of Rearrangements. Repertoire gathers all of this information together into composite object, which can be easily accessed by computer programs for data entry, analysis and visualization. AIRR Repertoire Schema has been implemented in YAML/JSON, which provides mechanism to share AIRR Repertoire metadata between research projects." .
SCR:022594 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adaptive Immune Receptor Repertoire Data Model" ;
definition: "Defines schema for MiAIRR data elements, structuring them within schema objects, defining relationship between those objects, and defining file format. Increased interest in immune system's involvement in pathophysiological phenomena coupled with decreased DNA sequencing costs have led to explosion of antibody and T cell receptor sequencing data collectively termed \"adaptive immune receptor repertoire sequencing\" (AIRR-seq or Rep-Seq). AIRR Community has been actively working to standardize protocols, metadata, formats, APIs, and other guidelines to promote open and reproducible studies of immune repertoire." .
SCR:022595 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adaptive Immune Receptor Repertoire Software Guidelines" ;
definition: "AIRR Software Guidelines were created by AIRR Software Working Group to promote standards for AIRR software tools and resources in order to enable rigorous and reproducible immune repertoire research at largest scale possible.Established standards for software tools. Authors whose tools comply with this standard will, subject to ratification from AIRR Software WG, be permitted to advertise their tools as being AIRR compliant. Guidelines include compliance checklist, list of compliant tools, and recommended software evaluation data sets." .
SCR:022596 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Minimal information about Adaptive Immune Receptor Repertoires" ;
NIFRID:abbrev "MiAIRR" ;
definition: "Checklist of minimally required information that we recommend journals adopt, and that could form requirements for submission to public data repository. AIRR sequencing studies apply high throughput sequencing technologies to profile B cell receptors (BCRs) and T cell receptors (TCRs). Standards were developed by AIRR Community Minimal Standards Working Group." .
SCR:022597 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AIRR Data Commons" ;
definition: "Network of distributed repositories that adhere to standards set out by AIRR Community. This collection contains standards and repositories either created by the AIRR community or approved for use within AIRR community." .
SCR:022598 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AIRR Community" ;
NIFRID:synonym "Adaptive Immune Receptor Repertoire Community",
"Adaptive Immune Receptor Repertoire Community of The Antibody Society" ;
definition: "Research driven group that is organizing and coordinating stakeholders in use of next generation sequencing technologies to study antibody/B-cell and T-cell receptor repertoires. Develops and promotes standards and recommendations for obtaining, analyzing, curating and comparing/sharing AIRR-seq datasets;using and validating tools for analyzing AIRR-seq data;relating AIRR-seq datasets to other “big data” sets, such as microarray, flow cytometric, and MiSeq and single-cell gene-expression data; legal and ethical issues involving use and sharing of AIRR-seq data sets derived from human sources." .
SCR:022599 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VDJbase" ;
definition: "Open source adaptive immune receptor genotype and haplotype database. Core collection is inferred from immune receptor repertoire sequences and genomically derived material. Provides customisable reports, which allow users to study gene and allele usage in various ways." .
SCR:022600 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCORCH" ;
NIFRID:synonym "Single Cell Opioid Responses in the Context of HIV" ;
definition: "Data coordination, analysis, and scientific outreach center to standardize and share single cell molecular HIV/SUD data by ensuring that data is FAIR. Program with mission of generating resources that would enable comprehensive tissue characterization at single cell level. This includes generating single nucleus transcriptomic data for identification of novel rare cell types, and enrichment of key cellular populations to inform pathophysiological understanding of CNS effects of SUD and HIV. Interdisciplinary effort, involving teams of investigators at ten institutions including Yale, Boston University, Mount Sinai, University of Nebraska Medical Center, Broad Institute, University of California San Diego, Weill Cornell Medicine, Allen Institute, Scripps Research as well as a Data Coordination Center hosted at Institute for Genome Sciences, University of Maryland Baltimore School of Medicine." .
SCR:022601 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Minian" ;
definition: "Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output." .
SCR:022602 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hydractinia Genome Project Portal" ;
NIFRID:synonym "NHGRI Hydractinia Genome Project Portal" ;
definition: "Portal provides genomic and transcriptomic data for researchers interested in Hydractinia genomics and molecular biology. Includes browsers for the H. symbiolongicarpus and H. echinata genome assemblies and interactive interface for interrogating H. symbiolongicarpus single cell gene expression atlas. Provides gene pages with functional annotation data for every gene model for both species, including protein domain composition and orthology predictions." .
SCR:022603 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rphenograph" ;
definition: "Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis." .
SCR:022604 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PharmMapper" ;
NIFRID:synonym "PharmMapper 2017" ;
definition: "Web server for potential drug target identification using pharmacophore mapping approach.Designed to identify potential target candidates for given probe small molecules including drugs, natural products, or other newly discovered compounds with binding targets unidentified using pharmacophore mapping approach. Used for potential drug target identification with comprehensive target pharmacophore database." .
SCR:022605 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Texas Southwestern Medical Center Quantitative Light Microscopy Core Facility" ;
NIFRID:synonym "Quantitative Light Microscopy Core" ;
NIFRID:abbrev "QLMC" ;
definition: "Provides access to variety of microscope modalities including laser scanning and spinning disk confocal, multiphoton, wide field deconvolution, CFP/YFP FRET, TIRF, single molecule imaging, and more. Offers customized microscopy training, advise and help with sample preparation, image quantification, and offer basic microscope maintenance. Can streamline your data handling and image visualization as well as automate your image analysis workflow through customized Fiji macros." .
SCR:022606 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1540" ;
rdfs:label "Fred Hutchinson Cancer Center Genomics and Bioinformatics Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Genomics and Bioinformatics Shared Resource Core" ;
definition: "Provides set of services that encompass experimental design, data generation and data interpretation. Expert genomics and bioinformatics teams are available to consult and collaborate at every step of process and work closely together to develop optimized experimental strategies to ensure that appropriate technology and data analysis tools are used to address each unique scientific question." .
SCR:022607 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fred Hutchinson Cancer Center Shared Resources" ;
definition: "Through Shared Resources, investigators in Fred Hutch/University of Washington Cancer Consortium and external academic and industry organizations can access services tailored to their specific research goals, including novel assay development or early access to new technologies." .
SCR:022608 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1538" ;
rdfs:label "Fred Hutchinson Cancer Center Antibody Technology Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Antibody Technology",
"Fred Hutchinson Cancer Center Antibody Technology Shared Resource" ;
definition: "Designs campaign strategies for generation and identification of novel monoclonal antibody compositions. Our projects encompass range of applications in oncology, viral therapeutics and diagnostics." .
SCR:022609 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1537" ;
rdfs:label "Fred Hutchinson Cancer Center Cellular Imaging Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Cellular Imaging Shared Resource" ;
definition: "Provides advanced light microscopy services for biomedical and translational research including workflow, training for independent work, assistance and technical support in microscopy techniques, quantitative image analysis. Offers training and support for imaging and analyzing gels and blots." .
SCR:022610 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1536" ;
rdfs:label "Fred Hutchinson Cancer Center Comparative Medicine Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Comparative Medicine Shared Resource" ;
definition: "Core teams of technicians, veterinarians, pathologists and operations specialists offer services in diagnostic and research pathology and support development and maintenance of preclinical mouse models, including mice bearing humanized immune system. Provides access to high quality technical services and immune deficient mice. Can perform individual technical services or complete entire in vivo experiments. Facilities are fully accredited by Association for Assessment and Accreditation of Laboratory Animal Care International and comply with all U.S. Department of Agriculture, Public Health Service, Washington state and local area regulations." .
SCR:022611 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1535" ;
rdfs:label "Fred Hutchinson Cancer Center Electron Microscopy Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Electron Microscopy Shared Resource" ;
definition: "Offers techniques to resolve structures from cellular ultrastructure to molecular interactions. Offers expertise in EM sample preparation and imaging, cryogenic electron microscopy, technologies and services, training through complexities of electron microscopy workflow, from sample preparation to image processing. All users must be trained by core staff." .
SCR:022612 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1534" ;
rdfs:label "Fred Hutchinson Cancer Center Experimental Histopathology Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Experimental Histopathology Shared Resource" ;
definition: "Provides expertise in anatomic pathology technologies. Offers routine and special staining, immunohistochemistry, in situ hybridization and digital pathology in support of internal and external investigators who rely on histological analysis." .
SCR:022613 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1533" ;
rdfs:label "Fred Hutchinson Cancer Center Flow Cytometry Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Flow Cytometry Shared Resource" ;
definition: "Includes services from sterile cell sorting for therapeutic applications to whole cell mass spectrometry, diagnostics and early stage clinical trials. Provides expertise from experimental design to data analysis and troubleshooting, therapeutic cell sorting. Supports isolation of cells for Phase 1 clinical trials of cellular immunotherapies." .
SCR:022614 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fred Hutchinson Cancer Center Hutch Data Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Hutch Data Core Shared Resource",
"Hutch Data Core" ;
definition: "Helps investigators integrate, interpret and explore large and diverse datasets. Provides services that support analysis of large scale datasets for biomedical researchers, drawing on expertise in computational biology, software engineering and cloud architecture. Offers project based scientific analysis by bioinformaticians, automation of analytical pipelines using workflow management platforms, publication of complex datasets with web accelerated graphics, training and documentation to enable scientist driven computation." .
SCR:022615 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1531" ;
rdfs:label "Fred Hutchinson Cancer Center Immune Monitoring Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Immune Monitoring Shared Resource" ;
definition: "Supports investigators seeking evaluations of immunologic responses in basic and early stage clinical research settings. Provides resources and expertise to evaluate cellular immunologic processes and responses through reagents, molecular and cellular assays, assay development support and research consulting services." .
SCR:022616 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1530" ;
rdfs:label "Fred Hutchinson Cancer Center Preclinical Imaging Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Preclinical Imaging Shared Resource" ;
definition: "Provides in vivo imaging technology and infrastructure to support basic and preclinical research. Offers diverse array of imaging modalities, including ultrasound and optical imaging, MRI, micro-CT and multiphoton microscopy." .
SCR:022617 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1529" ;
rdfs:label "Fred Hutchinson Cancer Center Preclinical Modeling Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Preclinical Modeling Shared Resource" ;
definition: "Supports development and maintenance of preclinical mouse models, including patient derived xenografts, cell line xenografts and genetically engineered mouse models." .
SCR:022618 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1528" ;
rdfs:label "Fred Hutchinson Cancer Center Proteomics and Metabolomics Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Proteomics and Metabolomics Shared Resource" ;
definition: "Provides support for mass spectrometry based proteomics and metabolomics research. With advanced instrumentation and highly trained staff, core offers consultation and services in sample preparation, sample separation, data collection and data analysis." .
SCR:022619 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fred Hutchinson Cancer Center Specimen Processing and Research Cell Bank Core Facility" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Specimen Processing and Research Cell Bank Shared Resource" ;
definition: "Provides biospecimen sample processing, extraction and biorepository services. Offers expertise to advance preclinical and clinical studies." .
SCR:022620 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UNC School of Medicine Integrated Genomics Cores High Throughput Sequencing Core Facility" ;
NIFRID:synonym "UNC School of Medicine HighThroughput Sequencing Facility",
"UNC School of Medicine Integrated Genomics Cores HighThroughput Sequencing Facility",
"University of North Carolina at Chapel Hill School of Medicine Integrated Genomics Cores High-Throughput Sequencing Facility" ;
NIFRID:abbrev "HTSF" ;
definition: "Full service sequencing facility to assist with genetic and genomic research. Part of Integrated Genomics Cores. Offers comprehensive library services, NextGen sequencing and alternative technologies including long reads. Offers library preparations and multiple sequencing platforms including MiSeq, HiSeq, NovaSeq, NextSeq, BioNano, Oxford Nanopore. Services also include using techniques and data analyses via sister core BARC." .
SCR:022621 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1473" ;
rdfs:label "Cincinnati Children's Hospital Animal Behavior Core Facility" ;
NIFRID:synonym "Animal Behavior Core",
"Cincinnati Children's Hospital Animal Behavior Core" ;
NIFRID:abbrev "ABC" ;
definition: "Offers behavioral phenotyping of rodent models as well as characterizing nervous system function in mouse and rat models through behavioral assays." .
SCR:022622 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1474" ;
rdfs:label "Cincinnati Children's Hospital Biomedical Informatics Core Facility" ;
NIFRID:synonym "Biomedical Informatics Core",
"Cincinnati Children's Hospital Biomedical Informatics Core" ;
definition: "Provides computational resources, services, and support to investigators including clinical research informatics, application and technology development, and bioinformatics analyses." .
SCR:022623 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1477" ;
rdfs:label "Cincinnati Children's Hospital Cell Processing Core Facility" ;
NIFRID:synonym "Cell Processing Core",
"Cincinnati Children's Hospital Cell Processing Core" ;
NIFRID:abbrev "CPC" ;
definition: "Supplies mononuclear cells, stem cells or other enriched cell populations. Provides stem cells and other tissue samples from normal donor or patient populations such as disease specific repositories or specific research studies requiring sample processing. Samples are provided fresh or cryopreserved according to availability, unprocessed or with further lab processing.Common processing techniques include PBMC isolation,Serum and plasma isolation,Separation of marker specific populations,Flow cytometric characterization of samples,Interferon gamma EliSpot.Additional services may be available upon request" .
SCR:022624 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1478" ;
rdfs:label "Cincinnati Children's Hospital Comprehensive Mouse and Cancer Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Comprehensive Mouse and Cancer Core",
"Comprehensive Mouse and Cancer Core" ;
NIFRID:abbrev "CMCC" ;
definition: "Offers services for researchers exploring cancer systems through animal models. Provides animals from specific inbred mouse strains primarily used in cancer and hematopoietic research, offers cell transplant, harvest and irradiation services and can handle animal cancer model systems involving xenotransplant procedures." .
SCR:022625 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1480" ;
rdfs:label "Cincinnati Children's Hospital Data Management and Analysis Center Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Data Management and Analysis Center",
"Data Management and Analysis Center" ;
NIFRID:abbrev "DMAC" ;
definition: "Centralized resource for clinical research data management, programming for clinical research databases, and statistical analysis." .
SCR:022626 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1475" ;
rdfs:label "Cincinnati Children's Hospital Cardiovascular Imaging Core Facility" ;
NIFRID:synonym "Cardiovascular Imaging Core Research Laboratory",
"Cincinnati Children's Hospital Cardiovascular Imaging Core Research Laboratory" ;
NIFRID:abbrev "CICRL" ;
definition: "Offers imaging techniques using imaging and measurement tools. Offers consulting services ranging from educational seminars to assistance with grant and industry funding support." .
SCR:022627 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1476" ;
rdfs:label "Cincinnati Children's Hospital Cell Manipulation Laboratory Core Facility" ;
NIFRID:synonym "Cell Manipulation Lab",
"Cincinnati Children's Hospital Cell Manipulation Laboratory" ;
NIFRID:abbrev "CML" ;
definition: "Supports development, scale -up and processing of innovative cell based therapies for clinical studies." .
SCR:022628 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1479" ;
rdfs:label "Cincinnati Children's Hospital Confocal Imaging Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Confocal Imaging Core",
"Confocal Imaging Core" ;
definition: "Provides Cincinnati Children s Hospital Medical Center; Cincinnati; Ohio resources in confocal, wide-field, and spatial technique applications." .
SCR:022629 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1485" ;
rdfs:label "Cincinnati Children's Hospital Critical Care Media Lab Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Critical Care Media Lab",
"Media Lab" ;
definition: "Develops high quality video and animation to enhance medical education." .
SCR:022630 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1482" ;
rdfs:label "Cincinnati Children's Hospital DNA Sequencing and Genotyping Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital DNA Sequencing and Genotyping",
"DNA Sequencing and Genotyping" ;
definition: "Supports production and analysis of DNA and RNA related data. Provides DNA and RNA sequencing, Next Generation sequencing, DNA extraction and high and low throughput SNP genotyping." .
SCR:022631 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1483" ;
rdfs:label "Cincinnati Children's Hospital Imaging Research Center Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Imaging Research Center",
"Imaging Research Center" ;
NIFRID:abbrev "IRC" ;
definition: "Provides access to advanced analytical imaging and image post-processing methods for collaborators involved in basic and clinical research." .
SCR:022632 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1481" ;
rdfs:label "Cincinnati Children's Hospital Discover Together Biobank Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Discover Together Biobank Core",
"Discover Together Biobank" ;
definition: "Provides access to services for standardized and centralized acquisition, processing, storage and distribution of biospecimens for research." .
SCR:022633 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1487" ;
rdfs:label "Cincinnati Children's Hospital Office for Clinical and Translational Research Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Office for Clinical and Translational Resarch",
"Office for Clinical and Translational Reearch" ;
NIFRID:abbrev "OCTR" ;
definition: "Clinical research support center for investigators and industry sponsors.Provides support services, research tools, experienced research personnel, and facilities to conduct or facilitate pediatric and adult clinical research from identification and development of research opportunities to phase I through phase IV clinical research trials." .
SCR:022634 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1489" ;
rdfs:label "Cincinnati Children's Hospital Pluripotent Stem Cell Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Pluripotent Stem Cell Facility",
"Pluripotent Stem Cell Facility" ;
NIFRID:abbrev "PSCF" ;
definition: "Supports all aspects of human pluripotent stem cell research, providing access to well characterized human embryonic stem cells and induced pluripotent stem cells for distribution to researchers. Consists of tissue culture facilities, access to microscopy and histology equipment, as well as equipment for cellular and molecular analysis of hESCs." .
SCR:022635 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1490" ;
rdfs:label "Cincinnati Children's Hospital Research Flow Cytometry Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Research Flow Cytometry Core",
"Research Flow Cytometry Core" ;
NIFRID:abbrev "RFCC" ;
definition: "Shared resource lab for flow cytometry instrumentation, training, education and analyte measurement (ELISA, Luminex, IsoLight). New users need to be trained for their instrument of choice." .
SCR:022636 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1486" ;
rdfs:label "Cincinnati Children's Hospital NMR based Metabolomics Core Facility" ;
NIFRID:synonym "NMR-based Metabolomics Core Facility" ;
NIFRID:abbrev "NBMC" ;
definition: "Provides all NMR related metabolomics services on human and animal cells, biopsies and body fluids." .
SCR:022637 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1488" ;
rdfs:label "Cincinnati Children's Hospital Pathology Research Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Pathology Research Core",
"Pathology Research Core" ;
NIFRID:abbrev "PATH" ;
definition: "Provides technical support for routine morphology based techniques. Pathologists are on hand to help guide projects, interpret results and collaborate on publications. Core personnel provide technical support for routine morphology based techniques including tissue processing and embedding, routine and special histochemical staining, immunohistochemistry, in situ hybridization, and electron microscopy." .
SCR:022638 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1484" ;
rdfs:label "Cincinnati Children's Hospital Mass Spectrometry Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Mass Spectrometry",
"Mass Spectrometry" ;
definition: "Provides analytical resource focusing on application of mass spectrometry and allied chromatographies to analysis of small molecules, generally of less than 1,000 daltons molecular weight, in complex clinical and biological samples." .
SCR:022639 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1493" ;
rdfs:label "Cincinnati Children's Hospital Vector Production Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Vector Production Facility",
"Vector Production Facility" ;
definition: "Facility manufactures lentiviral and retroviral vectors in support of early phase clinical trials.Services include large scale GMP lentiviral and retroviral vector and small to mid scale GMP like manufactured products. Supports certification and stability studies." .
SCR:022640 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1492" ;
rdfs:label "Cincinnati Children's Hospital Translational Trial Development and Support Laboratory Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Translational Trial Development and Support Laboratory",
"Translational Trials and Development Lab" ;
NIFRID:abbrev "TTDSL" ;
definition: "Provides facilities and expertise to support clinical assay development from technology developed in academic laboratories.Provides assay development and testing support for early phase clinical trials with focus on cell and gene therapy." .
SCR:022641 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1494" ;
rdfs:label "Cincinnati Children's Hospital Viral Vector Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Viral Vector Core",
"Viral Vector Core" ;
NIFRID:abbrev "VVC" ;
definition: "Provides research grade retroviral, lentiviral and adeno associated virus vectors. Offers generation of stable producer lines, and non-GMP quality control testing including vector titer by functional assay FACS or PCR, endotoxin, mycoplasma, and USP sterility testing.Provides standard packaging plasmids, the investigator provides the viral vector to be used for the production run." .
SCR:022642 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1491" ;
rdfs:label "Cincinnati Children's Hospital Transgenic Animal and Genome Editing Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Transgenic Animal and Genome Editing Core",
"Transgenic Animal and Genome Editing Core" ;
NIFRID:abbrev "TAGE" ;
definition: "Offers comprehensive CRISPR services to generate gene edited rodents and cells, and helps generate transgenic and chimeric mice via our microinjection service, cryopreserving unique mouse lines, and recovering them from liquid nitrogen storage via IVF and embryo transfer services." .
SCR:022643 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Cincinnati Children's Hospital Medical Center; Cincinnati; Ohio" ;
definition: "Nonprofit academic medical center established in 1883. One of the oldest and most distinguished pediatric hospitals in the United States. Affiliated with the University of Cincinnati Academic Health Center." .
SCR:022645 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Radiant" ;
NIFRID:synonym "Radiant v2.2",
"Radiant v2.3" ;
definition: "Software tool used to control Plexon pattern generator for optogenetic stimulation." .
SCR:022646 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sparse Inverse Covariance Estimation for Ecological Association Inference" ;
NIFRID:synonym "SParse InversE Covariance Estimation for Ecological Association Inference" ;
NIFRID:abbrev "SPIEC-EASI" ;
definition: "Software R package estimates inverse covariance matrix from sequencing data.Statistical method for inference of microbial ecological networks from amplicon sequencing datasets." .
SCR:022647 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PICRUSt2" ;
NIFRID:synonym "Phylogenetic Investigation of Communities by Reconstruction of Unobserved States" ;
definition: "Software for predicting functional abundances based only on marker gene sequences.Used for prediction of metagenome functions. Contains updated and larger database of gene families and reference genomes, provides interoperability with any operational taxonomic unit (OTU)-picking or denoising algorithm, and enables phenotype predictions. Allows addition of custom reference databases." .
SCR:022648 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1497" ;
rdfs:label "Cincinnati Children's Hospital Magnetoencephalography Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital MEG Core",
"MEG Core" ;
NIFRID:abbrev "MEG" ;
definition: "Core facilitates study of normal and pathologic brain processes using magnetoencephalography.The purpose of the core is to make magnetoencephalography available to researchers across the institute." .
SCR:022649 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1498" ;
rdfs:label "Cincinnati Children's Hospital Microbial Metagenomics Analysis Center Microbial Genomics and Metagenomics Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Microbial Metagenomics Analysis Center Microbial Genomics and Metagenomics Laboratory",
"Microbial Genomics and Metagenomics Laboratory" ;
NIFRID:abbrev "MMAC" ;
definition: "Provides solutions in areas of study design, bioinformatic processing of amplicon and shotgun metagenomic sequencing data, integration of metagenomic and clinical data structures, and statistical analyses of microbial community samples. MMAC works closely with Microbial Genomics and Metagenomics Laboratory to streamline workflows for metagenomic sequencing, bioinformatic processing, and statistical analysis of microbiome projects." .
SCR:022650 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1496" ;
rdfs:label "Cincinnati Children's Hospital Investigational Pharmacy Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Investigational Pharmacy",
"Investigational Pharmacy" ;
definition: "Our Investigational Pharmacy team is responsible for dispensing both inpatient and outpatient investigational medication for industry-sponsored, grant-funded and investigator-initiated protocols. We provide pharmacy services customized to each research protocol conducted at Cincinnati Children�s." .
SCR:022651 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_208" ;
rdfs:label "Oregon Health and Science University Integrated Genomics Laboratory Core Facility" ;
NIFRID:synonym "Integrated Genomics Laboratory",
"Oregon Health and Science University Integrated Genomics Laboratory" ;
NIFRID:abbrev "IGL" ;
definition: "Lab houses three cores providing support and services from nucleic acid isolation through data generation on multiple genomic and molecular analysis platforms. Nucleic acid extraction, qPCR, and Nanostring profiling services are available through the Gene Profiling Shared Resource for gene expression profiling, microRNA profiling, DNA genotyping and copy number analysis, and DNA methylation analyses. Currently running QuantStudio real-time PCR system. Comprehensive RNA and DNA extraction and quality assessment services available. Massively parallel sequencing (NGS) services, including library preparation, are available through Massively Parallel Sequencing Shared Resource on Illumina NovaSeq 6000 and NextSeq platforms. 10x Genomics single-cell and single-nuclei analysis services available. Cell line authentication, DNA plating, and custom oligo services are available through DNA Services Core." .
SCR:022653 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1495" ;
rdfs:label "Cincinnati Children's Hospital Single Cell Genomics Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Single Cell Genomics Core",
"Single Cell Genomics Core" ;
NIFRID:abbrev "SCGC" ;
definition: "Core to perform expression level analysis of thousands of genes in parallel.Uses RNA-Seq assays from Tecan Genomics, Takara and Illumina for samples with limited amounts of starting RNA. Microarray technology utilizing the Affymetrix GeneChip platform is also available." .
SCR:022655 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NutriSurvey" ;
definition: "Software tool for nutrition calculations and surveys." .
SCR:022656 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_558" ;
rdfs:label "Harvard University Bauer Core Facility" ;
NIFRID:synonym "Bauer Core",
"Harvard University Bauer Core",
"The Bauer Core Facility at Harvard University" ;
definition: "Helps to advance research efforts in life sciences that cannot readily be accomplished in the traditional academic laboratory because of need for expensive instrumentation or automation, scientific or organizational infrastructure, or multidisciplinary expertise. Provides expertise and hands-on training and use of instrumentation for nominal fee. Researchers can sign up to use instrumentation through on-line scheduling system and conduct their experiments independently." .
SCR:022657 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NPI | Pressure Application Module" ;
NIFRID:synonym "NPI Electronics PDES",
"PDES",
"PDES Pressure Application Module",
"Pressure Application Module (NPI Electronic)" ;
definition: "Pneumatic drug ejection. Used to apply ionic and non-ionic substances in small amounts. Locally precise application with microJECT pipette holder with built-in valve. Also available as 19″ stand alone device." .
SCR:022658 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Standard BioTools | Biomark HD system" ;
NIFRID:synonym "BioMark HD",
"Biomark HD system (Fluidigm)",
"Biomark™ HD system",
"Fluidigm Biomark HD system" ;
definition: "Automated, high performance PCR/qPCR system that uses microfluidics technology to process samples at nanoliter scale volumes for gene expression, genotyping, sample identification, copy number variation analysis and digital PCR. With wide range of integrated fluidic circuit (IFC) formats available, scaling from mid to high throughput on single system." .
SCR:022659 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Witwatersrand South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit" ;
NIFRID:synonym "South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit" ;
NIFRID:abbrev "Wits-VIDA" ;
definition: "African led research unit in field of epidemiology of vaccine preventable diseases, and clinical development of life saving vaccines. Conducts translational research that informs local and global policy recommendations on infectious diseases and use of next generation and novel vaccines. Collaborates with core facilities on various trials and studies." .
SCR:022660 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_A365" ;
rdfs:label "WPI | Constant Current Stimulus Isolator" ;
NIFRID:synonym "Constant Current Stimulus Isolator",
"Stimulus Isolator",
"WPI Constant Current Stimulus Isolator" ;
definition: """Automated bipolar pulsing for zero net charge on biological preparations. Includes Constant current,
Unipolar and bipolar stimulation modes, Built-in non-compliance alarm, Optically isolated input
Standard TTL triggering, DC test mode. Powered by 9 V alkaline or rechargeable batteries.""" .
SCR:022661 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Murdoch Children’s Research Institute" ;
NIFRID:abbrev "MCRI" ;
definition: "Australia’s largest child health research centre.Research health conditions include diabetes, allergies, asthma, premature birth and mental health problems,cancer and genetic disorders. Located in Royal Children’s Hospital in Melbourne." .
SCR:022662 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "National Institute for Communicable Diseases; South Africa" ;
NIFRID:synonym "NICD The National Institute for Communicable Diseases",
"South Africa" ;
NIFRID:abbrev "NICD" ;
definition: "National public health institute for South Africa, providing disease surveillance, specialised diagnostic services, outbreak response, public health research and capacity building to support the government’s response to communicable disease threats." .
SCR:022663 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OligoCalc" ;
definition: "Web tool as oligonucleotide properties calculator. Computational engine for reporting DNA and RNA single stranded and double stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter molecular self complementarity estimation and intra molecular hairpin loop formation." .
SCR:022664 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyFDAP" ;
NIFRID:synonym "Python Fluorescence Decay After Photoconversion" ;
definition: "Software tool as automated analysis of fluorescence decay after photoconversion (FDAP) experiments." .
SCR:022665 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:pyfrap" ;
rdfs:label "PyFRAP" ;
NIFRID:synonym "Python Fluorescence Recovery After Photobleaching" ;
definition: "Software Python package for FRAP analysis. Simulation based analysis software that makes use of PDE simulations to analyze FRAP experiments in 3D geometries. Used to assess molecular diffusion." .
SCR:022666 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioMerieux | NucliSens easyMAG system" ;
NIFRID:synonym "BioMérieux NucliSens easyMAG",
"BioMérieux NucliSens R easyMAG" ;
definition: "System for total nucleic acid extraction from variety of sample types and volumes. System automates enhanced magnetic silica version of bioMérieux’s proprietary BOOM technology gold standard for universal extraction of RNA and DNA.Clinical use includes nucleic acid extraction in front of molecular infectious disease assays, molecular oncology assays, molecular genetics assays." .
SCR:022668 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TABNET" ;
definition: "Portal to find all informations about epidemiology regarding public and suplementary health in Brazil." .
SCR:022669 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_356" ;
rdfs:label "University of Texas Health Science Center at San Antonio Mass Spectrometry Core Facility" ;
NIFRID:synonym "University of Texas Health Science Center at San Antonio Mass Spectrometry Institutional Core Laboratory",
"University of Texas Health Science Center at San Antonio UTHSCSA Mass Spectrometry Laboratory",
"UTHSCSA Mass Spectrometry Laboratory" ;
definition: "Mass Spectrometry for protein and small molecule analyses. Services cover full range from sample preparation through data processing and interpretation. Analyses include molecular mass determination, protein identification, protein relative quantification, localization of covalent protein modification and targeted quantitative metabolomics.Uses iLab." .
SCR:022670 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneRecommender" ;
NIFRID:abbrev "GenRec" ;
definition: "Platform for helping science researchers by recommending gene symbol obtained by AI neural proprietary network able to scan millions of papers. Web tool to extract hidden patterns and correlations among genes and diseases from scientific papers." .
SCR:022671 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Design-Expert" ;
definition: "Statistical software package from Stat-Ease Inc. to perform design of experiments. Offers comparative tests, screening, characterization, optimization, robust parameter design, mixture designs and combined designs." .
SCR:022672 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Drug and Statistics" ;
NIFRID:synonym "Drug and Analysis System" ;
NIFRID:abbrev "DAS" ;
definition: "Software pharmacokinetic tool. Used to calculate pharmacokinetic parameters, fit curves, calculate AV models, and conduct pharmaceutical statistics, including dissolution analysis, slice weight difference analysis, acceleration test." .
SCR:022673 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciReq | flexiVent system" ;
NIFRID:synonym "SCIREQ flexiVent system" ;
definition: """System for small animal pulmonary function. Used for in vivo respiratory mechanics measurements. Goes beyond traditional resistance and compliance mechanics of pulmonary ventilation, and captures details about mechanical properties of conducting airways, terminal airways and parenchyma.
Achieves sensitivity and reproducibility by precisely controlling experimental conditions.""" .
SCR:022674 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FACSymphony_A5_SE" ;
rdfs:label "BD Biosciences | FACSymphony A5 SE Cell Analyzer" ;
NIFRID:synonym "BD FACSymphony A5 SE",
"BD FACSymphony™ A5 SE Cell Analyzer" ;
definition: "Flow cytometer gains full visible spectrum coverage to collect all light emitted without need for filter changes, increasing dye flexibility and number of simultaneous colors. Uses unmix spectral data live in BD FACSDiva Software while retaining familiar compensation workflow. May improve resolution of difficult cells and populations using autofluorescence unmixing." .
SCR:022675 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Peptides" ;
definition: "Software R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences." .
SCR:022676 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eagle Atlas Compilation for Vestibular Research" ;
definition: "Collection of 1mm isotropic atlases for vestibular MRI research consisting of ROIs from Eickhoff et al. and Indovina et al., Brainnetome Atlas, Diedrichsen/SUIT Cerebellar Atlas, Najdenovska Thalamic Atlas, brainstem and diencephalon ROIs from Brainstem Navigator, and Neudorfer Anatomical Hypothalamus Atlas." .
SCR:022677 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "taxize" ;
definition: "Software R package for taxonomic information from around web. Interacts with suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more." .
SCR:022678 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "seqinr" ;
definition: "Software R package for exploratory data analysis and data visualization for biological sequence, DNA and protein, data." .
SCR:022679 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "reshape2" ;
definition: "Software R package to flexible rearrange, reshape and aggregate data. Reshape2 is reboot of reshape package." .
SCR:022680 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DNAmClassMeta" ;
definition: "Source code for paper \"Disease classification for whole blood DNA methylation: meta-analysis, missing values imputation, and XAI\" by A. Kalyakulina, I. Yusipov, M.G. Bacalini, C. Franceschi, M. Vedunova, M. Ivanchenko." .
SCR:022681 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1499" ;
rdfs:label "Northeastern University Institute for Chemical Imaging of Living Systems Core Facility" ;
NIFRID:synonym "Northeastern University NU-Institute for Chemical Imaging of Living Systems Core Facility",
"NU-Institute for Chemical Imaging of Living Systems" ;
NIFRID:abbrev "CILS" ;
definition: "Located in ISEC research center and includes advanced imaging instruments. CILS has three core facilities: Microscopy Core (confocal/multi-photon/lightsheet microscopes), Flow Cytometry Core (cell analyzer/sorter) and Preclinical Imaging Core (3T small animal MRI and ultrasound)." .
SCR:022682 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1503" ;
rdfs:label "Wayne State University School of Medicine Lipidomics Core Facility" ;
NIFRID:synonym "Wayne State University Lipidomics Core Facility" ;
NIFRID:abbrev "WSU-LCF" ;
definition: "Conducts comprehensive analysis of cellular lipids that encompass fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, and prenol lipids." .
SCR:022683 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1501" ;
rdfs:label "University of Nebraska Medical Center Echocardiography Imaging Core Facility" ;
NIFRID:synonym "Echocardiography Imaging Facility",
"University of Nebraska Medical Center Echo Facility",
"University of Nebraska Medical Center Echocardiography Imaging Facility",
"UNMC-Small Animal Ultrasound Core" ;
definition: "Preclinical ultrasound imaging. Provided instruments include Vevo 3100, Vevo 3100 LAZR-X, Perkin Elmer Vega." .
SCR:022684 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1502" ;
rdfs:label "Drexel University Materials Characterization Core Facility" ;
NIFRID:synonym "Drexel University Materials Characterization Core",
"Materials Characterization Core" ;
NIFRID:abbrev "MCC" ;
definition: "Facility provides technical expertise and instrumentation including nanoscience and engineering, polymer research, biomedical engineering, and chemistry and physics of solid materials.Houses electron microscopes, X-ray diffractometers, X-ray photoelectron spectrometer and suite of sample preparation tools. Staff members provide expert consultation, training and assistance to MCC users. Core is involved in teaching both undergraduate and graduate level courses in Materials Science and Engineering, Mechanical Engineering and Mechanics, Biomedical Engineering, and Biology. Trained and certified users are welcome to work independently on our instruments." .
SCR:022685 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1500" ;
rdfs:label "Van Andel Institute Flow Cytometry Core Facility" ;
NIFRID:synonym "VAI Flow Cytometry Core Facility",
"Van Andel Institute VAI Flow Cytometry Core Facility" ;
definition: "Core provides cell analysis and sorting services. Instruments include Cytek Aurora, Beckman Coulter CytoFLEX S, Thermo Fisher Attune CytPix, SONY MA900, and BD FACSSymphony S6." .
SCR:022686 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IBM SPSS Amos" ;
NIFRID:synonym "SPSS Amos" ;
definition: "Structural equation modeling software helping support your research and theories by extending standard multivariate analysis methods, including regression, factor analysis, correlation and analysis of variance." .
SCR:022687 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1504" ;
rdfs:label "Purdue Electron Microscopy Center" ;
NIFRID:synonym "Life Science Microscopy Core Facility",
"Purdue Electron Microscopy Facility",
"Purdue University Electron Microscopy Core Facility",
"Purdue University Life Science Microscopy Facility",
"Purdue University West Lafayette Purdue Electron Microscopy Facility" ;
NIFRID:abbrev "PEMC" ;
definition: "Provides Purdue researchers access to electron microscopy instrumentation including scanning electron microscopes, small dual beams and transmission electron microscopes. Expert staff scientists help with training and project support." .
SCR:022688 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1505" ;
rdfs:label "University of Texas at Austin Computational Biology and Bioinformatics Core Facility" ;
NIFRID:synonym "CBRS-Bioinformatics Consulting Group" ;
definition: "Provides support for students, postdoctoral fellows, and faculty interested in the use of computational approaches to solving biological problems. Our goal is to lower as much as possible the threshold to enter the -omics area of the life sciences." .
SCR:022689 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1506" ;
rdfs:label "Drexel University Cell Imaging Center Core Facility" ;
NIFRID:synonym "Cell Imaging Center",
"Drexel University Cell Imaging Center" ;
definition: "Facility housed in purpose built imaging suites in Papadakis Integrated Sciences Building and in Bossone Research Center. Serves light microscopy needs of Drexel researchers and supports teaching missions of Biology and Biomedical Engineering curricula and provides service to users from local biotech companies.Provides facility, expertise, and education in advanced quantitative light microscopy." .
SCR:022690 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1508" ;
rdfs:label "Howard Hughes Medical Institute at Janelia Research Campus Flow Cytometry Shared Resource Core Facility" ;
NIFRID:synonym "Howard Hughes Medical Institute at Janelia Research Campus Flow Cytometry Shared Resource" ;
NIFRID:abbrev "FCSR" ;
definition: "Provides range of instrumentation and expertise for cell sorting and analysis that can support experimental needs related to single cells, cell line production, biosensor development, and dye analysis. Offers expertise in flow cytometry experimental design, operation of instruments, distribution of raw data and sort reports, interpretation of results, and preparation of graphics for presentation and publication." .
SCR:022691 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1510" ;
rdfs:label "Texas A and M University Center for Educational Technologies Core Facility" ;
NIFRID:synonym "TAMU-The Center for Educational Technologies",
"Texas A&M University TAMU-The Center for Educational Technologies" ;
definition: "Offers services to researchers looking for collaborators or contractors for their educational or training projects.Offers development tools and hosting services to educators creating their own online training resources." .
SCR:022692 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Celleste" ;
NIFRID:synonym "Celleste 5.0 Image Analysis Software",
"Invitrogen™ Celleste™ 5.0 Image Analysis Software" ;
definition: "Image analysis software for florescence microscopy." .
SCR:022693 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SYNPRED" ;
NIFRID:synonym "synpred" ;
definition: "Web tool for prediction of drug combination effects in cancer using different synergy metrics and ensemble learning. Allows user to input two drugs, in form of two distinct SMILE files and attain prediction of their synergistic effects on specific cancer cell lines." .
SCR:022694 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1507" ;
rdfs:label "Howard Hughes Medical Institute at Janelia Research Campus Quantitative Genomics Core Facility" ;
NIFRID:synonym "Howard Hughes Medical Institute at Janelia Research Campus Quantitative Genomics",
"Quantitative Genomics" ;
definition: "Provides services to anything related to genomic analysis, such as RNAseq, genome sequencing, ATACseq etc, from experiment design all the way down to data analysis.Provides expert services for cell isolation, transcriptome and epigenetic profiling, and de novo genome assembly using next generation sequencing platforms from Illumina." .
SCR:022695 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:gpu-enabled_docker_container_with_jupyterlab_for_ai" ;
rdfs:label "Docker based GPU enabled Jupyterlab" ;
definition: "Open source, docker based, and GPU enabled jupyterlab notebook infrastructure that runs on public compute infrastructure of Galaxy Europe for rapid prototyping and developing end-to-end AI projects. Jupyterlab notebook in GPU enabled docker container for machine learning and deep learning." .
SCR:022696 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_459" ;
rdfs:label "University of Vermont Larner College of Medicine Advanced Genome Technologies Massively Parallel Sequencing Core Facility" ;
NIFRID:synonym "Advanced Genome Technologies Core Massively Parallel Sequencing Facility",
"University of Vermont Advanced Genome Technologies Core Massively Parallel Sequencing Facility" ;
definition: "Provides support for design, execution, and analysis of experiments involving Next Generation Sequencing through access and use of Illumina HiSeq 1500. Sequencer performs wide range of analysis including target preparation for RNAseq, Exome Seq, ChIP seq, Methyl Seq, whole genome sequencing, and small RNA sequencing.Core is involved in all aspects of Nanopore sequencing." .
SCR:022697 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miQC" ;
definition: "Software tool as flexible, probablistic metrics for quality control of scRNA-seq data. Adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. Data driven QC metric that jointly models proportion of reads mapping to mtDNA and number of detected genes with mixture models in probabilistic framework to predict which cells are low quality in given dataset." .
SCR:022698 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenMeta" ;
NIFRID:synonym "OpenMeta[Analyst]" ;
definition: "Cross platform software for advanced meta analysis." .
SCR:022699 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Zagreb School of Medicine; Zagreb; Croatia" ;
definition: "Public croatian university and the oldest continuously operating university in the area covering Central Europe south of Vienna and all of Southeastern Europe." .
SCR:022700 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scDblFinder" ;
definition: "Software package for detection and handling of doublets/multiplets in single cell sequencing data." .
SCR:022701 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1512" ;
rdfs:label "University of Zagreb School of Medicine Laboratory for Regenerative Neuroscience Core Facility" ;
NIFRID:synonym "UZSM - Laboratory for Regenerative Neuroscience / GlowLab" ;
definition: "Multimodal preclinical in vivo imaging facility for small laboratory animals such as mice and rats. Expertise is in brain research, however it is possible to provide imaging services on any part of or on animal.Instruments include magnetic resonance imager (Bruker BioSpec 70/20 USR) and optical bioluminescence/fluorescence imager (Perkin Elmer IVIS Spectrum), fully equipped with anesthesia delivery and physiological monitoring/control system.Imaging unit is complemented by cell culture laboratory and small animal surgery room, allowing to set up and perform entire experimental protocols as needed. Provides longitudinal imaging services owing to animal housing unit within same space, equipped with individually ventilated cages for both rats and mice (Tecniplast Green line and Emmerald line). Home cage monitoring is also possible for mice as an additional service with our Tecniplast DVC cages." .
SCR:022702 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1514" ;
rdfs:label "University of North Carolina at Chapel Hill Functional Genomics Core Facility" ;
NIFRID:synonym "UNC-Functional Genomics Core",
"University of North Carolina at Chapel Hill Functional Genomics Core",
"University of North Carolina at Chapel Hill UNC-Functional Genomics Core" ;
definition: "Core performs expression profiling, SNP genotyping and copy number microarray (Thermo Fisher) services." .
SCR:022703 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1513" ;
rdfs:label "University of North Carolina at Chapel Hill Systems Genetics Core Facility" ;
NIFRID:synonym "UNC Systems Genetics",
"UNC- Systems Genetics Core Facility",
"University of North Carolina at Chapel Hill UNC- Systems Genetics Core Facility" ;
NIFRID:abbrev "SGSF" ;
definition: "Provides access to multi parental genetic reference mouse population derived from eight founder inbred strains, encompassing genetic diversity. Strains have been sequenced and have much genomic data. All of CC strains are kept as live mouse strains. Provides breeding stock for internal use unless other permission is acquired, or experimental cohorts." .
SCR:022704 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Modular LED Displays project" ;
NIFRID:synonym "Modular LED Displays" ;
definition: "Provides customized display systems used in neuroscientific studies in insects and other small animals. System includes custom built modular LED panels and software. LED panels of various sizes can be arranged/grouped in different shapes for diverse setups. System provides millisecond refresh, precise synchronization, customizable color combinations, and varied display configurations and addresses most technical challenges of small animal vision experiments and is thoroughly documented for replicability." .
SCR:022705 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EBSCO Dentistry and Oral Sciences Source" ;
NIFRID:synonym "Dentistry and Oral Sciences Source" ;
definition: "Full text research database for dental practitioners and researchers. Offers top dental and oral sciences journals commonly purchased by dental schools and related institutions." .
SCR:022706 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Web of Science" ;
NIFRID:synonym "Web of Knowledge" ;
definition: "Database of bibliographic citations of multidisciplinary areas that covers various journals of medical, scientific, and social sciences including humanities.Publisher independent global citation database." .
SCR:022707 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EBSCO CINAHL" ;
definition: "Database indexes top nursing and allied health literature available including nursing journals and publications from the National League for Nursing and the American Nurses Association." .
SCR:022708 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chemotaxis and Migration Tool" ;
NIFRID:synonym "Chemotaxis and Migration Tool version 2.0" ;
definition: "Software tool for data analysis from time stack chemotaxis experiments. Based on NIH ImageJ image processing system." .
SCR:022709 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HDMF-Zarr" ;
NIFRID:synonym "Hierarchical Data Modeling Framework-Zarr" ;
definition: "Software hdmf-zarr library implements Zarr backend for Hierarchical Data Modeling Framework as well as convenience classes for integration of Zarr with PyNWB to support writing of NWB files to Zarr. Library is intended to be used in conjunction with Hierarchical Data Modeling Framework." .
SCR:022710 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RMBlast" ;
definition: "Software tool to support RepeatMasker searches by adding necessary features to stock NCBI blastn program. RepeatMasker compatible version of standard NCBI blastn program." .
SCR:022711 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CORAL" ;
NIFRID:synonym "Contextual Ontology based Repository Analysis Library" ;
definition: "Software tool as framework for rigorous self validated data modeling and integrative, reproducible data analysis." .
SCR:022712 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpiecEasi" ;
NIFRID:synonym "SParse InversE Covariance Estimation for Ecological Association Inference" ;
definition: "Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse." .
SCR:022713 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mvabund" ;
NIFRID:synonym "mvabund-package" ;
definition: "Software R package for multivariate microbiome analysis. Statistical methods for analysing multivariate abundance data." .
SCR:022714 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1516" ;
rdfs:label "California Institute of Technology Water and Environment Laboratory Core Facility" ;
NIFRID:synonym "California Institute of Technology Caltech Water and Environment Laboratory",
"Caltech Water and Environment Laboratory" ;
definition: "Provides access to chromatography and mass spectrometry techniques including GC and GC-MS, IC and IC-MS, ICP-MS, LC and LC-MS, and other environmentally relevent techniques such as isotope ratio measurements of water, TIC/TOC, and laser diffraction particle size analysis." .
SCR:022715 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1519" ;
rdfs:label "University of Pennsylvania Electronic Phenotyping Resource Core Facility" ;
NIFRID:synonym "Electronic Phenotyping Resource",
"University of Pennsylvania Electronic Phenotyping Resource" ;
NIFRID:abbrev "EPR" ;
definition: "Shared resource dedicated to unlocking power of electronic health records for clinical and translational research in cancer care. Electronic phenotyping involves querying electronic health record systems and other clinical information systems and databases to identify patients who meet specific set of clinical characteristics. Can be used to support clinical and translational research pursuits, such as hypothesis generation, retrospective data gathering and hypothesis testing, research planning and grant preparation, subject recruitment for prospective clinical trials, and development of prospective research registries. Provides consultative and technical services." .
SCR:022716 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1518" ;
rdfs:label "University of North Carolina at Chapel Hill Mammalian Genotyping Core Facility" ;
NIFRID:synonym "Mammalian Genotyping Core",
"University of North Carolina at Chapel Hill Mammalian Genotyping Core" ;
NIFRID:abbrev "MGC" ;
definition: "Core is component of Integrated Genomics Core/High Throughput Sequencing Facility. Supports population, basic, clinical and translational research by providing centralized cost efficient, high quality genotyping and methylation services using Illumina BeadArray and Infinium microarray assay technologies for Single Nucleotide Polymorphism Genotyping, Copy Number Variant, Loss of Heterozygosity, Insertions Deletion (indel), Structural Variant, and DNA Methylation Analysis. Can assist with selecting appropriate arrays to meet your needs." .
SCR:022717 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GDSC Single Molecule Localisation Microscopy" ;
NIFRID:synonym "GDSC SMLM ImageJ Plugins" ;
NIFRID:abbrev "GDSC SMLM" ;
definition: "Open source Java based software designed for single molecule localisation microscopy. Software can be used as stand alone library or as plugins for ImageJ image processing software." .
SCR:022718 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1520" ;
rdfs:label "University of Warsaw Center of New Technologies Genomics Core Facility" ;
NIFRID:synonym "Genomics Core Facility" ;
definition: "Core is dedicated to analysis of RNA and DNA sequence, structure and interactions in biological and biochemical processes.Specializes in Genomics, Metagenomics, Transcriptomics, Epigenomics, Interactomics, Oncogenomics, Structural Genomics and other fields. Equippment includes NovaSeq 6000, NextSeq 500 and MiSeq next generation sequencing systems and instruments for fractionation, quality and quantity assessment. Services include consultation and assistance, preparation of libraries from DNA (WGS, WES, Amp-seq, ATAC-Seq, ChIP-seq etc.) and RNA (different fractions: mRNA-seq, mRNA-seq, total RNA-seq, miRNA-seq, RIP-seq etc.), sequence custom libraries and conduct bioinformatic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:022719 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SNPRelate" ;
definition: "Software R package as parallel computing toolset for relatedness and principal component analysis of SNP data." .
SCR:022720 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1523" ;
rdfs:label "Fred Hutchinson Cancer Center Leica Center of Excellence Core Facility" ;
NIFRID:synonym "FH-Leica Center of Excellence",
"Fred Hutch Leica Center of Excellence",
"Fred Hutch Leica Center of Excellence Core Facility" ;
NIFRID:abbrev "CoE" ;
definition: "Leica Microsystems and Fred Hutch established Leica Center of Excellence in Pacific Northwest to provide researchers with advanced microscopy technologies, support generating scientific discoveries and developing new approaches to preventing and treating cancer and related diseases." .
SCR:022721 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1524" ;
rdfs:label "University of Massachusetts Medical School Sanderson Center for Optical Experimentation Core Facility" ;
NIFRID:synonym "UMass Chan - SCOPE",
"University of Massachusetts Medical School UMass Chan - SCOPE" ;
definition: "Offers tools and expertise for quantitative microscopy techniques including super resolution imaging, multi photon intravital and live tissue imaging, confocal microscopy, and high speed time lapse imaging.Offers commercial and custom built microscopes, training and access to light microscopes, imaging services including whole slide scanning, MERFISH spatial transcriptomics, NanoString GeoMx DSP services, and image analysis support. Wet lab facilities, including cell culture, are also available at this BL2 facility. Imaging at BSL3 is available upon request.Offers remote imaging and data analysis sessions, including remote control of all instruments and workstations. All users are trained individually prior to use of the SCOPE equipment and workstations." .
SCR:022722 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenSync" ;
definition: "Open source platform for synchronizing multiple behavioral and physiological signals in neuroscience experiments." .
SCR:022723 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Joint Acquisition, Recording and Voxel based Inference System" ;
NIFRID:synonym "JARVIS-MoCap" ;
NIFRID:abbrev "JARVIS" ;
definition: "Software markerless 3D motion capture toolbox. Used for capturing precise 3D motion." .
SCR:022724 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1526" ;
rdfs:label "Mayo Clinic Immune Monitoring Core Facility" ;
NIFRID:synonym "Immune Monitoring Core",
"Mayo Clinic Immune Monitoring Core" ;
definition: "Provided services include Designing assays to identify and quantify immune cell subpopulations; Characterizing and measuring immune function; Monitoring immunological changes in response to both specific and nonspecific stimulation; Mass Cytometry (CyTOF, Helios); Imaging Mass Cytometry (IMC, Hyperion). Supports experimental systems to study human and mouse models by providing expertise and standardized assays to evaluate immune functions in broad range of diseases and therapies in models as well as in healthy human subjects with variable demographics.Provides services to all Mayo Clinic faculty and staff engaged in research. Selective services are available to investigators outside Mayo Clinic." .
SCR:022725 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1541" ;
rdfs:label "Fred Hutchinson Cancer Center Therapeutic Products Core Facility" ;
definition: "Provides facilities and services in process development and manufacturing of Good Manufacturing Practice grade biologic and cellular therapeutic products for Phase 1/2 clinical trials. Supports the translation of ideas from academic laboratories to clinical trials." .
SCR:022726 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1542" ;
rdfs:label "University of Montreal CRCHUM Cell Imaging Core Facility" ;
NIFRID:synonym "CRCHUM-Cell Imaging" ;
NIFRID:abbrev "CRCHUM" ;
definition: "Optical and fluorescence microscopy facility. Provided instruments include range of microscopes from regular brightfield microscopes to high performence LSM900- Airyscan confocal microscope. Provides Image Analysis with Imaris Full Spectrum and ClearDeconvolution software." .
SCR:022727 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:brumir" ;
rdfs:label "BrumiR" ;
definition: "Software toolkit for de novo discovery of microRNAs from sRNA-seq data. Used for miRNA discovery." .
SCR:022728 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1004" ;
rdfs:label "Purdue University West Lafayette Metabolite Profiling Core Facility" ;
NIFRID:synonym "Metabolite Profiling Facility",
"Purdue University Metabolite Profiling Facility",
"Purdue University West Lafayette Metabolite Profiling Facility" ;
NIFRID:abbrev "MPF" ;
definition: "Provides technologies that enable both qualitative (defining all components of metabolome) and quantitative (determining differential concentrations of metabolites) metabolomics in complex biological systems.Provides sensitive mass spectrometry coupled with liquid chromatography and gas chromatography for precise sample analysis. Empowers researchers with new technologies, methods development, sample analysis, expert training, and consultation." .
SCR:022729 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Enhancing Quality In Preclinical Data Quality System" ;
NIFRID:synonym "EQIPD Quality System" ;
definition: "Preclinical research quality system that can be applied in public and private sectors to ensure that early drug development research proceeds along structured lines. Used for ensuring generation of reliable preclinical data. Proposes guidance on expectations for quality related measures, defines criteria for adequate processes like performance standards, and provides examples of how such measures can be developed and implemented. EQIPD certification was established by EQIPD consortium and is now managed by its legacy organisation GoEQIPD." .
SCR:022730 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ISGPRE" ;
definition: "Software package for predicting interferon stimulated human genes." .
SCR:022731 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UpSet" ;
NIFRID:synonym "UpSet Plot" ;
definition: "Software tool to visualize set intersections in matrix layout. Interactive, web based visualization technique designed to analyze set based data. Visualizes both, set intersections and their properties, and elements in dataset. Used for quantitative analysis of data with more than three sets." .
SCR:022732 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CryoStar_NX50" ;
rdfs:label "Epredia | CryoStar NX50 Cryostat" ;
NIFRID:synonym "CryoStar NX50 Cryostat",
"Epredia™ CryoStar™ NX50 Cryostat" ;
definition: "Manual cryostat designed to accommodate needs of routine clinical laboratory by offering form fitting ergonomic design, with optional height adjustment, vacutome and cold D disinfection." .
SCR:022733 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NetShift" ;
NIFRID:synonym "Netshif" ;
definition: "Web tool for identification of driver nodes between case control association networks.Methodology for understanding driver microbes from healthy and disease microbiome datasets." .
SCR:022734 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SparCC" ;
definition: "Inferring correlations from 16S sequencing data. Capable of estimating correlation values from compositional data." .
SCR:022735 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1544" ;
rdfs:label "University of Pittsburgh Center for Research Computing Core Facility" ;
NIFRID:synonym "Center for Research Computing" ;
definition: "Supports leading edge research with free access to advanced computing hardware and software." .
SCR:022739 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aiforia" ;
definition: "AI powered image analysis software platform for digital pathology and related applications. Enables pathologists and scientist to easily create their own custom AI models to identify, quantify or measure different features and patterns in digitized tissue images." .
SCR:022740 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1025" ;
rdfs:label "University of California at San Diego Institute for Genomic Medicine Genomics Center Core Facilitiy" ;
NIFRID:synonym "UCSD IGM Genomics Center" ;
definition: "Provides services including sequencing library preparation and sequencing on Illumina MiSeq and NovaSeq 6000 platforms. Supports single cell sequencing on 10X Genomics Chromium Controller. Provides Illumina Infinium Beadchips, which includes variety of whole genome genotyping arrays as well as Infinium MethylationEPIC BeadChip." .
SCR:022741 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1549" ;
rdfs:label "Oregon Health and Science University Biostatistics and Design Program Core Facility" ;
NIFRID:synonym "OHSU Biostatistics and Design Program" ;
NIFRID:abbrev "BDP" ;
definition: "Core provides designing studies and developing statistical analysis plans in clinical trials, clinical and community based intervention studies, laboratory experiments, and observational studies.Provides expertise in traditional and modern statistical methods.Can help with trial design and analysis, epidemiologic analysis, sample size and power, high dimensional data analysis, risk prediction, complex survey analysis, time-to-event and longitudinal models, and statistical simulation,data management and wrangling, analytic variable coding and data set creation, research database design, data visualization, manuscript preparation, statistical programming, and much more." .
SCR:022742 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1558" ;
rdfs:label "Oregon Health and Science University Small Animal Research Imaging Core Facility" ;
NIFRID:synonym "OHSU Small Animal Research Imaging Core" ;
NIFRID:abbrev "SARIC" ;
definition: "Provides in vivo imaging technology to evaluate anatomy, tissue function, cellular and molecular phenotype, blood/fluid flow, metabolism and to assess pharmacokinetics and stem cell function in small animal models.Offers spatial resolution, temporal resolution, tissue differentiation, sensitivity for contrast agent, and performance of contrast agents. Services include MicroPET/SPECT/CT imaging,Ultra-high frequency small animal ultrasound imaging,Biophotonics imaging." .
SCR:022743 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1072" ;
rdfs:label "University of Notre Dame Integrated Imaging Core Facility" ;
NIFRID:synonym "NDIIF- Notre Dame Integrated Imaging Facility",
"Notre Dame Integrated Imaging Facility (NDIIF)" ;
NIFRID:abbrev "NDIIF" ;
definition: "Provides microscopes and imaging stations. Expert staff offers guide to non-expert users. Facility offers imaging expertise in Electron Microscopy, Optical Microscopy, In Vivo Imaging, and Histology." .
SCR:022744 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1550" ;
rdfs:label "Oregon Health and Science University Biophysics Core Facility" ;
NIFRID:synonym "OHSU Biophysics Core" ;
definition: "Core services including ensurance that purified proteins and other biomolecules of interest are uncompromised in terms of their structure and stability. Facilitates analyses of catalytic activities and functional interactions.Examines thermodynamic and kinetic parameters for association between proteins and small molecules.Facilitates hypothesis generation through coalescence of experimental data and computational modeling.Assists in setting up protein crystallization assays." .
SCR:022745 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1551" ;
rdfs:label "Oregon Health and Science University Center for Radiochemistry Research Core Facility" ;
NIFRID:synonym "OHSU Center for Radiochemistry Research" ;
definition: "Provides access to tools for imaging with short lived radionuclides, data analysis and is integrated with campus centers SARIC and nuclear medicine clinic for quantitative imaging of these tracers in vivo that provides spatial and temporal data in order to improve our basic understanding of biochemical pathways, disease processes and help select personalized treatments that enhance clinical care. Highlights of our center include On-campus capacity to develop and produce radiopharmaceuticals to address specific research questions using in-vivo, real-time imaging;PET/CT, SPECT/CT (and soon PET/MRI) imaging capability to quantify organ perfusion, assess metabolic pathways, receptor function and density, and measure pharmacodynamics.Applications are directed toward range of models, ranging from small animals to non-human primates, to humans." .
SCR:022746 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1552" ;
rdfs:label "Oregon Health and Science University Elemental Analysis Core Facility" ;
NIFRID:synonym "OHSU Elemental Analysis Core" ;
definition: "Provides highly sensitive elemental quantification, including sample preparation, data analysis, and experimental guidance, through Inductively Coupled Plasma Mass Spectrometry (ICP-MS) technology." .
SCR:022747 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "USVCAM" ;
NIFRID:synonym "ultrasonic vocalizations camera",
"USVCAM project" ;
definition: "Open source acoustic camera system for measuring ultrasound communication in rodents. System includes small phased microphone array combined with camera and comprises USV segmentation algorithms with modification for overlapping vocalizations that results in high accuracy. Enables simpler and faster USV localization and assignment." .
SCR:022748 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RefSeq non-redundant proteins" ;
definition: "Non-redundant RefSeq protein records are currently provided for archaeal and bacterial RefSeq genomes, with exception of selected reference genomes, by NCBI prokaryotic genome annotation pipeline. This scope definition may change in the future to include additional RefSeq sub-kingdoms or other organism groups and some GenBank conceptual translation protein records may provide cross-links to RefSeq non-redundant proteins." .
SCR:022749 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IsoSeq3" ;
definition: "Software package for scalable de novo isoform discovery from single molecule PacBio reads. Contains tools to identify transcripts in PacBio single molecule sequencing data." .
SCR:022750 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ALLHiC" ;
definition: "Software pipeline for phasing and scaffolding polyploid genomes based on Hi-C data. Hi-C-based scaffolding algorithm that integrates pruning, partition, optimization and building functions to select contigs specific for polyploid genome assembly." .
SCR:022751 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Toyama; Toyama; Japan" ;
definition: "Japanese national university in Toyama Prefecture established in 1949. University of Toyama has three campuses, namely Gofuku, Sugitani, and Takaoka campuses." .
SCR:022752 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ComplexUpset" ;
definition: "Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries." .
SCR:022753 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eulerr" ;
definition: "Software package to generate area proportional Euler diagrams using numerical optimization that display set relationships (intersections, unions, and disjoints) with circles or ellipses. Area Proportional Euler and Venn Diagrams with Ellipses." .
SCR:022754 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rank Rank Hypergeometric Overlap2" ;
NIFRID:synonym "Rank–rank hypergeometric overlap2" ;
NIFRID:abbrev "RRHO2" ;
definition: """Software R package with new, more intuitive visualization of concordant and discordant gene overlap
where all regions in RRHO plots are meaningful. Used for identification of statistically significant overlap between gene expression signatures.""" .
SCR:022755 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "shinyhelper" ;
definition: "Software R package to add markdown helpfiles to shiny apps, using modal dialog boxes, with no need to observe each help button separately." .
SCR:022756 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ShinyCell" ;
definition: "Software R package to create interactive Shiny based web applications to visualise single cell data via visualising cell information and/or gene expression on reduced dimensions e.g. UMAP, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information e.g. nUMI / module scores using violin plots / box plots, visualising composition of different clusters / groups of cells using proportion plots and visualising expression of multiple genes using bubbleplots / heatmap.Shiny Interactive Web Apps for Single-Cell Data." .
SCR:022757 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "shinythemes" ;
definition: "Software R package Themes for use with Shiny." .
SCR:022758 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sholl Analysis" ;
definition: "Open source program for ImageJ/Fiji. Automated and multithreaded Sholl for direct analysis of fluorescent images and/or traced morphologies. Features quantifications based on curve fitting. Analysis of profiles obtained by other software is also possible." .
SCR:022759 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Surgisphere" ;
definition: "American healthcare analytics company established in 2008. Originally textbook marketing company, it came under scrutiny in May 2020 after it had provided large datasets of COVID-19 patients which were subsequently found to be extremely unreliable. The questionable data was used in studies published in The Lancet and The New England Journal of Medicine in May 2020. On 15 June 2020, company website was taken offline." .
SCR:022760 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "trinetx" ;
definition: "Network of healthcare organizations, together with data partners in Brazil, South Korea, and Japan, to bring clinical facts on more than 250 million patients around the world. Federated model so users of this data are ensured new patients, observations, and results every day, all harmonized to standard terminology like ICD-10 and LOINC without any data wrangling required at the point of care. The raw data is not available to authors of papers and papers in medicine are being retracted." .
SCR:022761 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yoda Project" ;
NIFRID:synonym "Yale University Open Data Access Project",
"Yale university Open Data Access project",
"YODA Project" ;
definition: "Project to promote and facilitate sharing of clinical trial data. Provides set of policies to set standards to enhance data availability and transparency in support of strong scientific research which aims to advance scientific and medical knowledge with goal of improving public health and healthcare delivery. Project has the final decision making rights regarding these policies and granting or denial of data requests, as per contractual agreements between the YODA Project and its partners." .
SCR:022762 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PCA Matching " ;
NIFRID:synonym "PCA_Matching" ;
definition: "Software R script for identifying x controls within t distance of each case based on weighted PCA data." .
SCR:022763 a "Research",
owl:NamedIndividual ;
rdfs:label "Hugo Data" ;
definition: "Platform for individuals who want to make their own data available for research. Used by people to join network with others who wish to contribute to vital research in partnership with and alongside leading scientists. Personal tool for saving and displaying medical information." .
SCR:022764 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1563" ;
rdfs:label "University of Pennsylvania Penn Vet Imaging Core Facility" ;
NIFRID:synonym "Penn Vet Imaging Core" ;
NIFRID:abbrev "PVIC" ;
definition: "Core provides access to light microscope systems to perform widefield, confocal, 2-photon/multiphoton, second harmonic generation, total internal reflection (TIRF), and high content imaging." .
SCR:022765 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Napari" ;
definition: "Multi dimensional image viewer for Python. Used for browsing, annotating, and analyzing large multi dimensional images. Can be coupled to machine learning and image analysis tools enabling more user friendly automated analysis." .
SCR:022766 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MicrobiomeDB" ;
NIFRID:synonym "MicrobiomeDB.org" ;
definition: "Systems biology platform for integrating, mining and analyzing microbiome experiments.Data discovery and analysis web based resource that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. Used to mine complex microbiome and metagenome studies." .
SCR:022767 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AOData" ;
definition: "Software tool as framework for adaptive optics data analysis. Object oriented framework for organizing data, metadata and code related to adaptive optics experiment." .
SCR:022768 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TMExplorer" ;
NIFRID:synonym "Tumour Microenvironment Explorer" ;
definition: "Software package to improve studying tumour microenvironment with single cell sequencing. Developers may use this package to obtain data for validation of new algorithms and researchers interested in tumour microenvironment may use it to study specific cancers more closely. Curated collection of scRNAseq datasets sequenced from tumours." .
SCR:022769 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scATAC.Explorer" ;
definition: "Software package to improve the ease of studying and integrating scATAC-seq datasets. Developers may use this package to obtain data for analysis of multiple tissues, diseases, cell types, or developmental stages. It can also be used to obtain data for validation of new algorithms." .
SCR:022770 a owl:NamedIndividual ;
rdfs:label "Cell Morphology Labelling Tool" ;
NIFRID:synonym "22CellMorphologyLabelingTool" ;
definition: "Software tool for image quality. Used for labeling quality of images and labeling center point of 3D RI images. Used to mange 3D RI cell images taken from holotomography." .
SCR:022771 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hifiasm-meta" ;
NIFRID:synonym "hifiasm_meta" ;
definition: "Software tool as metagenome assembler that exploits high accuracy of recent data. De novo metagenome assembler, based on haplotype resolved de novo assembler for PacBio Hifi reads. Workflow consists of optional read selection, sequencing error correction, read overlapping, string graph construction and graph cleaning." .
SCR:022772 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_09013" ;
rdfs:label "Bandage" ;
NIFRID:synonym "Bioinformatics Application for Navigating De novo Assembly Graphs Easily" ;
definition: "Software tool for visualising de novo assembly graphs. By displaying connections which are not present in contigs file, opens up new possibilities for analysing de novo assemblies. Used for interactive visualization of de novo genome assemblies." .
SCR:022773 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RDP Classifier" ;
NIFRID:synonym "Ribosomal Database Project Classifier" ;
definition: "Software tool as naive Bayesian classifier that can rapidly and accurately provide taxonomic assignments from domain to genus, with confidence estimates for each assignment." .
SCR:022774 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "viralVerify" ;
definition: "Software viral contig verification tool. Classifies contigs as viral, non-viral or uncertain, based on gene content. Also for non-viral contigs it can optionally provide plasmid/non-plasmid classification." .
SCR:022775 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kaiju" ;
definition: "Software tool for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing or metatranscriptomics experiments." .
SCR:022776 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_022781",
;
rdfs:label "Histological E data Registration in rodent Brain Spaces" ;
NIFRID:abbrev "HERBS" ;
definition: "Open source, extendable, intuitive and interactive software platform for image visualisation and image registration. Python based GUI for histological E-data registration in brain space." .
SCR:022779 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Megadepth" ;
definition: "Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts." .
SCR:022780 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DivBrowse" ;
definition: "Web tool for interactive visualization and analysis of diversity of genomic variants. Used for interactive exploration and analysis of very large SNP matrices based on VCF files." .
SCR:022782 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1565" ;
rdfs:label "MDC and BIH Technology Platform Genomics Core Facility" ;
NIFRID:synonym "MDC&BIH Technology Platform Genomics" ;
definition: "Facility comprises Next Generation Sequencing, Single Cell Technologies and Data Management teams. Offers professional project counseling, library preparation, and sequence production support for Max Delbruck Center for Molecular Medicine and Berlin Institute of Health at Charite institutes in Berlin." .
SCR:022783 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DataLyser" ;
definition: "A software to display, record and data processing of physiological signals. DataLyser is custom-built software developed at Walter Reed Army Institute of Research, Silver Spring, MD. It is not copyrighted." .
SCR:022784 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Subsemble Cell Type Classifier" ;
definition: "Supervised ensemble machine learning classifier. Classification performance benchmark scripts." .
SCR:022787 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenAlex" ;
definition: "Open index of scholarly works, authors, venues, institutions, and concepts. Catalog of scholarly papers, researchers, journals, and institutions along with all the ways they are connected to one another." .
SCR:022788 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1566" ;
rdfs:label "National Cancer Institute of Mexico Advanced Microscopy Applications Unit Core Facility" ;
NIFRID:synonym "Advanced Microscopy Applications Unit (ADMiRA)",
"Instituto Nacional de Cancerolog ADMiRA",
"National Cancer Institute of Mexico Research Support Network Advanced Microscopy Applications Unit" ;
NIFRID:abbrev "ADMiRA" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 26,2025. Imaging Core Facility located within National Cancer Institute of Mexico. Provides scientific and technical support in imaging and image analysis to any community. Imaging technologies in ADMiRA include: Confocal, Widefield, Super-Resolution, Lightsheet, FIB-SEM, Laser Microdisection, and Automated digital scanning." .
SCR:022789 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1567" ;
rdfs:label "University of California at Los Angeles California NanoSystems Institute Advanced Light Microscopy and Spectroscopy Core Facility" ;
NIFRID:synonym "Advanced Light Microscopy & Spectroscopy Core",
"UCLA CNSI Advanced Light Microscopy & Spectroscopy Core" ;
NIFRID:abbrev "ALMS" ;
definition: "Offers microscopy services, consultation, and support for application of novel microscopic and spectroscopic methods and advanced image analysis techniques for study of macromolecules, cellular dynamics and nano-scale characterization of bio-materials. Provides collection of customized biological fluorescence microscopes and small-animal imaging devices to study biological processes with high spatial and temporal resolution in whole organisms and in living cells down to single molecule detection level with nanometer accuracy. Located in basement and second floor of CNSI building, two optical suites designed to house microscopes with the required environment control (low vibration, air-filtered, air-conditioned and light-tight) and services. Services include Wide-field Fluorescence Imaging Microscopy (on a limited basis), Confocal One-Photon and Two-Photon Laser Scanning Microscopy, (both point scanning and spinning disk), Fluorescence Correlation Spectroscopy (FCS), Fluorescence Resonance Energy Transfer (FRET), microscopic and macroscopic Fluorescence Lifetime Imaging (FLIM) with Time-Correlated-Single-Photon-Counting (TCSPC) and Near-Infrared (NIR) Detection, Stimulated Emission Depletion laser-scanning microscopy (STED) (a super-resolution technique), both microscopic and macroscopic (small animal) spectral unmixing and laser capture microdissection." .
SCR:022790 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1568" ;
rdfs:label "British Columbia Children's Hospital Research Institute Flow Cytometry Core Facility" ;
NIFRID:synonym "BCCHR-FLOWCORE" ;
definition: "Core provides equipment for flow cytometric analysis, full service cell sorting, training, and dissemination." .
SCR:022791 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mBrainAligner" ;
definition: "Software package provides cross modality image registration pipeline to support whole brain mapping projects. Contains three modules: (1) image preprocessing and global registration, (2) Coherent Landmark Mapping (CLM) based automatic registration, and (3) optional semi-automatic refinement." .
SCR:022793 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Type Knowledge Explorer" ;
NIFRID:synonym "Allen Brain Map Cell Type Knowledge Explorer" ;
definition: "Software to examine multimodal data from thousands of cells across 3 mammalian species." .
SCR:022794 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BRAIN Initiative Cell Atlas Network " ;
NIFRID:abbrev "BICAN" ;
definition: "Provides molecular and anatomical foundational framework for study of brain function and disorders.Comprehensive Center on Human and Non-Human Primate Brain Cell Atlases with goal to build reference brain cell atlases that will be used throughout research community." .
SCR:022795 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CloudReg" ;
definition: "Software automated, terascale, cloud based image analysis pipeline for preprocessing and cross modal, nonlinear registration between volumetric datasets with artifacts. Automatic terabyte scale cross modal brain volume registration." .
SCR:022796 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Epiviz" ;
definition: "Software package as interactive visualization tool for functional genomics data. Interactive visual analytics for functional genomics data." .
SCR:022797 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Annotation Platform" ;
definition: "Centralized, community driven platform for creation, exploration, and storage of cell annotations for single cell RNA sequencing datasets." .
SCR:022798 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "harmonypy" ;
definition: "Software algorithm for integrating multiple high dimensional datasets. Port of harmony R package." .
SCR:022799 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1572" ;
rdfs:label "Pennsylvania State University Hershey College of Medicine Custom Antibody Core Facility" ;
NIFRID:synonym "Custom Antibody Core",
"Penn State College of Medicine PSU-COM Antibody Core",
"Penn State Hershey College of Medicine Custom Antibody Core",
"Penn State Hershey College of Medicine Custom Antibody Core Facility",
"PSU-COM Antibody Core" ;
definition: "Provides service for production and purification of custom antibodies.Primary services include immunization of mice and rabbits to make mouse and rabbit monoclonal antibodies to select targets. Primary screening of hybridomas will be conducted using standard ELISA technology and positive lines will be preserved for cloning. Supernatants containing antibody selected as positive will be made available to investigators for secondary analyses in their labs (Westerns, immunofluorescence, functional assays). Investigator selected lines will be cloned, isotyped, and adapted to serum free culture for future production of high titer antibody if investigator requires large quantities of antibody. Standard purifications will be conducted as needed, and various modifications (fluorochrome, enzyme, biotin) are also provided as Antibody Core services." .
SCR:022800 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TALOS-N" ;
definition: "Software package for prediction of protein backbone and sidechain torsion angles from NMR chemical shifts." .
SCR:022801 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LDSC" ;
definition: "Command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores." .
SCR:022802 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "monaLisa" ;
definition: "Software R package to work with sequence motifs in analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of obtained results are also provided." .
SCR:022803 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scglue" ;
NIFRID:synonym "single cell graph linked unified embedding" ;
definition: "Software Python package implemented Graph Linked Unified Embedding framework for single-cell multi-omics data integration." .
SCR:022804 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MUON" ;
NIFRID:synonym "multimodal omics Python framework" ;
definition: "Software Python framework designed to work with multimodal omics data. Aims to provide convenience and speed to its users enabling standardised analysis while staying flexible and expandable. Muon stands on shoulders of and integrates with annotated data object specification and scanpy library for single cell analysis in Python." .
SCR:022805 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "philentropy" ;
definition: "Software R package for similarity and distance quantification between probability functions. Information Theory and Distance Quantification with R. Provides framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions." .
SCR:022806 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyNNDescent" ;
NIFRID:synonym "Python Nearest Neighbor Descent" ;
definition: "Software Python tool for approximate nearest neighbors. Provides Python implementation of Nearest Neighbor Descent for k-neighbor-graph construction and approximate nearest neighbor search." .
SCR:022807 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BBKNN" ;
NIFRID:synonym "Batch Balanced KNN" ;
definition: "Software to identify each cell’s top neighbours in each batch separately instead of entire cell pool with no accounting for batch. Nearest neighbours for each batch are then merged to create final list of neighbours for cell. Aligns batches in a quick and lightweight manner." .
SCR:022808 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH Heal Project" ;
NIFRID:synonym "Addiction Long-term Initiative",
"NIH HEAL Initiative" ;
definition: """Project to help to end opioid addiction. Addiction Long-term Initiative or NIH HEAL Initiative, to speed scientific solutions to stem national opioid public health crisis. Initiative is funding hundreds of projects nationwide. Researchers are taking variety of approaches to tackle opioid epidemic through
understanding, managing, and treating pain, and also through improving prevention and treatment for opioid misuse and addiction.""" .
SCR:022809 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Simplicity " ;
definition: "Software for Berthold ORION II (LB 965) microplate luminometers." .
SCR:022810 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SINGLe" ;
definition: "Software R package to correct systematic errors in nanopore sequencing reads of gene libraries. Retrieves true consensus sequences of variants identified by barcode, needing only few reads per variant." .
SCR:022811 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Paradigmika" ;
NIFRID:synonym "presenter" ;
definition: "Simple PC application for present audio/visual stimuli for fmri paradigms." .
SCR:022812 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lwgeom" ;
definition: "Software R package for bindings to liblwgeom library." .
SCR:022813 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "stringr" ;
definition: "Software package to provide set of functions designed to make working with strings easy. Consistent wrappers for common string operations." .
SCR:022814 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Pro_6-FS" ;
rdfs:label "Motic | MoticEasyScan Pro 6-FS" ;
definition: "MoticEasyScan digital slides scanner." .
SCR:022815 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allen Brain Map BICCN Data Catalog" ;
NIFRID:synonym "Allen Brain Map BRAIN Initiative Cell Census Network Data Catalog",
"BICCN Data Inventory Catalog",
"BRAIN Initiative Cell Census Network Data Catalog" ;
definition: "BRAIN Initiative Cell Census Network data catalog. Provides access to all major data sets of the BICCN with descriptions." .
SCR:022816 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Highly segmented anatomical labels in the adult mouse brain common coordinate framework." ;
definition: """Labels provide resource to isolate and identify mouse brain anatomical structures. Cell type specific transgenic mice and an MRI atlas were used to adjust and further segment the labels.
Highly segmented anatomical labels in the adult mouse brain common coordinate framework.""" .
SCR:022817 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MorphoHub" ;
definition: "Software package to streamline workflow of imaging data management, visualization, reconstruction and collaboration, and data sharing." .
SCR:022818 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QuickNII and VisuAlign" ;
definition: "EBRAINS service for image registration. Spatially register mouse and rat serial 2D brain images to 3D reference atlases." .
SCR:022819 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hi5App" ;
definition: "Software cross platform mobile application that supports 2D/3D/4D image visualization, multi-morphometry annotation, proofreading, interactive imaging system controlling, and distributed collaboration." .
SCR:022820 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CloudVolume" ;
definition: "Software Python package for reading and writing of image data in Neuroglancer precomputed format. Used to read and write Neuroglancer datasets programmatically." .
SCR:022821 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "neuroXiv" ;
definition: "Platform to search neurons of interest by neuron anatomy, morphology, and connectivity patterns. Used to Explore morphology and connectivity features of neurons of interest, Upload neuron (swc file or eswc file) and calculate morphology features, Search similar neurons, Explore 3D visualization of neurons, Explore cross species atlas. Open source pan-neuron table of morphology and connectivity." .
SCR:022822 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Data Standards Ontology " ;
definition: "Repository for co-ordinating work on ontologies for Brain Data Standards Project. Automate data driven cell type ontology development for Brain Data Standards initiative." .
SCR:022823 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pittsburgh Supercomputing Center" ;
NIFRID:abbrev "PSC" ;
definition: """Joint computational research center with Carnegie Mellon University and University of Pittsburgh.
Provides university, government and industrial researchers with access to several systems for high performance computing, communications and data storage available to scientists and engineers nationwide for unclassified research.""" .
SCR:022824 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Molecular Biosensor and Imaging Center" ;
NIFRID:synonym "Carnegie Mellon University Molecular Biosensor and Imaging Center" ;
NIFRID:abbrev "MBIC" ;
definition: "Center for collaboration of biologists, chemists, and engineers to develop fluorescence technologies for biomedical applications used in drug discovery, neuroscience, biomedical imaging and cancer biology programs. Technologies launched from MBIC include the Cyanine Dyes (Cy3, Cy5, Cy7), High Content Screening (Cellomics, Inc), Difference In-Gel Electrophoresis (DIGE), Qdots for In-vivo imaging, Fluorogen Activating Proteins, and DNA Nanotags." .
SCR:022825 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Generative Diffeomorphic Mapping" ;
definition: "Web portal that explains technique of Diffeomorphic Mapping and Shape Analysis." .
SCR:022826 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneSwitches" .
SCR:022827 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellRank" ;
definition: "Software package for directed single cell fate mapping in diverse scenarios, including regeneration, reprogramming and disease. Automatically detects initial, intermediate and terminal populations, predicts fate potentials and visualizes continuous gene expression trends along individual lineages. Applied to lineage traced cellular reprogramming data, predicted fate probabilities correctly recover reprogramming outcomes." .
SCR:022828 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CytoTRACE" ;
NIFRID:synonym "Cellular (Cyto) Trajectory Reconstruction Analysis using gene Counts and Expression" ;
definition: "Software tool that predicts differentiation state of cells from single cell RNA sequencing data. Used for predicting differentiation states from scRNA-seq data." .
SCR:022829 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harvard Tissue Atlas" ;
NIFRID:synonym "tissue-atlas.org" ;
NIFRID:abbrev "HTA" ;
definition: "Gathers together imaging and omic datasets into molecular maps of normal and diseased tissue from human and animal models, with emphasis on cancer. Used to access datasets, educational curriculum and talks, and recommended methods and software." .
SCR:022830 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Minimum Information about Tissue Imaging" ;
NIFRID:synonym "MITI Consortium" ;
NIFRID:abbrev "MITI" ;
definition: "Consortium provides guidelines for highly multiplexed tissue images. Standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology. Data and metadata standards consistent with Findable, Accessible, Interoperable, and Reusable (FAIR) standards that guide data deposition, curation and release." .
SCR:022831 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harvard Medical School Center for Cancer Systems Pharmacology" ;
NIFRID:synonym "Center for Cancer Systems Pharmacology" ;
NIFRID:abbrev "CCSP" ;
definition: "Center includes studies for responsiveness and resistance to anti cancer drugs. Committed to training students and postdocs, promoting junior faculty and ensuring that data and software are reproducible, reliable and publicly accessible. Member of National Cancer Institute’s Cancer Systems Biology Consortium." .
SCR:022832 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCMICRO" ;
NIFRID:synonym "mcmicro.org",
"Multiple Choice MICROscopy" ;
definition: """Software tool as scalable, modular image processing pipeline for multiplexed tissue imaging.
Transforms multi channel whole slide images into single cell data.""" .
SCR:022833 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.5064",
"DOI:10.17616/r3cs51",
"DOI:10.25504/FAIRsharing.bmz5ap",
"r3d100011038" ;
rdfs:label "Qualitative Data Repository" ;
NIFRID:synonym "Qualitative Data Repository at Syracuse University" ;
NIFRID:abbrev "QDR" ;
definition: "Archive for storing and sharing digital data (and accompanying documentation) generated or collected through qualitative and multi method research in social sciences. QDR provides data management consulting services and actively curates all data projects, maintaining value and usefulness of data over time, and ensuring their availability and findability for re-use." .
SCR:022834 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pi USB Cam project" ;
NIFRID:synonym "Pi USB Cam",
"Pi USB Cam system" ;
definition: "Project related to video recording.Provides system for high throughput video capture. Pi USB Cam system includes low cost Raspberry Pi microcomputer, DIY electronics peripherals, freely available open-source firmware, and custom 3D-printed casings." .
SCR:022835 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EpiTools" ;
NIFRID:synonym "Ausvet EpiTools",
"Epidemiological Calculators",
"Epitools Epidemiological Calculators" ;
definition: "Web application for use by epidemiologists and researchers involved in estimating disease prevalence or demonstrating freedom from disease through structured surveys, or in other epidemiological applications." .
SCR:022836 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ModelRisk" ;
definition: "Monte Carlo simulation software that makes quantitative risk analysis intuitive. Monte Carlo simulation Excel add-in that allows user to include uncertainty in their spreadsheet models." .
SCR:022837 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "atRISK" ;
NIFRID:synonym "@RISK",
"Palisade @RISK" ;
definition: "Software is add-in tool for Microsoft Excel that computes and tracks many different possible scenarios in model using Monte Carlo simulation.Helps make better decisions through risk modeling and analysis." .
SCR:022838 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scShapes" ;
definition: "Software tool as statistical framework for identifying distribution shapes in single-cell RNA-sequencing data." .
SCR:022839 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BIDScoin" ;
definition: "Software Python tool to convert your source level neuroimaging data to BIDS. Application to convert source data to Brain Imaging Data Structure." .
SCR:022840 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PopTools" ;
definition: "Software to allow construction, analysis, and simulation of complex models in spreadsheet format." .
SCR:022841 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PEAKS Studio" ;
NIFRID:synonym "PEAKS Studio Xpro" ;
definition: "Software platform with complete solutions for discovery proteomics, including protein identification and quantification, analysis of post translational modifications and sequence variants (mutations), and peptide/protein de novo sequencing." .
SCR:022849 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FlowSorted.CordBloodCombined.450k" ;
definition: "Software package includes combination of four cell references for umbilical cord blood deconvolution using IlluminaHumanMethylation arrays 450K and EPIC." .
SCR:022850 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IBD Detection Tool Benchmark Tool" ;
definition: "Software package as open source project benchmarks IBD detection tools with multiple measurements." .
SCR:022851 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Research on Calculus Kinetics Society" ;
NIFRID:abbrev "ROCK" ;
definition: "Special interest society focused on basic mechanisms involved in human urinary stone formation." .
SCR:022852 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford University School of Medicine O’Brien Urology Research Center Biospecimen/Bioimaging Core Facility" ;
definition: "Core leverages infrastructure of Stanford Urology and Pathology Departments to provide services to benefit O’Brien Center investigators in CAIRIBU Network. Procures and provides biospecimens, including fresh, freshly-frozen, and formalin-fixed paraffin-embedded (FFPE) prostate issues.Provides tissue characterization services, including histology, tissue microarrays, laser microdissection, and multiplex immunohistochemistry (IHC) using MIBI-TOF (Multiplexed Ion Beam Imaging by Time of Flight). Stores and provides access to images including prostate MRIs, whole-mount histology and IHC, and MIBI-TOF data, as well as integrated multiscale data platform." .
SCR:022853 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bio_contrast_subgraph" ;
definition: "Software package for implementing algorithms proposed in Lanciano et al. \"Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data\"." .
SCR:022854 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LipiDexSpectrumAnnotator" ;
definition: "Software for annotation of lipidomics spectra." .
SCR:022855 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pediatric KIDney Stone Care Improvement Network" ;
NIFRID:abbrev "PKIDS" ;
definition: "Community of patients, caregivers, clinicians, and researchers who perform collaborative studies of kidney stones at pediatric healthcare systems in North America. Network to better understand treatment of kidney stones specifically comparative effectiveness of different surgical approaches to remove kidney stones, impact of these surgeries of patients’ lives, and insight into recovery period." .
SCR:022856 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ordinal" ;
NIFRID:synonym "Regression Models for Ordinal Data" ;
definition: "Software R package implementation of cumulative link models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered logit/probit models." .
SCR:022857 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "afex" ;
NIFRID:synonym "Analysis of Factorial EXperiments",
"Analysis of Factorial Experiments" ;
definition: "Software R package with convenience functions for analyzing factorial experiments using ANOVA or mixed models." .
SCR:022858 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Just the Docs Website Template LSP Edition" ;
NIFRID:synonym "Just-the-Docs Website Template: LSP Edition" ;
definition: "Platform containing documentation to create scientific websites using Just the Docs with Jekyll. This documentation includes overview of Markdown and instructions for configuring the site." .
SCR:022859 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Jekyll Tutorial" ;
definition: "Website tutorial for creating Jekyll-based scientific website, including editing in GitHub, working locally with Jekyll and applying Jekyll and Markdown formatting basics, and using custom themes." .
SCR:022860 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_217" ;
rdfs:label "University of Nebraska Medical Center Center for Collaboration on Research Design and Analysis Core Facility" ;
NIFRID:synonym "Center for Collaboration on Research Design and Analysis",
"University of Nebraska Medical Center Center for Collaboration on Research Design and Analysis" ;
NIFRID:abbrev "CCORDA" ;
definition: "Provides advance clinical, translational and public health research at UNMC and in the community and region. Provides expertise in quantitative sciences, including biostatistics, epidemiology, and health services research, and coordinates collaborative design, planning, conduct, analysis and interpretation of laboratory, clinical, and public health research studies.Provides educational training opportunities for graduate students and educational opportunities for public health, clinical, and translational investigators." .
SCR:022861 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1577" ;
rdfs:label "University of Delaware Flow Cytometry Core Facility" ;
NIFRID:synonym "UD Flow Cytometry Core" ;
definition: "Facility, located at the University of Delaware Main campus (UD) in Newark, Delaware, provides flow cytometry and hematology services. Facility is equipped with 15-color FACSAria Fusion high-speed cell sorters,BD Rhapsody Express Cell Processing Unit,VetScan HM5c veterinary hematology analyzer, Nexcelom Cellometer Vision cell counter, Zeiss Axiovert 200 inverted fluorescent microscope,Thermo Shandon Cytospin 4 & a Beckman Spinchron DLX centrifuge,General Laboratory facilities for Mammalian Cell Culture and Sample preparation,Laminar flow BSL-2 biosafety cabinets, microscopes and centrifuges." .
SCR:022862 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1578" ;
rdfs:label "University of California at Davis Veterinary Medicine Advanced Imaging Core Facility" ;
NIFRID:synonym "Health Sciences District Advanced Imaging Facility",
"University of California at Davis Health Sciences District Advanced Imaging Facility",
"University of California at Davis Veterinary Medicine Advanced Imaging Facility" ;
NIFRID:abbrev "HSDAIF" ;
definition: "Fluorescence microscopy facility with two Leica confocal microscopes, one with superresolution capability,second with multi-photon imaging capability, and Zeiss Lightsheet microscope. Facility offers consultation, training, and support." .
SCR:022863 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1580" ;
rdfs:label "University of Pennsylvania School of Dental Medicine Tissue Processing Laboratory Core Facility" ;
NIFRID:synonym "Tissue Processing Laboratory",
"University of Pennsylvania School of Dental Medicine Tissue Processing Laboratory" ;
definition: "Laboratory is located in Room 429 of the Levy Building.Services include tissue processing; H&E staining, trichrome, and other staining; creation of frozen sections; and deparaffinization. Provides cryostat for use by investigators within Penn Dental Medicine; cryostat training is available for a fee. Investigators requiring the services of the Tissue Processing Laboratory should contact the facility to arrange a meeting to set up the appropriate protocols. Special handling, specimen orientation, and any unique aspects of the tissue being processed will be discussed at that time; in some instances, it may be advantageous for the investigator to be present initially when the specimens are being oriented in the hot paraffin prior to the actual sectioning." .
SCR:022864 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fragpipe" ;
NIFRID:synonym "FragPipe" ;
definition: "Java Graphical User Interface for suite of computational tools enabling comprehensive analysis of mass spectrometry based proteomics data." .
SCR:022865 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DIA-NN" ;
definition: "Software tool for processing of data independent acquisition proteomics experiments. Universal automated software suite for DIA proteomics data analysis. Neural networks and interference correction enable deep proteome coverage in high throughput." .
SCR:022867 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1581",
"SCR_022881" ;
rdfs:label "Penn State University Center for Applications of Artificial Intelligence and Machine Learning to Industry Core Facility" ;
NIFRID:synonym "AIMI - Center for Applications of AI/ML to Industry",
"Penn State University Center for Applications of Artificial Intelligence and Machine Learning to Industry" ;
NIFRID:abbrev "AIMI" ;
definition: "Connects industry members with Penn State research community of artificial intelligence and machine learning researchers and their students to solve real world problems and seize market opportunities." .
SCR:022868 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fMOST Atlas" ;
definition: "Reference atlas for mice. Contains both average and annotation templates." .
SCR:022870 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "msigdbr" ;
definition: "Software R package contains Molecular Signatures Database (MSigDB) gene sets for multiple organisms in tidy data format. Gene sets in standard R data frame with key value pairs. Package includes human genes as well as corresponding symbols and IDs for frequently studied model organisms such as mouse, rat, pig, fly, and yeast." .
SCR:022871 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "What the Phage" ;
NIFRID:abbrev "WtP" ;
definition: "Parallel multitool approach for phage prediction combined with annotation and classification downstream strategy. Used for identification and analysis of phage sequences. Phage identification via nextflow and docker or singularity." .
SCR:022872 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Endourological Society" ;
definition: "Non-profit organization founded in 1983 by group of international urologists. Society sponsors annual meetings held at different sites of the world. Endourological Society has sub-societies through out the world including the British Society of Endourology, the Mexican Endourological Society, and the Korean Endourology and ESWL Society." .
SCR:022873 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Laboratory of Systems Pharmacology program" ;
NIFRID:abbrev "LSP" ;
definition: "Research and education program in Harvard Program in Therapeutic Science at Harvard Medical School to advance science and to develop technology needed to accelerate invention of new medicines and personalization of patient care. Used to study molecular causes of disease, ways drugs exert their therapeutic and adverse effects, design and interpretation of clinical trials." .
SCR:022874 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Society of Urodynamics, Female Pelvic Medicine and Urogenital Reconstruction (SUFU)" ;
definition: "Organization to optimize the care of women, men, and children with lower urinary tract dysfunction and/or pelvic floor disorders through education, research and involvement in health care policy. To improve the art and science of Urology through basic and applied clinical research in urodynamics and neurourology, voiding function and dysfunction, female urology and pelvic floor dysfunction, and to disseminate and teach these concepts." .
SCR:022875 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Society of Benign Prostate Disease" ;
NIFRID:abbrev "SoBPD" ;
definition: "Organization focused on disorder of men with benign prostate disease, and promote health and well-being of men by advancing the best care to every patient through integrated clinical practice, education and research. Provides collaborative platform to elevate knowledge base of members about pathophysiology, diagnosis, management, and treatment of prostate disease." .
SCR:022876 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Collaborating for the Advancement of Interdisciplinary Research in Benign Urology" ;
NIFRID:abbrev "CAIRIBU" ;
definition: "Community of researchers studying benign urology diseases at U54 O’Brien Cooperative Research Centers, P20 Exploratory Centers, and K12 Career Development Programs funded by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), one of the institutes within the National Institutes of Health (NIH). CAIRIBU Centers and Programs are united around the overall objectives of improving our understanding of the mechanisms of urogenital diseases and developing clinical therapies for treating them by building collaborative and interactive research platforms that span the gamut from basic to translational to population research." .
SCR:022877 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FreeStyle 1.8 SP1" ;
definition: "Software to visualize and qualitatively analyze mass spectrometry data. Used to display chromatograms and spectra, detect and integrate chromatographic peaks, search mass spectral libraries, simulate mass spectra, subtract background spectra, apply scan filters, annotate plots with text and graphics, create and save layouts, view the status of various instrument parameters during data acquisition, and create a 2D or 3D representation of an analysis displaying the acquired mass/wavelength scans. Part of liquid chromatography mass spectrometry system." .
SCR:022878 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_436" ;
rdfs:label "University of Hawaii at Manoa ABSL3/BSL3 Biocontaminant Core Facility" ;
NIFRID:synonym "ABSL_3/BSL_3 Biocontaminant Core",
"University of Hawaii at Manoa ABSL_3/BSL_3 Biocontaminant Core" ;
definition: "Research on microbial agents, which cause lethal diseases in humans and for which effective drugs or preventive vaccines are not available, must be conducted by well-trained investigators in specially built, well-maintained laboratories. Core provides the triad of service, research and development, and education and training." .
SCR:022879 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_373" ;
rdfs:label "Wayne State University Proteomics Core Facility" ;
NIFRID:synonym "Wayne State University WSU Proteomics Core",
"WSU Proteomics Core" ;
definition: "Protein identification and proteome analysis using Orbitrao Eclipse,Fusion and Q Exactive LC-MS/MS platforms. Affinity selection for phosphopeptides with analysis using HCD, CID and ETD. Validation and quantitation of proteins using MRM with a TSQ Vantage triple quad." .
SCR:022880 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_527" ;
rdfs:label "University of Georgia Georgia Genomics and Bioinformatics Core Facility" ;
NIFRID:synonym "Georgia Genomics and Bioinformatics Core",
"University of Georgia Georgia Genomics and Bioinformatics Core" ;
definition: "Core laboratory for nucleic acid sequencing and bioinformatics. Mission includes research support, education, and training.Services encompass range of genomic techniques and applications, sequencing technologies, and bioinformatics analyses. GGBC operates multiple platforms for short-, long-, and single-molecule sequencing reads (i.e., Illumina MiSeq and NextSeq, PacBio Sequel, and Oxford Nanopore MinIon). We also write letters of support (LOS) to offer our capabilities and expertise for grant applications submitted to funding agencies." .
SCR:022882 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Ottawa Behaviour and Physiology Core Facility" ;
NIFRID:synonym "University of Ottawa Behaviour and Physiology Core" ;
definition: "Core provides access to state-of-the-art rodent behavioural testing equipment in facility optimized for behavioural testing. Provides expert assistance in project development, test design and execution, data analysis and interpretation, and novel test development." .
SCR:022883 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1582" ;
rdfs:label "University of Arizona Electron Paramagnetic Resonance Core Facility" ;
NIFRID:synonym "Electron Paramagnetic Resonance (EPR) Facility",
"University of Arizona Electron Paramagnetic Resonance (EPR) Facility" ;
NIFRID:abbrev "EPR" ;
definition: "Research facility for studying paramagnetic centers by continuous wave and pulsed EPR techniques to obtain information on electronic, chemical, and geometric molecular structures." .
SCR:022884 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1583" ;
rdfs:label "University of Arizona W.M. Keck Center for Nano Scale Imaging Core Facility" ;
NIFRID:synonym "University of Arizona W.M. Keck Center for Nano-Scale Imaging",
"W.M. Keck Center for Nano-Scale Imaging" ;
definition: "Interdisciplinary research facility in areas of imaging, nano-science and spectroscopy for measuring surface topography, surface properties, electrical measurements, fluorescence, sub-monolayer visible spectroscopy, and molecular structures." .
SCR:022885 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1584" ;
rdfs:label "University of Arizona Laboratory for Electron Spectroscopy and Surface Analysis Core Facility" ;
NIFRID:synonym "Laboratory for Electron Spectroscopy and Surface Analysis (LESSA) Facility",
"University of Arizona Laboratory for Electron Spectroscopy and Surface Analysis (LESSA)" ;
NIFRID:abbrev "LESSA" ;
definition: "Core for surface science, thin films studies, and nano scale characterization. Provides analytical and educational services to department and university on preparation, modification, and study of solid surfaces." .
SCR:022886 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1587" ;
rdfs:label "University of Arizona Xray Diffraction Core Facility" ;
NIFRID:synonym "University of Arizona X-Ray Diffraction (XRD) Facility",
"X-Ray Diffraction (XRD) Facility" ;
NIFRID:abbrev "XRD" ;
definition: "Facility for investigation of single crystal and powder/thin film samples by X-Ray diffraction techniques." .
SCR:022887 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1588" ;
rdfs:label "University of Arizona Electron Photoemission Spectroscopy and Imaging Laboratory for Observation at the Nanoscale Core Facility" ;
NIFRID:synonym "Electron Photoemission Spectroscopy and Imaging Laboratory for Observation at the Nanoscale (EPSILON)",
"University of Arizona Electron Photoemission Spectroscopy and Imaging Laboratory for Observation at the Nanoscale (EPSILON)" ;
NIFRID:abbrev "EPSILON" ;
definition: "Facility offers imaging spectroscopy. Equipped with Xray Photoemission Spectroscopy, Ultraviolet Photoemission Spectroscopy, Inverse Photoemission Spectroscopy, energy filtered Photoelectron Emission Microscopy, and spatially resolved Angle Resolved Photoemission Spectroscopy and spatially resolved Xray Photoemission Spectroscopy." .
SCR:022888 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1585" ;
rdfs:label "University of Arizona Molecular Structures Core Facility" ;
NIFRID:synonym "Molecular Structures Core (MSC)",
"University of Arizona Molecular Structures Core (MSC)" ;
NIFRID:abbrev "MSC" ;
definition: "Core enables researchers to determine structures and dynamics, or motions, of large biomolecules such as proteins and DNA to understand how they interact with each other and with small molecules such as drugs." .
SCR:022889 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1591" ;
rdfs:label "University of Miami Sylvester Comprehensive Cancer Center Biospecimen Shared Resource Core Facility" ;
NIFRID:synonym "Sylvester Biospecimen Shared Resource",
"University of Miami Sylvester Comprehensive Cancer Center Biospecimen Shared Resource" ;
NIFRID:abbrev "BSSR" ;
definition: "Provides biorepository resources, services and expertise in support of oncology research.Facilitates translational cancer research with standard operating procedures for patient consenting; protection of patient personal and clinical data; specimen procurement and processing; quality control of specimens; secured specimen storage, retrieval, and distribution; and provision of relevant de-identified clinical data. BSSR services include: biospecimen collection, annotation, processing, storage and distribution (including tissue, blood, and other fluids); plasma, serum, and peripheral blood mononuclear cell processing and cryopreservation; rapid acquisition of surgical tissue and fresh biopsies; participant screening and enrollment for biospecimen collection studies;formalin-fixed, paraffin embedded and frozen tissue retrieval, processing, sectioning, histological staining, and digital whole slide scanning; tissue microarrays production; support for non-therapeutic trials; consultation on project design, data analysis and interpretation. Offers access tobiobank of diverse tissue types, including clinically annotated neoplastic and non-neoplastic samples from diverse anatomical sites, and provides banked specimen as well as fresh specimen procurement at institution wide level.Through BSSR, investigators have access to specimens collected fromUniversity of Miami Hospital, Sylvester Comprehensive Cancer Center, Bascom Palmer Eye Institute, Jackson Memorial Hospital, as well as to specimens collected in more broadly based multi-site studies." .
SCR:022890 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1590" ;
rdfs:label "University of Miami Sylvester Comprehensive Cancer Center Biostatistics and Bioinformatics Shared Resource Core Facility" ;
NIFRID:synonym "Sylvester Biostatistics and Bioinformatics Shared Resource",
"University of Miami Sylvester Comprehensive Cancer Center Biostatistics and Bioinformatics Shared Resource" ;
NIFRID:abbrev "BBSR" ;
definition: "Provides expertise and analysis support for basic and translational research, clinical trials, and both interventional and non-interventional population-based studies. Offers support for data and large scale data analysis projects. Services include support for data analysis and interpretation; software access; algorithm and database development; support of scientific review, monitoring, and oversight of clinical and population science research protocols; consultation, training, educational workshops, lectures and seminars.Biostatistics services include support for statistical design of clinical trials, population studies, and laboratory experiments; sample size determination and justification; statistical analysis plans; statistical support for data and safety monitoring of clinical trials; data analysis and interpretation; prediction model development using machine learning techniques; and database design and data management. Bioinformatics services include project design for high-throughput genomics studies; support for next generation sequencing data analysis (including whole transcriptome profiling; targeted region gene expression and single-cell RNA-seq; epigenomics profiling such as ChIP-seq and ATAC-seq; and exome or whole genome sequencing analysis); pathway analysis; microbiome data analysis; functional metagenomics analysis; drug sensitivity and genomic association analysis; genomic data integration using public databases; integration analysis of genomic data across multiple platforms; genomic data visualization; and bioinformatics methods, analysis pipeline, software and algorithm development. BBSR services can be utilized for QA/QC, including quality assessment of sequencing data, sample outlier detection, batch effect determination, evaluation of spike-in control methods, randomized block design, and other strategies for data normalization. T" .
SCR:022891 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1592" ;
rdfs:label "University of Miami Sylvester Comprehensive Cancer Center Cancer Modeling Shared Resource Core Facility" ;
NIFRID:synonym "Sylvester Cancer Modeling Shared Resource",
"University of Miami Sylvester Comprehensive Cancer Center Cancer Modeling Shared Resource" ;
NIFRID:abbrev "CMSR" ;
definition: "Provides small animal cancer modeling services to foster cancer research and to accelerate discovery of tailored anti-tumor therapies, including preclinical data for drug development, proof of principle for novel therapies, preclinical imaging, and disease biomarker studies. Services include facilitating in vivo modeling of human disease using mouse models; supporting preclinical in vivo efficacy and toxicity studies; devising treatment protocols; using noninvasive imaging for diagnosis and evaluation of responses to treatment; and performing histopathological analysis of targeted cancer therapies. Specific services include (1) support for the development of experimental murine models of cancer, including with cell line and patient-derived xenografts (PDXs), genetically engineered mouse models, and humanized models; (2) support for devising and implementing treatment protocols in a pre-clinical setting using murine models of human disease (e.g., drug toxicology and efficacy studies, drug formulation and delivery, and related assessments, like cell blood count, clinical chemistry, and flow cytometry analysis); and (3) diagnosis and evaluation of responses to treatment, using noninvasive small animal imaging for diagnosis and evaluation of responses to treatment, including in vivo bioluminescence and fluorescence optical imaging, high-frequency ultrasound imaging, structural and functional nuclear imaging, and magnetic resonance imaging (MRI); and (b) research histopathological analysis of targeted cancer therapies, including H&E and immunohistochemistry (IHC) sectioning, staining, scanning and analysis, and data storage of digital slide images. The CMSR also offers consultation, training, educational workshops and seminars. CMSR radiotherapy services support both small animal total body and image-guided radiation treatment delivery with sub-millimetric accuracy for development of radiation therapy regimens in a preclinical setting." .
SCR:022892 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1594" ;
rdfs:label "University of Miami Sylvester Comprehensive Cancer Center Molecular Therapeutics Shared Resource Core Facility" ;
NIFRID:synonym "Sylvester Molecular Therapeutics Shared Resource",
"University of Miami Sylvester Comprehensive Cancer Center Molecular Therapeutics Shared Resource" ;
NIFRID:abbrev "MTSR" ;
definition: "Provides preclinical drug discovery and development services to facilitate discovery of small molecules that have potential to become cancer therapeutics.Offers expertise in drug discovery and facilitates process of uncovering novel treatments for cancer. Services include target evaluation and assay development; small molecule library preparation, screening, and curation; high throughput screening enablement; plate imaging and transfers; assay identification, development and implementation; standard and customized assays (including live cell metabolic assays, cell death assays, clonogenic assays, and alphascreen); support for hit-to-lead pharmacology (including pharmacokinetics and ADME/T); data analytics for hit-picking; investigational new drug (IND) enablement; and full pipeline project management.Offers consultation, training, educational workshops and seminars." .
SCR:022893 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1589" ;
rdfs:label "University of Miami Sylvester Comprehensive Cancer Center Behavioral and Community Based Research Shared Resource Core Facility" ;
NIFRID:synonym "Sylvester Behavioral and Community-Based Research Shared Resource",
"University of Miami Sylvester Comprehensive Cancer Center Behavioral and Community Based Research Shared Resource" ;
NIFRID:abbrev "BCSR" ;
definition: "Provides services and expertise that facilitate behavioral, psychosocial, community, translational, and population based oncology research. Services include coordinating recruitment and retention of diverse study participants representative of Sylvester South Florida catchment area;supporting development of culturally and linguistically tailored study materials; facilitating data collection and management, including for biospecimens, in clinical and community setting; assisting with development and delivery of evidence based interventions across cancer continuum from prevention to survivorship; offering, seminars, workshops and training.Offers consultation on culturally appropriate approaches for study implementation and provides translation of study materials into Spanish and/or Haitian Creole. Engages diverse stakeholders throughout South Florida in dialogue about cancer prevention and collaborative research opportunities." .
SCR:022894 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RadiAnt DICOM Viewer" ;
definition: "Software tool as Digital Imaging and Communications in Medicine (DICOM) viewer for medical images." .
SCR:022895 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BioSpec_70/20" ;
rdfs:label "Bruker | 7 Tesla Bruker BioSpec 70/20 USR MRI system" ;
NIFRID:synonym "7.0 Tesla Bruker BioSpec 70/20 USR",
"Bruker BioSpec 70/20" ;
definition: "Multipurpose research system for high resolution Magnetic Resonance Spectroscopy and Imaging. System is equipped with 7 Tesla superconducting magnet designed with Ultra Shielded Refrigerated magnet technology. USR technology significantly reduces stray field to close to magnet. Used for In Vivo Magnetic Resonance Imaging." .
SCR:022896 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "North Carolina Diabetes Research Center" ;
NIFRID:abbrev "NCDRC" ;
definition: """Interactive regional diabetes research community across four premiere research institutions in North Carolina, who currently garner over $70 million annually for support of their diabetes research:
Duke University (Duke), The University of North Carolina at Chapel Hill (UNC), Wake Forest School of Medicine (WF), and North Carolina A&T State University (NC A&T State). NCDRC supports Research Cores that represent unique strengths at each institution.""" .
SCR:022897 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Colorado Diabetes Research Center" ;
definition: "Center to facilitate diabetes research at University of Colorado by integrating interdisciplinary basic, translational, and clinical diabetes research base; providing infrastructure and resources that are indispensable for continued discovery and progress towards diabetes research and developing improved prediction and disease prevention;providing P&F and enrichment programs to support DRC investigators and their trainees, and recruit new and young investigators into diabetes research." .
SCR:022898 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FASTGenomics" ;
definition: "Open online platform for single cell RNA-seq. Provides data management and analytics. Used to analyze public and private datasets and you can choose between several best practices workflows and browse existing analyses." .
SCR:022899 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1598" ;
rdfs:label "University of Pennsylvania Perelman School of Medicine Neuroimaging and Cognitive Core Facility" ;
NIFRID:synonym "Neuroimaging and Cognitive Core",
"University of Pennsylvania Perelman School of Medicine Neuroimaging and Cognitive Core" ;
NIFRID:abbrev "NICC" ;
definition: "Core aims to facilitate research in cognitive neuroscience through use of Computerized Neurocognitive Battery and neuroimaging.CNB is comprised of series of tests that have been applied in neuroimaging studies and can be used either in scanner as part of functional neuroimaging study or outside scanner for measuring individual differences in performance. Tests measure accuracy and speed of performance in major domains of cognition, including executive control functions (abstraction, attention, working memory), episodic memory (verbal, facial, spatial), complex cognitive processing (language reasoning, nonverbal reasoning, spatial processing), social cognition (emotion identification, emotion intensity differentiation, age differentiation) and sensorimotor and motor speed." .
SCR:022900 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1596" ;
rdfs:label "University of California at Los Angeles California NanoSystems Institute Electron Imaging Center for Nanomachines Core Facility" ;
NIFRID:synonym "California NanoSystems Institute Electron Imaging Center for Nanomachines",
"Electron Imaging Center for Nanomachines" ;
NIFRID:abbrev "CNSI EICN" ;
definition: "Provides advanced electron imaging tools covering scale range from tens of micrometers to angstroms, and delivering valuable structural information for cell biology, microbiology, biomolecular, molecular, and materials sciences.Offers all major electron microscopy modalities." .
SCR:022901 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D Printed Superfusion Chamber" ;
NIFRID:synonym "3D Printed Superfusion Chamber project" ;
definition: "Project consists of suite of 3D-printed tools including superfusion chamber with independent brain presser and animal stand. Modular device that facilitates transfer of pharmacological agents and brain access for electrodes and/or lenses for imaging. Provides stable conditions for electrophysiological and neuroimaging recordings. Device can be print either in-house or through 3d-printing service." .
SCR:022902 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stoelting | Tissue Slicer" ;
NIFRID:synonym "Stoelting 51425 Tissue Slicer" ;
definition: "Tissue Slicer with conventional vernier micrometer, resolution 10 micron. Designed to prepare thin slices of living brain, slicing other tissues, blocking fixed tissue for histology, and slicing electrophoretic gels. Sections as thin as 150 microns can be prepared." .
SCR:022903 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Colorado Anschutz Medical Campus Diabetes Research Center Clinical Resource Core Facility" ;
NIFRID:synonym "University of Colorado Diabetes Research Center Clinical Resource Core" ;
NIFRID:abbrev "DRC CR" ;
definition: "Core leverages current clinical research facilities and equipment available at Barbara Davis Center for Childhood Diabetes, UC AMC Clinical Translational Research Center, University of Colorado Hospital, Denver Veteran Administration Medical Center and Children Hospital Colorado.Core integrates diabetes research across these institutions through communication and distribution of resources available, and creates shared sample and data biobanks and recruiting database of mothers, infants, children, adolescents and adults with diabetes, diabetes risk and controls." .
SCR:022904 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Colorado Anschutz Medical Campus Diabetes Research Center Tissue Procurement and Processing Core Facility" ;
NIFRID:synonym "University of Colorado Diabetes Research Center Tissue Procurement and Processing Core" ;
NIFRID:abbrev "TPP" ;
definition: "Core facilitates access and usage of tissues and services to meet specialized needs of diabetes research community to expedite and catalyze innovative diabetes research at UC AMC. Provides resources to assist DRC investigators with acquisition and processing of rodent and human tissue, and specialized cell lines that are broadly required for diabetes research." .
SCR:022905 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Colorado Anschutz Medical Campus Diabetes Research Center Disease Modeling Core Facility" ;
NIFRID:synonym "University of Colorado Diabetes Research Center Disease Modeling Core" ;
definition: "Provides diabetes researchers with access to novel human stem cell-derived in vitro cell models for investigating cellular and molecular features of both Type 1 and Type 2 diabetes. Recent progress in stem cell, organoid culture, gene editing and directed differentiation technologies has afforded opportunities to develop pre-clinical human models.Provides expertise, infrastructure and access to novel human model systems and technologies to DRC investigators. Provides expertise, resources and training in stem cell technologies together with quality control testing, validation standardization and authentication all model platforms and reagents." .
SCR:022906 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Colorado Anschutz Medical Campus Diabetes Research Center Cell and Tissue Analysis Core Facility" ;
NIFRID:synonym "University of Colorado Diabetes Research Center Cell and Tissue Analysis Core" ;
definition: "Provides diabetes researchers at University of Colorado with access to microscopy and mass cytometry systems. Provides expertise and training to use equipment effectively for diabetes related tissues; expertise and validated diabetes related resources to prepare samples appropriately; guidance to design experiments; resources to analyze data; assistance with data interpretation." .
SCR:022907 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "North Carolina Diabetes Research Center Genomics and Proteomics Core Facility" ;
NIFRID:synonym "North Carolina Diabetes Research Center Genomics and Proteomics Core" ;
NIFRID:abbrev "GPC",
"NCDRC GPC" ;
definition: "Provides resources and expertise in genomics and mass spectrometry at Wake Forest Center for Precision Medicine. Provides unique access to instrumentation and analytical expertise to NCDRC faculty in support of advancement of diabetes research.Overlooks the use of existing resources at NCDRC partner institutions (UNC, NC A&T, and Duke University) to coordinate work and data analysis with Metabolomics Core to provide omics analyses.Offers analytic services, expertise, and tools to integrate data to better understand interactive systems at play in disease processes." .
SCR:022908 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "North Carolina Diabetes Research Center Advanced Clinical Study Methods Core Facility" ;
NIFRID:synonym "North Carolina Diabetes Research Center Advanced Clinical Study Methods Core" ;
NIFRID:abbrev "ACSMC" ;
definition: "Core to leverage data, patient populations and investigators at each NCDRC institution, including accessing expertise and resources of regional Clinical and Translational Science Institute hubs (Duke, UNC, and Wake Forest). Research navigators in ACSMC provides input and navigation of clinical research resources available to diabetes investigators based on extensive experience in diabetes specific studies and methodology and deep knowledge of NCDRC resources available at each institution." .
SCR:022909 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "North Carolina Diabetes Research Center Metabolomics Core Facility" ;
NIFRID:synonym "North Carolina Diabetes Research Center Metabolomics Core" ;
definition: "Provides platform for quantitative targeted metabolic profiling by MS/MS and GC/MS, supported by library of stable isotope labeled standards as well as extensive scientific expertise to help researchers navigate core resources and use of services." .
SCR:022910 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ccf_streamlines" ;
definition: "Software Python package presents interface to use isocortical streamlines of Allen Mouse Common Coordinate Framework. Used to support projection of Allen Common Coordinate Framework mouse brain volumetric data and coordinate data on to 2D representations." .
SCR:022912 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1599" ;
rdfs:label "Van Andel Institute Pathology and Biorepository Core Facility" ;
NIFRID:synonym "VAI Pathology and Biorepository Core",
"Van Andel Institute VAI Pathology and Biorepository Core" ;
NIFRID:abbrev "PBC",
"VAI PBC" ;
definition: "Pathology and Biorepository Core (PBC) integrates anatomic pathology expertise with biorepository and biospecimen science. It provides emphasis on high-quality biospecimens and interpretable results to validate experimental models and extend them to clinical samples. The PBC offers a comprehensive range of biospecimen services, including histology, pathology, and biospecimen processing and storage." .
SCR:022913 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1600" ;
rdfs:label "Van Andel Institute Genomics Core Facility" ;
NIFRID:synonym "VAI - Genomics Core",
"Van Andel Institute VAI - Genomics Core" ;
definition: "Provides services including Next Generation Sequencing, single cell Genomics, and Spatial Transcriptomics facility. Provides experimental design support, library generation, and Illumina and Nanopore Sequencing." .
SCR:022914 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1601" ;
rdfs:label "Van Andel Institute Transgenic Core Facility" ;
NIFRID:synonym "VAI Transgenic Core",
"Van Andel Institute VAI Transgenic Core" ;
definition: "Provides genetically modified animal models for our collaborators. For preexisting models provides rederivation or reconstitution for purpose of importing animals into Vivarium barrier. In the absence of preexisting models core works closely with partnering labs to generate their ideal mutation de novo, often using CRISPR technology. Usually beginning with a brief consultation, this process involves discussing factors such as ideal background strain, molecular methods for optimizing the intended genetic change, mutation induction strategies, screening approaches and eventual QC of the new mutant line with the overall goal of giving our collaborators a fully informed, realistic picture of their projects timeframe, pitfalls and workflow. Core provides mouse sperm and embryo cryopreservation services for purpose of archiving and distributing valuable lines. Institute is an AAALAC-accredited facility. All procedures are conducted according to the NIH Guide for the Care and Use of Laboratory Animals." .
SCR:022917 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1602" ;
rdfs:label "University of Michigan Statistics Online Computational Resource Core Facility" ;
NIFRID:synonym "Statistics Online Computational Resource (SOCR)",
"University of Michigan Ann Arbor Statistics Online Computational Resource (SOCR)" ;
NIFRID:abbrev "SOCR" ;
definition: "SOCR designs, validates and freely disseminates knowledge. The Resource develops AI/ML tools, mathematical models, and end-to-end data analytic protocols for biomedical and health studies. It provides portable online aids for probability, statistics and health science education, promotes technology enhanced instruction, supports efficient statistical computing, supports AI-services, and advances predictive big data analytics. The SOCR platform includes repository of interactive apps, datasets and case-studies, computational tools, visualization approaches, instructional resources, learning materials, and curricular components. SOCR faculty, staff, and students support data and information science collaborations and analytic partnerships involving biomedical, healthcare, and biostatistical investigations." .
SCR:022918 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sirenia Sleep Pro" ;
NIFRID:synonym "Pinnacle Sirenia Sleep Pro" ;
definition: "Software tool to reduce scoring time and simplify data analysis. Offers automated power analysis, semi-automated scoring methods, and advanced tabular and graphical analysis for investigating sleep data sets. Custom scoring and analysis are also available. Scoring sessions between two or more users can be compared. All EEG/EMG and video data sets recorded with Pinnacle software, as well as third party EDF files, can be imported." .
SCR:022919 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D-Beacons" ;
NIFRID:synonym "3D-Beacons Network" ;
definition: "Software platform to provide programmatic access to experimentally determined and theoretical protein structures. Provides unified programmatic access to experimentally determined and predicted structure models. Used for open collaboration between providers of macromolecular structure models to provide model coordinates and meta information from all contributing data resources in standardised data format, on unified platform.3D Beacons API retrieves and combines data from member data providers, and returns data in JSON format according to 3D-Beacons API specification." .
SCR:022920 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ATLAS.ti" ;
NIFRID:synonym "ATLAS.ti version no. 5. 2" ;
definition: "Software qualitative analysis tool. Used by researchers and practitioners to uncover and systematically analyze complex phenomena hidden in unstructured data including text, multimedia, geospatial. Provides tools that let the user locate, code, and annotate findings in primary data material, to weigh and evaluate their importance, and to visualize relations between them. Consolidates documents and keeps track of all notes, annotations, codes and memos in all fields that require close study and analysis of primary material consisting of text, images, audio, video, and geo data. Provides analytical and visualization tools designed to open new interpretative views on material." .
SCR:022921 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fujifilm | VisualSonics Vevo 770 Imaging System" ;
NIFRID:synonym "Vevo 770 High-Resolution In Vivo Micro-Imaging System" ;
definition: "High resolution in vivo imaging system for small animal research. Provides visualization and measurement of anatomical and hemodynamic function in small animals down to 30 microns." .
SCR:022922 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "annotate my genomes" ;
NIFRID:synonym "annotate_my_genomes" ;
definition: "Software genome annotation pipeline using long sequencing reads alignments from animal genomes." .
SCR:022924 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1603" ;
rdfs:label "University of California at Los Angeles California NanoSystems Institute Nano and Pico Characterization Laboratory Core Facility" ;
NIFRID:synonym "California NanoSystems Institute Nano and Pico Characterization Laboratory",
"NPC- Nano & Pico Characterization Laboratory" ;
definition: "Offers curated collection of high end scientific instrumentation to enable physicochemical characterization of nanoscale materials, devices, and systems under wide range of experimental conditions.Technical capabilities and expertise include surface analysis by Scanning Probe Microscopy (SPM); hydrodynamic size and surface charge analysis by Dynamic Light Scattering (DLS) and Zeta Potential (ZP) measurements; elemental and chemical analysis by Inductively Coupled Plasma Mass Spectrometry (ICP-MS)." .
SCR:022925 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1605" ;
rdfs:label "University of California at Los Angeles California NanoSystems Institute Integrated NanoMaterials Laboratory Core Facility" ;
NIFRID:synonym "California NanoSystems Institute Integrated NanoMaterials Laboratory",
"INML- Integrated NanoMaterials Laboratory" ;
NIFRID:abbrev "INML" ;
definition: "Nanomaterials and nanostructures grown in INML are used in lasers, solar cells, detectors, transistors, modulators, and a wide range of other electronic and photonic devices." .
SCR:022926 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1606" ;
rdfs:label "Medical College of Wisconsin Mellowes Center for Genomic Sciences and Precision Medicine Core Facility" ;
NIFRID:synonym "MC-Mellowes Center for Genomic Sciences and Precision Medicine",
"Medical College of Wisconsin Mellowes Center for Genomic Sciences and Precision Medicine" ;
definition: "Core for advancing genomic sciences and precision medicine in fields of Omics, Data Science, and Systems Biology. Provides whole genome sequencing technologies to investigate how gene variants impact gene expression and to define genetic variants associated with rare and common disease, embryonic development, and effects of environmental factors and drugs upon gene expression and disease." .
SCR:022927 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PowerBi" ;
definition: "Microsoft software suite of business analytics tools to analyze data and share insights. Used for business and to get answers quickly with rich dashboards available on every device." .
SCR:022928 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1607" ;
rdfs:label "University of Chicago Proteomics Platform Core Facility" ;
NIFRID:synonym "Proteomics Platform",
"University of Chicago Proteomics Platform" ;
definition: "Core to develop and utilize proteomics techniques to answer both basic and translational scientific questions." .
SCR:022929 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1608" ;
rdfs:label "University of Oklahoma Samuel Roberts Nobel Microscopy Laboratory Core Facility" ;
NIFRID:synonym "Samuel Roberts Nobel Microscopy Laboratory",
"University of Oklahoma Samuel Roberts Nobel Microscopy Laboratory" ;
definition: "Offers access to instrumentation, training, and service using advanced light microscopy, scanning electron microscopy, and transmission electron microscopy. Provides access to core imaging and analytical characterization technologies. In addition to instrument access, SRNML personnel offer advice, hands-on training, education, and research collaboration. Provides range of sample preparation equipment." .
SCR:022930 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Compass for Simple Western" ;
definition: "Simple Western instrument software to analyze assay data and processes results." .
SCR:022931 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CompuSyn" ;
definition: """Software tool for single drug and drug combinations pharmacodynamics with automated simulations
or dose efffect data analysis from enzymes, receptors, microorganisms, cells, animals and clinical trials.""" .
SCR:022932 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1611" ;
rdfs:label "University of Chicago Metabolomics Platform Core Facility" ;
NIFRID:synonym "Metabolomics Platform",
"University of Chicago Metabolomics Platform" ;
definition: "Equipped with Thermo Scientific Orbitrap IQ-X Tribrid mass spectrometer(+UVPD)- Vanquish Horizon UHPLC system. Provides experience in quantifying diverse groups of metabolites in cells, culture medium, bodily fluid, animal tissue, exhaled breath condensate, etc., and performes stable isotope tracing experiments using 13C, 15N, and 2H-labeled substrates. Support hypothesis generating untargeted and hypothesis driven targeted metabolomics studies from experimental design stage through data acquisition, data analysis, and interpretation." .
SCR:022933 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1614" ;
rdfs:label "University of Chicago Biomolecular Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "Biomolecular Nuclear Magnetic Resonance Facility",
"University of Chicago Biomolecular Nuclear Magnetic Resonance Facility" ;
definition: "Facility houses Bruker AVANCE IIIHD 600 and Bruker AVANCE III 500 NMR spectrometer. These are equipped with high sensitivity inverse and broadband probes, single axis gradients, pulse shaping capabilities, variable temperature control(-50C to 150C), and automatic tuning and matching.Bruker AVANCE IIIHD 600 is also equipped with robotic sample changer (Bruker SamplExpress) allowing automated acquisition of up to 60 samples. Sample preparation can also be automated with Gilson sample preparation robot." .
SCR:022934 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1616" ;
rdfs:label "University of Chicago Gnotobiotic Research Animal Core Facility" ;
NIFRID:synonym "Gnotobiotic Research Animal Facility",
"University of Chicago Gnotobiotic Research Animal Facility" ;
NIFRID:abbrev "GRAF" ;
definition: "One of the largest academic gnotobiotic mouse facilities internationally.Centrally managed gnotobiotic/germ free mouse facility located within centrally managed Knapp Center for Biomedical Discovery vivarium.GRAF currently maintains over 80 flexible film isolators with capacity for greater than 1045 mouse cages." .
SCR:022935 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1612" ;
rdfs:label "University of Chicago Organoid and Primary Culture Research Core Facility" ;
NIFRID:synonym "Organoid and Primary Culture Research Core",
"University of Chicago Organoid and Primary Culture Research Core" ;
definition: "The mission is to facilitate access, generation, banking, and usage of organoids and primary cells derived from patients and model organisms." .
SCR:022936 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1613" ;
rdfs:label "University of Chicago Human Disease and Immune Discovery Core Facility" ;
NIFRID:synonym "Human Disease and Immune Discovery",
"University of Chicago Human Disease and Immune Discovery" ;
definition: "Provides expertise, equipment and physical space for researchers to perform cutting edge, high resolution investigations of human immune system. Leverages innovative technologies from field of flow cytometry for data generation and analysis and through close collaboration with Genomics core facility to provide cellular component solutions to even higher resolution genomic investigations." .
SCR:022937 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1615" ;
rdfs:label "University of Chicago Center for Research Informatics Bioinformatics Core Facility" ;
NIFRID:synonym "CRI Bioinformatics Core",
"University of Chicago Center for Research Informatics Bioinformatics Core" ;
definition: "Core offers services and expertise designed to allow BSD investigators to take full advantage of high throughput technologies." .
SCR:022938 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1623" ;
rdfs:label "Stanford Graduate School of Business Data, Analytics, and Research Computing Core Facility" ;
NIFRID:synonym "Analytics",
"and Research Computing",
"Stanford Graduate School of Business Data" ;
NIFRID:abbrev "DARC",
"GSB DARC" ;
definition: "DARC facility engages directly with faculty members, preparing large scale datasets, assisting with data analysis, and consulting on research design. Provides expertise on machine learning, text processing, and cloud services. DARC team also supports Yen compute environment, linux cluster designed for data intensive workloads in business research." .
SCR:022939 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "draw.io" ;
definition: "Software tool as diagramming application that enables collaboration in real time." .
SCR:022940 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyPhotometry" ;
definition: "Open source Python based hardware and software for fiber photometry data acquisition. System includes compact, low cost, data acquisition board built around Micropython microcontroller, and cross platform graphical user interface for controlling acquisition and visualising signals. Can acquire two analog and two digital signals, and control two external LEDs via built in LED drivers. Time division multiplexed illumination allows independent readout of fluorescence evoked by different excitation wavelengths from single photoreceiver signal." .
SCR:022941 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhysiPKPD" ;
NIFRID:synonym "Physi pharmacokinetics and pharmacodynamics" ;
definition: "Open source PhysiCell based software package that allows users to include pharmacokinetics and pharmacodynamics in PhysiCell models. Used for module template for drug treatment in PhysiCell." .
SCR:022942 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRIQC" ;
NIFRID:synonym "Image Quality in MRI" ;
definition: "Software tool as quality assurance workflow for Brain Imaging Data Structure compliant anatomical and functional MRI datasets. Used to extract no-reference image quality metrics from structural and functional magnetic resonance imaging data." .
SCR:022943 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EmaCalc" ;
definition: "Software package in Python for statistical analysis of Ecological Momentary Assessment data." .
SCR:022944 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1622" ;
rdfs:label "University of Chicago Engineering and Technical Support Group Core Facility" ;
NIFRID:synonym "UChicago - Engineering and Technical Support Group",
"University of Chicago Engineering and Technical Support Group" ;
NIFRID:abbrev "ETSG" ;
definition: "ETSG serves University of Chicago faculty led research projects. ETSG staff is available to help plan, design, build, test, and install mechanical and electro mechanical apparatus." .
SCR:022945 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1621" ;
rdfs:label "City University of New York Advanced Science Research Center Live Imaging and Bioenergetics Core Facility" ;
NIFRID:synonym "ASRC-Live Imaging and Bioenergetics Core",
"CUNY Advanced Science Research Center ASRC-Live Imaging and Bioenergetics Core" ;
definition: "Provides Zeiss LSM880 upright two photon confocal microscope with Airyscan, FAST model and CLARITY lens; LSM880 inverted live cell imaging confocal microscope with Airyscan and FAST model; Agilent Seahorse XFe24 live cell metabolic analyzer.Supported applications include in vivo imaging of live animals, time lapse live cell imaging with high resolution optical sectioning, deep imaging of fixed CLARITY tissues, calcium imaging, photo switching and photo uncaging, Fluorescence Recovery After Photobleaching, Forster Resonance Energy Transfer, laser ablation, and measuring mitochondrial respiration and glycolysis in live cells in real time.Provides advanced imaging analysis software Imaris for data processing." .
SCR:022946 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "International Brain Laboratory Data " ;
NIFRID:abbrev "IBL Data" ;
definition: "Data portal hosting access to behavioral data sets generated by International Brain Laboratory aiming to understand brain functions underlying decision making. Datasets are acquired in neuroscience laboratories performing experimental work. In each of these laboratories, mice are first trained in IBL decision making task following standardized training pipeline." .
SCR:022947 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of California at Santa Cruz Stable Isotope Laboratory Core Facility" ;
NIFRID:synonym "UC Santa Cruz Stable Isotope Laboratory" ;
NIFRID:abbrev "SiL" ;
definition: "Provides light stable isotope ratio analysis services to scientists from UCSC and from around the world." .
SCR:022949 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SignatureHeatmap" ;
NIFRID:synonym "BasalClassicalHeatmap",
"Signature Heatmap" ;
definition: "Software package that enables signature classification of tumor samples by generating heatmaps using transcriptomic data." .
SCR:022950 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1624" ;
rdfs:label "Harvard Medical School Dana Farber Harvard Cancer Center Mouse Engineering Core Facility" ;
NIFRID:synonym "DF/HCC Mouse Engineering Core",
"Harvard Medical School DF/HCC Mouse Engineering Core" ;
definition: "Core provides services for generation of transgenic and knockout mice.Provides Nikon Diaphot microscope equipped with Nomarski Optics and Narishige micromanipulators for microinjections, Nikon surgical microscopes for egg isolation and transfer, sutter needle puller and de Fonbrune microforge. Facility maintains mice necessary for egg donors, egg recipients, and vasectomized males.Core offers electroporation of targeting vectors into ES cells. Provides investigators with DNA to identify ES cells carrying desired recombination events and ES cell expansion for microinjection into blastocysts.Services also include CRISPR injections, sperm and embryo cryopreservation, and reanimation with fresh or frozen sperm via IVF or thawing and implanting embryos." .
SCR:022951 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1625" ;
rdfs:label "University of Texas at Austin Cryo Electron Microscopy Core Facility" ;
NIFRID:synonym "University of Texas at Austin UTA CBRS Sauer Structural Biology Laboratory",
"UTA CBRS Sauer Structural Biology Laboratory" ;
definition: "Offers training, assisted and unassisted use of microscopes and equipment, as well as consultations and collaborations. Support includes single particle cryo-EM, Cryo-ET, Micro-ED,simple characterization of samples in vitrified aqueous mixtures (e.g. nanoparticle size, etc.)." .
SCR:022952 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CouGaR-g" ;
definition: "Source code for \"Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation\"." .
SCR:022953 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1626" ;
rdfs:label "Penn State College of Medicine High Performance Computing Core Facility" ;
NIFRID:synonym "Penn State College of Medicine High Performance Computing",
"Penn State College of Medicine PSCOM-HPC",
"PSCOM-HPC" ;
definition: "Provides computational and storage tools needed to efficiently and effectively process data. High performance computing cluster housing compute cores, graphical processing unit cores, and directly attached high speed storage." .
SCR:022954 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1617" ;
rdfs:label "University of Ottawa Genome Editing and Molecular Biology Core Facility" ;
NIFRID:synonym "University of Ottawa UO-Genome Editing and Molecular Biology facility",
"UO-Genome Editing and Molecular Biology facility" ;
definition: "Facility assists researchers in mammalian genome editing and molecular biology, including CRISPR genetic libraries and screens as well as custom viral vector/particle production. Projects are customized to researchers needs, from full service cell line creation to design and cloning.Supported by Canadian Foundation for Innovation." .
SCR:022955 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1619" ;
rdfs:label "University of Chicago Pritzker Nanofabrication Core Facility" ;
NIFRID:synonym "UC - Pritzker Nanofabrication Facility",
"University of Chicago UC - Pritzker Nanofabrication Facility" ;
definition: "Facility is ISO Class 5 cleanroom that specializes in advanced lithographic processing of hard and soft materials. Facility is focused on supporting basic science, applied research, research and development, and prototype production using micro and nanofabrication." .
SCR:022956 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1618" ;
rdfs:label "University of Califorania at Los Angeles California NanoSystems Institute Molecular Screening Shared Resource Core Facility" ;
NIFRID:synonym "California NanoSystems Institute Molecular Screening Shared Resource Core Facility",
"California NanoSystems Institute MSSR- Molecular Screening Shared Resource",
"MSSR- Molecular Screening Shared Resource" ;
NIFRID:abbrev "MSSR" ;
definition: "Services include use of high throughput screening technology, compounds in various libraries, siRNA sets of druggable genome for mouse and human and database of results from screens. For compounds screens, data points are in singlets.For functional genomics screens we use duplicates. We typically utilize 384 well plates but are flexible in this regard. We can accomodate any plate type ranging from 96 to 1536 well plates. Specialty plates can be handled on needed base. We have special rates for consumables with many vendors based on volume we use. These reduced rates are passed on directly to our screeners." .
SCR:022957 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford University School of Medicine O’Brien Urology Research Center" ;
NIFRID:synonym "Stanford University O’Brien Urology Research Center" ;
definition: "Center for research to understand the network of cells that cause benign prostatic hyperplasia , the most common cause of urinary bother in men." .
SCR:022958 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Frontier" ;
NIFRID:synonym "Frontier Version 4.1" ;
definition: "Software tool to estimate stochastic frontier models. Used to obtain maximum likelihood estimates of parameters of variety of stochastic production and cost frontiers, and estimates of mean and individual technical or cost efficiencies." .
SCR:022960 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013646" ;
rdfs:label "BALSA" ;
NIFRID:synonym "Brain Analysis Library of Spatial maps and Atlases" ;
definition: "Database for hosting and sharing neuroimaging and neuroanatomical datasets for human and primate species. Includes 1) curated, user created Study datasets, extensively analyzed neuroimaging data associated with published figures/manuscripts, 2) Reference datasets mapped to brain atlas surfaces and volumes in human and nonhuman primates for use as general resources (e.g., published cortical parcellations), and 3) ConnectomeDB powered by BALSA for distributing HCP-Young Adult and related HCP-style processed imaging and phenotypic datasets. Datasets in BALSA may include PMID and/or DOI that links them directly to relevant publications." .
SCR:022961 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JupiterPlot" ;
definition: "Software pipeline for generating Circos based genome assembly consistency plot given set of contigs relative to reference genome. Intended to visualize large scale translocations or missassemblies in draft assemblies, but it can also be useful when trying to show synteny between whole genomes.Circos based tool to visualize genome assembly consistency" .
SCR:022962 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MMseqs2" ;
NIFRID:synonym "Many-against-Many sequence searching2" ;
definition: "Software suite for ultra fast and sensitive sequence search and clustering. Used to search and cluster huge protein and nucleotide sequence sets. Designed to run on multiple cores and servers." .
SCR:022963 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GetOrganelle" ;
definition: "Software toolkit to assembly of organelle genome from genomic skimming data. Used for accurate de novo assembly of organelle genomes." .
SCR:022964 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Merqury" ;
definition: "Software toolkit for reference free quality, completeness, and phasing assessment for genome assemblies. Genome assembly quality evaluation based on k-mers." .
SCR:022965 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "YaHS" ;
definition: "Software command line tool for construction of chromosome scale scaffolds from Hi-C data. Scaffolding tool using Hi-C or Omni-C data. Used to scaffold contig level assemblies into chromosome scale scaffolded assemblies." .
SCR:022966 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Collaborative Brain Wave Analysis Pipeline" ;
NIFRID:abbrev "Cobrawap" ;
definition: "Software adaptable and reusable analysis pipeline for multi scale, multi methodology analysis of cortical wave activity. Pipeline ingests data from multiple measurements types of spatially organized neuronal activity, such as ECoG or calcium imaging recordings. Pipeline returns statistical measures to quantify dynamic wave like activity patterns found in data." .
SCR:022967 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1257" ;
rdfs:label "Harvard Medical School Biomolecular Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "Harvard Medical School HMS-Biomolecular NMR Core",
"HMS-Biomolecular NMR Core" ;
definition: "Offers services in fragment based screening and drug discovery, characterization and QC of biologics and biosimilar drugs, metabolomics, protein NMR, small molecule NMR, and NMR of natural products. Offers 400-700MHz systems, many with cryogenic probes." .
SCR:022968 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1627" ;
rdfs:label "Carleton University Tissue Engineering and Applied Materials Hub Core Facility" ;
NIFRID:synonym "Carleton University Tissue Engineering and Applied Materials (TEAM) Hub",
"Tissue Engineering and Applied Materials (TEAM) Hub" ;
NIFRID:abbrev "TEAM Hub" ;
definition: "Core research facilities include BioImaging Research Node which houses commercial and custom imaging systems and is focused on optical imaging; Tissue Engineering and Biomaterials Testing Research Node equipped with microfluidics 3D bioprinter and mechanical testers, which facilitate development of artificial 3D biological tissue models and biomechanical testing of different biomaterials and biomedical samples; Biochemistry and Molecular Biology Research Node which houses hypoxia chamber and systems for characterization and quantification of proteins, peptides, and nucleic acids; Cellular Biology Research Node to support development and use of 3D tissue models.It houses instruments including flow cytometer for phenotyping and performing functional testing of cells and bacteria, Seahorse Analyzer for evaluation of metabolic activity of cells, and Incucyte for live cell imaging of cells and tissues in culture." .
SCR:022969 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1628" ;
rdfs:label "National Institute on Drug Abuse Genetic Engineering and Viral Vector Core Facility" ;
NIFRID:synonym "NIDA-Genetic Engineering and Viral Vector Core" ;
NIFRID:abbrev "GEVVC" ;
definition: "Provides support to NIDA-IRP researchers by facilitating studies of brain function under physiological and pathological conditions through developing and producing genetic tools capable of modulating and monitoring molecules, cells and circuits in nervous system.Provided services include custom design and/or production of viral vectors/nanoparticles;in vitro molecular and cell biology services; consultation and training." .
SCR:022970 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "UTHealth Brain Collection for Research in Psychiatric Disorders" .
SCR:022971 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1629" ;
rdfs:label "University of Virginia School of Medicine Biorepository and Tissue Research Core Facility" ;
NIFRID:synonym "Biorepository & Tissue Research Facility",
"University of Virginia School of Medicine Biorepository & Tissue Research Facility" ;
definition: "Core is involved in procurement and processing of human tissue and other biospecimens for basic, translational, and clinical research.Provides laboratory support services for clinical trials, tissue samples from remnant surgical resection and autopsy specimens linked to clinicopathologic data while maintaining patient confidentiality. Provides biorepository of human specimens.Offers advanced histology services including multi color immunohistochemistry, in situ hybridization, tissue microarrays, slide scanning, computerized image analysis, NanoString spatial profiling." .
SCR:022972 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Brain Consent" ;
definition: "Platform for informing research participants and obtaining consent to share brain imaging data. Provides suggested wording/templates for MRI studies human participant consent forms (including GDPR version), reference of tools for data anonymization, etc to make prospective data sharing possible." .
SCR:022973 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IOX2" ;
definition: "Software tool to acquire, analyze, view, and store physiological data generated during preclinical experiment. Has library of application specific analysis modules for real time signal processing." .
SCR:022974 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "APA-Scan" ;
definition: "Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data." .
SCR:022975 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PTNet" ;
definition: "Graph based learning model for protein expression estimation by considering miRNA-mRNA interactions. Estimates protein levels by considering miRNA-mRNA interaction network, mRNA expression and miRNA expression." .
SCR:022976 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OmicsGAN" ;
NIFRID:synonym "Omics Generative Adversarial Network" ;
definition: "Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals." .
SCR:022977 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mtradeR" ;
NIFRID:synonym "Metagenomic TRajectory Analysis with Disease Endpoint and Risk factors" ;
definition: """Software R package implements Joint model with Matching and Regularization and simulation pipeline.
Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually.""" .
SCR:022978 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ISLET" ;
NIFRID:synonym "Individual-Specific ceLl typE referencing Tool" ;
definition: "Software R package to conduct signal deconvolution for general omics data. Can estimate individual specific and cell type specific reference panels, when there are multiple samples observed from each subject. Can solve for reference panel on individual basis. Can conduct test to identify cell type specific differential expression genes." .
SCR:022979 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Precellys_24" ;
rdfs:label "Bertin Technologies | Precellys 24 tissue homogenizer" ;
NIFRID:synonym "Bertin Precellys 24 tissue homogenizer" ;
definition: "The Precellys 24 homogenizer with automatic tube locking system with the ability to process up to 24 tubes simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:022980 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ultracut | E ultramicrotome" ;
definition: "Reichert Jung Ultracut E, article number 131-960, is used to cut ultrathin and semithin sections of resin embedded samples for electron microscopy." .
SCR:022981 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FEI | Tecnai T12 electron microscope" ;
NIFRID:synonym "Max Planck Institute of Molecular Cell Biology and Genetics Electron Microscopy Facillity FEI Tecnai T12 electron microscope" ;
definition: "Tecnai T12 microscope combines all imaging, diffraction, and analytical techniques at good spatial resolution and detection efficiency. Transmission electron microscope with operating voltage range of 20 to 120 kV. FEI Tecnai T12 120kV TEM and 2k TVIPS camera." .
SCR:022982 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HTGQC" ;
definition: "Software R package for quality check of HTG EdgeSeq datasets." .
SCR:022983 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Common Metabolic Disease Genome Atlas" ;
NIFRID:abbrev "CMDGA" ;
definition: "Component of Accelerating Medicines Partnership Common Metabolic Diseases being developed at University of California San Diego as part of larger consortium of academic, industry and non-profit institutions worldwide. Resource is based on software developed by ENCODE DCC at Stanford University. Atlas provides epigenomics and other functional genomics data to promote understanding of genetic basis of common metabolic diseases." .
SCR:022984 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Starr Life Sciences MouseOx Plus" ;
NIFRID:synonym "MouseOx Plus",
"MOUSEOX PLUS 2.0" ;
definition: "Software is part of MouseOx Plus pulse oximeter system." .
SCR:022985 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "2Biol | BP-2000 Blood Pressure Analysis System for Mice and Rats" ;
NIFRID:synonym "BP-2000 Blood Pressure Analysis System",
"BP-2000 Blood Pressure Analysis System™ for Mice and Rats" ;
definition: "Computerized, non invasive system for measuring mouse and rat blood pressure. Blood pressure analyzer is standard in transgenic and knockout mouse research." .
SCR:022986 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2461" ;
rdfs:label "Stanford University Community of Shared Advanced Research Platforms" ;
NIFRID:synonym "Community of Shared Advanced Research Platforms" ;
NIFRID:abbrev "C-ShARP" ;
definition: "Center coordinates ideas and investments to advance and democratize access to Stanford cores, instrumentation, scientific and technical staff, allowing users to perform innovative, rigorous experiments." .
SCR:022987 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xAtlas" ;
definition: "Software tool as variant caller for SNVs and small indels. Implemented as software application written in C++ ." .
SCR:022988 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CNACS" ;
definition: "Software tool for copy number analysis." .
SCR:022989 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenomonPipeline" ;
definition: "Software DNA and RNA sequence analysis pipeline." .
SCR:022990 a owl:NamedIndividual ;
rdfs:label "Xenopus 1 " ;
NIFRID:synonym "Xenopus one" ;
NIFRID:abbrev "Xen1" ;
definition: "Supplier for research frogs for biomedical research community worldwide. Supplies: Xenopus laevis and tropicalis frogs, frog ovary, oocytes, eggs, testes." .
SCR:022991 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ParetoTI" ;
definition: "Software R toolbox for Archetypal Analysis and Pareto Task Inference for unsupervised characterisation of single cell data. Allows describing continuum of cell states by identifying representative cells with most distinctive expression. Detecting which genes and functional annotations make those cells distinctive gives marker genes and predicted functions for each state." .
SCR:022992 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MOFA" ;
NIFRID:synonym "Multi Omics Factor Analysis" ;
definition: "Software framework for unsupervised integration of multi-omics data sets. Used for discovering principal sources of variation in multi omics data sets." .
SCR:022993 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "quanTIseq" ;
NIFRID:synonym "quantification of the Tumor Immune contexture from human RNA-seq data" ;
definition: "Software pipeline for quantification of Tumor Immune contexture from human RNA-seq data." .
SCR:022994 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NGSCheckMate" ;
definition: "Software package for validating sample identity in next generation sequencing studies within and across data types. Used for identifying next generation sequencing data files from the same individual. Used for checking sample matching for NGS data." .
SCR:022995 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SURVIVOR" ;
NIFRID:synonym "StructURal Variant majorIty VOte" ;
definition: "Software tool set for simulating and evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs. Used for for SV simulation, comparison and filtering." .
SCR:022996 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BrainHealth Databank" ;
definition: "Repository of many types and sources of data including, but not limited to, assessments, imaging, wearable, and biological samples, collected from research projects at the Centre for Addiction and Mental Health. Data that individuals choose to share to advance mental health." .
SCR:022997 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Manta" ;
definition: "Software tool for rapid detection of structural variants and indels for germline and cancer sequencing applications. Used to call structural variants and indels from mapped paired end sequencing reads." .
SCR:022998 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SvABA" ;
definition: "Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements." .
SCR:022999 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PURPLE" ;
NIFRID:synonym "purity ploidy estimator" ;
definition: "Software tool as purity ploidy estimator for whole genome sequenced data. Used for copy number calling and determination of sample purity." .
SCR:023000 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain" ;
definition: "Project to develop and utilize imaging infrastructure to create human brain cell census and instantiate it in coordinate system that will enable immediate impact of all in vivo MRI studies of human brain. Consortium for creating cellular census of human cerebral cortex." .
SCR:023001 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tissue Studio" ;
NIFRID:synonym "Definiens Tissue Studio" ;
definition: "Software to detect regions of interests and distinguishes cells and sub-cellular objects within these target regions from immunohistochemistry specimen. Used for digital pathology image analysis." .
SCR:023002 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Data Envelopment Analysis Program" ;
NIFRID:synonym "Data Envelopment Analysis (Computer) Program",
"DEAP 2.1" ;
NIFRID:abbrev "DEAP" ;
definition: "Software tool to construct Data Envelopment Analysis frontiers for calculation of technical and cost efficiencies and also for calculation of Malmquist TFP Indices." .
SCR:023003 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Applied Biosystems | QuantStudio 1 RealTime PCR System" ;
NIFRID:synonym "QuantStudio™ 1 Real-Time PCR" ;
definition: "qPCR instrument with basic features ideal for those new to qPCR or those who have limited budget. System offers quality, reliability, and advanced user experience of QuantStudio family of instruments." .
SCR:023004 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Applied Biosystems | SimpliAmp Thermal Cycler" ;
NIFRID:synonym "SimpliAmp™ Thermal Cycler" ;
definition: "Bentchtop Thermal Cycler for everyday PCR. Features innovative, safe heated lid and large LCD color touch screen." .
SCR:023005 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | NanoDrop One/OneC Microvolume UV Vis Spectrophotometer" ;
NIFRID:synonym "NanoDrop One OneC Microvolume UV Vis Spectrophotometer",
"NanoDrop™ One/OneC Microvolume UV-Vis Spectrophotometer" ;
definition: "Benchtop spectrophotometer designed for DNA, RNA, and protein quantification, one sample at time using only 1–2 uL of sample without dilution, even for highly concentrated samples." .
SCR:023006 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "diffcyt" ;
definition: "Sotware R package for differential discovery analyses in high dimensional cytometry data including flow cytometry, mass cytometry or CyTOF, and oligonucleotide tagged cytometry." .
SCR:023007 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCD Viewer" ;
definition: "Software package for post acquisition data processing that allows users to visualize, review, and export Imaging Mass Cytometry data acquired with Hyperion Imaging System and CyTOF." .
SCR:023008 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SyRI" ;
NIFRID:synonym "Synteny and Rearrangement Identifier" ;
definition: "SyRI compares alignments between two chromosome level assemblies and identifies synteny and structural rearrangements." .
SCR:023009 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Polar Star" ;
NIFRID:synonym "Polar_Star" ;
definition: "Software pipeline to analyze read depth along long read contigs and to find outliers." .
SCR:023010 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EnTAP" ;
NIFRID:synonym "Eukaryotic Non-Model Transcriptome Annotation Pipeline" ;
definition: "Software package as eukaryotic non model annotation pipeline.Used for bringing functional annotation to non-model eukaryotic transcriptomes to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. Addresses fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates of protein-coding transcripts." .
SCR:023011 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gene Structure Display Server" ;
NIFRID:synonym "GSDS 2.0" ;
NIFRID:abbrev "GSDS" ;
definition: "Web gene structure display server. GSDS 2.0 is upgraded gene feature visualization server with newly designed interface, supports for more types of annotation features and formats, as well as an integrated visual editor for editing generated figure.User specified phylogenetic tree can be added to facilitate further evolutionary analysis." .
SCR:023012 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PBIL GOR4" ;
definition: "Web tool for secondary structural analysis. Used for secondary structure prediction." .
SCR:023013 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multi Loc2" ;
NIFRID:synonym "MultiLoc2" ;
definition: "Web application for integrating phylogeny and Gene Ontology terms into subcellular protein colalization prediction.Extensive high performance subcellular protein localization prediction system." .
SCR:023014 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Plant mPLoc" ;
NIFRID:synonym "Plant-mPLoc" ;
definition: "Web application for predicting subcellular localization of plant proteins including those with multiple sites.Top Down Strategy to Augment Power for Predicting Plant Protein Subcellular Localization." .
SCR:023015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "protein hydrophilicity analysis tool " ;
definition: "Web protein hydrophilicity analysis tool." .
SCR:023018 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TBtools" ;
NIFRID:synonym "Tools for Biologist" ;
definition: "Software integrative toolkit developed for interactive analyses of big biological data." .
SCR:023019 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brassicaceae Database" ;
NIFRID:abbrev "BRAD" ;
definition: "Database includes newly released genome sequences of Brassiceae species and published genomic data of most other Brassicaceae species.Data can be browsed in JBrowse or searched in BLAST. Offers service of searching for syntenic genes, which are generated based on their syntenic relationships to genes in Arabidopsis thaliana. Regularly updated with newly released reference genomes." .
SCR:023020 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CNS Genoscope" ;
definition: "Web tool as Brassica napus genome browser." .
SCR:023021 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BnTIR" ;
NIFRID:synonym "Brassica napus Transcriptome Information Resource" ;
definition: "Searchable database of Brassiceae genomic data hosted on the website." .
SCR:023022 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1632" ;
rdfs:label "New York University Langone Medical Center Research Software Engineering Core Facility" ;
NIFRID:synonym "New York University Langone Medical Center Research Software Engineering Core",
"Research Software Engineering",
"Research Software Engineering Core" ;
NIFRID:abbrev "RSE" ;
definition: "Core is resource launched by NYU Langone, based in Information Technology department in close collaboration with NYU Grossman School of Medicine.Used to design, develop, optimize, and customize software to accelerate research. Requires iLab log in." .
SCR:023023 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1633" ;
rdfs:label "Cold Spring Harbor Laboratory Microscopy Shared Resource Core Facility" ;
NIFRID:synonym "Cold Spring Harbor Laboratory CSHL-Microscopy Shared Resource",
"CSHL-Microscopy Shared Resource" ;
definition: "Provides access to microscopes, technical advice and expertise in preparing cells or tissues for immunofluorescence/confocal microscopy, live cell imaging, super resolution imaging, transmission electron microscopy, and immunoelectron microscopy." .
SCR:023024 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "meta4diag" ;
NIFRID:synonym "Meta Analysis for Diagnostic Test Studies" ;
definition: "Software R package for bivariate meta analysis of diagnostic test studies using integrated nested Laplace approximation with INLA." .
SCR:023025 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rtrack" ;
definition: "Software R package for analysis of paths from spatial tracking experiments such as Morris water maze and calculation of goal finding strategies. Used for in depth analysis of tracking coordinates from video." .
SCR:023026 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ColonyTrack" ;
definition: "Software R package to process raw data from ColonyRack system. In addition to generating pre processed data and quality control information, range of high level metrics are calculated together with convenient tools for analysis." .
SCR:023027 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DataSeer" ;
definition: "Web tool to identify generation and reuse of research outputs. Used to determine author compliance with Open Science policies in academic research texts." .
SCR:023028 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iNSCOPIX | nVoke System" ;
NIFRID:synonym "Inscopix nVoke System" ;
definition: "Miniature microscope system that integrates in vivo cellular resolution calcium imaging with simultaneous or sequential optogenetic manipulation to causally link neural circuit activity with behavior." .
SCR:023030 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "MAPI Research Trust" ;
definition: "Organization dedicated to improving patients’ quality of life by facilitating access to Patient-Centered Outcome information. Has access to any published COA article and subscribes to key journals in this field, such as Quality of Life Research and Value in Health. Library houses COAs, as well as their translations into some 130 languages. See PROQOLID on ePROVIDE for full range of availability." .
SCR:023031 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GAITOR Suite" ;
NIFRID:synonym "Gait Analysis Instrumentation and Technology Optimized for Rodents",
"GAITOR",
"GAITOR Suite system" ;
definition: "Software suite to analyse gait trials collected with Experimental Dynamic Gait Arena for Rodents. Used for rodent gait analysis." .
SCR:023032 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nTracer" ;
definition: "Software tool as plug-in for ImageJ software. Used for tracing microscopic images." .
SCR:023033 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1644" ;
rdfs:label "University of Nebraska Medical Center UNMC MEG Core Facility" ;
NIFRID:synonym "UNMC MEG Core Facility" ;
definition: "Equipped with magnetoencephalography (MEG) scanner to detect immediate changes in electrical brain activity. Provides 306 channel whole head MEG system (TRIUX, Neo, MEGin) and 128 channels EEG amplifier.MEG helmet does coverage for whole cortex, 1220 cm2. MEG system has three measurement positions:supine, lower and upper seated. MEG system is housed within magnetic shielded room equipped with active shielding and automated helium recycler." .
SCR:023034 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1646" ;
rdfs:label "University of Arizona CBC Machine Shop Core Facility" ;
NIFRID:synonym "CBC Machine Shop",
"University of Arizona CBC Machine Shop" ;
definition: "Provides full service precision machine shop specializing in design and construction of custom equipment for scientific research and teaching." .
SCR:023035 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1645" ;
rdfs:label "University of Arizona CBC Electronics Core Facility" ;
NIFRID:synonym "CBC Electronics Facility",
"University of Arizona CBC Electronics Facility" ;
definition: "Supporting the research community through troubleshooting, repair and new designs for electronic instrumentation, equipment and experiments." .
SCR:023036 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1647" ;
rdfs:label "University of Arizona CBC Glassblowing Core Facility" ;
NIFRID:synonym "CBC Glassblowing Facility",
"University of Arizona CBC Glassblowing Facility" ;
definition: "Provides full service facility for design and fabrication of specialized scientific glassware as well as repairs and modifications of existing glassware." .
SCR:023037 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HiRise " ;
NIFRID:synonym "Omni-C Scuffolder" ;
definition: "Software pipeline to identify poor quality joins and produce accurate, long range sequence scaffolds." .
SCR:023038 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pairtools" ;
definition: "Software command line framework to process sequencing data from Hi-C experiment. Used to process pair end sequence alignments." .
SCR:023039 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " funannotate" ;
definition: "Software package for genome annotation. Built specifically for fungi, but will also work with higher eukaryotes. Used for genome prediction, annotation, and comparison." .
SCR:023040 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Science Alliance" ;
definition: "Organization mission is to expand cooperative ventures in research with Oak Ridge National Laboratory and enhance science and engineering research programs at University of Tennessee. Organization is affiliated with Tennessee Center of Excellence. Funding resource." .
SCR:023041 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Anipose" ;
definition: "Software package for 3D pose estimation. Uses DeepLabCut for 2D tracking and uses triangulation methods to project pose estimations into three dimensions.Toolkit for robust markerless 3D pose estimation." .
SCR:023042 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Generate tools" ;
NIFRID:synonym "Gene[rate] tools",
"HLA-net GENE[RATE]" ;
definition: "Software pipeline for effective HLA data analysis and its application to 145 population samples from Europe and neighbouring areas. Tools for handling and analysing data with ambiquities." .
SCR:023043 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cancer Cell Map Initiative" ;
NIFRID:abbrev "CCMI" ;
definition: "Initiative to enable cancer discovery and treatment based on complete elucidation of molecular networks underlying cancer. CCMI leverages advanced interaction mapping and computational facilities to generate and analyze cancer networks." .
SCR:023045 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Scientific TraceFinder" ;
NIFRID:synonym "TraceFinder",
"TraceFinder Software" ;
definition: "Software set of acquisition and data processing tools. LC/MS analytical software. Enables control of multi-channel LC, single quadrupole, triple quadrupole and high-resolution LC-MS systems, as well as IC and GC systems." .
SCR:023046 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AccuCor" ;
definition: "Software as isotope natural abundance correction algorithm that is needed especially for high resolution mass spectrometers. Natural abundance correction of mass spectrometer data." .
SCR:023047 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggsignif" ;
definition: "Software package to indicate if two groups are significantly different. Used to add significance brackets to ggplots." .
SCR:023048 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1648" ;
rdfs:label "University of Florida UF Scripps Biomedical Research Bioinformatics and Statistics Core Facility" ;
NIFRID:synonym "UF Scripps Biomedical Research-Bioinformatics and Statistics Core",
"University of Florida UF Scripps Biomedical Research Bioinformatics and Statistics Core" ;
definition: "Core provides data management and analysis services for UF Scripps community as well as for external collaborators. Offers scientific support to assist in experimental design, analysis, integration and dissemination of biomedical data and knowledge. Supports data analysis for samples processed at Genomics, Proteomics, and Neurobehavior cores." .
SCR:023049 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LiftPose3D" ;
definition: "Software tool for transforming 2D poses to 3D coordinates on labaratory animals. Used for kinematic studies of laboratory animals. Tracking movements in three dimensions from behaving flies, mice, rats, and non-human primates." .
SCR:023050 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1649" ;
rdfs:label "Virginia Commonwealth University Genomics Core Facility" ;
NIFRID:synonym "VCU Genomics Core",
"Virginia Commonwealth University VCU Genomics Core" ;
definition: "Genomics Core facility in Richmond VA, maintains instrumentation to support advanced sample/library preparation, high-throughput sequencing, real-time PCR and analysis." .
SCR:023051 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1652" ;
rdfs:label "National Jewish Health Genomics Core Facility" ;
NIFRID:synonym "National Jewish Health Genomics Facility" ;
definition: "Facility housed within Center for Genes, Environment and Health, provides Next-Gen Sequencing services from expert planning through data analysis including RNA-Seq, Whole Exome Sequencing, Single-Cell sequencing and customized panels.Data is stored onsite and is ready for future data mining by our team or others when needed. Our team is trained to utilize both Illumina and Thermo Ion Sequencing Platforms, including many other technologies, to provide the best mix of capabilities for your genomics needs." .
SCR:023052 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1651" ;
rdfs:label "Ohio State University Wexner Medical Center Leukemia Tissue Bank Core Facility" ;
NIFRID:synonym "Leukemia Tissue Bank",
"Leukemia Tissue Bank Shared Resource",
"Ohio State University Wexner Medical Center Leukemia Tissue Bank" ;
NIFRID:abbrev "LTBSR" ;
definition: "Human tissue biorepository offering procurement and distribution services for samples obtained from patients with hematologic malignancies." .
SCR:023060 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReproRehab Research Education Course" ;
NIFRID:synonym "Reproducible Rehabilitation Research Education Course" ;
NIFRID:abbrev "ReproRehab" ;
definition: "Research education program to build sustainable national workforce of rehabilitation researchers equipped with basic data science skills in five years." .
SCR:023061 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DANNCE" ;
NIFRID:synonym "3-Dimensional Aligned Neural Network for Computational Ethology" ;
definition: "Convolutional neural network that calculates 3D positions of user-defined anatomical landmarks on behaving animals from videos taken at multiple angles. Works on recorded video data from multiple cameras. Used for 3D markerless pose estimation and tracking." .
SCR:023062 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Protofilament Bending Models " ;
definition: "Code is written to be run with Matlab version r2020b or higher. Model accepts wave assay pulse amplitude data, and simultaneously solves and fits protofilament deflection models to deduce fundamental biophysical properties of microtubule protofilaments." .
SCR:023068 a owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TC_344C" ;
rdfs:label "Warner Instruments | Dual Channel Temperature Controller Model TC-344C" ;
NIFRID:synonym "Dual Channel Temperature Controller" ;
definition: "Temperature controller. Each channel supplies up to 22 watts into load of 10 ohms. Heat set point is controlled automatically in Auto mode via thermistor feedback. Loop speed selector provides three feedback response times to optimize tp thermal stability of device being heated. Heat set-point may also be manually controlled in Manual mode." .
SCR:023069 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BX51WI" ;
rdfs:label "Olympus | BX51WI Fixed Stage Upright Microscope" ;
NIFRID:synonym "BX51WI Fixed Stage Microscope" ;
definition: "BX51WI is for all physiological experiments such as patch clamping and intravital microscopy. Fixed stage and vibration free frame design ensures stability throughout experiment. Use of infrared light protects living cells and offers high penetration depths of thick tissue slices, while high NA optics allow magnification changes without moving objective." .
SCR:023070 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "expam" ;
definition: "Open source software Python application for high resolution analysis of metagenomes using distance trees. Tree based, taxonomy agnostic tool for identification of biologically relevant clades from shotgun metagenomic sequencing. Used for phylogenetic analysis of shotgun metagenomic data." .
SCR:023071 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StatTech" ;
definition: "Web service for statistics with automated data analysis mode." .
SCR:023072 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multiband Censoring Optimization Tool" ;
NIFRID:abbrev "MCOT" ;
definition: "Software tool for resting state functional connectivity analyses. Allows to get optimal LPF-FD and GEV-DV volume censoring parameters for specified multiband resting state fMRI dataset." .
SCR:023073 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Toolkit for MIRA LAB Striatal Segmentation" ;
NIFRID:synonym "Toolkit_for_MIRA_LAB_Striatal_Segmentation" ;
definition: "Software MATLAB pipeline that produces CNN-based segmentations of striatal regions of brain based on structural T1w image." .
SCR:023074 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SALib" ;
definition: "Open source software Python library for sensitivity analysis. Useful in systems modeling to calculate effects of model inputs or exogenous factors on outputs of interest." .
SCR:023075 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OmicsAnalyst" ;
definition: "Web based tool for multi-omics integration via intuitive visual analytics. Web based platform for visual analytics of multi-omics data to allow researchers to fuse statistical and visual streams of evidence together to make more informed judgements. Enables to dissect large and complex multi-omics datasets by facilitating pattern recognition and cognitive reasoning through intuitive visual analytics." .
SCR:023076 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:ms_dial" ;
rdfs:label "MS-DIAL" ;
definition: "Software tool for data independent MS/MS deconvolution for comprehensive metabolome analysis. Universal program for untargeted metabolomics that supports multiple instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker, LECO, Sciex, Shimadzu, Thermo, and Waters). Used for untargeted metabolomics and lipidomics supporting any type of chromatography/mass spectrometry methods." .
SCR:023077 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LECO ChromaTOF" ;
NIFRID:synonym "ChromaTOF" ;
definition: "Software tool to analyze data that are acquired with LECO time-of-flight instruments. Used for processing and analyzing large amounts of data that are acquired with LECO instruments. Offers control of instrument and its accessories, as well as intuitive interface with highly integrated data processing. Mass spectrometry data system to fully accommodate multidimensional chromatographic data." .
SCR:023078 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DistillerSR" ;
definition: "Literature review software by DistillerSR Inc. Automates management of literature collection, screening, and assessment using AI and intelligent workflows. From systematic literature review to rapid review to living review, makes any project simpler to manage and configure to produce transparent, audit-ready, and compliant results." .
SCR:023079 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OncoMerge" ;
definition: "Software tool to integrate somatic mutation types into comprehensive integrated somatic mutation matrix for downstream analyses.Somatic mutation integration platform that tames allelic heterogeneity, discovers causal mutations, integrates binary PAM and fusion with quantitative CNA data types, and overcomes known obstacles in cancer genetics. Used for systematic integration of protein affecting mutations, gene fusions, and copy number alterations into comprehensive somatic mutational profile." .
SCR:023080 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SYGNAL" ;
NIFRID:synonym "SYstems Genetic Network AnaLysis" ;
definition: "Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts." .
SCR:023081 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Corrplot" ;
definition: "Software R package as visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables." .
SCR:023082 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EnrichedHeatmap" ;
definition: "Software R package for comprehensive visualization of genomic signal associations. Visualizes enrichment of genomic signals on specific target regions. Used to visualize e.g. how histone marks are enriched to specific sites." .
SCR:023083 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PACEMweb" ;
NIFRID:synonym "Probabilistic Aggregate Consumer Exposure Model Web" ;
definition: "Web tool for aggregate consumer exposure assessment. Model is based on realistic product usage information obtained from surveys. Information on usage, frequency and amount of personal care products and household cleaning products in various European countries is included." .
SCR:023084 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MERLIN-Expo" ;
definition: "Software tool contains set of models for simulating fate of chemicals in main environmental systems and in human body. Features include uncertainty and sensitivity analysis as well as consideration of pharmacokinetics." .
SCR:023085 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "S-Risk" ;
definition: "Web tool for assessing exposure and human health risks at contaminated sites. Fate and distribution of chemical pollutants in soil are calculated according to steady-state conservation of mass principles.Risks are calculated by comparing exposures with toxicological reference values and concentrations with toxicological or legal reference concentrations." .
SCR:023086 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Anne O'Tate" ;
definition: "Web search tool to gain overview of set of articles retrieved by PubMed query. Used to support user driven summarization, drill down and browsing of PubMed search results. Value-added PubMed search engine for analysis and text mining." .
SCR:023087 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PubMed PubReMiner" ;
definition: "Web tool used to analyse PubMed search results. Text mining tool. Will query PubMed with your specified searchquery, get all abstracts and generate frequency tables. The first table will show journals in which your query is published the most.The second table will show the authors which are most active in the field of your query.The third table will show words that have been used most in the title and abstract of the articles." .
SCR:023088 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QCAlign" ;
definition: "Software tool to detect regions that are affected by tissue damage, labelling defects, artifacts or errors in image acquisition, regions that are poorly registered, or where registration cannot be verified. Makes it easier for the user to explore the atlas hierarchy and decide on customized hierarchy level for investigation. QCAlign was developed to support QUINT workflow which supports spatial analysis of labelling in series of brain sections from mouse and rat based on registration to reference atlas." .
SCR:023089 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "immunarch" ;
definition: """Software R package for exploration of single-cell and bulk T-cell/antibody immune repertoires.
Framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires.""" .
SCR:023090 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Differential Enrichment analysis of Proteomics data" ;
NIFRID:abbrev "DEP" ;
definition: "Software R package provides integrated analysis workflow for analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment." .
SCR:023091 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1653" ;
rdfs:label "Montpellier GenomiX Core Facility" ;
NIFRID:synonym "Montpellier GenomiX" ;
NIFRID:abbrev "MGX" ;
definition: "Offers genomic technologies to academic laboratories and biotechnology companies.Application portfolio includes Whole genome (re)sequencing, including the identification of variants (SNVs, mutations, indels, CNVs);Targeted sequencing, for instance exomes; Transcriptome analyses (RNA-Seq, small RNA-Seq, microarrays), including in single cells (single-cell 3 RNA-seq); Determination of chromatin structure and dynamics (ChIP-Seq, FAIRE-Seq, Hi-C); Epigenetic analyses (ChIP-Seq, RRBS, Bisulphite-Seq);Genotyping (RAD-Seq, GBS, microarrays)." .
SCR:023092 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1654" ;
rdfs:label "Arpege Core Facility" ;
NIFRID:synonym "Arpege" ;
definition: "Offers functional and structural analysis of protein complexes.Offers possibility to characterize all types of molecular interactions: ligand-target binding, protein-protein interactions, signal transduction, and signalling complexes. Staff members are skilled specialists in luminescence-based techniques and in receptor biology.Application portfolio includes Analysis of cell signalling, by measuring signal transduction;Ligand-target binding (pharmacological analysis, affinity, selectivity); Protein-protein interactions (oligomerization, effectors...); Activation of signalling pathways (G proteins, GRK, arrestins & internalization); Intracellular production of second messengers (cAMP, IP1, Ca2+); Phosphorylation of signalling proteins (ERK, AKT...); Measurement of global cell functions and of different cell parameters (proliferation, migration, invasion...)." .
SCR:023095 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReMM score" ;
NIFRID:synonym "Regulatory Mendelian Mutation score" ;
definition: """Software tool that scores positions in human genome in terms of their regulatory probability.
Regulatory Mendelian Mutation score was created for relevance prediction of non-coding variations (SNVs and small InDels) in human genome (hg19) in terms of Mendelian diseases.""" .
SCR:023096 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1655" ;
rdfs:label "Montpellier Bacfly Core Facility" ;
NIFRID:synonym "Bacfly",
"Montpellier Bacfly" ;
definition: "Facility dedicated to expression of innovative recombinant proteins for all in vitro and in vivo studies. Innovative technology developed by the platform, called FlexiBac, uses baculovirus / insect cell expression system." .
SCR:023097 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_428" ;
rdfs:label "Rockefeller University CRISPR and Genome Editing Resource Center Core Facility" ;
NIFRID:synonym "CRISPR and Genome Editing Resource Center",
"Rockefeller University CRISPR and Genome Editing Resource Center" ;
definition: "Provides gene targeting and mouse embryonic stem cell technology for members of Rockefeller University, Memorial Sloan-Kettering Cancer Center and their collaborators.CRISPR and Genome Editing services include mouse genomic knock-out and knock-in, mouse conditional knock-out, establishing new ES lines for gene targeting services, establishing ES lines from mutant mouse embryos, preparing ES cells introduced from off campus resources for injection or other application, assisting in embryoid body culture and in vitro differentiation of ES cells, and purification and evaluation of DNA for pronuclear injection." .
SCR:023098 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_83" ;
rdfs:label "Rockefeller University Transgenic and Reproductive Technology Center Core Facility" ;
NIFRID:synonym "Rockefeller University Transgenic and Reproductive Technology Center",
"Transgenic and Reproductive Technology Center" ;
NIFRID:abbrev "TRTC" ;
definition: "Provides services such as Pronuclear Injection, Blastocyst Injection, Embryo and Sperm Cryopreservation, Strain Recovery and Rederivation. Provides assisted reproductive techniques such as IVF and ICSI used for strain recovery. Core facility to the university for creation and maintenance of all transgenic animal models, refinement and development of new transgenic techniques, as well as training center for research personnel." .
SCR:023099 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1657" ;
rdfs:label "Children's Hospital of Philadelphia CHOP-Penn Proteomics Core Facility" ;
NIFRID:synonym "Children's Hospital of Philadelphia Research Institute CHOP-PENN Proteomics Core",
"Children's Hospital of Philadelphia Research Institute Proteomics Core Facility",
"CHOP-PENN Proteomics Core" ;
definition: "Core facility specializes in mass spectrometry-based proteomics with a commitment to quality, rigor, problem-solving, and innovation. Provides expert guidance." .
SCR:023100 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ENCODE ATAC-seq pipeline" ;
definition: "Software pipeline to process ATAC-Seq data. Used for automated end-to-end quality control and processing of ATAC-seq and DNase-seq data." .
SCR:023101 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cytograph" ;
definition: "Software multistage analysis pipeline which progressively discovers cell types or states while mitigating impact of technical artifacts.Used for single cell analysis." .
SCR:023102 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroPep" ;
definition: "Comprehensive resource of neuropeptides, which holds non-redundant neuropeptide entries. Data collected from resources including MEDLINE abstracts, full papers, UniProt,database at www.neuropeptides.nl and Neuropedia. Contains detailed annotations for each entry, including source organisms, tissue specificity, families, names, post-translational modifications, 3D structures and literature references. Amino acid compositions, isoelectric points, molecular weight and other physicochemical properties of peptides are also provided. Search database with keywords such as sequence, name, family, etc.,User friendly web tools like browsing, sequence alignment and mapping are also integrated.Users can submit new entries online. Each new entry is validated before incorporating it." .
SCR:023103 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ATACseqQC" ;
NIFRID:synonym "Assays for Transposase-Accessible Chromatin using sequencing Quality Control" ;
definition: "Software R package for post alignment quality assessment of ATAC-seq data. Package also contains functions to preprocess aligned ATAC-seq data for subsequent peak calling." .
SCR:023104 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1660" ;
rdfs:label "University of Michigan Ann Arbor Center for Chemical Genomics Core Facility" ;
NIFRID:synonym "Center for Chemical Genomics",
"University of Michigan�Ann Arbor Center for Chemical Genomics" ;
definition: "Provides high throughput screening of extensive small molecule, natural product and siRNA libraries along with assay development and optimization for basic biology and drug discovery projects." .
SCR:023105 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1661" ;
rdfs:label "University of Michigan Ann Arbor Natural Products Discovery Core Facility" ;
NIFRID:synonym "Natural Products Discovery Core",
"University of Michigan�Ann Arbor Natural Products Discovery Core" ;
definition: "Core has developed library of natural product extracts derived from unique collection of diverse marine and terrestrial actinomycetes, fungi and cyanobacteria. Provides technology and expertise to develop candidates identified through high-throughput screening into unique, bioactive, patentable, small molecules." .
SCR:023106 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1659" ;
rdfs:label "University of Rochester Medical Center Mass Spectrometry Resource Laboratory Core Facilitiy" ;
NIFRID:synonym "Mass Spectrometry Resource Laboratory",
"University of Rochester Medical Center Mass Spectrometry Resource Laboratory",
"URMC Mass Spectrometry Resource Laboratory" ;
NIFRID:abbrev "MSRL" ;
definition: "Provides instrumentation and technical expertise to local researchers seeking to conduct MS-based protein or small molecule assays.Staff provide assistance with project design, sample preparation, collection and interpretation of mass spectrometric data.Common analyses services include identification of unknown proteins, characterization of protein complexes, mapping of post-translational modifications and relative quantitation of peptides and small molecules from range of sample types, including complex clinical matrices, tissue extracts and cell lysates. Specialized MS instrumentation include Fusion Lumos Tribrid Orbitrap and Thermo Q Exactive Plus Hybrid Quadrupole-Orbitrap. In addition, the laboratory has access to a variety of automated database searching software as well as resources to facilitate discovery-based proteomics projects." .
SCR:023107 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "La Jolla Institute for Immunology Next Generation Sequencing Core Facility" ;
NIFRID:synonym "La Jolla Institute for Immunology Next Generation Sequencing Facility" ;
definition: "Core provides latest sequencing technology combined with Institute's expansive bioinformatics capabilities. Provides instrumentation including Illumina Miseq, Covaris Model E220, NovaSeq 6000, Agilent 2200 Tapestation, Beckman Coulter Biomek FXP, HiSeq 2500." .
SCR:023108 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1662" ;
rdfs:label "McLaughlin Research Institute for Biomedical Sciences Transgenic Core Facility" ;
NIFRID:synonym "McLaughlin Research Institute Transgenic Facility",
"MRI-Transgenic Facility" ;
definition: "Provides services to create, rederive or cryopreserve mouse models.Specific services include:CRISPR/Cas9-mediated gene editing (experimental design service and/or consulting also provided); pronuclear Injection; ES Cell Injection; In Vitro Fertilization; rederivation of mouse lines to specific pathogen free status; embryo and sperm cryopreservation and recovery." .
SCR:023109 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AgreeStat 360" ;
definition: "Web too that implements various methods for evaluating extent of agreement among two or more raters. For two raters, data can be organize either as contingency table (for categorical ratings only) or as two column table of raw categorical or quantitative ratings. For three raters or more, data can be in form of columns of raw scores (for categorical or quantitative ratings), or alternatively in form of distribution of raters by response category for categorical only. Data can be captured in two ways. You can key in ratings directly in data grid or import it from CSV text file or MS Excel. You can highlight portion of grid you want to analyze and click on red action button. Selected data will be described below associated red action button." .
SCR:023110 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Seattle Alzheimer Disease Brain Cell Atlas" ;
NIFRID:abbrev "SEA-AD" ;
definition: "Open atlas based on single cell profiling technologies with quantitative neuropathology and deep clinical phenotyping from middle temporal gyrus from neurotypical reference brains and brains from SEA-AD aged cohort that span spectrum of Alzheimer’s disease. Produced via collaboration between Allen Institute for Brain Science, University of Washington Alzheimer Disease Research Center and Kaiser Permanente Washington Health Research Institute." .
SCR:023111 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "10.57761",
"r3d100014398" ;
rdfs:label "Redivis" ;
NIFRID:synonym "Red Vis" ;
definition: "Commercial collaborative research platform for hosting and analyzing datasets.Data platform for academic research. Redivis provides organizations with central hub where researchers can easily discover, access, and analyze their data." .
SCR:023112 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ataqv" ;
definition: "Software package for QC and visualization of ATAC-seq results. Used to examine aligned reads and report basic metrics, including reads mapped in proper pairs, optical or PCR duplicates, reads mapping to autosomal or mitochondrial references, ratio of short to mononucleosomal fragment counts, mapping quality, various kinds of problematic alignments." .
SCR:023113 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GENERA" ;
NIFRID:synonym "GEN-ERA toolbox" ;
definition: "Software toolbox to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes." .
SCR:023115 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RNAcentral" ;
definition: "Non coding RNA sequence database. Comprehensive ncRNA sequence collection representing all ncRNA types from broad range of organisms." .
SCR:023116 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1663" ;
rdfs:label "University of Pittsburgh Medical Center Children Hospital of Pittsburgh Health Sciences Sequencing Core Facility" ;
NIFRID:synonym "Health Sciences Sequencing Core at UPMC Children Hospital of Pittsburgh",
"University of Pittsburgh Health Sciences Sequencing Core at UPMC Children Hospital of Pittsburgh" ;
definition: "Sequencing Core offers Illumina next generation sequencing services to University of Pittsburgh research community. Offers expertise in next generation sequencing technologies. Encourages to contact Assistant Director to arrange for consultation.Staff is available to share their experience and expertise to assist with development of projects of all sizes, standard or custom assay design, and other specialized application needs." .
SCR:023117 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1665" ;
rdfs:label "Cornell University Biotechnology Resource Center Biomolecular Interactions and Properties Core Facility" ;
NIFRID:synonym "BRC Biomolecular Interactions and Properties Facility",
"Cornell University BRC Biomolecular Interactions and Properties Facility" ;
definition: "Provides investigators with access to advanced tools for measuring biomolecular interactions and properties through variety of techniques from high throughput screening via automation to single reaction cuvette based methods.Facility complements technologies and techniques available through our Imaging facility and Proteomics and Metabolomics facility." .
SCR:023119 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ACTman" ;
NIFRID:synonym "Actigraphy Manager" ;
definition: "Software R library to automate labor intensive actigraphy data preprocessing and analyses steps while improving transparency, reproducibility, and scalability over software suites traditionally used in actigraphy research practice. Provides streamlined preprocessing while validating circadian rhythm and sleep analysis." .
SCR:023120 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SingleR" ;
NIFRID:synonym "Single-cell RNA-seq cell types Recognition" ;
definition: "Software R package for unbiased cell type recognition of scRNA-seq data. Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer cell of origin of each single cell independently." .
SCR:023121 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SigProfilerExtractor" ;
definition: "Software tool for de novo extraction of mutational signatures from data generated in matrix format. Identifies number of operative mutational signatures, their activities in each sample, and probability for each signature to cause specific mutation type in cancer sample." .
SCR:023122 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SigProfilerMatrixGenerator " ;
definition: "Software tool to create mutational matrices for all types of somatic mutations. Used to generate mutational matrices for set of samples with associated mutational catalogues. Used for optimized exploration and visualization of mutational patterns for all types of small mutational events. In addition to extending classification of single base substitutions, provides support for classifying doublet base substitutions and small insertions and deletions." .
SCR:023123 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dNdScv" ;
NIFRID:synonym "dN/dScv" ;
definition: "Software R package is group of maximum likelihood dN/dS methods designed to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole-exome level.Used to detect cancer driver genes on datasets ranging from few samples to thousands of samples, in whole-exome/genome or targeted sequencing studies." .
SCR:023124 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Algorithms and Framework for Nonnegative Matrix Factorization" ;
NIFRID:synonym "Non-negative Matrix Factorization" ;
NIFRID:abbrev "NMF" ;
definition: "Software R package for nonnegative matrix factorization. Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms." .
SCR:023125 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.4121",
"DOI:10.17616/R3VG6N",
"DOI:10.25504/FAIRsharing.zcveaz" ;
rdfs:label "4TU.ResearchData" ;
definition: "International data repository for science, engineering and design. Services include curation, sharing, long-term access and preservation of research datasets. These services are available to anyone around the world. In addition, 4TU.ResearchData also offers training and resources to researchers to support them in making research data findable, accessible, interoperable and reproducible (FAIR)." .
SCR:023126 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.48567" ;
rdfs:label "Antarctic Meteorological Research and Data Center Repository" ;
definition: "AMRDC Repository provides archival, preservation, access, and metadata authoring services for Antarctic meteorological data, managing data from submission to end-user retrieval. The repository hosts data collected by the Antarctic Meteorological Research Center and Automatic Weather Station projects, as well as campaign meteorological datasets deposited by other Antarctic investigators." .
SCR:023127 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.57995" ;
rdfs:label "Abertay University Datasets" ;
NIFRID:synonym "Abertay Datasets" ;
definition: "Open access repository. Contains research outputs and supporting data from staff and students, including published articles, conference papers, reports, datasets and theses." .
SCR:023128 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/r31njmv8",
"DOI:10.48623",
"r3d100013444" ;
rdfs:label "Aperta Turkey Open Archive" ;
definition: "Aperta is the name of the Turkish Open Archive.You can upload your scientific studies within the scope of Aperta to this portal or you can easily access the uploaded studies." .
SCR:023129 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.4878" ;
rdfs:label "Aston Publications Explorer" ;
definition: "Aston Publications Explorer is Aston University's repository for their open access publications. You may also be interested in Aston Data Explorer for Aston's research data and Aston Research Explorer for broader information about Aston's research work including research staff, awards and activities projects and research groups." .
SCR:023130 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R31NJMGT",
"DOI:10.21985",
"DOI:10.25504/FAIRsharing.52b22c",
"r3d100012925" ;
rdfs:label "Arch" ;
definition: "Arch is an open access repository for the research and scholarly output of Northwestern University. Log in with your NetID to deposit, describe, and organize your research for public access and long-term preservation. We'll use our expertise to help you curate, share, and preserve your work." .
SCR:023131 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.5884",
"DOI:10.17616/R3QK86",
"r3d100010953" ;
rdfs:label "Polar Data Catalogue" ;
NIFRID:synonym "ArcticNet" ;
definition: "Repository of metadata and data that describes and provides access to diverse data sets generated by Arctic and Antarctic researchers. The metadata records follow ISO 19115 and Federal Geographic Data Committee (FGDC) standard formats to provide exchange with other data centres. The records cover a wide range of disciplines from natural sciences and policy, to health and social sciences. The PDC Geospatial Search tool is available to the public and researchers alike and allows searching data using a mapping interface and other parameters." .
SCR:023132 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17036",
"DOI:10.17616/R3H073",
"r3d100012285" ;
rdfs:label "Aston Data Explorer" ;
definition: "Aston University's repository for their research data. It is one of three services providing information about Aston University�s research. Aston Publications Explorer holds Aston's research publications and Aston Research Explorer has broader information about Aston's research work including research staff, awards and activities, projects and research groups.Metadata will be accessible to anyone free of charge. The metadata may be re-used in any medium without prior permission and re-sold commercially provided the repository is mentioned.Aston�s repository holds datasets and corresponding metadata that have been produced by Aston University staff and students. The datasets deposited in Aston Publications Explorer range from metadata records only through to full datasets. Content is the sole responsibility of the authors, and any questions over content should be directed to them.Aston Data Explorer, Aston Publications Explorer AND Aston Research Explorer allow users to re-use full-text and other full-data items under the terms of the Creative Commons Attribution Non-Commercial No Derivatives (CC BY NC ND) licence. This means that users must give appropriate credit to the authors and link to the licence. Users may not re-use the material for commercial purposes. Users cannot distribute material that has been remixed, transformed or built upon the original published output. Where a full-text or other full-data item has a licence that is more restrictive or permissive than the CC BY NC ND default licence, this licence should be adhered to." .
SCR:023133 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.48667" ;
rdfs:label "Astrobiology Habitable Environments Database" ;
definition: "Astrobiology Habitable Environments Database (AHED) is a new data system being developed as a long-term, open-access repository for astrobiology data. AHED is intended to store user-contributed results from NASA or externally-funded research in astrobiology, and to encourage sharing and synergy within the astrobiology community." .
SCR:023134 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R3CG82",
"DOI:10.25504/FAIRsharing.j5eden",
"DOI:10.26198",
"r3d100010914",
"r3d100011749" ;
rdfs:label "Australian Ocean Data Network" ;
definition: "Interoperable online network of marine and climate data resources.AODN Portal provides access to all available Australian marine and climate science data and provides the primary access to IMOS data." .
SCR:023135 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.3473",
"DOI:10.17616/R3VK72",
"DOI:10.25504/FAIRsharing.da9307",
"r3d100011394" ;
rdfs:label "B2SHARE Eudat" ;
NIFRID:synonym "B2SHARE" ;
definition: "Used to store, publish and share research data in FAIR way. Facilitates research data storage, guarantees long-term persistence of data and allows data, results or ideas to be shared worldwide.Supports community domains with metadata extensions, access rules and publishing workflows." .
SCR:023136 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.48361" ;
rdfs:label "SCAR Antarctic Biodiversity Portal" ;
definition: "International effort that seeks to increase our knowledge and understanding of Antarctic and Southern Ocean biodiversity.It is a community of researchers, data custodians and developers from around the world that supports the mobilisation publication, retrieval and analysis of Antarctic and Southern Ocean biodiversity data in a free and open manner in line with the Antarctic treaty and the FAIR data Principles (Finable, Accessible, Interoperable, Reusable). The SCAR Antarctic biodiversity Portal has a number of portals dedicated to specific types of data and information on Antarctic and Southern Ocean Biodiversity.We aim to create an information ecosystem of various data bases, data systems, web services tools etc that can be used by anyone with an interest in Antarctic and Southern Ocean biodiversity.Biodiversity.aq is an international initiative of the Scientific Committee on Antarctic Research (SCAR). It finds it roots in the Census of Antarctic Marine Life and started in 2005. The central facilities are hosted by the Royal Belgian Institute for Natural sciences (RBINS, www.naturalsciences.be) and the Belgian Biodiversity Platform (BBPf, www.biodiversity.be).The SCAR Antarctic Biodiversity Portal is the regional thematic node of the Ocean Biodiversity Information System (OBIS, www.obis.org), the Global Biodiversity Information Facility (GBIF, www.gbif.org) and works closely together with the Southern Ocean Observation System (SOOS, www.soos.aq)." .
SCR:023137 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R3K897",
"DOI:10.17909",
"r3d100010403" ;
rdfs:label "Barbara A. Mikulski Archive for Space Telescopes" ;
definition: "Astronomical data archive focused on optical, ultraviolet, and near infrared. Used for maximizing scientific accessibility and productivity of astronomical data. MAST hosts data from over dozen missions like Webb, Hubble, TESS, Kepler, and in the future Roman." .
SCR:023138 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.34636" ;
rdfs:label "BioData Management Portal" ;
definition: "Portuguese distributed infrastructure for biological data and Portuguese node of ELIXIR." .
SCR:023139 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R31NJLW9",
"DOI:10.18743",
"r3d100012185" ;
rdfs:label "Birkbeck Research Data" ;
definition: "Repository allows all researchers at Birkbeck to upload data, and get DOI.Data in the Birkbeck Data Repository is stored on Arkivum server.This is a very secure storage space, which will allow our data to remain unchanged and accessible for many years after it is deposited." .
SCR:023140 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.48478" ;
rdfs:label "BRAIN Commons" ;
definition: "Scalable cloud-based platform for computational discovery designed for the brain health community.The BRAINCommons empowers the global research community by providing access to multi-model data, state-of-the-art tools and a secure interoperable system for data sharing." .
SCR:023141 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17616/R31NJN01",
"DOI:10.34721",
"r3d100013617" ;
rdfs:label "BioHeritage National Science Challenge Data Repository" ;
definition: "Data catalogue and repository for New Zealand's Biological Heritage National Science Challenge." .
SCR:023142 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.17043",
"DOI:10.17616/R3PP99",
"DOI:10.25504/FAIRsharing.3356e8",
"r3d100011699" ;
rdfs:label "Bolin Centre Database" ;
definition: "Provides open access to Climate and Earth System Data from scientists at the centre and their collaborators. Helps to make your data open, FAIR and visually appealing. Each dataset and source code in the Bolin Centre Database is assigned a unique DOI. This makes it easy to cite and find your data. If dataset has more than one version, each version will have its own DOI." .
SCR:023143 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.5443" ;
rdfs:label "Canadian Polar Data Network" ;
definition: "Repository of metadata and data that describes and provides access to diverse data sets generated by Arctic and Antarctic researchers.Metadata records follow ISO 19115 and Federal Geographic Data Committee standard formats to provide exchange with other data centres.Records cover wide range of disciplines from natural sciences and policy, to health and social sciences. The PDC Geospatial Search tool is available to the public and researchers alike and allows searching data using mapping interface and other parameters." .
SCR:023144 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.7301",
"DOI:10.17616/R3193B",
"r3d100011654" ;
rdfs:label "Brown Digital Repository" ;
definition: "Collection contains open and publicly funded data sets created by Brown University faculty and student researchers. Increasingly, publishers, and funders are requiring that protocols, data sets, metadata, and code underlying published research be retained and preserved, their locations cited within publications, and shared with other researchers and the public. The deposits here endeavor to be in line with FAIR Principles (Findable, Accessible, Interoperable, Reusable). If you would like to deposit data set into this collection for the purposes of citation/linking within publication and public dissemination, then please log in, zip up and upload your file, and request digital object identifier (DOI) for your data citation." .
SCR:023145 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyPI" ;
NIFRID:synonym "Python Package Index" ;
definition: "Software repository for Python programming language.Used to find and install software developed and shared by Python community." .
SCR:023146 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.5281/zenodo.7507492" ;
rdfs:label "IQAS" ;
NIFRID:synonym "Integrated Quality Assurance System MDL-LDA Component Resources",
"Integrated Quality Assurance System Modeling document labels using Latent Dirichlet Allocation Component Resources",
"IQAS:MDL-LDA Component Resources" ;
NIFRID:abbrev "iqas" ;
definition: "Modeling document labels using Latent Dirichlet Allocation is component tool under Integrated Quality Assurance System of Camarines Sur Polytechnic Colleges which categorizes text of particular document and use it for auto-tagging." .
SCR:023147 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Sartorius | IncuCyte S3 Live Cell Analysis System" ;
NIFRID:synonym "Incucyte Live-Cell Analysis System",
"Incucyte S3 Live-Cell Analysis Instrument",
"Incucyte S3 System" ;
definition: "System that automatically captures and analyzes images of living cells around-the-clock for days, weeks, or months, while cells remain undisturbed inside standard tissue culture incubator. Kinetic, image-based measurements. Used for cell monitoring and surveillance, cell health and viability, migration and invasion, phenotypic cell based assays." .
SCR:023148 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ERMA | Automatic blood cell counter PCE-210N" ;
NIFRID:synonym "Automatic blood cell counter PCE-210N" ;
definition: "Automatic cell counting instrument. Used to count blood cells." .
SCR:023149 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CycleViz" ;
definition: "Software Python package to visualize outputs of AmpliconArchitect in style of Circos plots. General circular visualizations of genomic regions. Used to visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos style images." .
SCR:023150 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AmpliconArchitect" ;
definition: "Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers." .
SCR:023151 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PafR" ;
NIFRID:synonym "Pairwise mApping Format' data in R" ;
definition: "Software package to read, manipulate and visualize 'Pairwise mApping Format' data in R." .
SCR:023152 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "synchCams" ;
definition: "Software toolbox for synchronized dual camera acquisition. Library for acquisition of synchronized dual camera video. Videos are saved with alternate acquisition of frames what ensures equal number of frames." .
SCR:023153 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openFPGALoader" ;
definition: "Universal utility for programming FPGAs. Compatible with many boards, cables and FPGA from major manufacturers (Xilinx, Altera/Intel, Lattice, Gowin, Efinix, Anlogic, Cologne Chip). Works on Linux, Windows and macOS." .
SCR:023154 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "clevRvis" ;
definition: "Software tool provides visualization techniques for clonal evolution. Available plots include shark plots as basic trees, showing phylogeny and optionally cancer cell fraction; dolphin plots as advanced visualization, showing phylogeny and development of CCFs over time; plaice plots as novel visualization, showing phylogeny, development of CCFs and development of remaining healthy alleles, influenced by bi-allelic events, over time. Provides algorithms for fully automatic interpolation of time points and estimation of therapy effect to approximate tumor's development in presence of few measured time points, as well as exploring alternative trees." .
SCR:023155 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lonza | 4D Nucleofector X Unit" ;
NIFRID:synonym "4D Nucleofector X Unit",
"4D Nucleofector X Unit Amaxa technology" ;
definition: "One of four functional modules of 4D-Nucleofector System. It supports Nucleofection of various cell numbers cells in different formats." .
SCR:023156 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Rad | Trans Blot Turbo system" ;
definition: "Rapid protein transfer apparatus that can transfer protein to membrane in 3 minutes.High performance western blotting transfer system designed to provide rapid transfers with high efficiency." .
SCR:023157 a NLX:63400,
owl:NamedIndividual ;
NIFRID:abbrev "RPG" .
SCR:023158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NicheNet" ;
definition: "Software tool as R implementation of NicheNet method to predict active ligand-target links between interacting cells. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest." .
SCR:023159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChIP-X Enrichment Analysis 3" ;
NIFRID:synonym "ChIP-X Enrichment Analysis Version 3 (ChEA3)" ;
NIFRID:abbrev "ChEA3" ;
definition: "Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries." .
SCR:023161 a owl:NamedIndividual ;
rdfs:label "Nikon | Eclipse TE2000 inverted microscope system" ;
NIFRID:synonym "Eclipse TE2000",
"Nikon Eclipse TE2000",
"Nikon Eclipse TE2000 inverted microscope" ;
NIFRID:abbrev "TE2000" ;
definition: "TE2000 was developed as full system with 3 models, the S, the U and the E. TE2000E is high precision Z-focus automated model that features 5 output ports and 5-way motorized light path changer. Used for advanced research that requires image capture in 3D, including confocal microscopy and deconvolution processing.TE2000U is universal model that comes with 4 output ports as standard, plus optional fifth user defined position, thereby providing unprecedented 5-way light path.The U model also features integrated magnification changer module providing 1x or 1.5x magnification to all ports." .
SCR:023163 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Princeton Instruments | Teledyne SpectraPro 2150 imaging spectrograph" ;
NIFRID:synonym "SpectraPro 2150",
"SpectraPro 2150 imaging spectrograph",
"SpectraPro 2150i" ;
definition: "150 mm focal length monochromator/spectrograph. It features astigmatism corrected optical system, dual indexable gratings and interchangeable grating turrets." .
SCR:023164 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_023167" ;
rdfs:label "Heka Elektronik | InstruTECH ITC-18" ;
definition: "Second generation low noise 16 bit computer interface from Instrutech Corporation. 16-bit Multi-Channel Data Acquisition Interface with PCI or USB host adapter." .
SCR:023165 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Andor | Luca S EMCCD camera" ;
definition: "Luca-S camera of single photon sensitive imaging Andor family scientific cameras with Electron Multiplying Charge Coupled Device detector, designed for most challenging low-light imaging applications." .
SCR:023166 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Andor | iXon Ultra EMCCD camera" ;
definition: "Scientific camera with EMCCD image sensor that is capable of detecting single photon events without image intensifier, achievable by way of unique electron multiplying structure built into the chip." .
SCR:023168 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Children's Hospital Association Pediatric Health Information System" ;
NIFRID:synonym "Pediatric Health Information System" ;
NIFRID:abbrev "PHIS" ;
definition: "Comparative database with clinical and resource utilization data for inpatient, ambulatory surgery, emergency department and observation unit encounters for more than 49 children's hospitals." .
SCR:023170 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurodegenerative Disease Knowledge Portal" ;
NIFRID:abbrev "NDKP" ;
definition: "Portal includes human genetic and functional genomic results generated via consortia based science focusing on neurodegenerative diseases such as ALS, Parkinson's disease, and Alzheimer's disease." .
SCR:023171 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Musculoskeletal Knowledge Portal" ;
NIFRID:abbrev "MSK-KP" ;
definition: "Portal enables browsing, searching, and analysis of human genetic and genomic information linked to musculoskeletal traits and diseases, while protecting the integrity and confidentiality of underlying data." .
SCR:023172 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:genomethreader" ;
rdfs:label "GenomeThreader" ;
definition: "Software tool to compute gene structure predictions.Gene structure predictions are calculated using similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments." .
SCR:023173 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openMINDS metadata framework" ;
NIFRID:synonym "open Metadata Initiative for Neuroscience Data Structures",
"openminds",
"openMINDS framework" ;
NIFRID:abbrev "openMINDS" ;
definition: "The openMINDS metadata framework comprises: schema specifications for multiple, interlocked metadata models for Linked Data, instance libraries for serviceable, well defined terms and constructs, as well as supportive tooling. openMINDS is developed as open source project by Open Metadata Initiative on GitHub. The framework is distributed over multiple, interlinked GitHub projects with one main GitHub repository for central access and maintenance." .
SCR:023174 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Google Forms" ;
definition: "Software for creating surveys and questionnaires." .
SCR:023175 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Intraclass Correlations for Quantifying Inter Rater Reliability" ;
NIFRID:synonym "Intraclass Correlations for Quantifying Inter-Rater Reliability" ;
NIFRID:abbrev "irrICC" ;
definition: "Software R package to calculate various intraclass correlation coefficients. Used to quantify inter-rater and intra-rater reliability." .
SCR:023176 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Computing Chance Corrected Agreement Coefficients" ;
NIFRID:synonym "Computing Chance-Corrected Agreement Coefficients" ;
NIFRID:abbrev "irrCAC" ;
definition: "Software R package to calculate various chance-corrected agreement coefficients among 2 or more raters. Among CAC coefficients covered are Cohen's kappa, Conger's kappa, Fleiss' kappa, Brennan-Prediger coefficient, Gwet's AC1/AC2 coefficients, and Krippendorff's alpha. Multiple sets of weights are proposed for computing weighted analyses." .
SCR:023177 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_557" ;
rdfs:label "University of Rochester Light Microscopy Resource Core Facility" ;
NIFRID:synonym "University of Rochester URMC Light Microscopy Resource",
"URMC Light Microscopy Resource" ;
NIFRID:abbrev "URMC" ;
definition: "Core for conventional brightfield microscopy and confocal microscopy." .
SCR:023178 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1669" ;
rdfs:label "University of Rochester Medical Center Biosafety Level 3 Core Facility" ;
NIFRID:synonym "Biosafety Level 3" ;
definition: "Core facility is available for use by any researcher at university whose work requires manipulation of biological agents that may cause serious or potentially lethal disease as result of exposure by inhalation route." .
SCR:023179 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1668" ;
rdfs:label "Penn State Hershey College of Medicine Comparative Medicine Imaging Core Facility" ;
NIFRID:synonym "Penn State Hershey College of Medicine Comparative Medicine Imaging" ;
definition: "Core provides equipment and expertise for bioluminescence and fluorescence imaging, in-vivo, full-body, 3D anatomical, functional and molecular imaging and MRI." .
SCR:023180 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Taiwan Bioresource Collection and Research Center" ;
NIFRID:synonym "Bioresource Collection and Research Center",
"Taiwan (BCRC)" ;
NIFRID:abbrev "BCRC" ;
definition: "Systematic and service oriented BioResource Center in Asia. Member of World Federation for Culture Collections from 1984 until now. BCRC is the first BRC certified by international organization of ISO quality system. Approved by Taiwan Biodiversity Information Facility." .
SCR:023181 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rio de Janeiro Cell Bank" ;
NIFRID:synonym "Banco Células do Rio de Janeiro (BCRJ)" ;
NIFRID:abbrev "BCRJ" ;
definition: "Collection as result of joint work of scientists, technicians and students from Federal University of Rio de Janeiro and Technical-Scientific Association Paul Ehrlich. Center of reference and excellence in cell culture in Brazil and in our continent. Collection of human and animal cells that operates as service provider in Brazil and is the largest in South America. " .
SCR:023182 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Collection of Cell Lines in Veterinary Medicine" ;
NIFRID:abbrev "CCLV" ;
definition: "Generates, characterises and collects cell lines which are of interest for veterinary research and diagnostics. Collection includes cell lines of farm animals such as cattle, pig, horse, sheep, goat and poultry and other mammals, birds, reptiles, fishes and insects (70 species).Authentication and quality-control tests (tests for contamination with mycoplasms, bacteria, BVDV) of the cultures are done routinely.Cell cultures are provided to scientists of the Friedrich-Loeffler-Institute and other non-commercial institutions worldwide after consultation of a scientific staff member of the CCLV." .
SCR:023183 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Lines Service" ;
NIFRID:abbrev "CLS" ;
definition: "Independent cell repository with rigorous monitoring, quality control and cell authentications to ensure that your cells are free of contaminations and with genuine genetic profile. " .
SCR:023184 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:iclc" ;
rdfs:label " Interlab Cell Line Collection " ;
NIFRID:abbrev "ICLC" ;
definition: "Was established in 1994 as core facility of National Institute of Cancer Research. Supplies human and animal cell lines; Short Tandem Repeat (STR) profiling of human cell lines; quality control service; mycoplasma detection and eradication service; safe deposit service and patent deposit service of cell lines and hybridomas. The catalogue of services is on-line, and the cell lines are distributed all over the world. Search allows to query catalogue on the basis of any word that may be included in the description of cell lines, including both encoded terms and free text information." .
SCR:023185 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IZSLER Biobank" ;
NIFRID:synonym "Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna Biobank",
"IZLER Biobank",
"IZSLER Biobank of Veterinary Resources" ;
NIFRID:abbrev "IZSLER" ;
definition: "Provides maintaining and managing the largest veterinary biobank facility in Italy for the storage of biological resources. IZSLER Biobank of Veterinary Resources include mainly bacteria and viruses from different animal species isolated during the routine IZSLER diagnostic activity, carried out on biological samples from farm animals, pets and wildlife and from food and feed. Biobank includes more than 600 cell lines from human and animal origin. All the materials enrolled in our collection are submitted to different cultural and molecular biology control tests in order to evaluate their characteristics, purity and identity. IZSLER laboratories, that supply biological resources to IBVR, use testing methods performed according to UNI EN ISO/IEC 17025 quality system." .
SCR:023186 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Resource Information Network" ;
NIFRID:abbrev "RIN" ;
definition: "Integrated data set and analytics platform combining Research Resource Identifiers (RRIDs), text mining and data aggregation." .
SCR:023187 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Japanese Collection of Research Bioresources Cell Bank" ;
NIFRID:synonym "Japanese Collection of Research Bioresources (JCRB) Cell Bank" ;
NIFRID:abbrev "JCRB Cell Bank" ;
definition: "Collection of various human and animal culture cells including cancer and genetically modified cells. Cell resources are distributed to researchers across Japan and around the world. These cells are comprehensively qualified by testing microbial contamination, virus contamination and cross culture contamination. Some cells are characterized by karyotyping and/or cell surface markers. In collaboration with other major cell banks in the world, we are developing methods for cell culturing and quality control in order to support fundamental research on medical of pharmaceutical sciences." .
SCR:023188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kunming Wild Animal Cell Bank" ;
NIFRID:synonym "Kunming Cell Bank",
"Kunming Wild Animal Cell Bank of the Chinese Academy of Sciences" ;
definition: "Cell Bank provides high quality resources and services including cell lines/tissues/DNA samples; cell culture training/trouble-shooting; cell culture/genetic research equipment; cell line karyotype analysis; STR/mycoplasma contamination detection; chromosome painting; cell line preservation.Cell Bank is branch of National Platform of Experimental Cell Resources for Science and Technology, Wildlife Resource Bank of the Chinese Academy of Sciences, the China Germplasm Bank of Wild Species, and also affiliated with Institute’s State Key Laboratory of Genetic Resources and Evolution. " .
SCR:023189 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Korean Cell Line Bank" ;
NIFRID:abbrev "KCLB" ;
definition: "Bank is located at the Cancer Research Institute of the Seoul National University College of Medicine. Collects cell lines from diverse laboratories but also continually develops new cell lines. We as well distribute our cell lines and provide researchers with detailed information about the cell lines." .
SCR:023190 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Cancer Institute Developmental Therapeutics Program " ;
NIFRID:abbrev "NCI-DTP" ;
definition: "DTP supports number of Repositories for the acquisition, storage and distribution of chemical, and biological samples and standards to researchers worldwide. In many cases there is no, or only nominal fee for samples." .
SCR:023191 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " NIH AIDS Reagent Program " ;
NIFRID:abbrev "NIH-ARP" ;
definition: "NIH HIV Reagent Program has been managed under contract by American Type Culture Collection (ATCC) since 2020. ATCC shall maintain the NIH HIV Reagent Program through identification, acquisition, production, receipt, storage, maintenance, distribution and disposal of biological and chemical research organisms and materials for HIV and other infectious diseases for use in basic and translational research." .
SCR:023192 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Tohoku University Cell Resource Center for Biomedical Research Cell Bank" ;
NIFRID:synonym "Tohoku University Cell Bank" ;
NIFRID:abbrev "TKG" ;
definition: "Cell Resource Center for Biomedical Research, Cell Bank is the collection, establishment, quality control, distribution of useful cell lines, and construction of database for researchers. The cell lines include transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells. Available cell line are listed in The Cell Line Catalog." .
SCR:023193 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Confidence in network meta analysis" ;
NIFRID:synonym "Confidence in Network Meta-Analysis" ;
NIFRID:abbrev "CINeMA" ;
definition: "Web application that simplifies evaluation of confidence in findings from network meta analysis." .
SCR:023194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AMSTAR" ;
NIFRID:synonym "A measurement tool to assess systematic reviews" ;
definition: "Guide tool to assess methodological quality of systematic reviews. Used to evaluate systematic reviews of randomised trials. AMSTAR 2 enables more detailed assessment of systematic reviews that include randomised or non-randomised studies of healthcare interventions, or both." .
SCR:023195 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fluidigm | Hyperion Imaging System" ;
NIFRID:synonym "Hyperion™ Imaging System" ;
definition: "Imaging system enables comprehensive analysis of cellular phenotypes. Allows access to single cell insights. This includes deeper understanding of intricate spatial relationships of cells, pathways and phenotypes in tissue microenvironment." .
SCR:023196 a NLX:63400,
owl:NamedIndividual ;
definition: "Software toolkit that enables real-time basecalling and several post-processing features that works on Oxford Nanopore Technologies sequencing platforms. Data processing toolkit that contains Oxford Nanopore Technologies basecalling algorithms, and several bioinformatic post-processing features. Provided as binaries to run on Windows, OS X and Linux platforms, as well as being integrated with MinKNOW, Oxford Nanopore device control software." .
SCR:023197 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1670" ;
rdfs:label "University of Rochester Medical Center Cold Storage Core Facility" ;
NIFRID:synonym "Cold Storage Core",
"University of Rochester Medical Center Cold Storage Core" ;
definition: "Provides controlled environment designed for long term storage of clinical/research materials in -20C or -80C freezers and in liquid nitrogen freezers." .
SCR:023198 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1671" ;
rdfs:label "Karolinska Institute Live Cell Imaging Core Facility" ;
NIFRID:synonym "Live Cell Imaging core facility" ;
definition: "Light microscopy facility. Offers microscopes and training to image cell and tissues, live or fixed, BSL1/BSL2." .
SCR:023199 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Falcon" ;
definition: "Open source software tool for closed loop neuroscientific experiments capable of sub-millisecond response latency over high-rate streaming data acquired from high-count multi-electrode arrays. Used for processing and controlling closed-loop neuroscience data." .
SCR:023200 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Training Infrastructure as a Service " ;
NIFRID:synonym "tiaas",
"tiaas2" ;
NIFRID:abbrev "TIaaS" ;
definition: "Web service that works alongside the Galaxy SciWMS to enable dynamic training infrastructure." .
SCR:023201 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TAMPA" ;
NIFRID:synonym "TAxonoMic Profiling Analysis" ;
definition: "Software tool to interpret and interact with taxonomic profiles produced by different taxonomic profiler methods beyond standard metrics used by scientific community. Interpretable analysis and visualization of metagenomics based taxon abundance profiles." .
SCR:023202 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sapporo service" ;
NIFRID:synonym "Sapporo-service" ;
definition: "Software for standard implementation conforming to Global Alliance for Genomics and Health Workflow Execution Service API specification." .
SCR:023203 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sapporo web" ;
NIFRID:synonym "Sapporo-web" ;
definition: "Web application for managing and executing Workflow Execution Service (WES) services." .
SCR:023204 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yevis cli" ;
NIFRID:synonym "Yevis-cli" ;
definition: "Software CLI tool to support building and maintaining Yevis workflow registry." .
SCR:023205 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yevis web" ;
NIFRID:synonym "Yevis-web" ;
definition: "Web application for browsing Yevis workflow registry." .
SCR:023206 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tonkaz" ;
definition: "Software CLI tool to verify workflow reproducibility." .
SCR:023207 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011049" ;
rdfs:label "STOREDB" ;
NIFRID:synonym "STORE" ;
definition: "Platform for archiving and sharing of primary data outputs from research on low dose radiation. Provides directory of bioresources and databases containing information and materials that investigators are willing to share. Supports creation of low dose radiation research commons." .
SCR:023208 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TEtranscripts" ;
definition: "Software package for including transposable elements in differential enrichment analysis of sequencing datasets. Used for including transposable elements in differential expression analysis of RNA-seq datasets. RNAseq TE quantification tool." .
SCR:023209 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BD Biosciences | FACSMelody Cell Sorter" ;
NIFRID:synonym "BD FACS Melody Cell Sorter",
"BD FACSMelody™ Cell Sorter" ;
definition: "Cell sorter offers advanced automation technology with BD FACSChorus software and guides you through entire cell sorting process with its intuitive interface, on-screen instructions and tips and simple-to-read reports." .
SCR:023210 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1675" ;
rdfs:label "Van Andel Institute Cryo-Electron Microscopy Core Facility" ;
NIFRID:synonym "VAI Cryo-EM Core",
"Van Andel Institute VAI Cryo-EM Core" ;
definition: "Facility encompasses cryo-electron microscopes (Krios, Arctica), which are supported by expert staff and high performance computing cluster with extensive cloud capabilities.Provides wide range of cost effective and efficient biological EM services." .
SCR:023211 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1673" ;
rdfs:label "Van Andel Institute Vivarium Core Facility" ;
NIFRID:synonym "VAI Vivarium",
"Van Andel Institute VAI Vivarium" ;
definition: "Core provides and supports gold standard of high quality mouse, rat and zebrafish modeling services for VAI investigators, collaborators and greater research community.Facility includes high containment barrier. All procedures are conducted according to the National Institutes of Health Guide for the Care and Use of Laboratory Animals. The Institute is accredited at the highest standard of care through the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) International." .
SCR:023212 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1672" ;
rdfs:label "Johns Hopkins Medical Institute Clinical and Translational Research Laboratory Core Facility" ;
NIFRID:synonym "JHMI-ICTR Research Laboratory Core",
"Johns Hopkins Medical Institution JHMI-ICTR Research Laboratory Core" ;
definition: "Core performs high throughput assays for determination of proteins, peptides, hormones and other biochemical markers in support of preclinical and clinical research studies. Laboratory has equipment and capacity to perform standard immunoassays as well as multiplexed ELISAs. Provides standardized sample handling that upholds high quality control. Supports reduced investigator cost through batch analysis of samples and direct manufacturer pricing." .
SCR:023213 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FunGAP" ;
NIFRID:synonym "Fungal Genome Annotation Pipeline" ;
definition: "Software tool to predict protein coding genes in fungal genome assembly. Performs gene prediction on given genome assembly and RNA-seq reads. Runs multiple gene predictors, evaluates all predicted genes, and assembles gene models that are highly supported by homology to known sequences." .
SCR:023214 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " ROD-WGAN-and-ROD-WGAN-hybird" ;
definition: "Stable models to generate tertiary structures that mimic natural features including backbone, local and distal characteristics, found in real proteins." .
SCR:023215 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bamtofastq" ;
definition: "Software tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis." .
SCR:023216 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "subset bam" ;
NIFRID:synonym "subset-bam" ;
definition: "Software tool to subset 10x Genomics BAM file based on tag, most commonly cell barcode tag.Takes 10x Genomics BAM file, CSV file defining subset of cells you want to isolate, and produces new BAM file with only alignments associated with those cells.Subsets BAM files output from CellRanger by tag which is usually cell barcode." .
SCR:023217 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Asian Mouse Mutagenesis Resource Association" ;
NIFRID:abbrev "AMMRA" ;
definition: "Mouse genetics and laboratory animal resources in the Asia Pacific. Collaborative group of development, archiving/distribution, coordination of phenotyping and informatics of mutant mice in Asia. Facilitates access to mouse resources in Asia for use of mouse models for understanding genome function and improvement of human health." .
SCR:023218 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Meadows" ;
definition: "Online behavioral experiment platform." .
SCR:023219 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Oxford |Optronix GelCount" ;
NIFRID:synonym "GelCount" ;
definition: "Mammalian cell colony, spheroid and organoid counter. PC software operated colony counter that automates detection, counting and analysis of mammalian cell colonies in multi-well plates, Petri dishes and T25 flasks." .
SCR:023220 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CHISEL" ;
NIFRID:synonym "Copy-number Haplotype Inference in Single-cell by Evolutionary Links" ;
definition: "Software tool to infer allele and haplotype specific copy numbers in individual cells from low coverage single cell DNA sequencing data. Integrates weak allelic signals across individual cells, powering strength of single cell sequencing technologies to overcome weakness. Includes global clustering of RDRs and BAFs, and rigorous model selection procedure for inferring genome ploidy that improves both inference of allele specific and total copy numbers." .
SCR:023221 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "10x Genomics Cellranger DNA" ;
NIFRID:synonym "10x Genomics Cellranger DNA software",
"10x Genomics Cellranger software",
"Cell Ranger DNA" ;
definition: "Software analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation, and compare heterogeneity among cells. Used in processing of single cell DNA sequencing performed on 10x Chromium platform." .
SCR:023222 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TF-Prioritizer" ;
definition: "Software pipeline for analysis of nfcore chromatine accessibility data including ChIP-Seq, DNAse-Seq or ATAC-Seq and nfcore RNA-seq count data. Performs DESeq2, TEPIC and DYNAMITE including all preprocessing and postprocessing steps necessary to transform data and provides plots for deep analysis of data." .
SCR:023223 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "abSENSE" ;
definition: "Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally." .
SCR:023224 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Google Earth Engine" ;
NIFRID:synonym "Earth Engine" ;
NIFRID:abbrev "GEE" ;
definition: "Web application as public data catalog, compute infrastructure, geospatial APIs and interactive app server. Geospatial processing service." .
SCR:023225 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UpSetPlot" ;
definition: "Software Python implementation of UpSet plots to visualize set overlaps." .
SCR:023226 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Oracle Crystal Ball" ;
definition: "Software spreadsheet based application for risk measurement and reporting, Monte Carlo simulation, time series forecasting, and optimization.Provides realistic and accessible way of modeling uncertainty, enabling you to measure and report on risk inherent in your key metrics." .
SCR:023227 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LI-COR | Odyssey Fc Imaging System" ;
definition: "System used to image and analyze Western blots. Odyssey Fc imager has been discontinued." .
SCR:023228 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2462" ;
rdfs:label "Stanford Graduate School of Business Library" ;
NIFRID:synonym "Stanford Business Library",
"Stanford GSB Library" ;
NIFRID:abbrev "GSB-Library" ;
definition: "Provides resources and services to support business related research and teaching at Stanford University. As part of GSB Research Hub, helps foster scholarship, teaching, and innovation by committing to access, dissemination, creation, and preservation of information and knowledge." .
SCR:023229 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2465" ;
rdfs:label "Stanford System Prototyping Core Facility" ;
NIFRID:synonym "System Prototyping Facility" ;
NIFRID:abbrev "SNF-SPF",
"SPF" ;
definition: "Electronics Shop where researchers can access and share expertise to build specialized electronics. Offers support to electronic sub-system design for researchers across campus in departments of Physics, Applied Physics, Electrical Engineering, Psychology, Psychiatry and Behavioral Sciences and Bioengineering.Provides expertise from independently using tools to requesting turnkey solution." .
SCR:023230 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2466" ;
rdfs:label "Stanford Nano Shared Core Facility" ;
NIFRID:synonym "Stanford Nano Shared Facilities" ;
NIFRID:abbrev "SNSF" ;
definition: "Group of service centers (Nanofabrication, Electron & Ion Microscopy, X-ray & Surface Analysis and Soft & Hybrid Materials) that include Stanford Nanocharacterization Laboratory, Nanopatterning Cleanroom, Ginzton Microfab, and Soft and Hybrid Materials Facility. Core provides shared scientific instrumentation, laboratory facilities, and expert staff support." .
SCR:023231 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2463" ;
rdfs:label "Stanford Graduate School of Business Behavioral Lab Core Facility" ;
NIFRID:synonym "Behavioral Lab",
"GSB Behavioral Lab",
"Stanford Graduate School of Business Behavioral Lab" ;
NIFRID:abbrev "GSB B-Lab" ;
definition: "Interdisciplinary laboratory designed for study of human subjects.Lab resources are available to all Stanford GSB faculty and PhD students to support research that uses human participants, whether your focus is organizational behavior, behavioral marketing, political economics, or behavioral economics.Assists with research by programming study, posting study to one or more of the available subject pools, paying participants, running participants through experiments in the lab, or creating study materials.Engages with faculty members and doctoral students in preparing and carrying out human subjects research, both in-person laboratory experiments and online survey research.Provides expert consultation on behavioral experiments, and implementations of technology in behavioral research, such as eye-tracking, psychophysiology, and other specialized technology used in research with human subjects." .
SCR:023232 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2468" ;
rdfs:label "Stanford Sarafan Medicinal Chemistry Knowledge Center Core Facility" ;
NIFRID:synonym "ChEM-H Knowledge Centers Medicinal Chemistry",
"Medicinal Chemistry Knowledge Center (MCKC)" ;
NIFRID:abbrev "MCKC" ;
definition: "Core for drug discovery and prototyping. Provides chemical probes for biological pathways and supports small molecule custom synthesis.Provides expertise in medicinal chemistry to biologists and clinicians at Stanford. Expertise in each step of drug development process, including hit generation, drug design and optimization, and clinical selection. Provides instrumentation to support synthesis, purification and analysis of small molecules." .
SCR:023233 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2471" ;
rdfs:label "Stanford Sarafan Macromolecular Structure Knowledge Center Core Facility" ;
NIFRID:synonym "Macromolecular Structure Knowledge Center" ;
NIFRID:abbrev "MSKC" ;
definition: "Service center and teaching lab focusing on molecular structural-functional studies. Jointly established by Sarafan ChEM-H, School of Engineering and SLAC National Accelerator Laboratory. Provides Stanford researchers with expertise, training and instruments for techniques in spectroscopy, bioimaging, crystallography, and scattering and diffraction." .
SCR:023234 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2464" ;
rdfs:label "Stanford Nanofabrication Core Facility" ;
NIFRID:synonym "Stanford Nanofabrication Facility" ;
NIFRID:abbrev "SNF" ;
definition: "One of four labs that are part of nano@stanford, under NSF National Nanotechnology Coordinated Infrastructure program. SNF includes cleanroom housing tools for device fabrication, satellite labs supporting Metal Organic Chemical Vapor Deposition,Experimental Fabrication methods and electronics shop for Systems Prototyping. SNF supports researchers in applications ranging from medicine and biology to fundamental physics and astronomy." .
SCR:023236 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2473" ;
rdfs:label "Stanford Sarafan Metabolomics Knowledge Center Core Facility" ;
NIFRID:synonym "Metabolomics Knowledge Center" ;
NIFRID:abbrev "MKC" ;
definition: "Provides scientific expertise and instrumentation for measurement of small molecules such as metabolites and lipids to ChEM-H and Stanford communities. Leverages expertise in mass spectrometry and allied techniques to understand biology of small molecules both metabolites and xenobiotics and to apply that understanding to advances in human health." .
SCR:023237 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2474" ;
rdfs:label "Stanford Sarafan Protein Engineering Knowledge Center Core Facility" ;
NIFRID:synonym "Protein Engineering Knowledge Center" ;
NIFRID:abbrev "PEKC" ;
definition: "MSKC is main gateway for Stanford faculty and students interested to study biological molecules using SLAC X-ray facilities and other major bioimaging facilities." .
SCR:023238 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford Sarafan Chemistry, Engineering and Medicine for Human Health Knowledge Centers Core Facility" ;
NIFRID:synonym "Chemistry",
"Engineering & Medicine for Human Health (ChEM-H) Knowledge Centers",
"Knowledge Centers at Sarafan ChEM-H" ;
NIFRID:abbrev "CHEM-H" ;
definition: "Shared resource to provide instrumentation and scientific expertise to Stanford researchers.Each Knowledge Center is organized around specific scientific area and offers services to the research community. Services, advice, training and instrument access, include area in High-Throughput Screening, Medicinal Chemistry, Crystallography, Cryo-EM, Metabolomics, Protein engineering, Protein expression." .
SCR:023239 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FAIR Data Station" ;
NIFRID:abbrev "FAIR-DS" ;
definition: "Software metadata ingestion platform that helps to improve quality of metadata. Station allows users to record meta-data according to minimum information standards thereby ensuring FAIR scientific data management from the start." .
SCR:023240 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPM Cluster Size Threshold estimation" ;
definition: "Software tool as routine for given estimated SPM to find cluster extent threshold, such that only significant at defined corrected p-value clusters are displayed and listed." .
SCR:023241 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MaAsLin2" ;
definition: "SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features." .
SCR:023242 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Regression Modeling Strategies" ;
NIFRID:abbrev "rms" ;
definition: "Software R package as collection of functions that assist with streamline modeling. Works with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression." .
SCR:023243 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_808" ;
rdfs:label "Washington University School of Medicine Genome Engineering and Stem Cell Center Core Facility" ;
NIFRID:synonym "Genome Engineering & Stem Cell Center (GESC@MGI)",
"Washington University School of Medicine Genome Engineering & Stem Cell Center (GESC@MGI)" ;
definition: "Provides support with technologies for cell and animal model needs. Services are ranging from CRISPR reagents with or without validation, to cancer/iPS cell line modification or animal model creation. Works closely with mouse cores from design, reagent validation to genotyping, process improvement and troubleshooting, when necessary. Provides next-generation sequencing (NGS) based human cell authentication and NGS-based genotyping services and general molecular biology assistance. Offers to culture, bank and store primary fibroblasts and renal epithelial cells from patient samples for investigators, and iPSC reprogramming service is provided from fibroblasts, RECs as well as peripheral blood mononuclear cells. Provides differentiation services on growing list of cell types." .
SCR:023244 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1469" ;
rdfs:label "Penn State College of Medicine Biomolecular NMR Core Facility" ;
NIFRID:synonym "Penn State College of Medicine Penn State COM Biomolecular NMR",
"Penn State COM Biomolecular NMR" ;
definition: "Provides services for multiple modern NMR applications, including structure elucidation of small molecules, triple resonance experiments of biomolecules, fragment-based drug discovery, metabolomic and tissue analyses." .
SCR:023245 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1677" ;
rdfs:label "University of Colorado Anschutz Medical Campus Gnotobiotic Core Facility" ;
NIFRID:synonym "CU Anschutz Gnotobiotic Core",
"University of Colorado Anschutz Medical Campus CU Anschutz Gnotobiotic Core" ;
definition: "Provides germ free and gnotobiotic mice, space in which investigators can complete their own studies or hire core to complete experimental manipulations.Facility includes 12 large soft sided vinyl isolators for breeding and 8 small soft sided vinyl isolators for experiments. There is option between using Allentown positive pressure racks and static cage for experimental use." .
SCR:023246 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1678" ;
rdfs:label "University of North Carolina at Chapel Hill Human Pluripotent Cell Core Facility" ;
NIFRID:synonym "Human Pluripotent Cell Core",
"University of North Carolina at Chapel Hill Human Pluripotent Cell Core" ;
definition: "Provides services to conduct basic as well as translational research using human induced pluripotent cells. Offers Reprogramming, Genome editing and directed cell differentiation." .
SCR:023247 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1679" ;
rdfs:label "Oslo University Norwegian Human Pluripotent Stem Cells Core Facility" ;
NIFRID:synonym "Core Facility for Human Pluripotent Stem Cells",
"Norwegian Core Facility for Human Pluripotent Stem Cells" ;
definition: "Core assists with production, characterization and differentiation of human pluripotent stem cells. Offers services related to research on human ES and iPS cells. Provides reprogramming of iPS cell lines from patients and healthy donors, for example for in vitro disease modeling. Offers already established human ES cell lines and large bank of human iPS cell lines established through ongoing REK-approved projects. Provides ES and iPS cell characterization services, and training in the culture and maintenance of human ES and iPS cells." .
SCR:023248 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2475" ;
rdfs:label "Stanford Vincent V.C. Woo Sandbox Laboratory Core Facility" ;
NIFRID:synonym "Stanford Vincent V.C. Woo Sandbox Laboratory (SBCL)",
"Vincent V.C. Woo Sandbox Laboratory (SBCL)" ;
NIFRID:abbrev "SBCL" ;
definition: "Provides space and equipment for collaborative pilot projects between engineers and neuroscientists, workshops, training classes and product demonstrations as requested by members of Wu Tsai Neuro. Facility provides tissue culture suite with two biosafety cabinets, CO2 incubators, centrifuge and fluorescent microscope, in vivo procedure suite to allow animal surgeries, four curtained electrophysiological rig/microscope areas, two microscope rooms, -20C and -80C freezers and 4C cabinets for temporary sample storage." .
SCR:023249 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2476" ;
rdfs:label "Stanford Behavioral and Functional Neuroscience Laboratory Core Facility" ;
NIFRID:synonym "Behavioral and Functional Neuroscience Laboratory (BFNL)",
"Stanford Behavioral and Functional Neuroscience Laboratory (BFNL)" ;
NIFRID:abbrev "BFNL" ;
definition: "Laboratory at Wu Tsai Neursciences Institute provides preclinical discovery platform for central nervous system target validation in preclinical in vivo and in vitro models. Neurobehavioral assessment tools in CNS disease models provide platform for screening and profiling of experimental therapeutics and genetic rodent models. Used to support understanding of human CNS disorders and development of therapeutic interventions." .
SCR:023250 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2477" ;
rdfs:label "Stanford Neuroscience Gene Vector and Virus Core Facility" ;
NIFRID:synonym "Neuroscience Gene Vector and Virus Core (GVVC)",
"Stanford Neuroscience Gene Vector and Virus Core" ;
NIFRID:abbrev "GVVC" ;
definition: "Core centralizes process of producing and distributing viral vectors and cDNA plasmids." .
SCR:023251 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2479" ;
rdfs:label "Stanford Visualization Laboratory Core Facility" ;
NIFRID:synonym "Stanford Visualization Laboratory",
"Visualization Laboratory" ;
NIFRID:abbrev "VIZ" ;
definition: "Used to explore new visualization technologies related to study of brain.Provides equipment and expertiese to help with project setup and planning. Hosts adaptive optics system that uses optical principles originally developed for visualizing distant stars to enable high resolution imaging of retina in human subjects." .
SCR:023252 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2480" ;
rdfs:label "Stanford Geochronology Cluster Core Facility" ;
NIFRID:synonym "Geochronology Cluster",
"Stanford Geochronology Cluster" ;
NIFRID:abbrev "GCC" ;
definition: "Core for comprehensive examination of evolution of Earth's crust using geochronologic approaches. Provides spectrum of analytical facilities that are all housed within School of Earth, Energy and Environmental Sciences.Provides data to many disciplines throughout geosciences, including tectonics, geodynamics, petrology, geochemistry, geomorphology, sedimentology, stratigraphy, paleontology, and paleoclimatology." .
SCR:023253 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2481" ;
rdfs:label "Stanford Stable Isotope Biogeochemistry Laboratory Core Facility" ;
NIFRID:synonym "Stable Isotope Biogeochemistry Laboratory",
"Stanford Stable Isotope Biogeochemistry Laboratory" ;
NIFRID:abbrev "SIBL" ;
definition: "Stable Isotope Biogeochemistry Laboratory at Stanford University's School of Earth Sciences provides analytical facilities and technical expertise to members of Stanford community who need to determine stable isotope ratios of variety of organic and inorganic materials from both terrestrial and marine environments." .
SCR:023254 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2478" ;
rdfs:label "Stanford Neuroscience Preclinical Imaging Laboratory Core Facility" ;
NIFRID:synonym "Neuroscience Preclinical Imaging Laboratory",
"Stanford Neuroscience Preclinical Imaging Laboratory" ;
NIFRID:abbrev "NPIL" ;
definition: "Provides preclinical Magnetic Resonance Imaging technology and expertise to Stanford community. Offers range of support from full project to independent user operation and training." .
SCR:023255 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2484" ;
rdfs:label "Stanford Environmental Measurements Core Facility" ;
NIFRID:synonym "Environmental Measurements Facility",
"Stanford Environmental Measurements Facility" ;
NIFRID:abbrev "EMF" ;
definition: "Provides instruments for solid, aquouse and gas sample analyses, quantitative analysis, technical expertise to members of Stanford community." .
SCR:023256 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2482" ;
rdfs:label "Stanford Microchemical Analysis Core Facility" ;
NIFRID:synonym "Microchemical Analysis Facility",
"Stanford Microchemical Analysis Facility" ;
NIFRID:abbrev "MAF" ;
definition: "Facility is equipped with JEOL JXA-8230 SuperProbe electron microprobe. Electron microprobe measures elemental compositions of solid samples by detecting the X-rays emitted on excitation by focused electron beam, down to spatial resolution of about 1 micron. All elements heavier than beryllium can be detected, at concentrations as low as 10s of ppm. Highly quantitative analyses are made using 5 wavelength dispersive X-ray spectrometers (WDS) with calibrations based on known standard materials. Compositional images (maps) can readily be obtained with backscattered electrons (sensitive primarily to mean atomic number), or with WDS or EDS X-ray data. The instrument is adjacent to the Stanford Nanocharacterization Laboratory (SNL), at the west end of the first floor of the McCullough Building." .
SCR:023257 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_520" ;
rdfs:label "Stanford Neuroscience Microscopy Service Core Facility" ;
NIFRID:synonym "Neuroscience Microscopy Service",
"Stanford Neuroscience Microscopy Service" ;
NIFRID:abbrev "NMS" ;
definition: "Provides microscopy expertise and access to high resolution, state-of-the-art imaging technologies to Stanford University and surrounding academic and biotech researchers. Core provides training, design, implementation, and analysis assistance." .
SCR:023258 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2485" ;
rdfs:label "Stanford Doerr School of Sustainability Sample Preparation Laboratory Core Facility" ;
NIFRID:synonym "Sample Preparation Laboratory",
"SDSS Sample Preparation Laboratory",
"Stanford Doerr School of Sustainability Sample Preparation Laboratory" ;
NIFRID:abbrev "SPL" ;
definition: "Provides guidance, access, and hands-on training for rock preparation, equipment uses, and mineral separation techniques. The most common uses are Powdering samples for geochemical or isotopic analysis;Cutting/drilling/coring rocks for geophysical analysis or generating thin section billets;Separation of zircon and apatite from quartz and feldspar;Soil and/or sediment sieving." .
SCR:023259 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2483" ;
rdfs:label "Stanford SIGMA Shared Facility" ;
NIFRID:synonym "SIGMA Facility",
"Stanford SIGMA Facility" ;
NIFRID:abbrev "SIGMA" ;
definition: "Shared analytical facility specialized in areas of radiogenic isotope geochemistry, non-traditional stable isotope geochemistry, and low blank concentration determinations of natural and engineered materials. Provided equipment includes triple-quad ICP-MS (Agilent 8900) with laser ablation intake system (AS RESOlution laser system), multi-collector ICP-MS (Neptune XT), and specially designed Picotrace metal-free low particulate clean laboratory. Produces high quality isotopic and trace element data. Offers training." .
SCR:023260 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nationwide Children’s Hospital Abigail Wexner Research Institute Biopathology Center Core Facility" ;
NIFRID:abbrev "CHTN" ;
definition: "Provides services related to biospecimen procurement, banking, processing, and distribution. Housed biospecimen collections are from biorepositories of National Cancer Institute funded Children’s Oncology Group, NRG Oncology-Columbus (formerly the GOG Tissue Bank), SWOG, Pediatric Division of Cooperative Human Tissue Network, and Biospecimen Core Resource of Center for Cancer Genomics, as well as numerous biospecimen collections sponsored by funded NCH investigators. Cooperative Human Tissue Network is one of six institutions funded by National Cancer Institutes to access to remnant human tissues for biomedical researchers throughout the United States and Canada. Offers expertise in tissue preparation and preservation to meet the research needs of basic and applied scientists." .
SCR:023261 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Shengqiang Technology |SQS-40P slide scanning imaging system" ;
definition: "Slide scanning image analysis system independently developed and designed by Shengqiang Technology has flexible objective lens configuration, automatic slide loading, and super-large-size scanning. Can seamlessly stitch tens of thousands of pathological slice pictures into complete slice, and intelligently generate full-field digital slide can digitize, complete and permanently store slide information. Experts can browse from a macro image, and then place it at any position and any magnification to observe the details of the slice ." .
SCR:023262 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Roche | Cobas 6000 analyzer" ;
NIFRID:synonym "COBAS 6000 analyzer automated system",
"Roche COBAS 6000 analyzer automated system",
"Roche/Hitachi Cobas 6000 analyzer series" ;
definition: "Roche/Hitachi Cobas 6000 analyzer series is fully automated, random-access, software- controlled system for immunoassay and photometric analyses intended for qualitative and quantitative in vitro determinations of wide variety of tests. Cobas 6000 modular analyzer is composed of core unit and combination of up to 3 analytical modules to best suit your needs." .
SCR:023263 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1682" ;
rdfs:label "Texas A and M University Rodent Preclinical Phenotyping Core Facility" ;
NIFRID:synonym "Rodent Preclinical Phenotyping Core",
"Texas A&M University Rodent Preclinical Phenotyping Core" ;
definition: "Core houses various instruments to measure and quantify mouse and rat physiology and behavior. Offers equipment to help expedite comprehensive research in many fields, including Behavior, Cardiovascular, Cancer, Pathological, Metabolic, Skeletomuscular, and Histology." .
SCR:023264 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1683" ;
rdfs:label "Emory University Emory Stem Cell Core Facility" ;
NIFRID:synonym "Emory Stem Cell Core",
"Emory University Emory Stem Cell Core" ;
NIFRID:abbrev "ESCC" ;
definition: "Core is supported by Georgia Clinical and Translational Science Alliance and Emory University School of Medicine. One of Emory Integrated Core Facilities (EICF). Offers services for generating induced pluripotent stem cells from human somatic cells for research." .
SCR:023265 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GRIMER" ;
definition: "Software tool to perform analysis of microbiome studies and generates portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection." .
SCR:023266 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eppendorf | Mastercycler nexus PCR Thermal Cycler" ;
definition: "Thermal cycler conduct PCR runs with range of standard vessel types, from 0.2 mL tubes to 96 well plates using single 96-well aluminum block. Can accommodate 96-well PCR plates, 0.2 mL PCR tubes, 0.2 mL PCR tube strips, and 0.5 mL PCR tubes.Mastercycler nexus cycler can email you when PCR run is complete." .
SCR:023267 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Sartorius | Octet BLI systems" ;
NIFRID:synonym "Octet BLI systems",
"Octet BLI systems with Octet Analysis Studio" ;
definition: "Octet BLI systems enable real-time, label-free analysis for determination of kinetics, affinity and antibody/protein quantitation. Includes Octet Analysis Studio for analysis of assays measuring kinetics and affinity values for drug-target binding and high-throughput kinetic screening for lead identification. Typical applications include kinetic analysis of protein-protein, protein-small molecules, antibody-antigen, antibody-VLP, antibody-Fc gamma receptors, including antibody-neonatal receptor (FcRn) interactions. Additional applications supported include lot release and stability analysis of drug molecules based on binding kinetics and affinity." .
SCR:023268 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:curves" ;
rdfs:label "CURVES plus" ;
NIFRID:synonym "Curves+" ;
definition: "Web server for analyzing and visualizing helical, backbone and groove parameters of nucleic acid structures. Can also be used to analyse molecular dynamics trajectories., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:023269 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpBox" ;
definition: "Open source electrophysiology hardware and software package for simultaneous EEG and EMG acquisition from multiple subjects." .
SCR:023270 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yokogawa | CellVoyager CV8000" ;
NIFRID:synonym "CellVoyager CV8000",
"CellVoyager CV8000 High-Content Screening System" ;
definition: """High content screening system with improved built-in incubator to analyze extended live cell responses.
System includes proprietary Yokogawa High Speed Confocal Scanner, water immersion lens, up to four high field-of-vision cameras, microscopic stage with cell cultivation environment, integrated robotic pipetter and specialized analysis software, CellPathfinder.""" .
SCR:023271 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SAMI Ex" ;
definition: "Software tool provides automation and process control across wide variety of applications, creates planned data driven schedules in optimized and predictable scheduling environment." .
SCR:023272 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Data Acquisition and Reporting Tool" ;
NIFRID:abbrev "DART" ;
definition: "Software package that gathers data and synthesizes runtime information from Biomek log files to capture each manipulation of sample during course of method." .
SCR:023273 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Cytomat 10 Hotel Ambient Storage" ;
definition: "Storage used for high capacity random access storage (210 SBS microplates) at ambient conditions. The Cytomat 10 Hotel (PH) offers multiple transfer positions, dual access point (DAP) and as combined benchtop-under bench solution, it allows flexible placement within the laboratory." .
SCR:023274 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Akoya Biosciences | PhenoImager Fusion" ;
NIFRID:synonym "Akoya Biosciences PhenoImager Fusion" ;
definition: "Brightfield and fluorescent whole slide imager with Multispectral Imaging Technology." .
SCR:023275 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ROIforMSI" ;
NIFRID:synonym "Regions-Of-Interest for Mass Spectrometry Imaging" ;
definition: "Source codes for manuscript \"Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation\"." .
SCR:023276 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepAI" ;
definition: "Software application as machine learning model for image colorization." .
SCR:023277 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Julich-Brain Atlas" ;
NIFRID:abbrev "JBA" ;
definition: "Atlas presents cytoarchitectonic maps in several coordinate spaces, such as MNI colin27, MNI152, and freesurfer. These maps originate from peer-reviewed probability maps that define both cortical and subcortical brain regions and account for the brain's inter-individual variability by analyzing data from multiple post-mortem samples. For a whole-brain parcellation, the available probability maps are combined into a maximum probability map by considering for each voxel the probability of all cytoarchitectonic brain regions, and determining the most probable assignment. Atlas stands as reference atlas for the Human Brain Project and is embedded within the European research infrastructure platform, EBRAINS." .
SCR:023278 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NU-5700" ;
rdfs:label "NuAire | NU-5700 Direct Heat CO2 Incubator" ;
definition: "Direct heat, 160 liter capacity, closed loop HEPA filtration, IR sensor CO2 control incubator.Offers touch screen panel control and monitoring of temperature and CO2 levels.Can be stacked and still allow the user easy access to the top chamber." .
SCR:023279 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1684" ;
rdfs:label "University of Arizona Imaging Cores Electron Core Facility" ;
NIFRID:synonym "Imaging Cores - Electron",
"University of Arizona Imaging Cores - Electron" ;
definition: "Electron facility provides full Biological Transmission Electron Microscopy related research, consultation, and imaging services.Offers services using FEI Tecnai Spirit Transmission Electron Microscope." .
SCR:023280 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of North Carolina Neuroscience Center and the BRAIN Initiative Viral Vector Core Facility" ;
NIFRID:synonym "BRAIN Initiative NeuroTools Vector Core Facility",
"BRAIN Initiative NeuroTools Vector Core UNC",
"Neurotools Viral Vector Core Facility" ;
definition: "Core provides affordable, custom viral vectors for neuroscience." .
SCR:023281 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Virginia School of Medicine Spatial Biology Core Facility" ;
NIFRID:synonym "Spatial Biology Core",
"Spatial Biology Facility" ;
NIFRID:abbrev "SBC" ;
definition: "Core offers spatial analysis which combines single-cell, spatial RNA sequencing, high-throughput microscopy, and quantitative image data analysis to enable large-scale spatial genomics and proteomics studies. Services include Spatial Transcriptome and Proteome analysis (GeoMx and CosMx), multiplex analysis (nCounter and Isoplexis), BSL2 laboratory, Confocal and Non-confocal image (Operetta), cell raft technology, sample preparation." .
SCR:023282 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1685" ;
rdfs:label "Pittsburgh Quantum Institute PQI Core Facility" ;
NIFRID:synonym "PQI" ;
definition: "Leading collaborative interdisciplinary organization that advances research, education, and training in quantum science and engineering. Helps to unify and promote research in quantum science and engineering in the Pittsburgh area. PQI members have faculty appointments from Carnegie Mellon University, Duquesne University, and the University of Pittsburgh in physics, chemistry, and engineering disciplines. Connects with team based science intitiatives and shared facilities.Resources and Facilities for Quantum Research include Carnegie Mellon Nanofabrication Facility,Center for Research Computing, Gertrude E. and John M. Petersen Institute of NanoScience and Engineering (PINSE), Materials Characterization Facility, Pittsburgh Supercomputing Center,QCFD (Quantum Computing/Computational Fluid Dynamics)." .
SCR:023283 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1687" ;
rdfs:label "MRC Protein Phosphorylation and Ubiquitylation Unit MRC PPU Reagents and Services Core Facility" ;
NIFRID:synonym "MRC PPU Reagents and Services",
"MRC Protein Phosphorylation and Ubiquitylation Unit MRC PPU Reagents and Services" ;
definition: "Focused on cell signalling pathways, provides access to reagents and services involving kinase and ubiquitin targets and associated substrates and interacting proteins. Provides expertise and assistance in projects development. Offers services for protein generation and antibody development." .
SCR:023284 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1686" ;
rdfs:label "Albert Einstein College of Medicine Epigenomics Shared Core Facility" ;
NIFRID:synonym "Albert Einstein College of Medicine Epigenomics Shared Facility (ESF)",
"Epigenomics Shared Facility (ESF)" ;
NIFRID:abbrev "ESF" ;
definition: "Part of Einstein Center for Epigenomics and Illumina CSPro (certified service provider) laboratory, offers massively-parallel sequencing (MPS) including fully-automated library preparation, quality control and assurance, and number of assays to study the genome/epigenome. Data analytical services are provided by Computational Genomics Facility." .
SCR:023288 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OA.Report" ;
definition: "Open source web tool that identifies research outputs organizations have supported, analyzes their openness including OA policy compliance, and then streamlines taking action to make results more open. Covers almost any type of policy, e.g funder, university, and national. This includes policies that require submission dates, grant IDs, or other complex criteria to determine compliance." .
SCR:023289 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Ion OneTouch 2 System" ;
NIFRID:synonym "Ion OneTouch 2 Instrument",
"Ion Torrent OneTouch 2 system",
"Ion Torrent™ Ion OneTouch™ 2 Instrument" ;
definition: "Automated system used for generation of template positive Ion Sphere Particles for semiconductor sequencing. Performs template amplification as part of manual workflow for Ion PGM, Ion Proton, Ion S5, and Ion S5 XL systems. Provides scalable template preparation for all Ion semiconductor chips. Instrument has small footprint and fits easily on any bench top." .
SCR:023290 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ion Torrent | Ion OneTouch ES" ;
NIFRID:synonym "Ion OneTouch ES" ;
definition: "Part of Ion OneTouch System. Employs magnetic bead technology to isolate template positive Ion Sphere particles that can be loaded directly onto Ion semiconductor chip delivering automated, highly reproducible enrichment with every run." .
SCR:023291 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mouse Behavioral Analysis Toolbox" ;
NIFRID:abbrev "MouBeAT" ;
definition: "Software package to analyze different behavioral tests in rodents semi-automatically. These tests include Open Field (OF), Elevated Plus Maze (EPM), Y-maze (YM) test and Morris Water Maze (MWM)." .
SCR:023292 a NLX:63400,
owl:NamedIndividual ;
definition: "We aligned single-nucleus atlases of middle temporal gyrus (MTG) of 5 primates (human, chimp, gorilla, macaque and marmoset) and identified 57 consensus cell types common to all species. We provide this resource for users to: 1) explore conservation of gene expression across primates at single cell resolution; 2) compare with conservation of gene coexpression across metazoa, and 3) identify genes with changes in expression or connectivity that drive rapid evolution of human brain." .
SCR:023293 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCSC Cell Browser" ;
definition: "Web based tool to visualize gene expression and metadata annotation distribution throughout single cell dataset or multiple datasets. Interactive viewer for single cell expression. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster specific marker genes." .
SCR:023294 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Baptist Health South Florida" ;
NIFRID:synonym "MCI",
"MNI" ;
NIFRID:abbrev "BHSF" ;
definition: "Faith-based, not-for-profit healthcare organization and clinical care network in Miami-Dade, Broward, and Palm Beach counties. Baptist Health has 11 hospitals and in excess of 100 physician practices and outpatient facilities." .
SCR:023295 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Carolina Data Warehouse for Health" ;
NIFRID:abbrev "CDW-H" ;
definition: "Central data repository containing clinical, research, and administrative data sourced from UNC Health Care System. Both Epic and legacy hospital systems are represented, with ability to query most data elements as far back as mid-2004. Used to mine UNC Health Care data to aid with trial recruitment, retrospective analyses, inter-institutional data sharing and much more." .
SCR:023297 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "airr_tools" ;
definition: """Github repository for the paper "T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases" by Høye et al.
""" .
SCR:023299 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AICcmodavg" ;
NIFRID:synonym "Akaike's Information Criterion and the second-order AIC model selection and multimodel inference based on (Q)AIC(c)" ;
definition: "Software R package to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. Package implements classic model averaging for given parameter of interest or predicted values, as well as shrinkage version of model averaging parameter estimates or effect sizes. Package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities." .
SCR:023300 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Enroll-HD" ;
definition: "Clinical research platform and longitudinal observational study for Huntington’s Disease families intended to accelerate progress towards therapeutics. Collaboration between Huntington’s disease families, clinicians, and researchers to accelerate progress toward effective treatments." .
SCR:023302 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepCT" ;
definition: "Software tool can learn complex interconnections of epigenetic features and infer unmeasured data from any available input. Can learn cell type-specific properties, build biologically meaningful vector representations of cell types, and utilize these representations to generate cell type-specific predictions of effects of non-coding variations in human genome." .
SCR:023303 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Teddy study IA prediction" ;
definition: "Software package to impute gene expression for all participants, whether they have partially or completely missing gene expression." .
SCR:023304 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TSEst" ;
definition: "Multi-modal time series imputation model that can use additional modality (another cross-sectional or time-series data) to impute missing values in time series data. This multi-modal approach shows improved performance over uni-modal imputation models." .
SCR:023305 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhysiCOOL" ;
NIFRID:synonym "Physi Calibration and Optimization Of modeLing" ;
definition: "Software Python library tailored to perform model calibration studies with PhysiCell. Generalized framework for model Calibration and Optimization Of modeLing projects." .
SCR:023306 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1238" ;
rdfs:label "University of Ottawa Flow Cytometry and Virometry Core Facility" ;
NIFRID:synonym "Flow Cytometry & Virometry",
"Flow Cytometry and Virometry" ;
definition: "Facility located at the Faculty of Medicine providing cutting edge instrumentation and expertise to researchers in Ottawa and around the world." .
SCR:023307 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1688" ;
rdfs:label "Max Planck Institute of Molecular Cell Biology and Genetics Light Microscopy Core Facility" ;
NIFRID:synonym "MPI-CBG Light Microscopy Facility" ;
definition: "Provieds acess to light microscopy techniques and instruments, consultation, training, and assists with project collaborations.Provides support with selecting imaging techniques, microscope systems, and setting up imaging experiments.Offers expertise in imaging techniques, such as Spinning disk confocal microscopy,Laser scanning confocal microscopy, 2-photon microscopy, Light sheet microscopy,Wide-field microscopy,Total internal reflection fluorescence (TIRF) microscopy ,Laser capture microdissection,Extended resolution microscopy,Quantitative phase imaging,Live cell and organoid imaging,Photomanipulation" .
SCR:023308 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iGraph/M" ;
definition: "Software package for use in complex networks and graph theory research. Mathematica interface for igraph. Provides Mathematica interface to popular igraph network analysis package, as well as many other functions for working with graphs in Mathematica. IGraph/M comes pre-packaged and ready to use on Windows, OS X and Linux (64-bit Intel), as well as the Raspberry Pi computer. The code is open source and can be compiled on other platforms as well (such as 32-bit Windows)." .
SCR:023309 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QuestionPro" ;
definition: "Survey software to design and host questionaires. Used as survey creator. Enables to choose from survey question types ranging from net promoter score questions for efficient customer satisfaction surveys to advanced multiple-choice and logic-based research questions." .
SCR:023310 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "indico" ;
definition: "Open-source tool for event organisation, archival and collaboration. Event management system made at CERN." .
SCR:023311 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1691" ;
rdfs:label "University of Nebraska at Omaha Movement Analysis Core Facility" ;
NIFRID:synonym "University of Nebraska at Omaha UNO-Movement Analysis Core",
"UNO-Movement Analysis Core" ;
definition: "Provides expertise and access to measurements of behavioral function and movement analysis for human movement variability research. Core services include access to human behavioral function measurements (3-D kinematics, kinetics, electromyography, and imaging), neuromuscular control of movements using virtual reality environments, EEG and fNIRS capabilities, dual-task measurements, blood flow and ultrasound technologies, portable pulmonary and energy expenditure assessments, movement modelling and simulation, and muscle strength measurements." .
SCR:023312 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pynapple" ;
definition: "Software object oriented, lightweight and standalone Python toolbox for neural data analysis. Its core features five versatile timeseries objects from Pandas library, allowing it the versatility to be used with most raw neuroscience data types and produce some common analysis forms." .
SCR:023314 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Variant Prediction Tools Evaluation" ;
NIFRID:synonym "Variant prEdiction Tools evAluation" ;
NIFRID:abbrev "VETA" ;
definition: "Software tool that analyses performance of several variant prediction methods at different levels. Used to benchmark variant effect predictors from VCF files." .
SCR:023315 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Benchmark of human deep intronic variation" ;
NIFRID:synonym "Benchmark of deep intronic variation" ;
definition: "Repository of code, data, and documentation to reproduce computational evaluation performed to identify the best tools/models to predict genetic variation in deep intronic regions of human genome." .
SCR:023316 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Prepare_SplicingPredictors" ;
definition: "Software tool as set of scripts to prepare the input for several sequence-based RNA splicing methods from VCF files." .
SCR:023317 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xyz2swc" ;
definition: "Web service that converts all 30 reconstruction formats (and 65 variations) described in scientific literature into SWC standard. Service is available open-source through user-friendly browser interface and Application Programming Interface." .
SCR:023318 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ricu" ;
NIFRID:synonym "r intensive care unit" ;
definition: "Software R package for download, setup and access of Intensive Care Unit data sets. In addition to functions for running arbitrary queries against available data sets, a system for defining clinical concepts and encoding their representations in tabular ICU data is presented." .
SCR:023319 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ObjectFinder" ;
definition: "Software image analysis package for 3D object recognition in volumetric images developed for neuroscience research purposes. MATLAB application to recognize small structures in large volumetric image, plot their statistics and perform quantitative analysis such as nearest neighbor and colocalization analysis. Used to detect fluorescently labeled synapses in neuronal image stacks acquired using confocal or super resolution microscopes." .
SCR:023320 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pavlovia" ;
definition: "Web application as repository and launch platform for Psychopy experiments and other open-source tools." .
SCR:023321 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Cell Data Viewer" ;
NIFRID:synonym "Masoko lab Brain Cell Data Viewer" ;
definition: "Web application that allows users to view and explore brain cell data. Composed of three, interlinked tabs. GeneExp allows users to plot expression of one or two genes in Slide-seq atlas. SingleCell allows users to plot gene expression in snRNA-seq atlas. CellSpatial shows spatial localization of snRNA-seq cell types in Slide-seq dataset. Used to visualize, interact with, and download data." .
SCR:023322 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Face Research Toolkit" ;
NIFRID:abbrev "FaReT" ;
definition: "Software toolkit of three dimensional models and software to study face perception. Collection of plugins used with MakeHuman to create face stimuli for experiments." .
SCR:023323 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MakeHuman" ;
definition: "Software tool to create face stimuli for experiments. Used for making 3D characters." .
SCR:023324 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1693" ;
rdfs:label "University of Florida Scripps Florida Histology Core Facility" ;
NIFRID:synonym "UF Scripps Biomedical Research",
"University of Florida Scripps Florida Histology Core" ;
NIFRID:abbrev "SFHC" ;
definition: "Provides histological services as well as technical support. Equipped with ventilated working areas and equipment to prepare, process and stain frozen or paraffin embedded specimens. Instrumentation include VIP Tissue Processor, BIOCARE NxGen Decloaking Chamber, Rotary Microtome, Staining Center, Leica Cryostat, Zeiss Axio Microscope/Camera Software, Leica Bond-Max Immunostainer, Leica Autostainer XL, General Data Laser Cassette Marker." .
SCR:023325 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2486" ;
rdfs:label "Stanford University Chemistry Department NMR Facility" ;
NIFRID:synonym "Stanford University Chemistry Department NMR Laboratory" ;
NIFRID:abbrev "NMR" ;
definition: "Core houses 5 Varian NMR Spectrometers including Inova 300, Varian 400, Neo 400, Inova 600, Inova 500." .
SCR:023327 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford University School of Medicine Beckman Center for Molecular and Genetic Medicine Core Facility" ;
NIFRID:synonym "Stanford Medicine Beckman Center for Molecular and Genetic Medicine" ;
NIFRID:abbrev "CMGM" ;
definition: "Integrates laboratory research with clinical medicine.Creates and supports multidisciplinary programs that promote discovery and innovation in basic sciences and accelerates introduction and application of new technologies for use in basic research and clinical medicine." .
SCR:023328 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_776" ;
rdfs:label "Stanford School of Medicine Translational Applications Service Center Core Facility" ;
NIFRID:synonym "Translational Applications Service Center" ;
NIFRID:abbrev "TASC" ;
definition: "Offers analytical services, technical and scientific consulting and training, as well as pay-per-use research equipment.Provides scientific expertise and support for standard and customized assays, from initial study design to final interpretation and statistical analysis of experimental data. Services also include clinical sample acquisition, processing and archival for conducting inter-disciplinary translational research applications." .
SCR:023329 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RHRV" ;
NIFRID:synonym "R Heart Rate Variability" ;
definition: "Software R package for developing heart rate variability analysis. Allows to import data files containing heartbeat positions in broadly used formats; eliminating outliers or spurious points present in time series with unacceptable physiological values; plotting HRV data and performing time domain, frequency domain and nonlinear HRV analysis." .
SCR:023330 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SurvStat" ;
definition: "Database reports all data from German 'Protection against Infection Act'. Robert Koch Institute maintains database of cases of notifiable diseases, and confirmation of pathogens, reported under the German ‘Act on the Prevention and Control of Infectious Diseases in Man’. SurvStat@RKI 2.0 is application that allows retrieval of aggregated data from limited version of German notification system database. Queries can be created individually or customized from pre-defined queries to generate tables, charts, and maps." .
SCR:023331 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "roifile" ;
definition: "Software Python package to read, write, create, and plot ImageJ ROI format, an undocumented and ImageJ application specific format to store regions of interest, geometric shapes, paths, text, and whatnot for image overlays." .
SCR:023332 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "findmaxima2d" ;
definition: "Software Python 2D Maxima finding algorithm. Re-implementation of Java plugin for ImageJ/Fiji." .
SCR:023333 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bassoon" ;
definition: "Software tool as Python GUI and wrapper for control of visual stimuli designed using Psychopy libraries." .
SCR:023334 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xarray " ;
definition: "Open source project and Python package that introduces labels in form of dimensions, coordinates, and attributes on top of raw NumPy-like arrays, which allows for more intuitive, more concise, and less error-prone user experience. Includes large and growing library of domain agnostic functions for advanced analytics and visualization with these data structures." .
SCR:023335 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scijava" ;
definition: "Collection of foundational software libraries, upon which ImageJ2 and Fiji are built. It is a collaboration of projects providing software for scientific computing in effort to cooperate and reuse code." .
SCR:023336 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyImageJ" ;
NIFRID:synonym "Python wrapper for ImageJ2" ;
definition: "Software provides set of wrapper functions for integration between ImageJ2 and Python. Supports original ImageJ API and data structures. Used to combine ImageJ and ImageJ2 with other tools available from Python software ecosystem, including NumPy, SciPy, scikit-image, CellProfiler, OpenCV, ITK and many more." .
SCR:023337 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pillow" ;
definition: "Software Python Imaging Library adds image processing capabilities to your Python interpreter. This library provides extensive file format support, efficient internal representation, and image processing capabilities. Core image library is designed for fast access to data stored in few basic pixel formats. It should provide solid foundation for general image processing tool." .
SCR:023338 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.5281/zenodo.6795860" ;
rdfs:label "tifffile" ;
definition: "Software Python library to store NumPy arrays in TIFF (Tagged Image File Format) files, and read image and metadata from TIFF-like files used in bioimaging. Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, DNG, STK, LSM, SGI, NIHImage, ImageJ, Micro-Manager NDTiff, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, BIF, ZIF (Zoomable Image File Format), QPTIFF (QPI, PKI), NDPI, and GeoTIFF files." .
SCR:023339 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JupyterLab" ;
definition: "Software extensible environment for interactive and reproducible computing, based on Jupyter Notebook and Architecture. Next generation user interface for Project Jupyter offering all familiar building blocks of classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in flexible and powerful user interface. Can be extended using npm packages that use our public APIs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:023340 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2488" ;
rdfs:label "Stanford University School of Medicine Genetics Bioinformatics Service Center Core Facility" ;
NIFRID:synonym "Stanford Genetics Bioinformatics Service Center" ;
NIFRID:abbrev "GBSC" ;
definition: "School of Medicine service center operated by Department of Genetics.Set up to facilitate massive scale genomics at Stanford and supports omics, microbiome, sensor, and phenotypic data types." .
SCR:023341 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford University School of Medicine Human Pathology Histology Services Laboratory Core Facility" ;
NIFRID:synonym "Human Pathology Histology Services Laboratory" ;
definition: "Provides broad range of tissue processing services to Stanford investigators in human disease research.Consolidates and centralizes tissue processing. Provides advice and expertise in tissue processing." .
SCR:023342 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2489" ;
rdfs:label "Stanford University School of Medicine In Vitro Biosafety Level3 Service Center Core Facility" ;
NIFRID:synonym "In Vitro Biosafety Level-3 Service Center" ;
NIFRID:abbrev "BSL3" ;
definition: "Center consists of Virology BSL3 lab, separate BSL3 Bacteriology lab, and BSL2 lab. It is operated by School of Medicine as scientific service center and is open to all Stanford researchers after adequate training and subsequent use." .
SCR:023343 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2490" ;
rdfs:label "Stanford University School of Medicine PET/MRI Metabolic Service Center Core Facility" ;
NIFRID:synonym "PET/MRI Metabolic Service Center" ;
NIFRID:abbrev "PMMSC" ;
definition: "Houses whole-body PET/MRI scanner and carbon-13 hyperpolarizer device.Simultaneous PET/MRI scanner combines high spatial resolution and fine anatomical soft tissue detail of MRI with high molecular specificity of PET imaging.PMMSC is the World's first installation of a SpinLab hyperpolarizer along side a PET/MRI scanner.Individual researchers are required to undergo MR safety and radiation safety training." .
SCR:023344 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2491" ;
rdfs:label "Stanford University School of Medicine Richard M. Lucas Center for Imaging Core Facility" ;
NIFRID:synonym "Stanford Lucas MRI Service Center Richard M. Lucas Center for Imaging" ;
definition: "Houses four whole-body MRI systems (three 3.0T, one 7.0T). 3T2 and 3T3 are part of the Lucas Service Center. Individual researchers are trained in magnet safety and scanner operations by the magnet manager or MR research technologists." .
SCR:023345 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2493" ;
rdfs:label "Stanford University School of Medicine Center for Innovation in In vivo Imaging Core Facility" ;
NIFRID:synonym "Stanford Center for Innovation in In vivo Imaging (SCi3)" ;
NIFRID:abbrev "SCi3" ;
definition: "Small animal imaginig service center.Instruments range from systems typically found in clinical setting, but scaled for rodent usage (such as MRI, PET, CT and ultrasound), optical systems for measuring bioluminescence, fluorescence, and Cherenkov light (IVIS, Ami, Lago and Maestro systems), new modalities (MPI and photoacoustic), as well as access to advanced image analysis software, computer workstations, and surgical preparation areas. Scientists are trained to use instruments independently and can schedule studies as needed." .
SCR:023346 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2492" ;
rdfs:label "Stanford University School of Medicine Biobank Core Facility" ;
NIFRID:synonym "Stanford Biobank" ;
definition: "Provides infrastructure for self service sample management tools, centralized broad consent, standardized laboratory services, and long term sample storage solutions.Tracks biological samples collected in every study at Stanford and linking each with associated electronic health records (i.e., EPIC), REDCap, and molecular data." .
SCR:023347 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "menoci" ;
definition: "Lightweight, modular web-based data management platform for biomedical research projects. Introduces multiple extension modules that support scientific data management. Used for data collection, experiment documentation, data publication, sharing, and preservation in biomedical research projects." .
SCR:023348 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Luminex | xMAP Intelliflex DR-SE System" ;
definition: "Flow cytometry based multiplex bead array reader with ability to simultaneously acquire data for two reporter channels per analyte. Compact, flow based, multiplex platform that combines low- and high-plex capabilities, quick time to reliable results, and ability to simultaneously acquire data for two parameters per analyte." .
SCR:023349 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1694" ;
rdfs:label "Ottawa Hospital Research Institute Flow Cytometry and Cell Sorting Core Facility" ;
NIFRID:synonym "OHRI-Flow Cytometry & Cell Sorting Facility" ;
definition: "Facility, located at General Campus of Ottawa Hospital, was established in 1998 and now includes three flow cytometers, two of which have sorting capabilities. Offers sorting precision required for isolation of rare cell populations with high purity and yield, up to 20 000 events per second. Allows simultaneous analysis of variety of light scatter and fluorescence parameters on single cells." .
SCR:023351 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BlobTools2" ;
NIFRID:synonym "blobtoolkit" ;
definition: "Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier." .
SCR:023352 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Omni-C" ;
definition: "Software tool for aligning and filtering, library QC, generating contact map, and identifying chromatin structures from Omni-C data." .
SCR:023353 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Wheel Running Activity acQuisition" ;
NIFRID:synonym "Wheel Running Activity acQuisition system",
"WRAQ system" ;
NIFRID:abbrev "WRAQ" ;
definition: "Open source microcontroller based system for wheel running activity in mice.Used to track circadian rhythms of rodents using microcontroller, powered by lithium polymer battery, and surveys exercise activity for up to 30 days. Data can be stored on microSD card or using online server using WiFi connection. Python software provides system interface with ActogramJ to analyze chronobiological aspects of data.Repository includes guide for installing integrated developmental environment and dependent libraries for building and setting up WRAQ systems - WRAQ and WRAQ-Wifi. WRAQ and WRAQ-WiFi are based on Adafruit Adalogger and DFRobot FireBeetle ESP32 connected to 4- and 8-bit binary counters receiving signal from reed switch attached to 5-inch flying saucer respectively." .
SCR:023354 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Alfred" ;
definition: "Web application as interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencingas." .
SCR:023355 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1695" ;
rdfs:label "University of Arizona Imaging Cores Optical Core Facility" ;
NIFRID:synonym "UArizona Imaging Cores - Optical",
"University of Arizona UArizona Imaging Cores - Optical" ;
definition: "Facility with two locations:Marley and Life Sciences North. Dedicated to acquisition of images for research, industrial and clinical applications.Marley location features inverted point scanning confocal microscope, upright confocal/multiphoton microscope with superresolution capabilities, fluorescence stereo microscope and research quality microwave. Life Sciences North location features superresolution fluoresence microscope:structured illumination, SIM; inverted multifunction widefield microscope:color brightfield, polarized light, fluorescence; image analysis workstation." .
SCR:023356 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1696" ;
rdfs:label "Carnegie Mellon University Pitt Brain Imaging Data Generation and Education Center Core Facility" ;
NIFRID:synonym "Carnegie Mellon University CMU-Pitt BRIDGE Center",
"CMU-Pitt BRIDGE Center" ;
definition: "Collaborative MRI facility that is jointly operated by the University of Pittsburgh and Carnegie Mellon University. Research neuroimaging facility, with focus on advanced data analytics and basic science research. Designed to support basic science research and next generation of brain scientists." .
SCR:023357 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRISMA-S" ;
NIFRID:synonym "Preferred Reporting Items for Systematic reviews and Meta-Analyses literature Search extension" ;
definition: "Extension to PRISMA Statement for Reporting Literature Searches in Systematic Reviews. Preferred reporting items for systematic reviews and meta analyses literature search extension. Complements PRISMA Statement and its extensions by providing checklist that could be used by interdisciplinary authors, editors, and peer reviewers to verify that each component of search is completely reported and therefore reproducible." .
SCR:023358 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Applied Biosystems | ViiA 7 Real-Time PCR System" ;
definition: "Contains Viia7 RT-PCR system and QuantStudio software for running Viia7 RT-PCR system and processing data." .
SCR:023359 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FFTrees" ;
NIFRID:synonym "Fast-and-Frugal Trees" ;
definition: "Software package as decision algorithms for solving binary classification problems. Faster and more frugal because every node allows making decision. Apart from being faster and requiring less information, FFTs tend to be robust against overfitting, and are easy to interpret, use, and communicate." .
SCR:023360 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Catalog of Bias" .
SCR:023361 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adobe Acrobat Pro" ;
definition: "Productivity and collaboration PDF solution, combining Acrobat desktop software, mobile scan app, signature app and Acrobat Reader mobile app enhanced with premium mobile features and premium Document Cloud services." .
SCR:023362 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Elicit" ;
NIFRID:synonym "Elicit: The AI Research Assistant" ;
definition: "Research assistant using language models like GPT-3 to automate parts of researchers’ workflows. Main workflow is Literature Review. If you ask question, Elicit will show relevant papers and summaries of key information about those papers in easy-to-use table." .
SCR:023363 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AMSTAR 2" ;
NIFRID:synonym "A MeaSurement Tool to Assess systematic Reviews" ;
definition: "Software critical appraisal tool for systematic reviews that include randomised or non-randomised studies of healthcare interventions, or both.Measurement tool to assess systematic reviews." .
SCR:023364 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Tumor Atlas Network" ;
NIFRID:abbrev "HTAN" ;
definition: "HTAN is National Cancer Institute funded Cancer Moonshot initiative to construct 3-dimensional atlases of dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.Provides three dimensional atlases of cancer transitions for diverse set of tumor types. Efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at single point in time. Data portal for Human Tumor Atlas Network. Data available on HTAN Portal is open access. Certain data types with potential for re-identification are available in restricted access through dbGAP." .
SCR:023365 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Systematic Review Accelerator" ;
NIFRID:abbrev "SRA" ;
definition: "Software suite of automation tools, purpose-built to speed up multiple steps in systematic review process. Assist with many steps of systematic review, including searching for citations, citation screening and write-up of review findings, among others. Existing tools are being continuously reviewed and refined, and additional tools are being developed. Systematic Review Accelerator project is based at the Bond University Institute for Evidence-Based Healthcare." .
SCR:023366 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automated Fiber Quantification in Python" ;
NIFRID:abbrev "pyAFQ" ;
definition: "Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry." .
SCR:023367 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ODYN" ;
NIFRID:synonym "Open DYNamics" ;
definition: "Open source software analysis tool to investigate space plasma turbulence and nonlinear DYNamics. Wraps comprehensive set of advanced data analysis methods meant to facilitate study of turbulence, nonlinear dynamics, and complexity in space plasmas." .
SCR:023368 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neuroscience Data Interface" ;
NIFRID:abbrev "NDI" ;
definition: "Software tool as platform independent data interface and database for neuroscience physiology and imaging experiments. Platform independent standard that allows analyst to use and create software that functions independently from format of raw data or manner in which data are organized into files. Interface is rooted in simple vocabulary that describes common apparatus and storage devices used in neuroscience experiments. Results of analyses, and analyses of analyses, are stored as documents in scalable, queryable database that stores relationships and history among experiment elements and documents. Interface allows development of application ecosystem where applications can focus on calculation rather than data format or organization. This tool can be used by individual labs to exchange and analyze data, and it can serve to curate neuroscience data for searchable archives." .
SCR:023369 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "vhlab-TwoPhoton-matlab" ;
NIFRID:synonym "Van Hooser lab fluorescent time-series analysis software" ;
definition: "Software VH Lab tools for analysis of calcium imaging data. Allows selection of ROIs and extraction of time series data from raster-scanned, line-scanned, or CCD images, written in Matlab." .
SCR:023370 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1698" ;
rdfs:label "University of Arizona Analytical and Biological Mass Spectrometry Core Facility" ;
NIFRID:synonym "UArizona Analytical & Biological Mass Spectrometry Facility",
"University of Arizona UArizona Analytical & Biological Mass Spectrometry Facility" ;
NIFRID:abbrev "ABMS" ;
definition: "Provides equipment and expertise for analysis of variety of biological and small molecules.Services include protein analysis encompassing protein identification, protein and peptide sequence confirmation, intact protein molecular weight determination, complex protein sample analysis, and protein/antibody drug interactions.Developed metabolomics library to support metabolomic and lipidomics analysis. Can identify range of post-translational modifications, determining their presence or absence, as well as quantitating PTMs.Proteomics and small molecule services include workflows for label free,chemical labeling (iTRAQ/TMT) and metabolic labeling (SILAC).Service for molecular synthesis, with monitoring reaction steps,calculating percentage of product, testing for purity, and molecule characterization with high resolution and high mass accuracy.Provides molecular weight and chemical composition determinations, structure elucidations and compound identification analysis or confirmation and accurate mass measurements of synthetic products, measurement of polymers, nucleic acids (DNA/RNA), peptides, proteins, natural products, and assistance with determination of unknowns." .
SCR:023371 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1699" ;
rdfs:label "Centre for Genomic Regulation Advanced Light Microscopy Unit Core Facility" ;
NIFRID:synonym "Advanced Light Microscopy Unit",
"Advanced Light Microscopy Unit (ALMU)" ;
NIFRID:abbrev "ALMU" ;
definition: "Core provides support with experimental design, sample preparation, acquisition, bioimage analysis and visualization.Consists of microscope systems specifically designed for fluorescence microscopy ranging from confocal, widefield to super resolution systems and helps reveal structures from macro to nanoscale." .
SCR:023372 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1702" ;
rdfs:label "Centre for Genomic Regulation Flow Cytometry Unit Core Facility" ;
NIFRID:synonym "Centre for Genomic Regulation CRG/UPF Flow Cytometry Unit",
"CRG/UPF Flow Cytometry Unit" ;
NIFRID:abbrev "CRG/UPF" ;
definition: "Flow cytometry studies optical parameters emitted by particles (cells, cell fractions). Flow cytometers can study a series of parameters of individual particles simultaneously, quickly and on a large number of individualized particles in suspension. Flow cytometers use lasers as a source of light excitement; therefore, it must be possible to mark the particles with one or more fluorescent substances. Information is also collected regarding the size and structural complexity of each particle. This multiparameter study of each particle enables us to analyse subpopulations in complex samples through electronic sorting. Some cytometers are also equipped with sorting and collection modules for particles of interest. The most important applications of flow cytometry include those relating to the study of cell surface receptors, nuclear and cytoplasmic antigens, DNA content, enzyme activity, cell integrity and membrane permeability and calcium flows. The Unit currently hosts five analyzers and two sorters, and is therewith the largest Becton Dickinson site in Spain. The sorters are operated by the facility personnel, who also support the users in experimental design and data analysis. The analyzers are operated by the users themselves, after they have been trained. The facility personnel helps with the experimental design and supervises and monitors the experiments when necessary." .
SCR:023373 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1700" ;
rdfs:label "Centre for Genomic Regulation Bioinformatics Unit Core Facility" ;
NIFRID:synonym "Bioinformatics Unit",
"Centre for Genomic Regulation Bioinformatics Unit" ;
definition: "Provides services of consultation, planning NGS and other genomic experiments, NGS data processing, analysis and management, software and database development, bioinformatics training, and access to high-performance computing resources at CRG. The Unit works in synergy with the Genomics Unit and the Biomolecular Screening and Protein Technologies Unit to support users using high throughput sequencing technologies from experiment planning to delivery of timely and reliable results." .
SCR:023374 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1704" ;
rdfs:label "Centre for Genomic Regulation Genomics Unit Core Facility" ;
NIFRID:synonym "Centre for Genomic Regulation Genomics Unit",
"Genomics Unit" ;
definition: "Supports next generation sequencing technologies and provides several next generation sequencing instruments. Several high-throughput technologies have been implemented to assess differential expression, inter-individual genetic variation, microRNA discovery, genome sequencing, targeted resequencing, epigenetic profiling and identification of binding sites of DNA or RNA-associated proteins." .
SCR:023375 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1705" ;
rdfs:label "Centre for Genomic Regulation Tissue Engineering Unit Core Facility" ;
NIFRID:synonym "Centre for Genomic Regulation Tissue Engineering Unit",
"Tissue Engineering Unit" ;
definition: "Provides latests technologies for stem cell biology, stem cell differentiation, organoid formation and induced pluripotent stem cells.Tissue Engineering platform works in collaboration with Biomolecular Screening and Protein Technologies Unit to provide CRISPR/Cas9 genome editing technology service.Unit also includes Histology In-house Service (only for PRBB residents) provides histopathological analysis required for analysing tissues from research performed in in vivo models. Histology In-house Service performs and optimizes histological processing and analysis of tissue, from experimental animal models and human origin.Provides mentoring and training in common histological techniques." .
SCR:023376 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1701" ;
rdfs:label "Centre for Genomic Regulation Protein Technologies Unit Core Facility" ;
NIFRID:synonym "Centre for Genomic Regulation Protein Technologies Unit",
"Protein Technologies Unit" ;
definition: "Provides technology platform to perform protein production and automated processes in context of biomolecular and biochemical screening assays.Through staff assisted screening, users have access to equipment including liquid handlers, plate readers and small molecule libraries.Unit is aimed at supporting the researchers of the CRG institute by purchasing, seeking and maintaining valuable stocks of clones and strains." .
SCR:023377 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1703" ;
rdfs:label "Centre for Genomic Regulation Proteomics Unit Core Facilitiy" ;
NIFRID:synonym "Centre for Genomic Regulation CRG/UPF Proteomics Unit",
"CRG/UPF Proteomics Unit" ;
definition: "Proteomics Unit is joint effort of Universitat Pompeu Fabra and Center of Genomic Regulation. Provides proteomics services by offering state-of-the-art methods, advise and expertise to support basic and translational researchers; developing new methods and techniques that keep the unit up to date and at the forefront of the proteomics field; training community and actively disseminating proteomics science and methods.Part of Spanish National Infrastructure for Omics Technologies and European Proteomics Infrastructure Consortium, and it coordinates European innovative and interdisciplinary Research and Training network. The Proteomics Unit is also part of Spanish National Health System." .
SCR:023378 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Catholic University of Louvain Institute of Experimental and Clinical Research Imaging Platform Core Facility" ;
NIFRID:synonym "2IP",
"Institute of Experimental and Clinical Research Imaging platform",
"IREC Imaging platform",
"IREC Imaging platform (2IP)" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 5,2025. Core provided services include paraffin embedding, paraffin and cryo sectioning, histological stainings, immunostainings; Image acquisition includes brightfield, fluorescence and polarized light whole slide imaging,2D fluorescence microscopy, 3D fluorescence microscopy; Image analysis includes 2D images : ImageJ/Fiji support – ZEN Analysis (Zeiss),2D whole slide scans: Author (Visiopharm), Halo (Indicalab), QuPath, 3D images: Arivis (Zeiss), Imaris (Bitplane)." .
SCR:023379 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Slide-seq Pipeline" ;
NIFRID:synonym "Slide-seq",
"SlideSeq",
"slideseq",
"SlideSeq Pipeline" ;
definition: "Software pipeline developed in collaboration with BRAIN Initiative Cell Census Network and BRAIN Initiative Cell Atlas Network. Supports processing of spatial transcriptomic data generated with Slide-seq commercialized as Curio Seeker assay." .
SCR:023380 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1708" ;
rdfs:label "Yale University West Campus Imaging Core Facility" ;
NIFRID:synonym "Yale University West Campus Imaging Core",
"Yale West Campus Imaging Core" ;
NIFRID:abbrev "WCIC" ;
definition: """Provides access and training to instruments including optical microscopes with three confocal systems, two wide-field systems, light sheet system, laser-microdissection system, cell-culture microscope, stereomicroscope, optical tweezer system, and Atomic Force Microscope. Maintains cell culture equipment such as biosafety cabinet, incubators,
refrigerator, and microfuges and lab support areas for cell culture and sample preparation.""" .
SCR:023381 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2494" ;
rdfs:label "Stanford Canary Center Preclinical Imaging Core Facility" ;
NIFRID:synonym "Preclinical Imaging Core Facility" ;
NIFRID:abbrev "SCi3-P" ;
definition: "Provides access to ultrasound, MRI, CT, and PET, instruments developed specifically for small animal work and photoacoustic imaging. All instruments are designed to image living subjects and allow for repeated imaging. The flexibility and rapid analyses of such animal models greatly accelerate the development of molecular imaging strategies.Facility houses surgical procedure room, histology slide scanner that converts glass slides into digital slides using both brightfield and fluorescence, and advanced image analysis workstations.Instruments include MicroPET Imaging Systems,Optical Imaging Systems,UltraSound Imaging System,Photoacoustic Imaging System,X-Ray Computed Tomography Imaging System,Magnetic Resonance Imaging." .
SCR:023382 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2495" ;
rdfs:label "Stanford University School of Medicine Transgenic, Knockout and Tumor model Center Core Facility" ;
NIFRID:synonym "Knockout and Tumor model",
"Stanford School of Medicine Transgenic" ;
NIFRID:abbrev "TKTC" ;
definition: "Services include genome editing of mice, rats and cell lines, mouse line cryopreservation and re-derivation, ES cell targeting, PDX models, drug screening.Crispr Mediated KO/KI and Conditional KO Mice,KI mouse by mouse ES cell genome editing,Integrase Mediated Transgenesis,Conventional Transgenic Mouse,Mouse Line Services,Cell Line Services. Tumor Model Services include In vivo tumor models,In vivo pharmacology,In vitro and biochemical assays,Translational imaging services." .
SCR:023383 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford University Computer Science Department Computer Core Facility" ;
NIFRID:synonym "Stanford University Computer Science Department Computer Facilities" ;
NIFRID:abbrev "CSD-CF" ;
definition: "Academic service center specializing in planning, installation and maintenance of research computer systems." .
SCR:023384 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2497" ;
rdfs:label "Stanford University School of Medicine Animal Diagnostic Laboratory Core Facility" ;
NIFRID:synonym "Animal Diagnostic Laboratory",
"Stanford School of Medicine Animal Diagnostic Laboratory" ;
definition: "Offers clinical laboratory services including hematology, cytology, serum chemistry, electrolyte analysis, coagulation profiles, fluid analysis, serology/immunology, parasitology, and microbiology; Specializes in diagnostic and research needs of laboratory animals. Committed to improving diagnostics, developing additional reference ranges for various clinical pathology parameters in laboratory animals, and supporting health surveillance and disease management." .
SCR:023385 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford University School of Medicine Institute for Stem Cell Biology and Regenerative Medicine FACS Core Facility" ;
NIFRID:synonym "Stem Cell FACS Core" ;
definition: "Core manager provides oversight and training on user-friendly instrumentation so that each investigator is able to perform sorts and analysis on their own.Manager also provides technical help with more complex sorts, ensures that instruments are maintained properly, and will perform troubleshooting as necessary. This novel design will allow for critical stem cell sorts to be done efficiently and economically." .
SCR:023386 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2500" ;
rdfs:label "Stanford University School of Medicine Clinical and Translational Research Unit Core Facility" ;
NIFRID:synonym "Clinical and Translational Research Unit (CTRU)",
"Stanford University School of Medicine Clinical and Translational Research Unit (CTRU)" ;
NIFRID:abbrev "CTRU" ;
definition: "Collecting and banking freshly frozen tumor and normal tissue from surgical material and autopsy specimens.Provides fresh tumor tissue for viable cell studies,processes and banks blood from cancer patients,maintains tissue database with links to clinicopathological data,providing histological staining and pathological review,coordinating patient consent and assuring regulatory compliance." .
SCR:023387 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2499" ;
rdfs:label "Stanford University School of Medicine Cancer Institute Tissue Procurement Shared Resource Core Facility" ;
NIFRID:synonym "Stanford Cancer Institute Tissue Procurement Shared Resource" ;
definition: "Procures and provides needed tissue specimens to Stanford Cancer Institute investigators to support cancer related research. Services include collecting and banking freshly frozen tumor and normal tissue from surgical material and autopsy specimens;Providing fresh tumor tissue for viable cell studies;Processing and banking blood from cancer patients;Maintaining tissue database with links to clinicopathological data;Providing histological staining and pathological review;Coordinating patient consent and assuring regulatory compliance.Provides portal to virtual bank which links inventories of specialized satellite repositories, including collections of hematological and neurosurgical specimens." .
SCR:023388 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2496" ;
rdfs:label "Stanford University School of Medicine Veterinary Service Center Core Facility" ;
NIFRID:synonym "Stanford School of Medicine Veterinary Service Center" ;
definition: "Provides medical care, in vivo research support, and disease surveillance to laboratory animals at Stanford University . Our board certified and board eligible veterinarians offer consultation in appropriate animal modeling, animal care techniques, experimental methodology, anesthetic techniques, surgical techniques, pain management, humane euthanasia techniques, and animal use (APLAC) protocol consultation. AALAS certified veterinary technicians are available to provide technical support including dosing, biosampling, conducting anesthesia and post-operative care, for example." .
SCR:023389 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_023395" ;
rdfs:label "BE designer" ;
NIFRID:synonym "Base Editor designer",
"BE-designer" ;
definition: """Web-based design tool for CRISPR base editing. Guide RNA designer for CRISPR base editing.
Provides all possible base editor target sequences in given input DNA sequence with useful information including potential off target sites.""" .
SCR:023390 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cas OFFinder" ;
NIFRID:synonym "Cas-OFFinder" ;
definition: "Web application that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Enables searching for potential off-target sites in any sequenced genome rapidly without limiting PAM sequence or number of mismatched bases." .
SCR:023391 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "findCPcli" ;
definition: "Software command line Python package for computation of chokepoint reactions in genome scale metabolic models. Used to compute chokepoints by taking into account both topology and dynamic information of network. Can compute and remove dead-end metabolites, find essential reactions and update flux bounds of reactions according to results of Flux Variability Analysis." .
SCR:023392 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2683" ;
rdfs:label "Colorado School of Mines Shared Instrumentation Facility Atom Probe Tomography Core Facility" ;
NIFRID:synonym "3D nanoscale compositional analysis",
"atom probe tomography",
"light mass and heavy mass species identification",
"mass spectral data" ;
definition: "Core to capture mass spectral data obtained through time-of-flight measurements that can be used for 3D nanoscale compositional analysis to identify light mass and heavy mass species with equivalent sensitivity." .
SCR:023393 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Simple Features" ;
NIFRID:synonym "Simple Feature Access",
"simple features" ;
NIFRID:abbrev "sf" ;
definition: "Software R package as set of standards that specify common storage and access model of geographic features made of mostly two dimensional geometries used by geographic information systems. Standardized way to encode spatial vector data. Formalized by Open Geospatial Consortium and International Organization for Standardization." .
SCR:023394 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rworldmap" ;
definition: "Software R package for mapping country data.Enables mapping of country level and gridded user datasets by facilitating joining to modern world maps and offering visualisation options. Country borders are derived from Natural Earth data v 1.4.0." .
SCR:023398 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allen Cell and Structure Segmenter" ;
NIFRID:synonym "Allen Cell & Structure Segmenter",
"Segmenter",
"The Allen Cell and Structure Segmenter" ;
definition: "Software Python toolkit developed at Allen Institute for Cell Science for 3D segmentation of intracellular structures in fluorescence microscope images. Used for segmenting 3D intracellular structures in fluorescence microscopy images." .
SCR:023399 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CaT-z" ;
NIFRID:synonym "Classification and Tracking in depth (z)" ;
definition: "Software tool for 3D tracking and automatic classification of rodent behavior. Used for acquisition, annotation, and automatic behavioral profile characterization of laboratory rodents' RGB-D videos. Utilizes video segmentation, tracking of body parts, and automated classification of behaviors through machine learning and computer vision methods. Setup uses low costing RGB-D cameras for tracking behaviors in various environments. Software includes GUI interfaces for video acquisition, annotation, and processing of behavioral data. Software is capable of automated behavior detection with only 30 minutes of annotated video." .
SCR:023400 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneScan" ;
NIFRID:synonym "GeneScan 3.7" ;
definition: "Software tool as DNA sequence analyzer program." .
SCR:023401 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eHDprep" ;
NIFRID:synonym "electronic Health Data Preparation" ;
definition: "Software R package provides quality control and semantic enrichment tools for preparation of health datasets. Enables semantic enrichment of dataset where metavariables are discovered from relationships between input variables determined from user provided ontologies." .
SCR:023402 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetGENE" ;
definition: "Web tool identifies associations between genes and metabolites that are biosynthesized, metabolized, or transported by proteins coded by genes. Gene centric metabolomics information retrieval tool. Knowledge based, gene centric data aggregator that hierarchically retrieves information about genes, their related pathways, reactions,metabolites, and metabolomic studies from standard data repositories under one dashboard to enable ease of access through centralization of relevant information. Information can be contextualized by filtering along species, anatomy tissue and disease or phenotype." .
SCR:023403 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2501" ;
rdfs:label "Stanford University School of Medicine Laboratory for Cell and Gene Medicine Core Facility" ;
NIFRID:synonym "Laboratory for Cell and Gene Medicine (LCGM)",
"Stanford Laboratory for Cell and Gene Medicine",
"Stanford University School of Medicine Laboratory for Cell and Gene Medicine" ;
NIFRID:abbrev "LCGM" ;
definition: "Provides support and services to clinical investigators including consulting, technology transfer, process and analytical development, clinical manufacturing and regulatory affairs." .
SCR:023404 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_374" ;
rdfs:label "Stanford University School of Medicine Computational Services and Bioinformatics Core Facility" ;
NIFRID:synonym "Computational Services and Bioinformatics Facility",
"Stanford Computational Services and Bioinformatics Facility" ;
NIFRID:abbrev "CSBF" ;
definition: "Provides variety of Macintosh, Windows, and Linux software for scientific research.Obtains concurrent network licenses that work under control of software license manager.This allows facility to purchase limited number of copies of expensive software and distribute software within Stanford network.CSBF has user community of over 200 research labs in 36 different departments at Stanford. Staff members have many years of experience in providing computer support to biomedical researchers." .
SCR:023405 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2503" ;
rdfs:label "Stanford University Chemistry Department Optics Core Facility" ;
NIFRID:synonym "Stanford University Chemistry Department Optics Facility" ;
definition: "Houses optical spectroscopy instruments including Fluorolog 3 Fluorimeter,Vertex 70 FTIR with RAM II Raman accessory, Cary 6000i UV/Vis/NIR Spectrometer." .
SCR:023406 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2504" ;
rdfs:label "Stanford University Biomaterials and Advanced Drug Delivery Laboratory Core Facility" ;
NIFRID:synonym "Biomaterials and Advanced Drug Delivery (BioADD) Laboratory" ;
NIFRID:abbrev "BioADD" ;
definition: "Provides creation of biomaterials and drug delivery agents, expertise toward designing and analyzing biomaterials, development of drug delivery devices and formulations, pharmacokinetic and pharmacodynamic studies, and development of materials for biomedical applications." .
SCR:023407 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2505" ;
rdfs:label "Stanford University Cyclotron and Radiochemistry Core Facility" ;
NIFRID:synonym "Cyclotron and Radiochemistry Facility" ;
NIFRID:abbrev "CRF" ;
definition: "Provides clinical and pre-clinical radiotracers for understanding and detecting cancer, cardiac conditions, inflammatory disorders, and neurodegenerative diseases." .
SCR:023408 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2502" ;
rdfs:label "Stanford University Instrumentation Shop Core Facility" ;
NIFRID:synonym "MCP / NIS Engineering Shop",
"Stanford University instrumentation shop" ;
definition: "Core for assisting with custom instrumentation and equipment needs at affordable price.Projects devices include microcontrollers, LCD displays, keypad interfaces, serial communication, signal conditioning electronics, analog and digital computer interfaces, photomultiplier tube amplifiers, DC motor, stepper motor and linear motor controllers, servomotors, rotary encoders, timed sequenced equipment, temperature controllers, peltier devices, solenoid valves, actuators, force transducers, profusion chambers, microscope adapters as well as mechanical design and limited machine shop services." .
SCR:023409 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HetMatPy" ;
NIFRID:synonym "hetmatpy" ;
definition: "Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes." .
SCR:023410 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford Center for High Throughput Quantitative Biology Core Facility" ;
NIFRID:synonym "Stanford Center for High Throughput Biology",
"Stanford Center for High Throughput Quantitative Biology" ;
NIFRID:abbrev "SCIQUBE" ;
definition: "Provides access to technologies involving high-throughput microscopy, high-throughput biological assays, and microfluidics." .
SCR:023411 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2506" ;
rdfs:label "Stanford University High Performance Computing Center Core Facility" ;
NIFRID:synonym "Stanford High Performance Computing Center",
"Stanford University High Performance Computing Center" ;
definition: "Academic cost recovery center, operates number of HPC clusters to enable larger simulations, deeper analyses, and faster computation times than are possible using computers available to individual researchers. Provides mass data storage and archival systems to store data." .
SCR:023412 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2507" ;
rdfs:label "Stanford University Physics Machine Shop Core Facility" ;
NIFRID:synonym "Physics Machine Shop",
"Physics Varian Machine Shop",
"Stanford University Physics Machine" ;
NIFRID:abbrev "HPCC" ;
definition: "Provides services for all departments on campus, including library of materials and parts suppliers, arranging for off-campus services such as plating and specialized machining services,help with laboratory and research apparatus and repair of existing equipment, designs from sketches to final assembly by mechanical means (welding, brazing or soldering),computer numerically controlled mill and lathe, electro discharge machining." .
SCR:023413 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2508",
"ABRF_2916",
"SCR_025708" ;
rdfs:label "Stanford University Research Computing" ;
NIFRID:synonym "Stanford Research Computing" ;
NIFRID:abbrev "SRC" ;
definition: "Provides services with computing and data information for research proposals, data storage platforms,consultation,computational platforms and resources.Some services relate directly to physical hardware, including hosting and system administration. Hosting largely takes place at Stanford Research Computing Facility data center designed specifically to host high density, power consumptive computing equipment. SRCF is intended to meet research server hosting needs of campus for years to come." .
SCR:023415 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:coveffect" ;
rdfs:label "CoVEffect" ;
definition: """Web tool as interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning. User can search papers over COVID-19 literature using keywords or
or load specific paper through its DOI.""" .
SCR:023416 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Research Center Jülich; Jülich; Germany" ;
NIFRID:synonym "Forschungszentrum Jülich",
"Jülich Research Institute; Jülich; Germany",
"Research Centre Jülich" ;
definition: "One of the largest interdisciplinary research centers in Europe for inspiring science exchange from all over the world. It is member of the Helmholtz Association." .
SCR:023417 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GE Volume Viewer" ;
NIFRID:synonym "Volume Viewer" ;
definition: "Software tool to provide data 3D visualization and processing. Used for reading and comparing CT, MR, 3D X-ray, PET, and PET/CT datasets." .
SCR:023418 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vitrea Read Diagnostic Viewer" ;
NIFRID:synonym "Diagnostic Viewer",
"Vitrea EasyViz",
"Vitrea EasyViz Diagnostic Viewer",
"Vitrea Read" ;
definition: "Software application providing tools and features that may be used for general purpose radiological viewing and reading of image data from various imaging modalities, clinical review and performs functions of digital image processing, measurement, communications and storage." .
SCR:023419 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HOMA2 calculator" ;
NIFRID:synonym "HOMA Calculator" ;
definition: "Software tool used to calculate Homeostasis Model Assessment which takes account of variations in hepatic and peripheral glucose resistance, increases in insulin secretion curve for plasma glucose concentrations and contribution of circulating proinsulin. Provides access to HOMA2 model for researchers who wish to use model derived estimates of %B and %S, rather than linear approximations." .
SCR:023420 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1709" ;
rdfs:label "Drexel University Research Computing Core Facility" ;
NIFRID:synonym "Drexel University Research Computing Facility",
"University Research Computing Facility" ;
NIFRID:abbrev "URCF" ;
definition: "Provides high performance scientific computing and secure storage of protected health information to both Drexel community and other universities in Philadelphia area. Data center houses Picotte cluster, which consists of Standard CPU Nodes, Large Memory Nodes, GPU Nodes and secure scratch and persistent storage." .
SCR:023421 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1710" ;
rdfs:label "Fasteris Next Generation Sequencing Services" ;
NIFRID:synonym "Fasteris NGS Services" ;
definition: "Fasteris, the brand of Genesupport SA for all Life Science Services, provides Next Generation Sequencing and Sanger sequencing services.Offers customized approaches and consulting services at each step of your projects." .
SCR:023422 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1711" ;
rdfs:label "University of Iowa Institute of Human Genetics Genomics Division Core Facility" ;
NIFRID:synonym "IIHG-Genomics Division",
"Iowa Institute of Human Genetics (IIHG) Genomics Division" ;
NIFRID:abbrev "IIHG" ;
definition: "Provides broad spectrum of resources designed to make techniques of genomics, functional genomics, and recombinant DNA technology. Services include Next Generation sequencing, single cell analysis, spatial transcriptomics, Sanger Sequencing, qPCR, digital PCR, Nanostring, and microarray analysis." .
SCR:023423 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JPSurv" ;
NIFRID:synonym "JoinPoint Survival",
"joinpoint survival" ;
definition: "Web tool to analyze survival data by single year of diagnosis and estimates changes in survival trends and year over year trend measures." .
SCR:023424 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoString GeoMx Tools" ;
NIFRID:synonym "GeoMxTools" ;
definition: "Software package contains tools for analyzing data from NanoString GeoMx Digital Spatial Profiler. Provides functions to read, quality control and normalize starting from Nanostring DCC and PKC files generated from NanoString GeoMx DSP. Contains definition of NanoStringGeoMxSet class which inherits from Biobase’s ExpressionSet class and NanoStringRCCSet class." .
SCR:023425 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "M3 Platform" ;
NIFRID:synonym "McGill-Mouse-Miniscope (M3) Platform",
"McGill-Mouse-Miniscope platform" ;
definition: "Software neuroscience laboratory environment for simultaneous neuronal imaging and behavioral monitoring. McGill-Mouse-Miniscope Touchscreen Behavior Platform. Standardized approach for high throughput imaging of neuronal dynamics during behavior." .
SCR:023426 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "treemix_tree_with_bootstraps.py " ;
definition: "Phython script for bootstraping Treemix snp trees to generate confidance intervals in the main tree." .
SCR:023427 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus | Cell Counter model R1" ;
definition: "Automated cell counter with software algorithm to provide accurate counting results for variety of cell types by automatically declustering clumped cells, performing size and roundness based sorting, and identifying live and dead cells. Can confirm cell counts prior to experimental data acquisition, quality check, passaging, or induction of differentiation." .
SCR:023429 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RepFinder" ;
definition: "Software tool to find shared repeats between mitochondrial genomes." .
SCR:023430 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mitochondria simulator" ;
NIFRID:synonym "mitochondria-simulator" ;
definition: "Software repository for mtDNA assembly project." .
SCR:023431 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Virginia School of Medicine Molecular Imaging Core Facility" ;
NIFRID:synonym "Medicine Molecular Imaging Core" ;
definition: "Provides imaging small animals and samples with variety of modalities depending on needs including MRI, X-Ray CT, PET, SPECT, luminescence, and fluorescence. Works closely with Radiochemistry Core Lab which can synthesize custom, targeted PET and SPECT imaging agents.Offers preclinical imaging tools designed for imaging rodents." .
SCR:023432 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1713" ;
rdfs:label "University of Arizona Flow Cytometry and Human Immune Monitoring Shared Resource Core Facility" ;
NIFRID:synonym "UArizona Flow Cytometry and Human Immune Monitoring Shared Resource",
"University of Arizona UArizona Flow Cytometry and Human Immune Monitoring Shared Resource" ;
definition: "Flow cytometry facility provides instrumentation for data acquisition, analysis, and cell sorting, technical expertise to interpret results and develop methods. Offers information about new techniques, and applications of flow cytometry through workshops and seminars, and provides training to interested facility users. Individual consultation services are available.Human Immune Monitoring Facility provides immune profiling, sample preparation,clinical trial support, technical expertise to clinical investigators and research scientists.Services include multispectral flow cytometry, metabolic analysis, blood services such as PBMC isolation and serum/plasma extraction, and full spectrum of immunological services.Offers custom assays and biobanking services upon request.Offers training, assisted, unassisted, and technician operated modalities for all instruments and will meet investigators at their desired level of engagement." .
SCR:023433 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1714" ;
rdfs:label "University of Arizona Functional Genomics Core Facility" ;
NIFRID:synonym "UArizona Functional Genomics Core",
"University of Arizona UArizona Functional Genomics Core" ;
definition: "Offers to run high-throughput compound, RNAi, and deletion library based screens for purpose of network analysis, drug and/or target discovery. Offers assistance to develop assay, carryout screen and/or analyze data. Equipment is also available for general (low-throughput) use. Helps with developing custom pipeline. Biomek FX liquid handling workstation with integrated Liconic shaker incubator (temperature, humidity, and CO2 controlled) can be used to setup and grow most cell types in 96 well plates. This robot is equipped to add RNAi constructs, drugs or other stimuli to each plate. Biomek FX can also be used to perform high-throughput biochemical assays. Cell based assays can be carried out using either Operetta CLS high-content analysis system or CLARIOstar plus. Both instruments have powerful, but easy to use software for data analysis." .
SCR:023434 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DendroX" ;
definition: "Web application for multi-level multi-cluster selections in dendrogram. Provides interactive visualization of dendrogram in which users can divide dendrogram at any level and into any number of clusters." .
SCR:023435 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Southern HIV and Alcohol Research Consortium" ;
NIFRID:synonym "Southern HIV and Alcohol Research Consortium Biomedical Data Repository",
"The Southern HIV and Alcohol Research Consortium (SHARC)" ;
NIFRID:abbrev "SHARC" ;
definition: "Consortium to improve health outcomes and reduce HIV transmission among diverse range of populations affected by alcohol and HIV infection in Florida. Fosters interdisciplinary translational research, training and community engagement. One of five national Consortia for HIV/AIDS and Alcohol Research Translation (CHAART). Supports Researcher Hub for researchers interested in SHARC research, publication, presentations, and opportunity to access, and analyze datasets via SHARC Concepts System." .
SCR:023436 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HemOnc Knowledgebase" ;
NIFRID:synonym "Free Hematology/Oncology Reference",
"HemOnc",
"HemOnc.org" ;
definition: "Medical wiki of interventions, regimens, and general information relevant to fields of hematology and oncology. Knowledge base for hematology and oncology providers, containing details about hematology/oncology drugs and treatment regimens. Any healthcare professional can sign up to contribute. Acuracy and completeness of content is overseen by Editorial Board." .
SCR:023437 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ROBOKOP" ;
NIFRID:synonym "ROBOKOP Graph Knowledgebase; Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways",
"ROBOKOP KG",
"ROBOKOP KGB",
"ROBOKOP Knowledge Graph",
"ROBOKOP Knowledge Graph Builder (KGB)" ;
definition: "ROBOKOP system consists of web based user interface, API server, and several worker servers. Biomedical knowledge graph that integrates and semantically harmonizes important knowledge sources. Contains nodes representing entities such as genes, chemicals, and diseases, and edges representing relationships between them. Abstraction layer and user interface for knowledge graphs to support question answering. Used for reasoning over structured biomedical knowledge databases as part of NCATS translator and reasoner programs. ROBOKOP Knowledge Graph Builder constructs KG and provides extensible framework to handle graph query over and integration of federated data sources." .
SCR:023438 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GlyGen" ;
NIFRID:synonym "GlyGen Portal" ;
definition: "Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression." .
SCR:023439 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TeamTat" ;
definition: "Web based collaborative text annotation tool. Used for managing multi-user, multi-label document annotation. Project managers can specify annotation schema for entities and relations and select annotators and distribute documents anonymously to prevent bias. Document input format can be plain text, PDF or BioC (uploaded locally or automatically retrieved from PubMed/PMC), and output format is BioC with inline annotations. Displays figures from full text." .
SCR:023440 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Open Molecular Software Foundation" ;
NIFRID:abbrev "OMSF" ;
definition: "Nonprofit organization with mission to advance molecular sciences by building open source software and sustainable communities for research software development. Focuses on working with hosted projects to support their software development and provide operational support, while also pursuing own community-service and community-building projects. Uses fiscal sponsorship as business model available to nonprofit organizations to assemble resources, provide support and advance open source projects in molecular sciences aligned with charitable purpose and general public interest." .
SCR:023441 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ThermoFisher Connect Platform " ;
NIFRID:synonym "Connect Platform" ;
definition: "Platform for connecting people, software, data, and equipment. Helps integrating software, instruments, and data across your lab’s existing ecosystem. Provides: workflows guide users through processes involving multiple systems;Centralized access to Thermo Fisher Scientific instrument service and expertise;Connectivity to monitor and maintain instruments and equipment;Granular data sharing controls to enhance collaboration;Secure environment." .
SCR:023442 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1717" ;
rdfs:label "University of California Davis Campus Mass Spectrometry Core Facility" ;
NIFRID:synonym "Campus Mass Spectrometry Facilities",
"University of California Davis Campus Mass Spectrometry Facilities" ;
definition: "Mass spectrometry core is offering advanced mass spectrometry services including analysis of intact molecules including peptides, proteins, oligonucleotides, polymers and small organic molecules; MALDI, LCMS or direct loop injections; High resolution accurate mass measurements and tandem MS/MS;Routine quantitation." .
SCR:023443 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1720" ;
rdfs:label "University of California Davis Biological Electron Microscopy Core Facility" ;
NIFRID:synonym "Davis UCD-BioEM",
"UCD-BioEM",
"University of California",
"University of California Davis Biological Electron Microscopy Facility" ;
NIFRID:abbrev "BioEM" ;
definition: "Provides electron microscopy imaging services, expertise, training, training in sample preparation and equipment use." .
SCR:023444 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1723" ;
rdfs:label "University of California Davis Advanced Materials Characterization and Testing Laboratory Core Facility" ;
NIFRID:synonym "Advanced Materials Characterization and Testing Laboratory",
"Davis Advanced Materials Characterization and Testing Laboratory",
"University of California" ;
NIFRID:abbrev "AMCaT" ;
definition: "Provides electron microscopes, including aberration-corrected scanning transmission electron microscopes for characterization of hard and soft materials. Provides sample preparation equipment, high-resolution x-ray diffractometer, and different optical microscopes and image analysis software." .
SCR:023445 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1719" ;
rdfs:label "University of California Davis Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "Davis UCD-Nuclear Magnetic Resonance Facility",
"UCD-Nuclear Magnetic Resonance Facility",
"University of California" ;
definition: "Provides access to NMR instrumentation for spectroscopy and imaging. Spectrometers are multinuclear and variety of liquids, solids, surface, and imaging probes are available for use. Individual training, safety and operational training can be requested" .
SCR:023446 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1721" ;
rdfs:label "University of California Davis Center for Molecular and Genomic Imaging Core Facility" ;
NIFRID:synonym "Davis UCD - Center for Molecular and Genomic Imaging",
"UCD - Center for Molecular and Genomic Imaging",
"University of California" ;
NIFRID:abbrev "CMGI" ;
definition: "Provides in vivo animal imaging and biospecimen imaging. In Vivo Preclinical Imaging services." .
SCR:023447 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1718" ;
rdfs:label "University of California Davis West Coast Metabolomics Center Core Facility" ;
NIFRID:synonym "Davis WCMC-West Coast Metabolomics Center",
"University of California",
"WCMC-West Coast Metabolomics Center" ;
definition: "Provides services for analysis of small molecules in biological samples. Specializes in discovery, identification and quantitation of many metabolites and lipids. Provides metabolomics analysis services, professional courses in metabolomics analysis and data processing." .
SCR:023448 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NuAire | LabGard ES NU-425-600E Biosafety Cabinet" ;
NIFRID:synonym "NuAire LabGard ES (Energy Saver) NU-425 Class II",
"Type A2 Biosafety Cabinets" ;
definition: "Designed for laboratory safety, proper ergonomics, and energy efficiency.Models available from GMI are 2-ft. NU-425-200, 3-ft. NU-425-300, 4-ft. NU-425-400, and 6-ft. NU-425-600. LabGard NU-425 biosafety cabinets feature control system to control blower, lights, and outlets, Minihelic gauge that measures plenum performance, and Attenumount vibration control system for attenuation of sound and vibration. Cabinets are equipped with highly efficient, energy-saving motor/blower to increase filter life and cut electricity costs." .
SCR:023449 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GFL | Water Bath" ;
definition: "GFL Water Baths models 1002 to 1013 are used for incubations and inactivations of cultures, heating media, carrying out chemical reactions or thawing samples." .
SCR:023451 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpaGRN" ;
NIFRID:synonym "spatial Gene Regulatory Networks" ;
definition: "Software Python package for inferring gene regulatory networks based on spatial gene expression data. Used for analyzing spatially resolved gene expression data. Software tool to infer TF-centred, spatial gene regulatory networks for spatially resolved transcriptomic data." .
SCR:023452 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "poppr" ;
definition: "Software R package for analysis of populations with mixed modes of sexual and clonal reproduction. Used for genetic analysis of populations with mixed reproduction." .
SCR:023453 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "vcfR" ;
NIFRID:synonym "variant call format in R" ;
definition: "Software R package to read, write, manipulate and analyze variant call format data. Facilitates easy manipulation of variant call format (VCF) data." .
SCR:023455 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Applied Biosystems | StepOne Real Time PCR System" ;
NIFRID:synonym "Applied Biosystems StepOne Real-Time PCR System",
"Applied Biosystems StepOne™ Real-Time PCR System",
"StepOne™ Real-Time PCR System" ;
definition: "StepOne Real Time PCR System is 48-well plate, low throughput RT PCR instrument. Can be setup in variety of configurations and comes with intuitive data analysis and instrument control software." .
SCR:023456 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "inoLab | pH laboratory meter pH 7310" ;
NIFRID:synonym "pH–Meter" ;
definition: "Precise pH meter with documentation function to use in quality assurance, pharmaceutical industry and everywhere GLP supported documentation is required." .
SCR:023457 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tecan | HydroSpeed plate washer" ;
NIFRID:synonym "HydroSpeed",
"Tecan HydroSpeed" ;
definition: "Advanced plate washer, designed for quick, parallel washing of entire 96- and 384-well plates. This avoids time differences between wells for uniform results. Provides full control of wash power for optimized washing of cells, beads and ELISAs. Equipped with 96 and 384 indexing wash head and optimized magnetic carriers." .
SCR:023458 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "vtree" ;
NIFRID:synonym "variable tree" ;
definition: "Software R package for calculating and drawing variable trees. Variable trees display information about nested subsets of data frame." .
SCR:023459 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoEntek | EVE Automated Cell Counter" ;
NIFRID:synonym "EVE Automated Cell Counter",
"EVE™ Automated Cell Counter" ;
definition: "Bench top size cell counter that is designed to count cells and verify viability accurately and precisely, using standard trypan blue technique and provides image analysis for cell counting." .
SCR:023460 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GFL | 3013 Shaker" ;
NIFRID:synonym "GFL Gesellschaft Fuer Labortec GFL-3013 Shaker",
"GFL Gesellschaft Fuer Labortec™ GFL-3013 Shaker",
"GFL-3013 Shaker",
"Shaker GFL 3013" ;
definition: "Shaker with rocking movements, max. load capacity 15 kg. Angle platform shaker use slow and uniform rocking motion to create reproducible growth and processing conditions at low speeds." .
SCR:023461 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cytiva | AKTA pure 25 L chromatography system" ;
NIFRID:synonym "AKTA pure 25 L chromatography system",
"ÄKTA pure 25 L chromatography system",
"ÄKTA pure™ 25 L chromatography system" ;
definition: "Chromatography system for purification in research applications. Allows for customization due to its modular design with flow rate. Available with flow rate of up to 25 mL/min or flow rate of up to 150 mL/min. Offers more than 20 hardware options for custom system, including new UV monitor.Includes Air sensor L9;CELL 2 U KPL;Conductivity monitor C9n Cpl;Injection valve V9-Inj;Instrument control unit, I9, Äkta pure; Mixer M9;Pressure monitor R9-2 with pump restrictor; Pump P9 Cpl 2x; UV Monitor U9-L Cpl;Fraction collector F9-R, Cytiva, CAT# 29011362;Superdex 200 increase 10/300 GL, Cytiva, CAT# 28-9909-44." .
SCR:023462 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eppendorf | Research plus 30-300 uL 12 channel pipette" ;
NIFRID:synonym "Eppendorf Research plus",
"Eppendorf Research plus 30 to 300 uL 12 channel pipette",
"Eppendorf Research plus 300 uL 12 channel pipette" ;
definition: "Eppendorf multichannel, manual, autoclavable, air-cushion pipette for accurate ergonomic pipetting of aqueous solutions." .
SCR:023463 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automated 2 Photon Imaging Compatible Platform for Assessing Working Memory" ;
NIFRID:synonym "Automated 2-Photon Imaging-Compatible Platform for Assessing Working Memory" ;
definition: "Open source automated platform for assessing working memory and prefrontal circuit function. Designed for automated, high-throughput assessments of working memory and simultaneous two-photon imaging in chronic stress studies. Physiology compatible behavioral platform designed specifically for studying circuit mechanisms underlying working memory and related cognitive functions in chronic stress states." .
SCR:023464 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eppendorf | Research plus 20 ��� 200 ��L yellow 1 channel pipette" ;
NIFRID:synonym "Eppendorf Research® plus 20 – 200 µL",
"yellow 1-channel pipette" ;
definition: "Mechanical and autoclavable, manual, air cushion pipette for accurate, ergonomic pipetting of aqueous solutions." .
SCR:023465 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eppendorf | Research plus 2 ��� 20 ��L yellow 1 channel pipette" ;
NIFRID:synonym "Eppendorf Research® plus 2 – 20 µL yellow 1-channel pipette" ;
definition: "Mechanical and autoclavable, manual, air cushion pipette for accurate, ergonomic pipetting of aqueous solutions." .
SCR:023466 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eppendorf | Research plus 100-1000 uL 1 channel pipette" ;
NIFRID:synonym "Eppendorf Research® plus 100-1000 uL 1-channel pipette" ;
definition: "Eppendorf manual, autoclavable, air-cushion pipette for accurate ergonomic pipetting of aqueous solutions." .
SCR:023467 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rasberry rat" ;
NIFRID:synonym "Rasberry_rat" ;
definition: "Software Python platform for recording, converting, and uploading videos to cloud and for performing scheduled video recordings. Repository also includes wiki section with comprehensive guide to setting up Raspberry Pis for this purpose. Raspberry Pis are often cheaper than camcorder and can produce HD video. They are also equipped with infrared camera, making them ideal for recordings of animals that are active in low light conditions." .
SCR:023468 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CHRONO LOG | Model 700 Whole Blood Optical Lumi Aggregometer" ;
NIFRID:synonym "700 aggregometer",
"CHRONO-LOG® Model 700 Whole Blood/Optical Lumi-Aggregometer" ;
definition: "Aggregometer exclusively used in measuring platelet aggregation to observe phenotypes." .
SCR:023469 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GloMax Discover System Software and Firmware" ;
NIFRID:synonym "Promega GloMax Discover System Software and Firmware" ;
definition: "System includes firmware and plate reader software for reading absorbance, fluorescence, or luminescence in 96-well plates." .
SCR:023470 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Diagenode | Bioruptor" ;
NIFRID:synonym "Bioruptor" ;
definition: "Sonication system for optimal shearing of biological and chemical samples." .
SCR:023471 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MEGAX" ;
definition: "Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases." .
SCR:023472 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1727" ;
rdfs:label "Mexican National Laboratory for Advanced Microscopy Core Facility" ;
NIFRID:synonym "Laboratorio Nacional de Microscop�a Avanzada-UNAM",
"Mexican National Laboratory for Advanced Microscopy",
"National Laboratory for Advanced Microscopy" ;
NIFRID:abbrev "UNAM" ;
definition: "Mexican national facility open to all sectors of scientific research and education.Offers light microscopy and image analysis services and consulting, has original research program with incorporated undergraduate and postgraduate students, and supports development of bioimaging community in Mexico through training and outreach activities." .
SCR:023475 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Plasmid Vectors" ;
definition: "Portal provides link to design and order pMTL plasmid backbones created at BBSRC/EPSRC Synthetic Biology Research Centre, Nottingham, UK, for general cloning, expression and gene engineering (random and directed) in variety of chassis, including Clostridium sp and other anaerobes,hermophilic bacilli (Geobacillus),Cupriavidus (Ralstonia), and methanotrophs, such as Methylococcus capsulatus." .
SCR:023476 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1728" ;
rdfs:label "Georgia State University Imaging Core Facility" ;
NIFRID:synonym "Imaging Core Facility" ;
definition: "Facility is located in Petit Science Center in Georgia State University downtown Atlanta campus.Provides advanced light and electron microscopy imaging based analytical capabilities through use of laser scanning confocal microscopy, biological light microscopy, and electron microscopy, etc. Services include investigations in neurosciences, biology, biomedical sciences, chemistry, geosciences, physics, and other disciplines." .
SCR:023477 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Massachusetts Amherst Cell Culture Core Facility" ;
NIFRID:synonym "Amherst - Cell Culture Core Facility",
"UMass Amhrest Cell Culture",
"University of Massachusetts" ;
definition: "Core provides space, equipment, plant and animal cell cultures, media, supplies and training on recharge basis for both academic labs and corporate partners. Labs are equipped with laminar flow hoods, incubators, centrifuges, refrigerators/freezers, basic microscopes and automated cell counters. Offers technical expertise and hands on support for custom research projects. Services include Cell Line expansion and cryopreservation;Stem cell culture;Liquid nitrogen storage;Assay Development/optimization; CRISPR based gene editing and stable clone selection; Mycoplasma testing; Lentiviral packaging, titer, transduction;Molecular biology." .
SCR:023478 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1729" ;
rdfs:label "Dartmouth College Microscopy Shared Resource Core Facility" ;
NIFRID:synonym "Dartmouth College DCC - Microscopy Shared Resource",
"DCC - Microscopy Shared Resource" ;
definition: "Light microscopy imaging facility within Dartmouth Cancer Center. Services offered include confocal microscopy with Airyscan, multispectral imaging slide scanner, high thoughput brightfield and multichannel fluorescence microscopy of live cells, multichannel TIRF microscopy, photopatterning and microfabrication." .
SCR:023479 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1731" ;
rdfs:label "Dartmouth Hitchcock Medical Center Geisel School of Medicine Pathology Shared Resource Core Facility" ;
NIFRID:synonym "DH Pathology Shared Resource",
"Geisel School of Medicine at Dartmouth DH Pathology Shared Resource" ;
definition: "Facilitates project planning, clinical validation and implementation of novel translational technology and research in fields of molecular diagnostics, molecular therapeutics, pharmacogenomics, quantitative morphologic image analysis and immunohistochemistry in CLIA-certified, CAP-accredited laboratory ensuring optimal clinical quality assurance." .
SCR:023480 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RAiD" ;
NIFRID:synonym "Research Activity Identifier" ;
definition: "Project that aims to provide persistent, unique and resolvable identifiers for research projects based on global handle system, funded by Australian Research Data Commons." .
SCR:023481 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LocaliZoom" ;
definition: "Web application for displaying high resolution image series coupled with overlaid atlas delineations. Online pan and zoom type viewer with three operating modes including Display series with atlas overlay;Create or edit nonlinear alignments; Create markup which can be exported as MeshView point clouds or to Excel for further numerical analysis." .
SCR:023482 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RodentJoystick" ;
definition: "Project features single board real time input/output system including touch sensing joysticks to quantify mouse forelimb trajectories with micron millisecond spatiotemporal resolution, which resolves mouse forelimb kinematics and further allows extraction of primitives. Joystick increases spatial precision, and reduces displacement force. Joystick is then integrated into automated home cage system to train mice in center out reach task." .
SCR:023483 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UniprotR" ;
definition: "Software R package to retrieve, cluster and visualize protein data from UniProt knowledgebase. Used to process, parse and illustrate proteomics data to summarize all required protein information in readable data frame, Excel CSV file, and/or graphical output. Generates set of graphics including gene ontology, chromosomal location, protein scoring and status, protein networking, sequence phylogenetic tree, and physicochemical properties. Supports clustering of proteins based on primary gene name or chromosomal location, facilitating additional downstream analysis." .
SCR:023484 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "maser" ;
NIFRID:synonym "Mapping Alternative Splicing Events to pRoteins" ;
definition: "Software package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events. Mapping alternative splicing events to proteins." .
SCR:023485 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rMATS" ;
definition: "Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design." .
SCR:023486 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adaptive Shrinkage in R" ;
NIFRID:abbrev "ashr" ;
definition: "Software R package for adaptive shrinkage. Implements Empirical Bayes approach for large scale hypothesis testing and false discovery rate estimation." .
SCR:023487 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AnnotationDbi" ;
definition: "Software tool to implement interface for querying SQLite-based annotation data packages. Used for manipulation of SQLite-based annotations in Bioconductor." .
SCR:023488 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "org.Mm.eg.db" ;
definition: "Software package for genome wide annotation for mouse, primarily based on mapping using Entrez Gene identifiers." .
SCR:023489 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sargasso" ;
definition: "Software Python tool to disambiguate mixed species RNA-seq reads according to their species of origin." .
SCR:023490 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_160" ;
rdfs:label "Rhode Island Hospital Molecular Pathology Core Facility" ;
NIFRID:synonym "Molecular Pathology Core of the COBRE Center for Cancer Res. Dev." ;
NIFRID:abbrev "MPCL" ;
definition: "Core of COBRE Center at department of Pathology located on sixth floor of Aldrich building at Rhode Island Hospital.Provides services, instrumentation, training and support. Equipment includes ArcturusXT laser capture microdissector, Stratagene MX3005p realtime PCR instrument, BioRad iCycler, Agilent Bioanalyzer, Olympus fluorescence-capable microscope with image analysis software, Ventana Discovery immunohistochemistry processor, microtome, cryostat, Beecher tissue arrayer and Aperio ScanScope.Tissue bank has 40 cu ft of ultra-low freezer space and provides human tumor tissue samples to all interested investigators who have received IRB approval for academic testing and research.Services include Tissue Sample Processing,Histology,Immunohistochemistry,Digital slide scanning by Aperio ScanScope,Tissue Microarrays,DNA/RNA extraction, Microdissection,Macrodissection verification by pathologist,Digital image analysis,Visium Spatial Gene Expression Assay,RNAscope Assay,Enzyme Linked Immunosorbent Assays (ELISAs),Technical assistance,Pathologist consultation,Technical assistance, Equipment use and training." .
SCR:023491 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_240" ;
rdfs:label "Rensselaer Polytechnic Institute Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "NMR Core",
"Rensselaer Polytechnic Institute NMR Core" ;
definition: "Provides access to ultra high field NMR instrumentation including probes for solution and solid state NMR, and resonators and high power gradients for diffusion and magnetic resonance microimaging. Supports research programs including structure determination of small molecules, proteins, carbohydrates, nucleic acids, and macromolecular complexes at atomic resolution, quantitative analysis of complex mixtures, metabolomics applications, diffusion analysis, characterization of materials, and MR microimaging.Expert training and assistance is available in experiment design and/or pulse sequence customization, sample preparation, data acquisition, processing, analysis, and reporting of results e.g. manuscript and/or grant preparation, in addition to comprehensive support." .
SCR:023492 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_590" ;
rdfs:label "University of Miami School of Medicine Transmission Electron Microscopy Core Facility" ;
NIFRID:synonym "Transmission Electron Microscopy (TEM) Core Facility",
"University of Miami Transmission Electron Microscopy Core Facility" ;
NIFRID:abbrev "TEM" ;
definition: "Provides access to conventional transmission electron microscope and associated sample processing services." .
SCR:023493 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_668" ;
rdfs:label "University of Maryland School of Pharmacy Mass Spectrometry Center Core Facility" ;
NIFRID:synonym "University of Maryland School of Pharmacy Mass Spectrometry Center" ;
definition: "Provides access to cutting edge technologies in mass spectrometry, methodology, and instrumentation. Provided expertise include the fields of Chemical Biology,Pharmaceutical Biology,Cancer Biology,Microbial Biology,Infectious Disease,Metabolic Disease,Chronic Pain Research,Quantitative Biosciences, Drug Discovery and Drug Development,Translational and Regulatory Sciences,Nanotechnology,.Bioinformatics and Technology Development" .
SCR:023495 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_563" ;
rdfs:label "Charite University and Berlin Institute for Health Research Central Biobank Core Facility" ;
NIFRID:synonym "Central Biobank of the Charite",
"Charite - Central Biobank Charite/BIH (ZeBanC)",
"Charite/BIH (ZeBanC)" ;
NIFRID:abbrev "ZeBanC" ;
definition: "Integrated healthcare biobank that operates under certified conditions and strict SOPs. Enables biomedical and translational researchers to perform their analyses using high quality biospecimens and data to generate reliable and reproducible research data. Core offers modular biobanking portfolio that can cover workflow from blood collection to storage, including all pre-analytical steps and their documentation. Offers spectrum of additional services ranging from DNA/RNA extraction and virtual microscopy to entire management of sample and data flow for national and international research consortia. Provides secure conventional and automated storage of samples at various temperatures as well as secure data management." .
SCR:023496 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1734" ;
rdfs:label "University of Utah Cell Imaging Core Facility" ;
NIFRID:synonym "HSC Cell Imaging Core",
"University of Utah HSC Cell Imaging Core" ;
definition: "Core offers services, training and provides access to optical microscopes and imaging.Offers collaboration for complex projects." .
SCR:023497 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_392" ;
rdfs:label "University of Massachusetts Medical School Viral Vector Core Facility" ;
NIFRID:synonym "Viral Vector Core (VVC) of the Gene Therapy Center",
"Viral Vector Core Facility" ;
NIFRID:abbrev "VVC" ;
definition: "Core uses technologies to create and produce variety of high quality viral vectors.Provides investigators with the most suitable and efficient gene transfer vectors.Vectors produced include AD, AAV, and Lenti/retro. VVC staff can assist investigators with selection of gene transfer vector, its design and potential applications. Services include AdV vector creation and production, AAV vector production, Lentiviral vector production,AAV neutralizing antibody screening and titration." .
SCR:023498 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openMINDS SANDS metadata model" ;
NIFRID:abbrev "openMINDS SANDS",
"openMINDS_SANDS" ;
definition: "One of the metadata models of openMINDS metadata framework. Composed of modular metadata schemas for spatial anchoring of neuroscience data structures, including brain atlas definitions." .
SCR:023499 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_023813" ;
rdfs:label "Atlas Ontology Model" ;
NIFRID:synonym "AtOM: Atlas Ontology Model" ;
NIFRID:abbrev "AOM",
"AtOM" ;
definition: "Ontology for describing key metadata elements of spatial reference atlases. Ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures. Identifies and defines relationships between four common atlases and characterizes their properties and organization. This model can serve as suggestion for minimum requiremens for atlases and will accelerate neuroscience data integration." .
SCR:023501 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Dartfish" ;
definition: "Commercial organization provides software tools for video and data analysis used in healthare and education.Provides performance analysis solutions for team sports and individual athletes at every level." .
SCR:023502 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DESDEO" ;
NIFRID:synonym "Decision Support for computationally Demanding Optimization" ;
definition: "Software Python framework for interactive multiobjective optimization methods." .
SCR:023503 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RIsearch" ;
NIFRID:synonym "RIsearch1",
"RIsearch2" ;
definition: "Software tool for prediction of RNA–RNA, RNA–DNA, and DNA–DNA interactions. Both RIsearch1 and RIsearch2 enable quick localisation of potential near complementary interactions between given query and target sequences. RIsearch1 performs computation with whole sequences. RIsearch2 focuses on perfect complementary seed regions and extends them on both ends. User defined seed and extension constraints makes RIsearch2 applicable to all kinds of interaction predictions (e.g., siRNA and Cas9–gRNA off-target predictions)." .
SCR:023504 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Reactome Knowledgebase" ;
NIFRID:synonym "Reactome" ;
definition: "Open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. Core unit of Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form network of biological interactions and are grouped into pathways including classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. External domain expert provides expertise, curator formalizes it into database structure, and external domain expert reviews representation. System of evidence tracking ensures that all assertions are backed up by primary literature. Website is designed to give the user graphical map of known biological processes and pathways that is also an interface. Database and website enable to find, organize, and utilize biological information to support data visualization, integration and analysis." .
SCR:023506 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Katdetectr" ;
definition: "Software R package for detection, characterization and visualization of localized hypermutated regions, often referred to as kataegis. Aims to identify putative kataegis loci from common data formats housing genomic variants." .
SCR:023507 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Puerto Rico Central Cancer Registry" ;
NIFRID:abbrev "PRCCR" ;
definition: "Part of Department of Health program for collecting, analyzing, and publishing information on all cancer cases in Puerto Rico. Information collected is obtained through active search for cancer cases, in places where cancer patients are studied, diagnosed or treated." .
SCR:023508 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "jsPsych" ;
definition: "Software JavaScript library for creating behavioral experiments in Web browser. Used to create behavioral experiments in browser using JavaScript." .
SCR:023509 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LGBTQ Primary Care Toolkit" ;
definition: "Resource to enable providers and staff of primary care clinics to promote organizational change to reduce health and healthcare disparities for SGM patients." .
SCR:023511 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tmilltracker" ;
definition: "Open source computer vision controlled treadmill system for small running animals such as insects and mice. Treadmill is controlled by Python software, allowing for flexible control of video tracking parameters, behavioral triggers, distance ran, and feedback. Used for studying locomotor behavior." .
SCR:023513 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dolphin Ceph Tracing" ;
definition: "Software tool for computerized cephalometric tracing for research related to orthodontic or orthognathic surgery. Used to analyze cephalometric radiographs and create progress superimpositions." .
SCR:023514 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RE-JOIN HEAL Consortium" ;
NIFRID:synonym "Restoring Joint Health and Function to Reduce Pain" ;
NIFRID:abbrev "REJOIN HEAL" ;
definition: "Multi institutional consortium working to map network of sensory nerves that connect to temporomandibular joint and knee. Aims to understand how these types and patterns of sensory neuron networks in joints change with disease and aging. Part of larger HEAL consortium, trans agency effort to speed scientific solutions to stem national opioid public health crisis. Joint pain is recognized as contributing factor in the use of opioids." .
SCR:023515 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fujirebio | Lumipulse G600II" ;
definition: "Chemiluminescent enzyme immunoassay (CLEIA) analyzers from Fujirebio." .
SCR:023516 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VOSviewer" ;
NIFRID:synonym "VOSviewer version 1.6.19" ;
definition: "Software tool for constructing and visualizing bibliometric networks. These networks may for instance include journals, researchers, or individual publications, and they can be constructed based on citation, bibliographic coupling, co-citation, or co-authorship relations. Offers text mining functionality that can be used to construct and visualize co-occurrence networks of important terms extracted from body of scientific literature." .
SCR:023517 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dcm2niix" ;
definition: "Software tool as DICOM to NIfTI converter." .
SCR:023518 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCRuB" ;
NIFRID:synonym "Source tracking for Contamination Removal in microBiomes",
"Source-tracking for Contamination Removal in microBiomes" ;
definition: "Software R package to help researchers address common issue of contamination in microbial studies. Well aware MiSeq decontamination program." .
SCR:023519 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DADA2" ;
definition: "Open source software R package for modeling and correcting Illumina sequenced amplicon errors. Fast and accurate sample inference from amplicon data with single nucleotide resolution." .
SCR:023520 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRO-ACT database" ;
NIFRID:synonym "Pooled Resource Open Access ALS Clinical Trials Database" ;
definition: "Publicly available repository of merged ALS clinical trials data." .
SCR:023521 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1736" ;
rdfs:label "Emory University Biostatistics Collaboration Core Facility" ;
NIFRID:synonym "The Emory Biostatistics Collaboration Core (BCC)" ;
NIFRID:abbrev "BCC" ;
definition: """Core is housed in the Department of Biostatistics and Bioinformatics in the Rollins School of Public Health of Emory University. BCC personnel are available for discussion at all stages of research, including: preparation of grants and contracts, assistance in analyzing and presenting research data, and statistical review of manuscripts in publication process.
Provides access to computer hardware and software and personnel with expertise in using major statistical, graphics, and data management packages. Offers services from database development, implementation, and maintenance to production of publication quality graphic and tabular material.BCC tasks are classified into short term tasks that can be completed within three to six months with clear deliverables.""" .
SCR:023522 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1737" ;
rdfs:label "Emory University Center for Systems Imaging Core Facility" ;
NIFRID:synonym "Center for Systems Imaging Core (CSIC CORE)",
"Emory University Center for Systems Imaging Core" ;
NIFRID:abbrev "CSIC CORE" ;
definition: "Provides cross disciplinary scientific, administrative, and educational home for in vivo imaging at Emory University. Provides services for human and animal imaging studies.Supports advancement of scientific research focused on development of imaging biomarkers, and serves to build interdisciplinary educational symposia and training programs." .
SCR:023523 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1738" ;
rdfs:label "Emory University Division of Animal Resources Core Facility" ;
NIFRID:synonym "Division of Animal Resources (DAR)",
"Emory University Division of Animal Resources" ;
NIFRID:abbrev "DAR" ;
definition: "Provides integrated team of animal care specialists, administrative professionals, veterinarians, veterinary technicians, logistics deliverers and information technology experts dedicated to high quality and comprehensive care of research animals." .
SCR:023524 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1740" ;
rdfs:label "Emory University Emory Glycomics and Molecular Interactions Core Facility" ;
NIFRID:synonym "Emory Glycomics and Molecular Interactions Core (EGMIC)",
"Emory University Emory Glycomics and Molecular Interactions Core (EGMIC)" ;
NIFRID:abbrev "EGMIC" ;
definition: "Provides access to methods and technology in area of glycomics and molecular interactions.Provides individual consultation with investigators to address questions regarding glycosylation, the most common posttranslational modification, and protein glycan interactions.Provides access to mass spectrometry and glycan microarray technologies to help understand functions of glycans and glycan binding proteins." .
SCR:023525 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1742" ;
rdfs:label "Emory University Emory Integrated Computational Core Facility" ;
NIFRID:synonym "Emory Integrated Computational Core (EICC)",
"Emory University Emory Integrated Computational Core (EICC)" ;
NIFRID:abbrev "EICC" ;
definition: "Provides computational support to Emory investigators with large datasets." .
SCR:023526 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1741" ;
rdfs:label "Emory University Emory Gnobiotic Animal Core Facility" ;
NIFRID:synonym "Emory Gnobiotic Animal Core (EGAC)" ;
NIFRID:abbrev "EGAC" ;
definition: "Offers services to experimentally manipulate microbiomes of mice in controlled environment to gain insight into important biological mechanisms." .
SCR:023527 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1744" ;
rdfs:label "Emory University Emory Integrated Metabolomics and Lipidomics Core Facility" ;
NIFRID:synonym "Emory Integrated Lipidomics Core",
"Emory Integrated Metabolomics & Lipidomics Core",
"Emory University Emory Integrated Metabolomics and Lipidomics Core" ;
NIFRID:abbrev "EILC",
"EILMC" ;
definition: "Provides quantitative analysis of lipids and soluble metabolites using cutting-edge mass spectrometry methods as a service to both clinical and basic biomedical research efforts. We deliver quantitative lipidomics and metabolomics analyses on samples from a wide variety of biological matrices, e.g. blood, serum, plasma, solid tissues, fecal/urine samples, cell extracts, etc., to support both clinical and basic research efforts." .
SCR:023528 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1746" ;
rdfs:label "Emory University Emory Multiplexed Immunoassay Core Facility" ;
NIFRID:synonym "Emory Multiplexed Immunoassay Core",
"Emory University Emory Multiplexed Immunoassay Core" ;
definition: "Core provides services involved with the latest multiplexed immunoassays." .
SCR:023529 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1743" ;
rdfs:label "Emory University Emory Integrated Genomics Core Facility" ;
NIFRID:synonym "Emory Integrated Genomics Core (EIGC)",
"Emory University Emory Integrated Genomics Core (EIGC)" ;
NIFRID:abbrev "EIGC" ;
definition: "Core helps investigators use the latest genomics technologies in their research." .
SCR:023530 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1745" ;
rdfs:label "Emory University Emory Integrated Proteomics Core Facility" ;
NIFRID:synonym "Emory Integrated Proteomics Core (EIPC)",
"Emory University Emory Integrated Proteomics Core (EIPC)" ;
NIFRID:abbrev "EIPC" ;
definition: "Core is full service proteomics facility offering Emory researchers ability to use the latest technologies in their research." .
SCR:023531 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1749" ;
rdfs:label "Emory University Emory HPLC Bioanalytical Core Facility" ;
NIFRID:synonym "Emory HPLC Bioanalytical Core",
"Emory University Emory HPLC Bioanalytical Core" ;
definition: "Core offers services to identify and quantify monoamine neurotransmitters, amino acids, purine bases, and nucleotides from variety of biological samples. Provides expertise to develop and validate HPLC methods to measure other small molecule compounds, peptides, and proteins." .
SCR:023532 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1751" ;
rdfs:label "Emory University Emory Investigational Drug Service Core Facility" ;
NIFRID:synonym "Emory Investigational Drug Service (IDS)",
"Emory University Emory Investigational Drug Service (IDS)" ;
NIFRID:abbrev "IDS" ;
definition: "Provides research pharmacy services to Emory patients, investigators and sponsors, and ensures that research drugs are handled safely, accurately and effectively. IDS strives to provide quality and efficiency in research drug management, enhance patient care in research and ensure audit readiness at all times." .
SCR:023533 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1747" ;
rdfs:label "Emory University Emory Cellular and Immunotherapy Core Facility" ;
NIFRID:synonym "Emory Cellular and Immunotherapy Core",
"Emory University Emory Cellular and Immunotherapy Core" ;
NIFRID:abbrev "ExCITE" ;
definition: "Clinical cell manufacturing facility that prepares cell and immunotherapy products under current Good Manufacturing Practices for development of investigational new drugs and diagnostics methods.Provides GMP compliant cell manufacturing and/or consultation for translational of Emory based or external research collaborations into early phase clinical trials." .
SCR:023534 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1750" ;
rdfs:label "Emory University Emory Integrated Cellular Imaging Core Facility" ;
NIFRID:synonym "Emory Integrated Cellular Imaging Core (ICI)",
"Emory University Emory Integrated Cellular Imaging Core (ICI)" ;
NIFRID:abbrev "ICI" ;
definition: "Provides light microscopy. Offers expertise in imaging for experimental needs." .
SCR:023535 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1752" ;
rdfs:label "Emory University Mouse Transgenic and Gene Targeting Core Facility" ;
NIFRID:synonym "Emory University Mouse Transgenic and Gene Targeting Core (TMF)",
"Mouse Transgenic and Gene Targeting Core (TMF)" ;
NIFRID:abbrev "TMF" ;
definition: "Provides equipment and expertise for generating and characterizing genetically altered mouse models. Please contact us so that we can discuss your experimental needs." .
SCR:023536 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1739" ;
rdfs:label "Emory University School of Medicine Flow Cytometry Core Facility" ;
NIFRID:synonym "Emory Flow Cytometry Core (EFCC)",
"Emory University Emory Flow Cytometry Core" ;
NIFRID:abbrev "EFCC" ;
definition: "Core provides sorting, sample analysis and analyzer training.Provides quantitative flow cytometric analyses on samples including blood, bone marrow, spleen, serum, plasma, solid tissues, cell extracts to support both clinical and basic research efforts. These analyses will provide insight on cell function and precursors whose abundance can be monitored as biomarkers to predict and follow progression of a wide range of diseases, such as H1N1, yellow fever, dengue, neurodegenerative diseases, stem cell studies.Provides consultations, expert training, and support for all systems and provides access to equipment." .
SCR:023537 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1753" ;
rdfs:label "Emory University Robert P. Apkarian Integrated Electron Microscopy Core Facility" ;
NIFRID:synonym "Emory University Robert P. Apkarian Integrated Electron Microscopy Core (IEMC)",
"Robert P. Apkarian Integrated Electron Microscopy Core (IEMC)" ;
NIFRID:abbrev "IEMC" ;
definition: "Core helps investigators use the latest technologies on structural research in their projects. Provides expertise in experimental needs." .
SCR:023538 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1756" ;
rdfs:label "Vanderbilt University Medical Center Vanderbilt Diet, Body Composition, and Human Metabolism Core Facility" ;
NIFRID:synonym "and Human Metabolism Core",
"Body Composition",
"Vanderbilt Diet" ;
definition: "Core provides valid, reliable, appropriate and cost effective methods to investigators that facilitate all types of human research (T1, T2 and T3) and study designs. These methods include 24 hour diet recalls, diet histories, food records/diaries, food frequency questionnaires, observed intakes and weighed intakes of all forms of dietary and nutrient intake (foods, beverages, dietary supplements, liquid nutrition supplements, enteral tube feedings, parenteral support and medications)." .
SCR:023539 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1757" ;
rdfs:label "University of Nebraska Medical Center UNMC Genomics Core Facility" ;
NIFRID:synonym "UNMC Genomics Core Facility" ;
definition: "Provides Next Generation DNA and Sanger sequencing services; single cell genomics assays by 10x Genomics, and Nanostring technology targeted gene expression assays." .
SCR:023540 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1758" ;
rdfs:label "University of California BioPACIFIC MIP Core Facility" ;
NIFRID:synonym "and Integrated Chemistry Materials Innovation Platform Core Facility",
"Automated Cellular Infrastructure",
"BioPACIFIC MIP",
"BioPACIFIC MIP Core Facility",
"BioPolymers",
"Flow" ;
NIFRID:abbrev "NSF BioPACIFIC MIP" ;
definition: "BioPolymers, Automated Cellular Infrastructure, Flow, and Integrated Chemistry Materials Innovation Platform is platform dedicated to scalable production of bio-derived building blocks and polymers from yeast, fungi, and bacteria. Automated high-throughput synthesis and characterization of bio-derived polymers aims to accelerate discovery and speed development of new high-performance materials." .
SCR:023543 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harmony" ;
NIFRID:synonym "Harmony 5.0",
"Harmony 5.1",
"Harmony High-Content Imaging and Analysis Software" ;
definition: "Software tool designed by PerkinElmer for high content screening systems. Used to quantify complex cellular phenotypes. High content analysis software." .
SCR:023544 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EraSOR" ;
NIFRID:synonym "Erase Sample Overlap and Relatedness" ;
definition: "Software Python tool for removing bias introduced from having overlapped samples between base GWAS data and target genotype data for Polygenic Risk Score analyses. Used for adjusting inflation in PRS prediction and association statistics in presence of sample overlap or close relatedness between GWAS and target samples." .
SCR:023546 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_31" ;
rdfs:label "University of Vermont Functional Brain Imaging Core Facility" ;
NIFRID:synonym "Functional Brain Imaging Core",
"University of Vermont Functional Brain Imaging Core",
"UVM MRI Center for Biomedical Imaging" ;
definition: "Core to perform functional brain imaging studies collaboratively with Department of Radiology utilizing Tesla Phillips Achieva scanner and CNRU experimental image capture and analysis system. Works collaboratively with other laboratories within Psychiatry Department to serve mutual research interests. Collaborates across Neuroscience Consortium with investigators in Departments of Neurology, Anatomy, Psychology, as well as GCRC investigators to further develop brain imaging expertise at UVM. Functional imaging experimental and analysis expertise reside in CNRU-Psychiatry. Technical personnel necessary to operate imaging program including MR physicist, fMRI radiologist, and technicians are employed by Department of Radiology in College of Medicine." .
SCR:023548 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "The World Factbook " ;
NIFRID:abbrev "CIA Factbook" ;
definition: "Presents basic realities about world in which we live in and is one of the U.S. Government’s most accessed publications. Provides basic intelligence on history, people, government, economy, energy, geography, environment, communications, transportation, military, terrorism, and transnational issues for 266 world entities." .
SCR:023549 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Google Looker Studio" ;
NIFRID:synonym "Google Data Studio",
"Looker Studio" ;
definition: "Former name Google Data Studio, is online tool for converting data into customizable informative reports and dashboards introduced by Google on March 15, 2016 as part of enterprise Google Analytics 360 suite. Online service for graphic data visualization." .
SCR:023550 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SimplyAgree" ;
definition: """Software R package and jamovi module for simplifying agreement and reliability analyses.
Functions within this package include simple tests of agreement, agreement analysis for nested and replicate data, and provide robust analyses of reliability.Used for calculating absolute agreement and estimating required sample sizes for studies of absolute agreement.""" .
SCR:023551 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BIGSdb" ;
NIFRID:synonym "Bacterial Isolate Genome Sequence Database" ;
definition: "Platform for gene-by-gene bacterial population annotation and analysis. Designed to store and analyse sequence data for bacterial isolates. Used for scalable analysis of bacterial genome variation at population level." .
SCR:023552 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "22ActionRecognitionTool" ;
definition: "Software tool for multi view child motor development dataset for AI-driven assessment of child development project." .
SCR:023553 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CeleScope" ;
definition: "Software tool as collection of bioinfomatics analysis pipelines to process single cell sequencing data generated with Singleron products. Single cell analysis pipelines developed by Singleron Biotechnologies." .
SCR:023554 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Michigan Imputation Server" ;
definition: "Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4." .
SCR:023555 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FastIndep" ;
definition: "Software tool as algorithm for finding maximal independent set of nodes in arbitrary undirected graph along with efficient implementation in C++. Used to discover unlinked markers, and unrelated individuals in populations." .
SCR:023556 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Michigan Genomics Initiative" ;
NIFRID:abbrev "MGI" ;
definition: "Collaborative research effort among physicians, researchers, and patients at the University of Michigan with goal of combining patient electronic health record data with corresponding genetic data to gain novel biomedical insights. Biobank linking genotypes and electronic clinical records in Michigan Medicine patients. MGI participants agree to provide study team with access to EHR data for clinical information and biospecimen including blood or saliva." .
SCR:023557 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rprs" ;
NIFRID:synonym "Polygenic Risk Scores" ;
definition: "Software R package for computing Polygenic Risk Scores from dosages." .
SCR:023558 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Polygenic Score Catalog" ;
NIFRID:synonym "The Polygenic Score (PGS) Catalog" ;
definition: "Open database of polygenic scores and relevant metadata required for accurate application and evaluation. Used for reproducibility and systematic evaluation." .
SCR:023559 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DLEx" ;
definition: "Web tool for retrieving available lexicon. It comes in app format, which can be downloaded from the tool's website, and in web format, which can be completed online." .
SCR:023561 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_713" ;
rdfs:label "Northwestern University Immune Monitoring Core Facility" ;
NIFRID:synonym "Immune Monitoring Core",
"Northwestern University Immune Monitoring Core" ;
definition: "Core of Comprehensive Transplant Center provides translational mechanistic studies in human solid organ and cellular transplantations. Provides assistance with human immune monitoring needs for translational and clinical transplantation research projects.Offers immune monitoring services for translational mechanistic studies." .
SCR:023562 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1760" ;
rdfs:label "Colorado State University Experimental Pathology Core Facility" ;
NIFRID:synonym "Colorado State University Experimental Pathology Facility",
"Experimental Pathology Facility" ;
NIFRID:abbrev "EPF" ;
definition: "Core provides pathologic services ranging from animal model troubleshooting, and tissue fixation to stain slide prep and immunohistochemistry. Offers expertise in slide interpretations and quantitative histopathology in anatomic and clinical pathology. Offers molecular pathology services via Nanostring nCounter equipment." .
SCR:023563 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hardware Accelerated Read Until" ;
NIFRID:abbrev "HARU" ;
definition: "Software package as heterogenous compute solution for Oxford Nanopore Technologies adaptive sampling also known as selective sequencing and Read Until. Read Until allows genomic reads to be analyzed in real-time and abandoned halfway, if not belonging to genomic region of interest. HARU takes advantage of heterogenous edge compute platforms and provides hardware acceleration using reconfigurable hardware on Multiprocessor system on chip." .
SCR:023565 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Korea Statistical Information Service" ;
NIFRID:synonym "KOSIS" ;
definition: "Republic of Korea e-Government platform for major domestic, international and North Korean statistics. Web service provides official statistics produced by statistical agencies covering more than 500 subject matters as well as the latest data on international finance and economy from international organizations i.e. IMF, World Bank, OECD." .
SCR:023566 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "caTools" ;
definition: "Software R package containing several basic utility functions including moving, rolling, running,window statistic functions, read, write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder,decoder, round-off-error-free sum and cumsum." .
SCR:023567 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fqCleanER" ;
NIFRID:synonym "fastq Cleaning and Enhancing Routine" ;
definition: "Software tool written in Bash to ease different standard preprocessing steps of short high throughput sequencing reads. Runs on UNIX, Linux and most OS X operating systems." .
SCR:023568 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "randomizeR" ;
NIFRID:synonym "Randomization for Clinical Trials" ;
definition: "Software R package for randomization of clinical trials. Provides sound scientific evidence for choice of randomization procedure, on the basis of well founded criteria. Includes functions for generating randomization sequences from various randomization procedures as well as various issues for assessment of randomization procedures." .
SCR:023569 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ListDiff" ;
definition: "Software tool that performs SET Operations including Set Intersections, Set Unions and Set Differences over lists of words, numbers etc with formatted results . Used for comparing differences between two lists." .
SCR:023570 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "easyPubMed" ;
definition: "Software R package for query NCBI Entrez and retrieve PubMed records in XML or text format. Used to process PubMed records by extracting and aggregating data from selected fields. Large number of records can be downloaded via this simple-to-use interface to NCBI PubMed API. Used to search and retrieve scientific publication records from PubMed." .
SCR:023571 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "10x Genomics | Visium Spatial Gene Expression" ;
NIFRID:synonym "Visium Spatial Gene Expression" ;
definition: "Visium Spatial Gene Expression is next-generation molecular profiling solution for classifying tissue based on total mRNA. Allows to map whole transcriptome with morphological context in FFPE or fresh frozen tissues. Used to perform spatial transcriptomics, which combines histological information with whole transcriptome gene expression profiles to provide spatially resolved gene expression. System for classifying tissue based on total mRNA. Includes two software to analyze data. Space Ranger analysis software that automatically overlays spatial gene expression information on tissue image and identifies clusters of spots with similar transcription profiles. Loupe Browser visualization software to interactively explore results." .
SCR:023572 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Snippy" ;
NIFRID:synonym "snippy" ;
definition: "Software tool for rapid haploid variant calling and core genome alignment." .
SCR:023573 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DiagrammeR" ;
definition: """Software R package to create, modify, analyze, and visualize network graph diagrams.
Graph and network visualization using tabular data in R.""" .
SCR:023574 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1762" ;
rdfs:label "University of Montreal Health Centre Rodent Metabolic Phenotyping Core Facility" ;
NIFRID:synonym "Centre Hospitalier de University de Montr�al CRCHUM-Rodent Metabolic Phenotyping Core",
"CRCHUM-Rodent Metabolic Phenotyping Core" ;
definition: "Core facility offers services unique in Canada for study of carbohydrate and energy metabolism in rodents such as routine tolerance tests of glucose, lipids, pyruvate, insulin and metabolic cages.Provides expertise in performing hyperglycemic clamps as well as Hyperinsulinemic-euglycemic clamps. Offers services for research projects carried out at the cellular or tissue level and on animals,complete metabolic phenotyping of genetically modified rodents, evaluation of effect of pharmacological or molecular interventions on carbohydrate and/or energy metabolism in healthy rodent models or in obese or diabetic models.All surgical procedures, metabolic tests, dosing and data analyses are carried out by our staff." .
SCR:023575 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D Printed Multi Pump System" ;
NIFRID:synonym "3D Printed Syringe Pump Rack" ;
definition: "System includes 3D Printed Syringe Pump Rack composed by 5 Syringe Pumps to have 2 continuous flow systems and one remaining pump. Syringe Pump is used to gradually administer small amounts of fluid to patient or for use in chemical and biomedical research. Main features include Open hardware/software, Extremely compact size ( 7cm movement range ), High precision lead screw and nut, Simple to use (command line interface), Simple to replicate, Minimal clean Design." .
SCR:023576 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1763" ;
rdfs:label "University of Florida Health Mass Spectrometry and Proteomics Core Facility" ;
NIFRID:synonym "Mass Spectrometry and Proteomics",
"University of Florida Health Mass Spectrometry and Proteomics" ;
definition: "Core provides range of mass spectrometry based proteomics services to assist with protein characterization, identification and quantification, and apply these technologies to solve relevant biological problems. Equipment including Thermo Scientific Orbitrap Fusion Tribrid mass spectrometer, Thermo Scientific Q Exactive hybrid quadrupole-Orbitrap benchtopmass spectrometer, Agilent Technologies 1100 HPLC. Services include Mini SDS-PAGE,Gel Coomassie staining,Protein/Peptide Assay,Protein Precipitation,Solution or in-gel sample digestion and high resolution LC-MS/MS using 1-4Hr gradients,High resolution LC-MS/MS using 1-4Hr gradients (self-digested samples),High resolution MS and MS/MS via direct infusion,Protein digest clean up,TMT quantification,SILAC quantification,Label free quantification,HPLC peptide separation." .
SCR:023577 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IHC Profiler" ;
definition: "ImageJ plugin for quantitative evaluation and automated scoring of immunohistochemistry images of human tissue samples. IHC profiler has been developed as standard automated scoring tool." .
SCR:023578 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPRING" ;
definition: "Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data." .
SCR:023579 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "PromoCell" ;
definition: "Life Science company providing human cell culture and cell biology products." .
SCR:023580 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Vilber" ;
definition: "Life science company that develops and manufacture imaging and analyzing systems for fluorescence, chemiluminescence and bioluminescence applications." .
SCR:023581 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Cytiva" ;
definition: "Cytiva is the new name of the former GE Healthcare Life Sciences biopharma business following its acquisition by Danaher Corporation, according to an April 1, 2020 announcement. Provider of life sciences brands such as ÄKTA, Amersham, HyClone, MabSelect and Whatman." .
SCR:023582 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1764" ;
rdfs:label "Princeton University Chemistry Core Facility" ;
NIFRID:synonym "Chemistry Core Facileties",
"Princeton University Chemistry Core Facileties" ;
definition: "Department of Chemistry houses comprehensive array of research facilities to support diversity of scientific work. Staff members expertly maintain each facility and are available to help users set up experiments or interpret results. Our resources facilitate scientific progress from giving chemists deeper understanding of their data to providing essential characterization of compounds for publication." .
SCR:023583 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1765" ;
rdfs:label "University of California Davis Health Biorepository Shared Resource Core Facility" ;
NIFRID:synonym "UC Davis Biorepository Shared Resource",
"University of California Davis Health Biorepository Shared Resource" ;
NIFRID:abbrev "BRSR" ;
definition: "Provides specimens with annotated data for clinical and basic science research purposes.Biorepository functions as centralized tissue bank to provide researchers access to cancer- and non-cancer-related specimens including fresh or frozen tissue, paraffin blocks,sections and fluids, procured and stored using international standards of best practices and protocols compliant with Office for Human Research Protection. Specimens can be obtained prospectively as part of clinical trials or accessed through UC Davis Health Clinical Laboratories, where over 5.5 million blood specimens are processed annually." .
SCR:023584 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1767" ;
rdfs:label "University of California Davis Health Combinatorial Chemistry and Chemical Biology Shared Resource Core Facility" ;
NIFRID:synonym "Davis UC Davis Combinatorial Chemistry & Chemical Biology Shared Resource",
"UC Davis Combinatorial Chemistry & Chemical Biology Shared Resource",
"University of California" ;
NIFRID:abbrev "CCCBSR" ;
definition: "Provides high throughput screening platform to discover unique chemical probes against biological targets using various one bead one compound and one bead two compound combinatorial libraries.Interacts closely with resource users on optimization of the lead compounds via focused libraries and standard medicinal chemistry techniques. Provides custom synthesis of telodendrimer based micellar nanoparticle platform for efficient drug delivery." .
SCR:023585 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1766" ;
rdfs:label "University of California Davis Health Biostatistics Shared Resource Core Facility" ;
NIFRID:synonym "Davis UC Davis Biostatistics Shared Resource",
"UC Davis Biostatistics Shared Resource",
"University of California" ;
NIFRID:abbrev "BSR" ;
definition: "Provides expertise in design, analysis and reporting of cancer related studies, including basic, translational, clinical and population based research. BSR affiliated faculty and staff work with investigators from the earliest stages of study planning. The shared resource is especially committed to mentoring early career cancer researchers." .
SCR:023586 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1769" ;
rdfs:label "University of California Davis Health Genomics Shared Resource Core Facility" ;
NIFRID:synonym "Davis UC Davis Genomics Shared Resource",
"UC Davis Genomics Shared Resource",
"University of California" ;
NIFRID:abbrev "GSR" ;
definition: "Provides expertise and comprehensive services to accomplish virtually every application of next generation sequencing based genomics research, including gene expression profiling, mutation/variant analyses, copy number analysis, epigenomics, metagenomics, single cell sequencing and spatial transcriptomics services. GSR also specializes in development of custom protocols and extensive data analysis and integrative bioinformatics support. The shared resource provides wide range of additional services for translational and clinical genomics research." .
SCR:023587 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1770" ;
rdfs:label "University of California Davis Health Immune Modeling, Analysis and Diagnostics Shared Resource Core Facility" ;
NIFRID:synonym "Analysis and Diagnostics Shared Resource",
"Davis UC Davis Immune Modeling",
"UC Davis Immune Modeling",
"University of California" ;
NIFRID:abbrev "IMADSR" ;
definition: "Clinical Laboratory Improvement Amendments certified laboratory established to provide scientific support to investigators conducting clinical studies in humans, preclinical studies in animals and/or studies in veterinary medicine. Conducts immunology based assays needed to monitor patients in clinical immunotherapy trials. Offers molecular and cellular assays for investigators in different fields, including custom assays designes." .
SCR:023588 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1771" ;
rdfs:label "University of California Davis Health Molecular Pharmacology Shared Resource Core Facility" ;
NIFRID:synonym "Davis UC Davis Molecular Pharmacology Shared Resource",
"UC Davis Molecular Pharmacology Shared Resource",
"University of California" ;
NIFRID:abbrev "MPSR" ;
definition: "Provides services to support the development and implementation of clinical trials at UC Davis Comprehensive Cancer Center. Oversees high quality collection, processing, and analysis of clinical specimens,typically but not exclusively blood specimens, for pharmacokinetic and pharmacodynamics studies. Conducts preclinical modeling of novel anti cancer agents to test hypotheses and develop scientific rationale required for translation of laboratory concepts into clinical trials, including assessment of DM/PK/PD properties." .
SCR:023589 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1772" ;
rdfs:label "University of California Davis Health In Vivo Translational Imaging Shared Resource Core Facility" ;
NIFRID:synonym "Davis UC Davis In Vivo Translational Imaging Shared Resource",
"UC Davis In Vivo Translational Imaging Shared Resource",
"University of California" ;
NIFRID:abbrev "IVTISR" ;
definition: "Provides access to in vivo imaging technologies including molecular imaging, optical imaging, quantitative physiologic and anatomic imaging, and whole body PET/CT scanning in humans and animals. Provides targeted imaging probes and tracers as well as expertise in planning, executing and analyzing in vivo imaging studies. Supports imaging studies in small animals, large animals and humans.This resource is located in three adjacent buildings in the Health Sciences district of the Davis campus:Center for Molecular and Genomic Imaging (CMGI), Genome and Biomedical Sciences Facility (small-animal imaging);Nuclear Magnetic Resonance (NMR) Facility, Tupper Hall (small-animal MRI);Center for Imaging Sciences (CIS), Veterinary School (large-animal imaging)." .
SCR:023591 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MuLan-Methyl" ;
definition: "Web tool for predicting DNA methylation sites. Identifies methylation sites for three different types of DNA methylation, namely N6-adenine, N4-cytosine, and 5-hydroxymethylcytosine. MuLan-Methyl-Multiple transformer based language models for accurate DNA methylation prediction." .
SCR:023592 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BigSeqKit" ;
definition: "Software parallel Big Data toolkit to process FASTA and FASTQ files at scale. Used to manipulate FASTA/Q files at scale with speed and scalability at its core." .
SCR:023593 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Reads2Map" ;
definition: "Software package as collection of WDL workflows to build linkage maps from sequencing reads. WDL workflows to build genetic maps from sequencing reads." .
SCR:023594 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:veryfasttree" ;
rdfs:label "VeryFastTree" ;
definition: "Software tool for speeding up estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies." .
SCR:023595 a "Research",
owl:NamedIndividual ;
rdfs:label "KinasePhos 3.0" ;
definition: "Software tool for redesign and expansion of prediction on kinase specific phosphorylation sites. Machine learning based kinase specific phosphorylation site prediction tool." .
SCR:023596 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1773" ;
rdfs:label "Stellenbosch University Microscopy Unit Core Facility" ;
NIFRID:synonym "Stellenbosch University SU_CAF Microscopy Unit",
"SU_CAF Microscopy Unit" ;
definition: "Provides access to advanced light and electron microscopes as well as imaging expertise. Applications range from material science to biomedical research. Provides custom image analysis, comprehensive sample preparation for light and electron microscopy, and consultation." .
SCR:023597 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fastcluster" ;
definition: "Software Python library for hierarchical clustering. Fast Hierarchical, Agglomerative Clustering Routines for R and Python." .
SCR:023598 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "single cell RNA-seq Data Visualization and Analysis" ;
NIFRID:abbrev "scDVA" ;
definition: "Interactive web server to explore and analyze single cell RNA-seq data. R shiny based tool used for single cell RNA-seq data visualization and analysis." .
SCR:023602 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BehaviorDEPOT" ;
definition: "Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs." .
SCR:023603 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Leica Biosystems" ;
definition: "Medical devices company that develops and supplies clinical diagnostics to pathology market. It is also research, instrument, and medical device company as well as division of Danaher Corporation with headquarters Wetzlar, Germany." .
SCR:023604 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Keyence" ;
definition: "Direct sales organization that develops and manufactures automation sensors, vision systems, barcode readers, laser markers, measuring instruments, and digital microscopes. Founder Takemitsu Takizaki. Headquarters Osaka, Osaka, Japan." .
SCR:023605 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Ionpath" ;
definition: "Pioneer in high definition spatial proteomics, tissue imaging and analysis to accelerate medical discovery and improve human health. With MIBI technology and expertise of pathology and data science teams, Ionpath provides actionable insights to translational and clinical researchers at leading pharmaceutical, biotechnology, and research organizations in immuno-oncology, immunology, neuroscience, and infectious disease research." .
SCR:023606 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Standard BioTools" ;
NIFRID:synonym "Standard BioTools Inc." ;
definition: "American company engaged in design, manufacture and sale of biological research equipment based on integrated fluidic circuit technology. Founders leveraged their semiconductor experience to create integrated circuits that carried fluids rather than electrons." .
SCR:023607 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Zeiss Microscopy" ;
NIFRID:synonym "Carl Zeiss NTS Ltd.",
"ZEISS Microscopy" ;
definition: "Manufacturer of light, electron, X-ray and ion microscope systems. Offers solutions for correlative microscopy. Provides products and services for life sciences, materials and industrial research, as well as education and clinical practice." .
SCR:023608 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Bruker Daltonics" ;
definition: "Bruker Daltonics is subsidary of Bruker Corporation American. Bruker is manufacturer of scientific instruments for molecular and materials research, as well as for industrial and applied analysis." .
SCR:023609 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Andor" ;
definition: "Provides development and manufacture of high performance scientific digital cameras, microscopy systems and spectrographs for academic, industrial and government applications." .
SCR:023610 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Zyla 4.2" ;
rdfs:label "Andor | Zyla 4.2 sCMOS" ;
NIFRID:synonym "Zyla 4.2 PLUS",
"Zyla 4.2 sCMOS" ;
definition: "Zyla 4.2 PLUS is the latest sCMOS technology advancement from Andor. At its heart, Zyla 4.2 PLUS benefits from latest generation sCMOS sensor technology, delivering a further 10 % boost in QE, resulting in an unprecedented 82% QEmax." .
SCR:023611 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SCN400" ;
rdfs:label "Leica | SCN400 slide scanner" ;
definition: "Provides fully digitized image of speciment that can be viewed and edited from virtually anywhere." .
SCR:023612 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DAG-deepVASE" ;
NIFRID:synonym "Directed Acyclic Graphs using deep-learning VAriable SElection" ;
definition: "Software tool for identifying nonlinear causal relations and estimating their effect size help to understand complex disease pathobiology." .
SCR:023613 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ionpath | MIBIscope System" ;
NIFRID:synonym "MIBIscope",
"MIBIscope System" ;
definition: "Imaging platform, enabling phenotypic profiling and spatial analysis of tissue microenvironment. Enables over 40 markers to be visualized simultaneously with single step staining and single step imaging." .
SCR:023614 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NextSeq 2000" ;
rdfs:label "Illumina | NextSeq 2000 system" ;
definition: "Sequencing system supports range of methods such as exome sequencing, target enrichment, single-cell profiling." .
SCR:023615 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker timsTOF fleX with MALDI-2" ;
definition: "Instrument for probing molecular content of sample with MALDI-2. The timsTOF fleX is fully functional high speed, high sensitivity ESI instrument for all X-Omics analyses, combined with high spatial resolution Matrix-Assisted Laser Desorption Ionization (MALDI) source and stage specifically designed for resolving molecular distributions and bringing spatial dimension to OMICS analyses.MALDI-2 uses laser post-ionization to enhance and enrich the MALDI experiment providing access to chemical classes typically opaque to MALDI with enhanced sensitivities." .
SCR:023616 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GE: Healthcare | IN Cell Analyzer 2200" ;
NIFRID:synonym "GE IN Cell Analyzer 2200",
"IN Cell Analyzer 2200" ;
definition: "Cell imaging system for fast, automated imaging in fixed and live cells. Instrument can rapidly image cells using laser autofocusing, LED light source and CMOS camera." .
SCR:023617 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BZ-X800" ;
rdfs:label "Keyence | BZ-X800 Fluorescent Microscope" ;
NIFRID:synonym "BZ-X800 Fluorescent Microscope" ;
definition: "Automated high-resolution microscope for Life Science research. Provided with BZ-X800 Analyzer software. You can purchase different applications for the BZ-X800 analysis software to perform specific analyses, such as the BZ-H4C Hybrid Cell Count Application, which is used to count stained areas." .
SCR:023618 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Orbitrap Eclipse Tribrid mass spectrometer" ;
NIFRID:synonym "Orbitrap Eclipse Tribrid mass spectrometer" ;
definition: "Mass spectrometer designed for most difficult analytical challenges. Incorporates inventions in ion transmission and control, extended m/z range, and real-time decision making. System suited for proteomics, structural biology, small-molecule, and biopharmaceutical characterization experiments." .
SCR:023619 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mia" ;
definition: "Software R package with several tools for microbiome data analysis." .
SCR:023621 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TargetRanger" ;
definition: "Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines." .
SCR:023622 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneRanger" ;
definition: "Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types." .
SCR:023623 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kinase Enrichment Analysis 3" ;
NIFRID:abbrev "KEA3" ;
definition: "Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations." .
SCR:023624 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "X2K Web" ;
NIFRID:synonym "eXpression2Kinases (X2K) Web" ;
NIFRID:abbrev "X2K" ;
definition: "Web service to predict involvement of upstream cell signaling pathways, given signature of differentially expressed genes. Used to linking expression signatures to upstream cell signaling networks." .
SCR:023625 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "White Adipose Atlas" ;
definition: "Single cell atlas of human and mouse white adipose tissue." .
SCR:023626 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TIGER Data Portal" ;
NIFRID:synonym "Translational Human Pancreatic Islet Genotype Tissue-Expression Resource" ;
definition: "Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets." .
SCR:023627 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Liver cell atlas" ;
definition: "Portal to search liver single cell RNA-sequencing datasets. Datasets for expression of genes or proteins (when CITE-seq was performed). To search for gene enter the official gene name. To search for protein please click to see specific names to use for different markers included." .
SCR:023628 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IDF Diabetes Atlas" ;
definition: "Atlas aims to provide regular information on state of diabetes. Reports, produced annually, epidemiological and diabetes related impact data including the impact of type 2 diabetes in indigenous peoples, type 1 diabetes across all age groups, COVID-19 among people with diabetes, and diabetes foot-related complications." .
SCR:023629 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Diabetes Data and Hypothesis Hub" ;
NIFRID:synonym "Diabetes Data and Hypothesis Hub (D2H2)" ;
NIFRID:abbrev "D2H2" ;
definition: "Platform that facilitates data driven hypothesis generation for diabetes and related metabolic disorder research community. Curated transcriptomics datasets from various Type 2 Diabetes studies are made available for download, visualization, and enrichment analysis." .
SCR:023630 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hetnet Connectivity Search" ;
NIFRID:synonym "heterogeneous network",
"Heterogeneous network Connectivity Search" ;
NIFRID:abbrev "Hetnet" ;
definition: "Web app that allows users to search for the most important paths connecting any two nodes in Hetionet." .
SCR:023631 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microsoft PowerPoint" ;
definition: "Presentation software developed by Microsoft Corporation. Part of Microsoft Office suite. Used for creating slideshows and delivering presentations." .
SCR:023633 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "forestplot" ;
definition: "Software R package that allows for multiple confidence intervals per row, custom fonts for each text element, custom confidence intervals, text mixed with expressions, and more. Advanced Forest Plot using 'grid' graphics. Used to extend the use of forest plots beyond meta analyses." .
SCR:023634 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford University Quantitative Sciences Unit Core Facility" ;
NIFRID:synonym "Stanford University Quantitative Sciences Unit" ;
NIFRID:abbrev "QSU" ;
definition: "Collaborative unit of faculty and staff with diverse data science expertise in Biomedical Informatics Research Division in Department of Medicine. Members collaborate with investigators to address questions about disease and human health through leading in practice of data science. QSU members are data scientists with expertise including data inference, evidence synthesis, computational biology, missing data, prediction modeling, statistical computing, database creation, and software development. QSU leads and collaborates on large scale scientific projects that includes serving as data coordinating center for large multi center randomized clinical trials." .
SCR:023635 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "spark-xml-utils" ;
definition: "Software library to filter documents based on XPath expression, return specific nodes for XPath/XQuery expression, transform documents using XSLT stylesheet. By providing some basic wrappers to Saxon, spark-xml-utils library exposes some basic XPath, XQuery, and XSLT functionality that can readily be leveraged by any Spark application." .
SCR:023636 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "spark-xml" ;
definition: "Software library for parsing and querying XML data with Apache Spark, for Spark SQL and DataFrames. XML data source for Spark SQL and DataFrames." .
SCR:023637 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Apache Zeppelin" ;
definition: "Web based notebook that enables data driven, interactive data analytics and collaborative documents with SQL, Scala, Python, R and more. Multi purposed web based notebook which brings data ingestion, data exploration, visualization, sharing and collaboration." .
SCR:023638 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1777" ;
rdfs:label "University of Montreal CR-HMR Flow Cytometry Core Facility" ;
NIFRID:synonym "CR-HMR Flow Cytometry Core Facility" ;
definition: "Offers sorting and flow cytometry services. Equipment includes Cytek Aurora, BD ARIA III, SONY cell sorters and Cytek Aurora, 2 BD LSRFortessa X-20, BD FACSCelesta,BD LSR II, CANTO A analyzers. Individual mandatory training is necessary to access this facility. ARIA III cell sorter as well as SONY SH800 are equipped with negative pressure hood allowing sorting of potentially infectious samples including human cells from healthy donors." .
SCR:023639 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1778" ;
rdfs:label "Texas A and M University AggieFab Nanofabrication Core Facility" ;
NIFRID:synonym "AggieFab",
"AggieFab Nanofabrication Facility" ;
definition: "Shared nano/microfabrication facility located on the 1st floor of the Frederick E. Giesecke Engineering Research Building at Texas A&M University. Provides equipment for range of microscale and nanoscale fabrication of diverse materials, nanopatterning and deposition equipment. Equipment include Zeiss Orion Helium Ion Microscope/Nanofab, FEI Helios DualBeam Focused Ion Beam (FIB), ASM Atomic Layer Deposition (ALD) tool, Clustex Multi-target deposition tool, Oxford Estrelas DRIE tool, Heidelberg MLA150 Maskless Lithography tool." .
SCR:023640 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1776" ;
rdfs:label "Creative Biolabs Non-IgG Antibody Isotypes Services" ;
NIFRID:synonym "CBL (Germany) Non-IgG Antibody Isotypes",
"Non-IgG Antibody Isotypes" ;
definition: "Provides high quality custom non-IgG antibody services." .
SCR:023641 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CRISPR Target Finder" ;
definition: "Web tool for identifying CRISPR target sites and evaluating their specificity. CRISPR Target Finder uses TagScan and algorithms based on large scale analyses of CRISPR-Cas9 specificity in cell lines and animals published to date to identify potential off target cleavage sites for given CRISPR target." .
SCR:023642 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Face Homecage Running Wheel" ;
definition: "Open source, printable, open faced running wheels for mice residing in home cage that is automated to collect locomotor information such as distance traveled, wheel direction, and velocity. Running wheel system available on GitHub contains code and information to create and run running wheels. System consists of 3D printed wheel, Raspberry Pi 0 W, and supporting components." .
SCR:023643 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LabChart" ;
definition: "LabChart data analysis software creates platform for all of your recording devices to work together, allowing you to acquire biological signals from multiple sources simultaneously and apply advanced calculations and plots as your experiment unfolds.Used for collection and analysis of signals. Recommended for researchers and educators who want the capabilities without modules and automation of specific measurements." .
SCR:023644 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FACSymphony_A3" ;
rdfs:label "BD Biosciences | FACSymphony A3 Cell Analyzer" ;
NIFRID:synonym "BD FACSymphony A3" ;
definition: "Fluorescence activated cell analyzing instrument by BD Biosciences. Allows for the simultaneous detection of up to 30 parameters and 28 colors." .
SCR:023645 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1779" ;
rdfs:label "Pennsylvania State University Huck Institutes of the Life Sciences Genomics Core Facility" ;
NIFRID:synonym "HUC-Genomics",
"Huck Institutes Genomics Core Facility",
"Huck Institutes of the Life Sciencies Genomics Core Facility",
"PennState Huck Institutes of the Life Sciencies Genomics Core Facility",
"PennState UHC Genomics",
"PennState UHC Genomics Core Facility" ;
definition: "Genomics Core Facility provides services including Whole-genome and transcriptome sequencing of non-model organisms, Amplicon sequencing for metagenomic studies, Differential expression analysis of mRNA and miRNA, Degradome sequencing, ChIP and RIP sequencing." .
SCR:023648 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Natural Scenes Dataset" ;
NIFRID:abbrev "NSD" ;
definition: "Portal for large scale fMRI dataset conducted at ultra high field strength at Center of Magnetic Resonance Research at University of Minnesota. Dataset consists of whole brain, high resolution fMRI measurements of healthy adult subjects while they viewed thousands of color natural scenes over course of scan sessions. While viewing these images, subjects were engaged in continuous recognition task in which they reported whether they had seen each given image at any point in experiment. These data constitute massive benchmark dataset for computational models of visual representation and cognition, and can support wide range of scientific inquiry." .
SCR:023650 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EVOS_M5000" ;
rdfs:label "Thermo Fisher | EVOS M5000 Imaging System" ;
NIFRID:synonym "EVOS M5000 Imaging System" ;
definition: "Microsoft system includes integrated digital inverted benchtop microscope for four-color fluorescence, transmitted-light, and color imaging. Provides interchangeable optics with autofocus, single-click multi-channel image acquisition.3.2 Megapixels, monochrome, CMOS camera. Offers software for acquisition, analysis, and automated cell counting." .
SCR:023651 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sciex" ;
definition: "Manufacturer of mass spectrometry instrumentation used in biomedical and environmental applications. Originally started by scientists from the University of Toronto Institute for Aerospace Studies, it is now part of Danaher Corporation with the SCIEX R&D division still located in Toronto, Canada." .
SCR:023652 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BPG" ;
NIFRID:synonym "BoutrosLab.plotting.general" ;
definition: "Software R package contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in creation of these plots. Functions to create publication quality plots." .
SCR:023653 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bam readcount" ;
NIFRID:synonym "bam-readcount" ;
definition: "Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads." .
SCR:023654 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ConsensusCruncher" ;
definition: "Software tool that suppresses errors in next generation sequencing data by using unique molecular identifers to amalgamate reads derived from same DNA template into consensus sequence." .
SCR:023655 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MAVIS" ;
NIFRID:synonym "and Illustration of Structural variants",
"Annotation",
"Merging",
"Validation" ;
definition: "Software Python command line tool for post processing of structural variant calls. Framework for rapid generation of structural variant consensus, to visualize genetic impact and context as well as process both genome and transcriptome data." .
SCR:023656 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SViCT" ;
NIFRID:synonym "Structural Variant detection in Circulating Tumor DNA" ;
definition: "Software tool for detecting structural variations from cell free DNA containing low dilutions of circulating tumor DNA." .
SCR:023657 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "panelcn.mops" ;
NIFRID:synonym "panelcn.MOPS" ;
definition: "Software R package as CNV detection tool for targeted NGS panel data. Extension of cn.mops package. Used for detecting copy number variations in targeted next generation sequencing panel data. Suitable to use for clinical geneticists for routine clinical diagnostics." .
SCR:023658 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VarDict" ;
definition: "Software tool as variant caller for both single and paired sample variant calling from BAM files. Implements amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads.Novel and versatile variant caller for next generation sequencing in cancer research." .
SCR:023659 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kinase Associated Neural Phospho Signaling" ;
NIFRID:abbrev "KANPHOS" ;
definition: "Database system that provides phosphorylated sites and information about which substrates are phosphorylated by specific kinase and which extracellular stimuli activate or inhibit protein phosphorylation via intracellular signaling cascades." .
SCR:023660 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Minimum Information about Biosynthetic Gene cluster" ;
NIFRID:synonym "MIBiG 2.0",
"MIBiG 3.0" ;
NIFRID:abbrev "MIBiG" ;
definition: "MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters." .
SCR:023661 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Database Commons" ;
definition: "Curated catalog of worldwide biological databases to provide landscape of biological databases throughout the world and enable easy retrieval and access to specific collection of databases of interest. Catalog of worldwide biological databases as well as their curated meta information and derived statistics." .
SCR:023662 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100013615" ;
rdfs:label "AlphaFold Protein Structure Database" ;
NIFRID:abbrev "AlphaFold DB" ;
definition: "Database of protein structure predictions by AlphaFold that are freely and openly available to global scientific community. Included are nearly all catalogued proteins known to science. Provides programmatic access to and interactive visualization of predicted atomic coordinates, per residue and pairwise model confidence estimates and predicted aligned errors." .
SCR:023663 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Resting State Hemodynamic Response Function Retrieval and Deconvolution" ;
NIFRID:abbrev "rsHRF" ;
definition: "Software toolbox for resting state HRF estimation and deconvolution analysis. Matlab and Python toolbox that implements HRF estimation and deconvolution from resting state BOLD signal. Used to retrieve optimal lag between events and HRF onset, as well as HRF shape. Once that HRF has been retrieved for each voxel/vertex, it can be deconvolved from time series or one can map shape parameters everywhere in brain and use it as pathophysiological indicator. Input can be 2D GIfTI, 3D or 4D NIfTI images, but also on time series matrices/vectors. Output are three HRF shape parameters for each voxel/vertex, plus deconvolved time series, and number of retrieved pseudo events. All can be written back to GIfTI or NIfTI images." .
SCR:023664 a owl:NamedIndividual ;
NIFRID:synonym "Catholic University of Louvain Institute of Experimental and Clinical Research Flow Cytomerty Platform",
"CytoFlux",
"Flow Cytomerty Platform" .
SCR:023665 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1784" ;
rdfs:label "University of Pennsylvania Institute for RNA Innovation Engineered mRNA and Targeted Nanomedicine Core Facility" ;
NIFRID:synonym "Engineered mRNA and Targeted Nanomedicine Core" ;
definition: "Core focuses on exploring mRNA technology and lipid nanoparticles for various applications including tissue and cell targeting. Offers Optimization and production of in vitro transcribed mRNA, Small scale production of sequence optimized in vitro transcribed mRNA, Incorporation of modified nucleosides to modulate activity, Off the shelf in vitro transcribed mRNA encoding reporter genes or cancer antigens,Labelled mRNA for nanoparticle tracking and microscopy, Encapsulation into commercially available proprietary and non proprietary lipid nanoparticles through LNP core." .
SCR:023666 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cellsnake" ;
definition: "Software tool for single cell RNA sequencing analysis. Command line tool for easy and scalable single cell RNA sequencing analysis." .
SCR:023667 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RatHeadphones" ;
NIFRID:synonym "Ratphones" ;
definition: "Repository for highly controlled sound presentation in freely moving rats. Provides all necessary information for building, adjusting, and using Ratphones to reliably present auditory stimulation to freely moving rats. Used for 3D printing of headphones designed for auditory psychophysics in behaving rats." .
SCR:023668 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sequence Demarcation Tool" ;
NIFRID:synonym "SDTv1.2" ;
NIFRID:abbrev "SDT" ;
definition: """Software tool for classification of virus sequences based on sequence pairwise identity.
Virus classification tool based on pairwise sequence alignment and identity calculation.
Used to enable general virologists to consistently classify newly determined virus full genome sequences according to ICTV endorsed pairwise genetic identity based genus, species and strain demarcation recommendations. Also usable as amino acid sequence classifier for characterisation of novel highly divergent viruses.""" .
SCR:023669 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VirusDetect " ;
definition: "Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs." .
SCR:023670 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurocare | PowerMag View! System" ;
NIFRID:synonym "PowerMAG View! 3D-Neuronavigation system" ;
definition: "System visualizes electromagnetic hot spot of the coil at individual, anatomical data record. MR-based navigation system integrated into TMS flexible arm enables optimal alignment with camera. Used to carry out neuronavigation." .
SCR:023671 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ActiView" ;
definition: "Software tool writen in LabVIEW is acquisition program for BioSemi ActiveTwo system. Designed to display all ActiveTwo channels on screen and save all data to network disk in .BDF format. Basic acquisition program can be expanded with modules on client specification. Used for acquisition of EEG/ECG/EMG signals, as well as for data coming from additional sensors such as AnalogInputBox (AIB), digital triggers from USB2 receiver and extra sensors connected to AD-box. Several reference selections, filtering and downsampling options are provided." .
SCR:023672 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "10x Genomics" ;
definition: "American biotechnology company that designs and manufactures gene sequencing technology used in scientific research." .
SCR:023673 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1785" ;
rdfs:label "University of British Columbia Gut4Health Microbiome Core Facility" ;
NIFRID:synonym "UBC-Gut4Health Microbiome Core",
"University of British Columbia UBC-Gut4Health Microbiome Core" ;
definition: "Facilitates microbiome studies for researchers at British Columbia Children Hospital Research Institute and University of British Columbia. Core offers processing and storing biological specimens, and sequencing and analysis of microbial communities for various research studies, including basic science, clinical, translational, and epidemiological projects." .
SCR:023674 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "metaGOflow" ;
definition: "Software pipeline for marine Genomic Observatories data analysis. Used to address challenges of analysis of European Marine Omics Biodiversity Observation Network data." .
SCR:023675 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FuzDrop" ;
definition: "Web tool to predict probability of proteins to undergo liquid-liquid phase separation.Used to perform sequence based identification of both droplet promoting regions and of aggregation promoting regions within droplets. Used to predict droplet promoting regions and proteins, which can spontaneously phase separate." .
SCR:023676 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OmicsBox" ;
NIFRID:synonym "BioBam OmicsBox",
"OmicsBox v.3.0.29" ;
definition: "Software aplication for NGS data analysis of genomes, transcriptomes, and metagenomes. Allows researchers to easily process large and complex data sets, and streamline their analysis process. Software is structured in different modules, each with specific set of tools and functions designed to perform different types of analysis, such as de-novo genome assemblies, genetic variation analysis, differential expression analysis, and taxonomic classifications of microbiome data, including the functional interpretation and rich visualizations of results." .
SCR:023677 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MSMC2" ;
NIFRID:synonym "MSMC",
"Multiple Sequentially Markovian Coalescent" ;
definition: "Software application to infer population size history and population separation history from whole genome sequencing data. Used for inferring demographic history and population structure through time from genome sequences. MSMC2 is successor of MSMC." .
SCR:023678 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KGML-xDTD" ;
NIFRID:synonym "Knowledge Graph-based Machine Learning framework for explainably predicting Drugs Treating Diseases" ;
definition: "Software repository contains all scripts and instructions for running KGML-xDTD model, which is Knowledge Graph-based Machine Learning framework for explainably predicting Drugs Treating Diseases." .
SCR:023679 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COSMIIC HORNET" ;
NIFRID:synonym "Cleveland Open Source Modular Implant Innovators Community" ;
NIFRID:abbrev "COSMIIC" ;
definition: "Open source neurostimulation and recording hardware instrument platform. Part of the SPARC project. COSMIIC is based on the Networked Neuroprosthesis developed at Case Western Reserve University." .
SCR:023680 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Segment Anything Model" ;
NIFRID:synonym "Meta Segment Anything Model" ;
NIFRID:abbrev "SAM" ;
definition: "Promptable segmentation system with zero shot generalization to unfamiliar objects and images, without need for additional training. Github repository provides code for running inference with SegmentAnything Model, links for downloading trained model checkpoints, and example notebooks that show how to use the model." .
SCR:023681 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HORNET CENTER FOR AUTONOMIC NERVE RECORDING AND STIMULATION SYSTEMS" ;
NIFRID:abbrev "CARSS" ;
definition: "Parylene MEA Fabrication is related to SPARC. Repository for standard fabrication procedure for Parylene C microelectrode arrays and similar devices." .
SCR:023682 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RatInABox" ;
definition: "Software Python toolkit for modelling locomotion and neuronal activity in continuous environments. Used to model realistic rodent locomotion and generate synthetic electrophysiological data from spatially modulated cell types." .
SCR:023683 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1786" ;
rdfs:label "Dartmouth Geisel School of Medicine Biostatistics and Bioinformatics Shared Resource Core Facility" ;
NIFRID:synonym "Biostatistics and Bioinformatics Shared Resource",
"Dartmouth Geisel School of Medicine Biostatistics and Bioinformatics Shared Resource" ;
definition: "Core offers comprehensive statistical and bioinformatic analysis, consultation, collaboration, and technical services." .
SCR:023684 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gigapixel AI" ;
NIFRID:synonym "Gigapixel AI Image Enhancement Software" ;
definition: "Software to increase image resolution. Gigapixel AI’s neural networks are continuously trained on sample images to increase resolution of different subjects like portraits, wildlife, landscapes, architecture and image types like DSLR, web/compressed, CG." .
SCR:023685 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microsoft Windows Snipping Tool" ;
NIFRID:synonym "Snipping Tool to capture screenshots" ;
definition: "Platform about software application that helps you capture device's screenshot. Snipping Tool is used to make changes or notes, then save, and share. Used to make changes afer taking snapshot to copy words or images from all or part of PC screen." .
SCR:023686 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Arkansas MicroCT Imaging Consortium for Research and Outreach" ;
NIFRID:synonym "MicroCT Imaging Consortium for Research and Outreach" ;
NIFRID:abbrev "MICRO" ;
definition: "MicroCT Imaging Consortium for Research and Outreach is home of University of Arkansas’s micro computed tomography system. MICRO is nested within and managed by the Center for Advanced Spatial Technologies which is dedicated to applying geospatial technologies in research, teaching, and service." .
SCR:023687 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nikon | XT H 225 ST uCT system" ;
NIFRID:synonym "Nikon XTH 225 ST microfocus Computer Tomography system" ;
definition: "Provides insight into the inside of components and specimens, allowing users to visualize, analyze and measure complex internal geometry as well as surfaces, all non-destructively. Versatile microfocus CT system for high resolution inspection in R&D and failure analysis of components ranging from tiny plastic connectors up to aluminum castings." .
SCR:023688 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "TIANGEN" ;
definition: "Biological high-tech enterprise integrating R&D, production, sales and customer service. Provides services from sample storage to nucleic acid extraction and detection. Reagent supplier." .
SCR:023689 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ATHLATES" ;
definition: "Software package for determining HLA genotypes for individuals from Illumina exome sequencing data. Program applies assembly, allele identification and allelic pair inference to short read sequences, and applies it to data from Illumina platforms." .
SCR:023690 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LOHHLA" ;
NIFRID:synonym "Loss Of Heterozygosity in Human Leukocyte Antigen" ;
definition: "Software tool to evaluate HLA loss using next-generation sequencing data. Computational tool to determine HLA allele-specific copy number from sequencing data." .
SCR:023691 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PONDR" ;
NIFRID:synonym "Predictor of Natural Disordered Regions" ;
definition: "Web tool to predict order and disorder from amino acid sequence. Used to predict of natural disordered regions in proteins." .
SCR:023692 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Axio_Observer_5" ;
rdfs:label "Zeiss | Axio Observer 5" ;
NIFRID:synonym "Zeiss Axio Observer 5 microscope" ;
definition: "Inverted microscope Axio Observer 5 for transmitted light brightfield LED and differential interference contrast. Used for demanding multimodal imaging." .
SCR:023693 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss | Axio Observer 3" ;
NIFRID:synonym "Zeiss Axio Observer 3 microscope" ;
definition: "Inverted microscope Axio Observer 3 for transmitted light brightfield LED and differential interference contrast. Used for demanding multimodal imaging." .
SCR:023694 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Axio_Observer_7" ;
rdfs:label "Zeiss | Axio Observer 7" ;
NIFRID:synonym "Zeiss Axio Observer 7 microscope" ;
definition: "Inverted microscope Axio Observer 7 for transmitted light brightfield LED and differential interference contrast. Used for demanding multimodal imaging." .
SCR:023695 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford Spectrum Biostatistics Epidemiology and Research Design Core Facility" ;
NIFRID:synonym "Stanford CTSA-sponsored Biostatistics Epidemiology and Research Design (BERD)" ;
NIFRID:abbrev "BERD" ;
definition: "Core provides CTR investigators with support for study design development, data curation and management, and analytic strategies. Provides infrastructure through Data Studio; Clinical Office Hours; Data Science Navigation." .
SCR:023696 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2509" ;
rdfs:label "Stanford University School of Medicine Cancer Institute Biostatistics Shared Resource Core Facility" ;
NIFRID:synonym "Stanford Biostatistics Shared Resource",
"Stanford Cancer Institute Biostatistics Shared Resource" ;
NIFRID:abbrev "BSR" ;
definition: "Core provides statistical support to SCI members by engages them on their data related needs. Specifically, BSR members assist researchers at each stage of study’s lifecycle, including project design, mid study evaluation and interpretation and reporting of results. In addition, BSR members mentor SCI investigators in research methods. BSR assists with development and review of proposed studies and planning of research related data management systems." .
SCR:023697 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MR-PRESSO" ;
NIFRID:synonym "Mendelian Randomization Pleiotropy RESidual Sum and Outlier" ;
definition: "Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing." .
SCR:023699 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Global Alzheimers Association Interaction Network" ;
NIFRID:abbrev "GAAIN" ;
definition: "Open access integrated research platform, which links scientists, shared data, and analysis tools to accelerate Alzheimer’s disease research, disease preventions, treatments and cure. Unites diverse and geographically distributed network of data partners to foster cohort discovery, collaboration and sharing. Researchers can discover clinical, genetic, imaging and other data collected across many independent studies." .
SCR:023700 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "merTools" ;
NIFRID:synonym "mixed effect regression Tools" ;
definition: "Software R package for extracting results from mixed effect model objects fit with 'lme4' package. Allows construction of prediction intervals efficiently from large scale linear and generalized linear mixed effects models. Used for analyzing mixed effect regression models." .
SCR:023701 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Metaphor" ;
NIFRID:synonym "Metagenomic Pipeline for Short Reads" ;
definition: "Software workflow for streamlined assembly and binning of metagenomes. Used for assembly and binning of metagenomes. Performs quality control, basic functional and taxonomic annotation of assembled contigs, using NCBI COG database." .
SCR:023702 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IPEV" ;
NIFRID:synonym "Identification of Prokaryotic and Eukaryotic Virus" ;
definition: "Software tool to identify of Prokaryotic and Eukaryotic virus derived sequences in virome using deep learning. Used to calculate set of scores that reflect probability that input sequence fragments are prokaryotic and eukaryotic viral sequences." .
SCR:023703 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroBridge" ;
definition: "Platform for data discovery to enhance the reuse of clinical neuroscience and neuroimaging data. Provides NeuroBridge ontology, and combines machine learning with ontology based search of both neuroimaging repositories like XNAT databases and open access full text journals such as PubMed Central. Connects researchers with potential neuroimaging data, by searching text of papers describing neuroimaging studies that contain information on neuroimaging data." .
SCR:023704 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TIDE" ;
NIFRID:synonym "Tracking of Indels by DEcomposition" ;
definition: "Web tool to estimates spectrum and frequency of small insertions and deletions generated in pool of cells by genome editing tools such as CRISPR/Cas9, TALENs and ZFNs. Used for quantification of small indels in DNA of targeted cell pool. Provides rapid and reliable assessment of genome editing experiments of target locus." .
SCR:023705 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_583" ;
rdfs:label "University of Miami Miller School of Medicine Biomarkers and Immunoassay Laboratory Core Facility" ;
NIFRID:synonym "U of Miami Biomarkers and Immunoassay Laboratory",
"University of Miami Miller School of Medicine Biomarkers and Immunoassay Laboratory",
"University of Miami Miller School of Medicine Diabetes Research Institue Biomarkers and Immunoassay Laboratory",
"University of Miami U of Miami Biomarkers and Immunoassay Laboratory" ;
definition: "Provides biomarker testing for human clinilcal research studies across multiple disciplines.Provides expertise with chemistry, special chemistry, radioimmunoassay, nephelometric and ELISA and multiplexing assay methods utilizing automated and manual procedures. Laboratory has Clinical Laboratory Improvement Act certification and follows guidelines established by CLIA for quality control and proficiency testing to ensure results. Core coordinates proper pre-analytical sample collection and processing procedures with project leaders; performs biochemical assays on samples submitted to the laboratory by investigators in manner that assures strict quality control both within and between assay runs; reports results to project staff in timely fashion; makes available expertise and technical assistance for establishing and validating new methodologies to support University of Miami investigators." .
SCR:023706 a owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_710" ;
rdfs:label "Northwestern University Analytical BioNanoTechnology Equipment Core Facility" ;
NIFRID:synonym "Analytical BioNanoTechnology Equipment Core (ANTEC)",
"Northwestern University Analytical BioNanoTechnology Equipment Core (ANTEC)" ;
NIFRID:abbrev "ANTEC" ;
definition: """Facility houses research equipment for evaluating materials and biological preparations, and offers 3D printing and 3D scientific illustration services. Available instruments include
Cytation3 Automated Microscope Plate Reader, BioTek Inc.; Zetasizer Nano ZSP, Malvern Inc.; Lyophilizers FreeZone 6 and 6 Plus, Labconco; Azure300, Chemiluminescent Gel Imager, Azure Biosystems; Real-Time PCR I-cycler CFX-Connect, Bio-Rad Laboratories; Centrifuge Sorvall X1R, ThermoFisher; MCR302 Rheometer, Anton Paar Inc.; Plasma Cleaner, Harrick Plasma; NanoSight300, Malvern Instruments (Evanston); IncuCyte Live Cell Analysis System, Sartorius; Piuma Nanoindenter, Optics 11; Freezer/Mill, SPEX Sample Prep; J-1500 Circular Dichroism Spectrometer, JASCO.""" .
SCR:023707 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1788" ;
rdfs:label "Catholic University of Louvain Genomics platform Core Facility" ;
NIFRID:synonym "Catholic University of Louvain Genomics platform-PGEN",
"UCLouvain-PGEN",
"University Catholique de Louvain UCLouvain-PGEN" ;
NIFRID:abbrev "PGEN" ;
definition: "Core provides services including Sequencing (Sanger, NGS); Genotyping (micro array, fragment analysis); Molecular karyotyping (micro array); Bioinformatics (exomes [WES], genomes [WGS], gene panels [panels], transcriptome [RNAseq]). Equipment includes Illumina MiSeq sequencer;Ion Torrent Ion Proton sequencer and an Ion Chef for sample preparation;HPC cluster for bioinformatics processing of NGS data (WES, WGS, panels, RNASeq);Affymetrix microarray platform;Sanger sequencer and fragment analyser;Contracts for outsourcing WES, WGS and RNAseq, according to public procurement regulations;Highlander software, developed in-house, for variant analysis from NGS data." .
SCR:023708 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SODAR Core" ;
definition: "Software Django based framework for building scientific data management web apps. Framework for Django web application development." .
SCR:023709 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AltamISA" ;
definition: "Software Python API for ISA-Tab files. It is an alternative implementation of ISA-tools data model and ISA-Tab file format." .
SCR:023710 a owl:NamedIndividual ;
rdfs:label "VarFish" ;
definition: "Web application for quality control, filtering, prioritization, analysis, and user based annotation of DNA variant data with focus on rare disease genetics. Comprehensive DNA variant analysis for diagnostics and research." .
SCR:023711 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kiosc" ;
definition: "Software for web application to control Docker containers that run webserver. Used to facilitate presenting analysis results interactively by running Docker images that are constricting any application that offers web interface. Any image can be loaded, and Kiosc manages access to web interface of application." .
SCR:023712 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ;
rdfs:label "LabNet" ;
definition: "Open source software for parallel control over multiple behavioral systems.C++ optimized control layer software to give access to Raspberry Pi connected hardware. Suitable for time critical operations, and to be simple to expand. Used for general automation in experimental laboratories with its control PC located at some distance." .
SCR:023713 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Frictionless Data" ;
definition: "Open source software package for building data infrastructure including data management, data integration, data flows, etc. Includes various data standards and provides software to work with data." .
SCR:023714 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurodesk" ;
definition: "Open source platform provides containers to support suite of neuroimaging software. Provides containerised data analysis environment to facilitate reproducible analysis of neuroimaging data. Analysis pipelines for neuroimaging data rely on specific versions of packages and software, and are dependent on their native operating system." .
SCR:023716 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LipidSearch" ;
NIFRID:synonym "LipidSearch 5.0",
"LipidSearch 5.1" ;
definition: "Software for automated identification and relative quantitation of lipids. Provides automated identification of lipids and integrates entire dataset into concise report showing statistical differences between sample groups." .
SCR:023717 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1791" ;
rdfs:label "Texas A and M University Health Institute of Biosciences and Technology Microphysiological Lead Optimization and Toxicity Screening Core Facility" ;
NIFRID:synonym "TAMU-Microphysiological Lead Optimization and Toxicity Screening facility (MLOTS)",
"Texas A&M Health Science Center TAMU-Microphysiological Lead Optimization and Toxicity Screening facility (MLOTS)" ;
NIFRID:abbrev "MLOTS" ;
definition: "Supports lead optimization programs and has established roster of medium throughput microphysiologic screening platforms including tissue- and tumor-on-a-chip platforms, organoid, and spheroid culture systems that will be used to evaluate efficacy and toxicity of new lead compounds and drug combinations.Provides resources to identify toxic liabilities in lead series molecules before entering pre-clinical or clinical testing. MLOTS can evaluate NME for cardiovascular, neuro, or liver toxicity relative to reference standards using in vitro screening platforms. Facility will potentially enhance the effectiveness of CPRITs drug discovery programs." .
SCR:023718 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PoreSpy" ;
definition: "Software package as collection of image analysis functions used to extract information from 3D images of porous materials typically obtained from X-ray tomography. Software Python toolkit for quantitative analysis of porous media images." .
SCR:023719 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1793" ;
rdfs:label "University of Pittsburgh Dietrich School Glass Shop Core Facility" ;
definition: "Core is responsible for fabricating and repairing intricate pieces of glassware and apparatus, as well as constructing complete high vacuum systems." .
SCR:023720 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1794" ;
rdfs:label "University of Pittsburgh Dietrich School Machine Shop Core Facility" ;
definition: "Core specializes in mechanical design, fabrication, and repair of research equipment and instrumentation." .
SCR:023721 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JAX Animal Behavior System" ;
NIFRID:abbrev "JABS" ;
definition: "Video based phenotyping platform for laboratory mouse. Provides complete details of software and hardware, including 3D designs used for data collection. Data acquisition system consists of video collection hardware and software, behavior labeling and active learning app, and online database for sharing classifiers. Hardware and software solution collects high quality data for behavior analysis." .
SCR:023722 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "oncoboxlib" ;
definition: "Software library to calculate Pathways Activation Levels. It takes file that contains gene symbols in HGNC format, their expression levels for one or more samples and calculates PAL values for each pathway in each sample." .
SCR:023723 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OncoboxPD" ;
NIFRID:synonym "Oncobox Pathway Databank" ;
definition: "Structured curated collection of protein based and of metabolic human molecular pathways. Human molecular pathways database with tools for activity calculating and visualization.All pathways are functionally classified according to GO terms enrichment patterns. All pathway participants, their interactions and reactions are uniformly processed and annotated, and are ready for numeric analysis of experimental expression data.For every comparison graph is generated summarizing top up and down regulated pathways." .
SCR:023724 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lumenera | Infinity 2-1R USB Microscopy Camera" ;
NIFRID:synonym "INFINITY2-1R 1.4 Megapixel USB 2.0 Microscopy Camera CCD",
"Infinity2-1R 1.4 Megapixel USB 2.0 Microscopy Camera CCD" ;
definition: "Scientific microscope camera for documentation and image analysis. Has dynamic range of 64 dB allowing users to image unevenly lit samples. Allows for long exposure times of several minutes." .
SCR:023725 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus | CKX41 Inverted Microscope" ;
definition: "CKX41 inverted microscope suitable for regular cell observation including GFP and other fluorescence applications. High angle tilting head is for simple visual checks, while advanced Universal Infinity System 2 (UIS2) optics produce images. Olympus relief contrast increases visibility with non-glass cell culture vessels and improves productivity with its pre centered slider. Post acquisition analysis, documentation, and archiving can be achieved with digital cameras and software." .
SCR:023726 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Preprocessing tools for oligonucleotide arrays" ;
NIFRID:synonym "affycoretools" ;
definition: "Software R package to analyze oligonucleotide arrays at probe level. Supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). Used for annotation of Affymetrix Gene Array data." .
SCR:023727 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1449" ;
rdfs:label "Montpellier Imaging Resources Core Facility" ;
NIFRID:synonym "Montpellier Imaging Resources",
"Montpellier Ressources Imagerie" ;
definition: "Imaging and cytometry facility of the Montpellier area." .
SCR:023728 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AlcoR" ;
definition: "Software tool for simulation, computation, and visualization of low compexity regions in biological data. Used for alignment free simulation, mapping, and visualization of low complexity regions in FASTA data. Provides ability of fast sequence characterization through low complexity regions, ideally for scenarios entangling presence of new or unknown sequences. Effective in whole genomes, specifically those reconstructed with support of long reads." .
SCR:023729 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HTXImaging | Sublimator" ;
definition: "Automated MALDI matrix deposition system offering speed, reproducibility, and smallest available crystals for sub-micron resolution mass spectrometry imaging. Features rectangular vacuum chamber that achieve sublimation conditions extremely quickly to maximize efficiency for imaging MS sample preparation." .
SCR:023730 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HTXImaging | SepQuant dropletProbe" ;
definition: "Allows liquid surface extraction of analytes on surfaces and further analysis in HPLC-MS detector. Surface sample to be analyzed is mounted in custom sample tray. Then optical image of mounted sample is acquired using flatbed scanner controlled with DropletProbe Premium software." .
SCR:023731 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HTXImaging | M3+ Sprayer" ;
NIFRID:synonym "equipment",
"instrument",
"M3+ Sprayer TM MALDI Imaging Sample Preparation System",
"M3+ Sprayer™️ MALDI Imaging Sample Preparation System",
"MALDI matrix sprayer",
"sprayer",
"USEDit" ;
definition: "Sample preparation platform offering automated advanced MALDI matrix sprayer." .
SCR:023732 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HTXImaging | TM-Sprayer" ;
NIFRID:synonym "adjust both gas flow rate and nozzle velocity",
"control drying time",
"equipment",
"heat matrix solution",
"image resolution",
"intrument",
"preventing analyte delocalization",
"preventing large matrix crystals formation",
"TM-Spraye TM MALDI Sample Preparation System",
"TM-Sprayer™️ MALDI Sample Preparation System",
"USEDit" ;
definition: "Allows users to adjust both gas flow rate and nozzle velocity to control drying time, preventing analyte delocalization and formation of large matrix crystals, known to create hot spots on MALDI images. Allows to heat matrix solution as it is being applied to their sample. By increasing temperature of matrix solution, absorption of matrix into sample is increased, resulting in greater MALDI image resolution." .
SCR:023733 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HTXImaging | M5 Sprayer" ;
definition: "Sprayer builds on capabilities of HTX TM-Sprayer providing innovative M5 chassis, high velocity stage and heated sample holder drawer. Sample plate holder is mounted on drawer mechanism to allow easy loading of samples, better protection of user and better alignment of various plate types. New High-Velocity XY stage allows nozzle displacement speed of up to 5,600mm/min and expands process range. Super dry spray can be achieved at high flow rates of solvent further improving instrument performance. E/Z trough gutter design improves chemical containement and is easy to remove and clean. Bulkhead connectors are directly mounted on it to also allow easy access to in line filter." .
SCR:023734 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "HTX Technologies" ;
NIFRID:synonym "HTX Technologies LLC." ;
definition: "Company offers sample preparation solutions for Mass Spectrometry Imaging. HTX delivers customized solutions for sample preparation and workflow automation of advanced analytical platforms." .
SCR:023735 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1796" ;
rdfs:label "Dartmouth Health Hitchcock Medical Center Biorepository Core Facility" ;
NIFRID:synonym "DH Biorepository and ORO lab",
"The Dartmouth-Hitchcock Health Biorepository",
"The Dartmouth-Hitchcock Health Biorepository (DH-Biorep)" ;
NIFRID:abbrev "DH-Biorep" ;
definition: "Institutional resource collaboratively run by Office of Research Operations and Department of Pathology and Laboratory Medicine that provides services in support of Dartmouth Research Communities and in alignment with Institutional Review Board approved protocols including Clinical Trials. Provides collection, processing, storage, and distribution of annotated human bio-specimens to clinicians and other investigators in support of clinical trials, industry sponsored projects, and scientific investigations." .
SCR:023738 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCOM" ;
NIFRID:synonym "Synergistic COMpetition" ;
definition: "Software application to Pan-cancer characterization of ncRNA synergistic competition. Used to predict ncRNA synergistic competition network from gene expression data and predicted ncRNA-related ceRNA networks." .
SCR:023739 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Automated Lightweight Provenance Capture" ;
definition: "Software Python package for the capture of provenance information during the execution of Python scripts that process data. Alpaca provides a simple API for recording the details of the functions being executed, the data flow, and a description of parameters used. Using simple Python decorators, this is accomplished with minimal code instrumentation and user intervention. Provenance information is structured and serialized according to a model based on the W3C PROV format. In addition, provenance information can be simplified and prepared for interactive visualization by the researcher." .
SCR:023740 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1797" ;
rdfs:label "University of Texas at Austin Advanced Protein Therapeutics Core Facility" ;
NIFRID:synonym "The University of Texas at Austin UT Austin Advanced Protein Therapeutics Core",
"UT Austin Advanced Protein Therapeutics Core" ;
NIFRID:abbrev "APT" ;
definition: "Core catalyzes translation of scientific discoveries into novel protein cancer therapies. Offers therapeutic antibody and enzyme discovery, engineering, and optimization services." .
SCR:023741 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1798" ;
rdfs:label "University of California Berkeley QB3 Cell and Tissue Analysis Core Facility" ;
NIFRID:synonym "QB3 Cell and Tissue Analysis Facility",
"University of California Berkeley QB3 Cell and Tissue Analysis Facility" ;
definition: "Facility provides cell culture equipment and instrumentation needed to grow and assess mammalian cells including flow cytometry, automated epifluorescence, confocal, and multiphoton imaging, as well as histology suite with cryosectioning equipment." .
SCR:023742 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TrumpetPlots" ;
definition: "Software R package to visualize relationship between allele frequency and effect size in genetic association studies." .
SCR:023743 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "clusterSim" ;
definition: "Software R package used for searching for optimal clustering procedure for data set." .
SCR:023744 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bibliometrix" ;
definition: "Software R package for comprehensive science mapping analysis. Used for quantitative research in scientometrics and bibliometrics that includes all main bibliometric methods of analysis." .
SCR:023745 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zonation 5" ;
NIFRID:synonym "Zonation 5 v1.0" ;
definition: "Spatial prioritization software used to identify priority areas to support conservation planning, land use planning, ecological impact avoidance and other similar tasks." .
SCR:023746 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GADM" ;
NIFRID:synonym "Database of Global Administrative Areas" ;
definition: "Platform provides maps and spatial data for all countries and their sub-divisions. You can browse maps or download data to make your own maps." .
SCR:023747 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss Zen Lite" ;
NIFRID:synonym "ZEISS ZEN lite" ;
definition: "Software tool for basic image acquisition and analysis. Zeiss ZEN microscopy software to control of axiocam microscope cameras, image transformation and measurements, image processing, image alignment for correlative microscopy, various visualization options." .
SCR:023748 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1799" ;
rdfs:label "University of Texas at San Antonio Stem Cell Core Facility" ;
NIFRID:synonym "UTSA Stem Cell Core" ;
definition: "Provides service, advice and training across spectrum of induced pluripotent stem cell workflow, from adult tissue to gene edited differentiated progeny. Provided services include Isolation and cryopreservation of cells from adult tissues, Reprogramming of adult tissues to IPSCs, Full quality control panel ensuring high quality iPSCs, Gene editing of pluripotent stem cells, Custom research utilizing pluripotent stem cells and their 2D and 3D differentiated progeny, Consultation and project planning assistance." .
SCR:023750 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ViewPoint MicroZebraLab" ;
NIFRID:synonym "MicroZebraLab" ;
definition: "Software tool to extract cardiovascular parameters from transmitted light videos of zebrafish embryos or larvae. Used to investigate live and in non-invasive way scope of zebrafish larvae physiological parameters. Measures heartbeat and blood flow." .
SCR:023752 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cancer Genome Interpreter" ;
NIFRID:abbrev "CGI" ;
definition: "Platform that systematizes interpretation of cancer genomes and makes it automatic. Web tool to annotate genomic alterations and interpret their possible role in tumorigenesis and in response to anti cancer therapies. Used to support identification of tumor alterations that drive disease and/or which may be therapeutically actionable. Analyses mutations including single nucleotide changes and small insertions/deletions, copy number alterations including gene amplifications and deletions and translocations." .
SCR:023753 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuralGlider | Inserter" ;
NIFRID:synonym "NeuralGlider Neural Implant Inserter" ;
definition: """Inserter for precise electrode positioning, reduced tissue damage and standardized insertions, enabling researchers to obtain single and multi unit recordings immediately following insertion. Used to simplify surgical procedures and data analysis pipelines.
Inserter uses ultrasonic micro vibration to reduce forces and resultant dimpling during neural implant insertions. Reduced insertion force facilitates slow 0.1 mm/s, accurate implant insertions while minimizing displacement/dimpling of cortical surface, helping to preserve integrity of underlying neural tissue.""" .
SCR:023754 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Similarity Ensemble Approach" ;
NIFRID:abbrev "SEA" ;
definition: "Web tool to relate proteins based on set wise chemical similarity among their ligands. Used to rapidly search large compound databases and to build cross target similarity maps." .
SCR:023755 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Relative Expression Software Tool" ;
NIFRID:abbrev "REST" ;
definition: "Software tool for group wise comparison and statistical analysis of relative expression results in real-time PCR. Used to compute expression ratio, based on real-time PCR efficiency and crossing point deviation of unknown sample versus control. Compares two groups, with up to 16 data points in sample and 16 in control group, for reference and up to four target genes." .
SCR:023756 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SwissTargetPrediction" ;
definition: "Web tool to estimate the most probable macromolecular targets of small molecule, assumed as bioactive. Prediction is founded on combination of 2D and 3D similarity with library of known actives on proteins from three different species." .
SCR:023757 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform" ;
NIFRID:synonym "TCMSP database" ;
NIFRID:abbrev "TCMSP" ;
definition: "Pharmacology platform of Chinese herbal medicines that captures relationships between drugs, targets and diseases. Database includes chemicals, targets and drug-target networks, and associated drug-target-disease networks, as well as pharmacokinetic properties for natural compounds involving oral bioavailability, drug-likeness, intestinal epithelial permeability, blood-brain-barrier, aqueous solubility." .
SCR:023758 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hamamatsu | FDSS/uCELL Kinetic Plate Imager" ;
definition: "Laboratory screening system that compactly integrates technologies developed in drug discovery screening. Simultaneous measurement and analysis of kinetics of a sample’s fluorescence or luminescence intensity in all wells at the time of compound addition are made possible by the high sensitivity two-dimensional sensor camera and dispenser head (96 tip type / 384 tip type). Screening various compounds at high throughput is enabled by measurement under the same conditions with no time lag between wells." .
SCR:023759 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hamamatsu | FDSS-GX Kinetic Plate Imager" ;
NIFRID:synonym "FDSS-GX Kinetic Plate Imager" ;
definition: "Kinetic plate imager optimized for 96-, 384-, and 1536-well for high throughput screening, enabling whole microplate imaging and simultaneous injections to all wells. System achieves high sensitivity imaging with qCMOS sensor, and highly accurate and repeatable micro-dispensing by adopting 1536 ch dispensing unit capable of dispensing variable volumes. By combining optional parts, robot free semi automation system can be built according to user's purpose." .
SCR:023760 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hamamatsu | NanoZoomer S210 Digital slide scanner" ;
NIFRID:synonym "NanoZoomer S210 Digital slide scanner" ;
definition: "NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S210 provides high performance capable of handling large number of slides." .
SCR:023761 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hamamatsu | NanoZoomer S360 Digital slide scanner" ;
NIFRID:synonym "NanoZoomer S360 Digital slide scanner" ;
definition: "NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S360 is ideal for use in hospitals and clinical laboratories." .
SCR:023762 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hamamatsu | NanoZoomer S60 Digital slide scanner" ;
NIFRID:synonym "NanoZoomer S60 Digital slide scanner" ;
definition: "NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S60 supports brightfield imaging, fluorescence imaging and double size slides., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:023763 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hamamatsu | NanoZoomer-SQ Digital slide scanner" ;
NIFRID:synonym "NanoZoomer-SQ Digital slide scanner" ;
definition: "NanoZoomer is a family of whole slide scanners that convert glass slides into high resolution digital data by high speed scanning. Desktop single slide compact scanner for creating whole slide images of single tissue slides." .
SCR:023764 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hamamatsu | NanoZoomer S20 Digital slide scanner" ;
NIFRID:synonym "NanoZoomer S20 Digital slide scanner" ;
definition: "NanoZoomer series is family of whole slide scanners that rapidly scan glass slides to convert them to digital data. NanoZoomer S20 is compact, high speed, and adaptable scanner." .
SCR:023765 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LI-COR | Odyssey Classic Imager" ;
NIFRID:synonym "Odyssey Classic",
"Odyssey Classic Imaging System" ;
definition: "Odyssey Classic Imaging System provides flexible, multifunctional platform to accommodate variety of applications. Western blot imager, plate reader, slide scanner, luminescence imager. Performs membrane-, plate-, gel-, and slide based assays." .
SCR:023766 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cytiva | Biacore 4000" ;
NIFRID:synonym "Biacore 4000",
"Biacore TM 4000",
"Biacore™ 4000 surface plasmon resonance system" ;
definition: "High throughput Surface Plasmon Resonance system with high quality interaction data for better informed decision making in antibody selection, drug discovery and more., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:023767 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1802" ;
rdfs:label "University of Nebraska Medical Center Bioinformatics and Systems Biology Core Facility" ;
NIFRID:synonym "Bioinformatics and Systems Biology Core",
"University of Nebraska Medical Center Bioinformatics and Systems Biology Core" ;
NIFRID:abbrev "BSBC" ;
definition: "Core fosters research and teaching activities related to bioinformatics and systems biology at UNMC. Provides infrastructure, resources, and educational training in bioinformatics with ultimate goal of promoting synergistic research activities at the intersection of computational and experimental disciplines. Used to analyze biomolecular datasets including DNA, RNA, proteins, etc." .
SCR:023768 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1804" ;
rdfs:label "Children's Hospital of Philadelphia Research Institute CHOP Biorepository Resource Center Core Facility" ;
NIFRID:synonym "Biorepository Resource Center (BioRC)",
"CHOP Biorepository Resource Center" ;
NIFRID:abbrev "BioRC" ;
definition: "Core with capacity for approximately 2 million to 3 million samples, serves CHOP’s biobanking needs, avoiding specimen duplication, preserving precious materials, and providing organized data and materials. The BioRC operates under the following principles: An Operational Committee, which coordinates central and investigator-specific biobanking resources and programs at CHOP, governs and approves requests to utilize the BioRC; BioRC facilitates integration and enhancement of access to information about biorepository specimens and resources; BioRC assists investigators in developing new projects that require the collection and processing of shareable samples not currently available, or helps investigators with existing projects who would like to migrate storage and management of their shareable banked specimens and data to the BioRC. BioRC institutes and follows best-practice standard procedures for collection, processing, and storage of samples to ensure high quality specimens and data for all CHOP investigators." .
SCR:023769 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1803" ;
rdfs:label "University of Nebraska Medical Center Biosafety Level 3 Core Facility" ;
NIFRID:synonym "Biosafety Level 3 Core Facility" ;
definition: "Facility provides safe and secure work area for qualified and authorized researchers to perform studies that involve work with biohazarad materials. Negative air pressure handling system, secure entrance and exit doors, five individual and secure Principal Investigator (PI)-assigned working suites, two pass-through autoclaves, annually certified biosafety cabinets, and personal protective equipment contribute to biosafety of each researcher using this facility." .
SCR:023770 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ContainerProfiler" ;
definition: "Software tool supports profiling resource utilization including CPU, memory, disk, and network metrics of containerized tasks. Resource utilization metrics are obtained across three levels: virtual machine (VM)/host, container, and process. Implementation leverages facilities provided by Linux operating system that is integral with Docker containers." .
SCR:023772 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Akoya Biosciences | PhenoImager" ;
NIFRID:synonym "PhenoImager" ;
definition: "Digital pathology imager for spatial phenotyping.Provides accurate quantitative assessment of multiple immune phenotypes while capturing their tissue context and spatial distribution within tumor microenvironment." .
SCR:023773 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Akoya Biosciences | PhenoCycler-Fusion" ;
NIFRID:synonym "Akoya PhenoCycler Fusion" ;
definition: "PhenoCycler-Fusion system is integrated platform combining automated, ultrahigh-plex cycling platform, Akoya PhenoCycler, and its high-speed imaging platform, PhenoImager (formerly Phenoptics), into end-to-end, integrated workflow." .
SCR:023774 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Akoya Biosciences" ;
definition: "Spatial biology company offering solutions for high parameter tissue analysis from discovery through clinical and translational research, enabling development of more precise therapies for immuno-oncology and other drug development applications." .
SCR:023775 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChatGPT" ;
definition: "Artificial Iinteligence chatbot that uses natural language processing to create humanlike conversational dialogue. Notable for enabling users to refine and steer conversation towards desired length, format, style, level of detail, and language used. Sibling model to InstructGPT, which is trained to follow instruction in prompt and provide detailed response." .
SCR:023776 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Poly Peak Parser" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 25,2025. Web tool to parse Sanger sequencing chromatograms with double peaks into wildtype and alternative allele sequences. Used to separate chromatogram data containing ambiguous base calls into wildtype and mutant allele sequences.Used for identification of unknown indels using sanger sequencing of polymerase chain reaction products." .
SCR:023777 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CRISPRscan" ;
definition: "Web tool for predictive sgRNA-scoring that captures sequence features affecting Cas9/sgRNA activity in vivo. Scoring algorithm to help select the best gRNAs for CRISPR." .
SCR:023778 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Grammarly" ;
definition: "Software to correct spelling and grammar." .
SCR:023780 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Azure_600" ;
rdfs:label "Azure Biosystems | 600 Western Blot Imaging System" ;
NIFRID:abbrev "AZURE 600" ;
definition: "System offers two channel, laser based IR and chemiluminescent detection, with speed and sensitivity of film, with ability to image visible fluorescent dyes, standard EtBr and protein gels, and infrared laser excitation for quantitative Western blot imaging in NIR." .
SCR:023781 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lnc2cancer" ;
NIFRID:synonym "lnc2Cancer 3.0" ;
definition: "Manually curated database of experimentally supported lncRNAs associated with various human cancers. Cancer long non coding RNA database. Lnc2Cancer 3.0 is updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data." .
SCR:023782 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Wind Integration National Dataset Toolkit" ;
NIFRID:synonym "WIND Toolkit" ;
NIFRID:abbrev "WIND" ;
definition: "United States national wind dataset. Provides high spatial and temporal resolution wind power, wind power forecast, and meteorological data for 7-year period at over 126,000 locations throughout continental United States. The largest publicly available wind power data set in the world. Used for wind energy integration studies. It is accessible through Web-based API." .
SCR:023783 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Life Sciences Institute Imaging Core",
"LSI Imaging Advanced Bioimaging Core",
"LSI Imaging Core",
"LSI Imaging Facility",
"UBC LSI Imaging Core Facility" .
SCR:023784 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AnimalTA" ;
NIFRID:synonym "Animal Tracking and Analysis" ;
definition: "Software video tracking tool for tracking and analysing animal movement in different environments." .
SCR:023785 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1806" ;
rdfs:label "University of Freiburg Medical Center Lighthouse Core Facility" ;
NIFRID:synonym "UF-Lighthouse Core Facility",
"University of Freiburg UF-Lighthouse Core Facility" ;
NIFRID:abbrev "LCF" ;
definition: "Core specializes in areas of flow cytometry and cell sorting; light microscopy including confocal, widefield fluorescence, high content screening, lightsheet, slide scanning, highly multiplexed microscopy; and digital PCR / QPCR. It is located at University of Freiburg Medical Center and hosts institutions including Dept. of Medicine I, Center for Chronic Immunodeficiency (CCI), CCCF / DKTK, and Medical Faculty of University of Freiburg." .
SCR:023786 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1807" ;
rdfs:label "South Dakota State University Functional Genomics Core Facility" ;
NIFRID:synonym "SDSU-Functional Genomics Core Facility",
"South Dakota State University SDSU-Functional Genomics Core Facility" ;
definition: "Core provides access and training on range of instruments in areas of genomics, molecular biology, imaging, and chemical/metabolite analysis to support research on the SDSU campus." .
SCR:023787 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneWalk" ;
definition: "Software for individual genes functions determination that are relevant in particular biological context and experimental condition. Quantifies similarity between vector representations of gene and annotated GO terms through representation learning with random walks on condition specific gene regulatory network. Similarity significance is determined through comparison with node similarities from randomized networks." .
SCR:023788 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KEGGgraph" ;
NIFRID:synonym "Kyoto Encyclopedia of Genes and Genomes graph" ;
definition: "Software R package interface between KEGG pathway and graph object as well as collection of tools to analyze, dissect and visualize these graphs." .
SCR:023789 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PathVisio " ;
NIFRID:synonym "PathVisio 3" ;
definition: "Software visualization tool for biological pathways. Pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. Developed in Java and can be extended with plugins." .
SCR:023790 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenSAFELY" ;
definition: "The code that runs the OpenSAFELY platform used for analysis of electronic health records data." .
SCR:023791 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_354" ;
rdfs:label "University of Lethbridge Canadian Center for Hydrodynamics Core Facility" ;
NIFRID:synonym "Canadian Center for Hydrodynamics (CCH)",
"University of Lethbridge Canadian Center for Hydrodynamics (CCH)" ;
definition: "Provides comprehensive solution characterization of macromolecules or macromolecular interactions and assemblies. This includes description of stoichiometry, size composition, cargo loading.Core is equipped with analytical ultracentrifuges featuring multi-wavelength UV-visible detection, as well as Rayleigh interference optics and fluorescence emission detection for fluorescent tags with 488 nm excitation." .
SCR:023792 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of Lethbridge; Alberta; Canada" ;
definition: "University of Lethbridge with campuses in Lethbridge and Calgary, is one of Canada\"s leading research institutions." .
SCR:023794 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | Thunder Imager Live Cell system" ;
NIFRID:synonym "THUNDER Imager",
"Thunder Imager",
"THUNDER Imager Live Cell",
"Thunder Imaging system" ;
definition: "Advanced widefield microscope enabling use of 3D specimens with camera based fluorescence microscopes. System ensures low phototoxicity and photobleaching, i.e., higher throughput with optimal conditions." .
SCR:023795 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Malvern Panalytical MicroCal PEAQ-ITC analysis" ;
NIFRID:synonym "Malvern Panalytical MicroCal PEAQ-ITC Analysis software",
"MicroCal PEAQ-ITC",
"MicroCal PEAQ-ITC Analysis software",
"MicroCal PEAQ-ITC Analysis Software v1.41" ;
definition: "Software application for isothermal titration calorimetry performed on MicroCal PEAQ instrument by Malvern." .
SCR:023796 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DriverMP" ;
NIFRID:synonym "Multiomics based Pair driver genes" ;
definition: "Software tool for effectively prioritizing altered genes on cancer type level by considering mutation pair genes. Used to prioritize cancer genes on cancer-type level by utilizing somatic mutation data, protein‒protein interaction networks, and differential expression data." .
SCR:023797 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Beckman Coulter | Navios EX flow cytometer" ;
definition: "Designed specifically for clinical laboratory NAVIOS EX 10-color flow cytometer delivers performance with improved sample traceability and reporting functions. Navios EX has two optional ready-to-use IVD reagent systems, the Navios Tetra System for simultaneous identification and enumeration of T, B and NK lymphocytes and the ClearLLab 10C System – the first FDA cleared and CE marked integrated leukemia and lymphoma immunophenotyping system." .
SCR:023798 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BB15" ;
rdfs:label "Thermo Fisher | BB15 CO2 incubator" ;
NIFRID:synonym "BB15 CO2 Incubator",
"Thermo Scientific™ BB15 CO2 incubator" ;
definition: "CO2 Incubator for cell and tissue cultures grow. Offers precise temperature and CO2 control, humidification system to reduce recovery time and internal solid copper construction for durable contamination control." .
SCR:023799 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Rad | iMark Microplate Absorbance Reader" ;
NIFRID:synonym "iMark™ Microplate Absorbance Reader" ;
definition: "Absorbance reader offers reading speeds of 6 sec at single wavelength detection, onboard software capabilities including protocols for kinetic assays, preprogrammed validation protocol, built-in plate shaker, and built-in thermal printer. Instrument can read flat-, U-, or V-bottom microplates or 8- or 12-well strip plates. Includes 415, 450, 490, 595, 655, and 750 nm filters, onboard software, USB and power cables." .
SCR:023800 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TAM" ;
NIFRID:synonym "TAM 2.0" ;
definition: "Web server for miRNA set enrichment analysis. TAM 2.0 is updated version of this web server. Allows to test functional and disease annotations of miRNAs by overrepresentation analysis and to compare input de-regulated miRNAs with those de-regulated in other disease conditions via correlation analysis." .
SCR:023801 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miRNA Enrichment Analysis and Annotation Tool" ;
NIFRID:synonym "miEAA 2.0",
"miRNA Enrichment Analysis and Annotation Tool (MiEAA)" ;
NIFRID:abbrev "MiEAA" ;
definition: "Web tool for functional analysis of sets of miRNAs. Tailored for miRNA precursors and mature miRNAs of multiple frequently investigated species. Used for miRNA set enrichment analysis. miEAA 2.0 is updated version for integrating multi-species microRNA enrichment analysis and workflow management systems." .
SCR:023802 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lick Instance Quantifier Home cage Device" ;
NIFRID:synonym "LIQ HD system",
"LIQ HD: Lick Instance Quantifier Home cage Device" ;
NIFRID:abbrev "LIQ HD" ;
definition: """Arduino code, 3D print design files, and tutorial video on how to build LIQ HD system.
Open source tool for recording undisturbed two-bottle drinking behavior in home cage environment. All designs and software are open source to allow other researchers to build on the system and adapt LIQ HD to their animal home cages.""" .
SCR:023803 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nikon | N-SIM S Super Resolution Microscope" ;
NIFRID:synonym "N-SIM S Super Resolution Microscope" ;
definition: "Microscope enables super solution imaging of live cells at ten times the speed of conventional SIM. Powered by ECLIPSE Ti2-E Inverted Research Microscope, taking advantage of its advanced optics, stability and features." .
SCR:023805 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1805" ;
rdfs:label "Florida Atlantic University FAU Laboratory Schools Marcus Research and Innovation Center Core Facility" ;
NIFRID:synonym "FAU Laboratory Schools Marcus Research and Innovation Center",
"FAUHS Owls Imaging Lab",
"Florida Atlantic University FAUHS Owls Imaging Lab" ;
definition: "Provides access to equipment to work on research projects, including cancer treatment research, vaccine development, and prosthetic creation. Instruments including micro-computed tomography (CT) scanner; scanning electron microscope (SEM); histology equipment; inverted fluorescence compound microscope; and stereoscope is available to FAU students (high school, undergraduate, graduate), post doctoral researchers, and faculty." .
SCR:023806 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1809" ;
rdfs:label "Creighton University Integrated Biomedical Imaging Core Facility" ;
NIFRID:synonym "Creighton University CU-Integrated Biomedical Imaging Facility",
"CU-Integrated Biomedical Imaging Facility" ;
definition: "Provides instruments for performing widefield light microscopy, multiphoton microscopy, and confocal microscopy. Offers software for analyzing imaging data." .
SCR:023808 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Florida Atlantic University; Florida; USA" ;
NIFRID:abbrev "FAU" ;
definition: "Public research university with its main campus in Boca Raton, Florida and satellite campuses in Dania Beach, Davie, Fort Lauderdale, Jupiter, and Fort Pierce. The university is a member of the State University System of Florida." .
SCR:023809 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hippo-ATESC" ;
NIFRID:synonym "Automatic Texture Extraction from the Hippocampal region using Soft Computing",
"Hippo-ATESC:Automatic Texture Extraction from the Hippocampal region using Soft Computing" ;
definition: "Software pipeline aiming at detecting transcripts enriched in hippocampal neuropil of adult mice, by systematically exploring high resolution images contained in Mouse Brain Atlas. Data mining tool that can provide information to select target genes whose nature will be studies and confirmed using biological tests." .
SCR:023810 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atlasplot" ;
definition: "Software package to simplify process of producing graphics for expression data available in the Allen Institute's Brain Atlases. Related to Allen Mouse Brain Atlas." .
SCR:023811 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allen Brain Atlas-Driven Visualizations" ;
NIFRID:abbrev "ABADV" ;
definition: "Web based gene expression energy visualization tool.Created for visualizing expression energy data from the Allen Brain Atlas.ABADV generates simple-to-analyze visualizations of numerous mouse gene expression data across brain structures." .
SCR:023812 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AllenDigger" ;
definition: "Software tool for spatial expression data visualization, spatial heterogeneity delineation and single cell registration based on Allen Brain Atlas. Software toolkit to collect and preprocess expression data from Allen Brain Atlas and allow query to visualize spatial distribution of genes of interest, characterize spatial heterogeneity of brain, and register cells from single-cell transcriptomics data to fine anatomical brain regions via machine learning methods with high accuracy." .
SCR:023814 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ABAEnrichment" ;
definition: "Software R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing human brain, together with ontologically organized structural information about the brain, both provided by the Allen Brain Atlas.Used to test for gene set expression enrichment in adult and developing human brain." .
SCR:023815 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain heatmap" ;
definition: "Custom Brain Heatmaps on top of the Allen Brain Atlas. Platform to generate brain heatmaps for the human or mouse brain ontop of the Allen Brain Atlas by editing google spreadsheet template with specific brain region and gene information." .
SCR:023816 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brainmapr" ;
definition: "Software R package to the infer spatial location of neural progenitor subpopulations within the developing mouse brain by integrating single-cell RNA-seq data with in situ RNA patterns from the Allen Developing Mouse Brain Atlas." .
SCR:023817 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cocoframer" ;
NIFRID:synonym "COmmon COordinate FRAMEwork in R" ;
definition: "Software R package contains various functions for using the data from the Allen Mouse Brain Atlas that is registered to the Common Coordinate Framework. The functionality includes retrieving 3D, CCF aligned, gridded ISH data from the Allen Brain Atlas API, rendering 2D plots of slices of ISH data, retrieving the Mouse Brain Atlas structural ontology, and generating 3D plots of brain structures like those presented in the Allen Brain Explorer." .
SCR:023818 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AIDAhisto" ;
definition: "Software atlas based imaging data analysis tool for quantitative mouse brain histology. Can automatically detect cells in histological mouse brain and spinal cord sections of interest." .
SCR:023819 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MeshGen" ;
definition: "Software tool to simplify creation of procedural meshes. Used to generate separate mesh files for each label present in segmentation volume, simplifying creations of procedural meshes." .
SCR:023820 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "goi2roimapping" ;
NIFRID:abbrev "GOI2ROI" ;
definition: "Software Python package utilizes spatial, anatomical, microarray expression data from the Allen Institute for Brain Science. This program maps genes of interest (Goi) by their levels of expression to brain regions (Roi). The identified regions that co-express the input Goi can, in turn, be studied further with many experimental modalities. This program can be customized to map gene expression data and identify significant Roi from similar reference expression data in other contexts outside of neuroscience." .
SCR:023821 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PET-CT mouse brain toolbox" ;
definition: "Software toolbox provides multi-modality murine image templates, all of which are spatially registered to the Allen Common Coordinate Framework. The images have been optimized for in-vivo preclinical imaging in terms of resolution and region-of-interest size. The ROIs have been derived from the Allen Brain Atlas. This image analysis tool can be used to facilitate the analysis of mouse PET-CT brain images." .
SCR:023822 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multimodal Environment for Neuroimaging and Genomic Analysis" ;
NIFRID:synonym "MENGA: Multimodal Environment for Neuroimaging and Genomic Analysis" ;
NIFRID:abbrev "MENGA" ;
definition: "Software platform for integration of imaging data and Allen Human Brain Atlas mRNA data. MENGA investigates correlation patterns between various imaging modalities and gene expression profiles based on the Allen Brain Atlas in order to create comprehensive, integrated data platform." .
SCR:023823 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Process Genes List" ;
NIFRID:abbrev "PGL" ;
definition: "Software R package which links genetics and human brain imaging by using genes associated with disease and calculating normalized mRNA expression average of those genes in each brain region. By uploading lists of genes and brain regions of interest, this package will return csv with the results." .
SCR:023824 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CutNII" ;
definition: "Software provides visualization and slicing of 3D isotropic image data as well as various atlases. Through orthogonal views of three standard planes (coronal, sagittal, horizontal) and custom-angle slice cut through the volume, CutNII produces custom-angle atlas slices that match histological sections with non-standard cutting angles. Custom slicing then allows for the inspection of anatomical features from non-conventional angles.Custom-angle slicer for brain atlas volumes." .
SCR:023825 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spatiotemporal pattern Exploration of Brain" ;
NIFRID:abbrev "STEB" ;
definition: "Web based visual analytics tool for the comprehensive exploration of genomic and phenotypic patterns, especially for the spatiotemporal patterns, in the developing mouse brain. The tool is designed in JavaScript and D3.js, the data is based on Allen Developing Mouse Brain Atlas (ADMBA) data." .
SCR:023826 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ARA Tools" ;
definition: "Software package for analysis of mouse brain STP data with respect to the Allen Reference Atlas. Collection of MATLAB functions to analyze mouse whole brain imaging data and the associated \"sparse\" point data such as cell locations, traced neurite trees, or traced projections from a bulk injection. This package relates sparse data to the Allen Mouse Brain Reference Atlas." .
SCR:023827 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allen Mouse Brain ImageLoader" ;
definition: "Respository contains two small software tools which render annotation and images of the Allen Mouse Brain Atlas. Both tools generate 1304 images of the Mouse Brain (456 sagital, 528 coronal and 320 axial)." .
SCR:023828 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genomic-and-High-Dimensional-Data" ;
NIFRID:synonym "Genomic-and-High-Clustering-Data" ;
definition: "Software tool analyzes single-cell RNA-seq dataset from the Allen Mouse Brain Atlas to isolate the analysis of hierarchical structure and the discovery of important genes in the mouse neocortex." .
SCR:023829 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VoxHunt" ;
definition: "Software package for assessing brain organoid patterning, developmental state, and cell composition through systematic comparisons of single cell transcriptomes to three-dimensional in situ hybridization data from the Allen Brain Atlas and number of other useful reference datasets." .
SCR:023830 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "allenCCF" ;
NIFRID:synonym "Allen CCF tool",
"allen CCF tools" ;
definition: "Software tools to work with Allen Inst CCF data in Matlab. MATLAB code to work with the Allen Mouse Brain CCF data." .
SCR:023831 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mouse_abi_tool" ;
definition: "Software tool to pull gene expression from Allen Brain Institute API in same annotation space as structural connectome." .
SCR:023832 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Abagen" ;
definition: "Software package provides Python interface for aquiring and analyzing Allen Human Brain Atlas microarray expression data.Includes reproducible workflow for processing microarray expression data for further analysis.Used for the Allen Brain Atlas genetics data." .
SCR:023833 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ABAnnotate" ;
definition: "Software toolbox for ensemble-based multimodal gene-category enrichment analysis of human neuroimaging data.Performs ensemble-based gene-category enrichment analysis on volumetric human neuroimaging data via brain-wide gene expression patterns derived from Allen Human Brain Atlas. Utilizes nonparametric method using spatial autocorrelation-corrected phenotype null maps for estimation of gene-category null ensembles." .
SCR:023834 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ABI-expression-data-generator" ;
definition: "Software to download expression data from Allen Mouse Brain data portal ABI. This script will query database, download available data, convert it from the raw/mhd format to NIfTI, and register it to standard space. Package-manager-friendly archive of gene expression maps registered in SMRI standard space from the Allen Mouse Brain Atlas." .
SCR:023835 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GCEA_FalsePositives" ;
definition: "Software toolbox for gene category enrichment analysis false positives available. Used for analysis of statistical biases in Gene Set Enrichment Analysis applied to transcriptomic atlas data." .
SCR:023836 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BrainRegionMarkers" ;
definition: "Software R package provides matrix of predefined set of marker genes for many regions of the human brain, using data from the Allen Human Brain Atlas." .
SCR:023837 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Alleninf" ;
definition: "Software package to test hypotheses about relation of patterns found in statistical maps with gene expression measured in postmortem brains. Refines corregistration coordinates provided by the Allen Institute.Used to compare statistical map of brain with gene expression patterns from Allen Human Brain Atlas." .
SCR:023838 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JuGEx" ;
definition: "Software tool for integrating tissue transcriptome and cytoarchitectonic segregation. Combines data from Allen Human Brain Atlas and the EBRAINS Human Brain Atlas, specifically to discover how gene activities and microanatomical architectures contribute to brain function and dysfunction. Both tissue transcriptome and probabilistic brain segregation data allow for integrating genetic expression, brain structure, and function knowledge." .
SCR:023839 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atlas Densities" ;
definition: "Software tools to compute densities in context of brain atlases. Used to create BBP Cell Atlas, using Allen Mouse Brain Atlas and collected literature density values.Provides list of volumetric files that provides cell type density estimates for each voxel of mouse brain volume." .
SCR:023840 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pinpoint" ;
definition: "Software electrophysiology tool for planning Neuropixels recordings. Neuropixels trajectory planner for designing multi-probe insertions,utilizing the Allen Mouse Brain Common Coordinate Framework." .
SCR:023841 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atlas Direction Vectors" ;
NIFRID:synonym "Allen Density Vectors" ;
definition: "Software tools to compute direction vectors in context of brain atlases." .
SCR:023842 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atlas Splitter" ;
definition: "Software tools to split brain atlas regions and refine annotations accordingly. Applicable to the Allen Mouse Brain Atlas" .
SCR:023843 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atlas Alignment Meter" ;
definition: "Software Python CLI and library to measure jaggyness of brain parcellation volume. Used to measure slice-to-slice jaggedness of volumetric dataset, only in form of NRRD file." .
SCR:023844 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SageBionetworks Portals" ;
definition: "Platform provides web interfaces for research institutions to exchange, share, and publish curated data and other digital resources." .
SCR:023845 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "brain-mapping" ;
definition: "Software tool to map histological slice sequences to Allen Mouse Brain Atlas without 3D Reconstruction. Automatically maps histological slice to its corresponding plane in Allen Mouse Brain Atlas to build plane wise mapping and then perform 2D nonrigid registration to build pixel wise mapping." .
SCR:023846 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BRain area Input Output" ;
NIFRID:synonym "BRain area Input Output (BRIO)" ;
NIFRID:abbrev "BRIO" ;
definition: "Software visualization and analysis tool based on the Allen Brain Atlas connectivity database. Produces custom visualizations and figures for input output strength of specific brain area." .
SCR:023847 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AP-histology" ;
definition: "Software data pipeline which aligns histology images to the Allen CCF." .
SCR:023848 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BrainGlobe Atlas API" ;
NIFRID:synonym "BrainGlobe Atlas API (bg-atlasapi)" ;
NIFRID:abbrev "bg-atlasapi" ;
definition: "Software lightweight python module to interact with atlases for systems neuroscience. Provides consistent way to process brain atlas data from various sources." .
SCR:023849 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Segmenting Brain Regions" ;
NIFRID:synonym "SeBRe-Segmenting Brain Regions" ;
NIFRID:abbrev "SeBRe" ;
definition: "Software high-throughput Mask R-CNN based toolbox to generate brain atlas through deep learning. Used for segmenting brain regions of interest." .
SCR:023850 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BrainModules" ;
definition: "Web interactive visualization tool of brain architecture based on tracer database.There are four modes of visualization: surfarce, flat, coronal, and saggital." .
SCR:023851 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MorphAPI" ;
definition: "Software Python package for downloading neurons morphological reconstructions from publicly available datasets. With the provided APIs, the user can download data of selected neurons and functionality to create 3d meshes with the neuronal reconstruction for visualization." .
SCR:023852 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Type Analysis Toolbox" ;
definition: "Software toolbox is cell counting and distribution mapping platform which can be used to analyze serial two-photon tomography (STPT) data." .
SCR:023853 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brainreg-segment" ;
definition: "Software tool for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first. Used for segmentation of 3D shapes in common anatomical space." .
SCR:023854 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepSlice" ;
definition: "Software Python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning." .
SCR:023855 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allen Brain Atlas Tools" ;
NIFRID:synonym "ABAT (Allen Brain Atlas Tools)" ;
NIFRID:abbrev "ABAT" ;
definition: "Software stores mutiple MATLAB functions to read, analyze, and visualize various kinds of data from Allen Brain Atlas." .
SCR:023856 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QUINT" ;
definition: "Software workflow includes suite of various software to form analysis pipeline of atlas-based quantifuication of labbeled features in histological images from mouse or rat brain. This workflow also suggests and explains with instructional videos the way these software work together. Used for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases." .
SCR:023857 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aligning Big Brains and Atlases" ;
NIFRID:synonym "ABBA (Aligning Big Brains & Atlases)" ;
NIFRID:abbrev "ABBA" ;
definition: "Software Fiji plugin for registering thin serial sections: coronal, sagittal, horizontal, to compatible atlases including Allen Mouse Common Coordinate Framework, Waxholm Rat Brain Atlas, and all BrainGlobe atlases." .
SCR:023858 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brainreg " ;
definition: "Software Python based tool that registers the template brain (e.g. from the Allen Reference Atlas) to the sample image.Automated 3D brain registration with support for multiple species and atlases." .
SCR:023862 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "brms" ;
definition: "Software package implements Bayesian multilevel models in R using probabilistic programming language Stan." .
SCR:023863 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "National Bureau of Statistics of China" ;
definition: "Deputy cabinet level agency directly under the State Council of China. Responsible for collection, investigation, research and publication of statistics concerning the nation's economy, population and other aspects of the society." .
SCR:023864 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2447" ;
rdfs:label "Pennsylvania State University Huck Institutes of Life Sciences Metabolomics Core Facility" ;
NIFRID:synonym "Huck Institues' Metabolomics Facility",
"Penn State Huck Metabolomics Core Facility" ;
definition: "Core for conducting metabolomics studies on variety of biofluids and tissue extracts from plant and animal sources. Provided instruments include Agilent 5975C series GC-MSD, Bruker NEO 600 NMR, Thermo Exactive Plus, Thermo Orbitrap Exploris 120, Thermo Orbitrap Exploris 240, Thermo TSQ Quantis Plus, Thermo Orbitrap Fusion Lumos Tribrid." .
SCR:023865 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agricultural Production Systems sIMulator" ;
NIFRID:abbrev "APSIM" ;
definition: "Software platform for modelling and simulation of agricultural systems. Contains suite of modules that enable simulation of systems for diverse range of plant, animal, soil, climate and management interactions. Used to simulate biophysical processes in agricultural systems, particularly as it relates to the economic and ecological outcomes of management practices in the face of climate risk." .
SCR:023866 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1810" ;
rdfs:label "Creighton University Auditory and Vestibular Technology Core Facility" ;
NIFRID:synonym "Creighton University CU-AVT Core Imaging Facility",
"CU-AVT Core Imaging Facility" ;
NIFRID:abbrev "AVT" ;
definition: "Core was established to provide infrastructure to support Research Project Leaders and principle investigators associated with the Dr. Richard J. Bellucci Translational Hearing Center to conduct auditory and vestibular research across the full range of experimental model systems, from single molecule analysis to whole organism models. We also offer access to our services and instruments to outside users." .
SCR:023867 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1811" ;
rdfs:label "University of Notre Dame ND Biophysics Instrumentation Core Facility" ;
NIFRID:synonym "Biophysics Instrumentation Core",
"ND Biophysics Instrumentation Core Facility" ;
NIFRID:abbrev "BIC" ;
definition: "Offers instrumentation dedicated to characterizing biomolecular conformations and interactions, as well as equipment for isolation and purification of macromolecules for subsequent detailed biophysical analysis." .
SCR:023869 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Immunedeconv" ;
definition: "Software R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data." .
SCR:023870 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miRCode" ;
definition: "Web tool for transcriptome wide microRNA target prediction including lncRNAs.Used for whole transcriptome human microRNA target predictions based on the comprehensive GENCODE gene annotation, including long non-coding RNA genes. Coding genes are also covered, including atypical regions such as 5'UTRs and CDS. MicroRNA family definitions and names are consistent with TargetScan. Site conservation is aluated based on 46 vertebrates species.Map of putative microRNA target sites in the long non-coding transcriptome." .
SCR:023871 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DrInsight" ;
definition: "Software connectivity mapping based drug repurposing tool that identifies drugs that can potentially reverse query disease phenotype or have similar functions with query drugs." .
SCR:023872 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "oncoPredict" ;
definition: "Software tool bridges in vitro drug screening with in vivo drug and biomarker discovery. Predicts in vivo or cancer patient drug response and biomarkers to enrich for response from cell line screening data. Builds model using ridge regression, and enables biomarker discovery by imputing drug response in large cancer molecular datasets. Enables drug specific biomarker identification by correcting for general level of drug sensitivity shared among the population." .
SCR:023873 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miRBaseConverter" ;
definition: "Software R package for converting and retrieving information of miRNAs in different miRBase versions. Used for converting and retrieving miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. Can process huge number of miRNAs in short time without other depends." .
SCR:023874 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Forum Literature Propagation" ;
definition: "Method extending ’guilt by association’ principle to literature information by using Bayesian framework to suggest diseases associated with overlooked metabolites." .
SCR:023875 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1813" ;
rdfs:label "Beatson Institute for Cancer Research United Kingdom Beatson Advanced Imaging Resource Core Facility" ;
NIFRID:synonym "Beatson Advanced Imaging Resource (BAIR)",
"Cancer Research UK Beatson Institute Beatson Advanced Imaging Resource (BAIR)" ;
NIFRID:abbrev "BAIR" ;
definition: "Core to uncover and interrogate important molecular pathways in cancer. Offers training scientists in all stages of modern microscopical research from advice on experimental design and sample preparation, basic and advanced microscope operation and data acquisition through to quantitative image analysis and interpretation." .
SCR:023876 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1814" ;
rdfs:label "Aarhus University Bioimaging Core Facility" ;
NIFRID:synonym "Aarhus University Bioimaging Core Facility at the Department of Biomedicine",
"AU Bioimaging Core Facility" ;
definition: "Core Facility offers equipment for wide range of light microscopy applications as well as access to advanced bioimaging software. Specialized staff offers personal training and assistance." .
SCR:023878 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Circulating Cell-free Genome Atlas project" ;
NIFRID:synonym "Circulating Cell-free Genome Atlas (CCGA)" ;
NIFRID:abbrev "CCGA" ;
definition: "Prospective, observational, longitudinal, study designed to characterize landscape of genomic cancer signals in blood of people with and without cancer. Sudy includes people in the USA and Canada who had cancer at the time of enrollment, newly diagnosed, and not yet received treatment, and people who did not have known cancer diagnosis." .
SCR:023879 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1815" ;
rdfs:label "University of Arizona Phenotyping Core Facility" ;
NIFRID:synonym "UA Phenotyping Core (UAPC)",
"University of Arizona UA Phenotyping Core (UAPC)" ;
NIFRID:abbrev "UPAC" ;
definition: "Core provides resources to investigate phenotypes of genetically altered mice and small animal models of disease. Offers investigators full service support of in vivo cardiovascular and physiology studies in normal and diseased states through surgical models, imaging techniques, and functional physiological assessments.Core provides services to assist researchers with phenotyping of small laboratory animals including mice, rats, guinea pigs, rabbits with focus on cardiovascular neuromuscular and respiratory function, and exercise tolerance. Services include Experiments with cardiovascular ultrasound, plethysmography, exercise studies, small animal surgeries LAD-ligation, transaortic constriction, and data analysis; Training with equipment, small animal surgeries or data analysis; Equipment rent to measure cardiovascular, neuromuscular, respiratory function, and exercise tolerance;Consultation on experimental design, physiological data-collection, analysis, interpretation and IACUC protocols, grant- and manuscript writing." .
SCR:023880 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tfcheckpoint" ;
definition: "Collection of transcription factors annotated according to experimental and other evidence on their function as true DbTFs. Provides reference for both small scale experiments and genome scale studies. Curated compendium of specific DNA-binding RNA polymerase II transcription factors." .
SCR:023881 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1816" ;
rdfs:label "Pasteur Institute Human Disease Models Core Facility" ;
NIFRID:synonym "Human Disease Models Core Facility",
"Human disease models core facility",
"Institut Pasteur",
"Paris Human disease models core facility" ;
definition: "Core Facility produces mice harboring human immune system and provides expertise for possible applications of this model. HIS mice engrafted with human Hematopoietic stem cells are advantageous in vivo models for long term studies in field of human immune cells biology, immune oncology and infectious disease. They constitute small animal model in which to analyze potency and safety of small animal model modulating immune system." .
SCR:023882 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bioawk" ;
definition: "Software tool as modified awk version for biodata. Extension to Brian Kernighan's awk, adding support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds few built-in functions and command line option to use TAB as the input/output delimiter." .
SCR:023884 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "B-CALM" ;
definition: "Open source system for behavioral control based on Arduino Mega microcontroller and MATLAB based graphical interface and analysis code. Behavior controller optimized and customized for associative learning and memory tasks. Provided software should be able to control many different types of hardware for different task configurations." .
SCR:023885 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hierarchical Genome Assembly Process" ;
NIFRID:synonym "HGAP: Hierarchical Genome Assembly Process",
"PacBio Hierarchical Genome Assembly-Process (HGAP)" ;
NIFRID:abbrev "HGAP" ;
definition: "Software for High-quality de novo microbial genome assemblies using only single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:023886 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpheroScan" ;
definition: "Software tool for analyzing images of spheroids. Designed to streamline process of spheroid segmentation, area calculation, and downstream analysis of spheroid image data, and can help to standardize and accelerate analysis of spheroid assay results." .
SCR:023887 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1817" ;
rdfs:label "University of California at Davis Bioinformatics Core Facility" ;
NIFRID:synonym "Davis UC Davis Bioinformatics Core",
"UC Davis Bioinformatics Core",
"University of California" ;
definition: "UC Davis Bioinformatics Core helps researchers with their projects, from experimental design, through all analyses and to publication.Provides expertise in analyzing data from omics technologies, and other projects. Regularly offers bioinformatics training." .
SCR:023888 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hitachi | 16-bit 3-CCD color camera HV-F203GV / HV-F203SCL" ;
NIFRID:synonym "HV-F203GV / HV-F203SCL camera" ;
definition: "High resolution 1/1.8\" 3 CCD Progressive Scan Color Camera with 1600 x 1200 pixel (UXGA) that is installed in the ZEISS Axioscan Z1 slide scanner. Integrated functions include electronic shutter from 1/30s to 1/100000s, Long term Integration up to 4s, AGC, external Trigger, Auto Shading, 6 Colour Masking, Frame-On-Demand Function, White Balance, AGC, Black Level Adjustment and Partial Scan Function." .
SCR:023890 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automated Record Analysis" ;
NIFRID:synonym "ARA.v1.6.0",
"ARA:Automated Record Analysis" ;
NIFRID:abbrev "ARA" ;
definition: "Software automatic pipeline for exploration of Sequence Read Archive datasets with sequences as query." .
SCR:023891 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LW Scientific | ZipCombo centrifuge" ;
NIFRID:synonym "ZipCombo Centrifuge" ;
definition: "Multi-function microcentrifuge available with choice of three rotors. The flat microhematocrit rotor spins shorter capillary tubes and eliminates angled separation lines, clay blow-outs, and broken tubes. The six place microtube rotor spins 1.5 to 2.0ml tubes for serum and urine separations and comes with adapters for smaller sized tubes (0.2ml-1.5ml). The optional 16-place PCR strip rotor spins two 8-place strips. The ZipCombo is well-suited to accomplish blood and urine separations, microfiltrations, and DNA preparations." .
SCR:023892 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rainin | Pipet-Lite LTS Pipette L-200XLS+" ;
NIFRID:synonym "Pipet-Lite™ XLS+",
"Rainin Pipet-Lite™ XLS+" ;
definition: """Pipet-Lite™ XLS+ manual single-channel pipette, 20-200 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-200XLS+)
""" .
SCR:023893 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rainin | Pipet-Lite LTS Pipette L-100XLS+" ;
NIFRID:synonym "Pipet-Lite LTS Pipette L-100XLS+" ;
definition: "Pipet-Lite™ XLS+ manual single-channel pipette, 10-100 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-100XLS+)" .
SCR:023894 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rainin | Pipet-Lite LTS Pipette L-1000XLS+" ;
NIFRID:synonym "Pipet-Lite LTS Pipette L-1000XLS+" ;
definition: "Pipet-Lite™ XLS+ manual single-channel pipette, 100-1000 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-1000XLS+)" .
SCR:023895 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rainin | Pipet-Lite LTS Pipette L-10XLS+" ;
NIFRID:synonym "Pipet-Lite LTS Pipette L-10XLS+" ;
definition: "Pipet-Lite™ XLS+ manual single-channel pipette, 0.5-10 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-10XLS+)." .
SCR:023896 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "epitools" ;
NIFRID:synonym "Epidemiology Tools",
"epitools: Epidemiology Tools" ;
definition: "Software R package for training and practicing epidemiologists including methods for two-way and multi-way contingency tables." .
SCR:023897 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Ranger ARC " ;
NIFRID:synonym "10x Genomics Cell Ranger ARC" ;
definition: "Software analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate variety of analyses pertaining to gene expression , chromatin accessibility, and their linkage. Used to perform analyses that link chromatin accessibility and GEX." .
SCR:023898 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GERONIMO" ;
NIFRID:synonym "GEnomic RNA hOmology aNd evolutIonary MOdeling" ;
definition: "Software pipeline to conduct high-throughput homology searches of structural genes using covariance models. Utilises covariance models to conduct homology searches of RNA sequences across wide range of gene families in broad evolutionary context." .
SCR:023900 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rainin | E4 Pipette Multi E8-1200XLS+" ;
NIFRID:synonym "E4 Pipette Multi E8-1200XLS+" ;
definition: "8-channel pipette, 100-1200 μL, uses LTS™ LiteTouch™ tips. Consistent sample pickup, all channels. Simple operation, advanced modes. Password-protection (E8-1200XLS+)." .
SCR:023902 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VWR | Lab Dancer Vortex Mixer" ;
definition: "Vortex mixer suitable for single, small containers up to 30 mm in diameter." .
SCR:023903 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1819" ;
rdfs:label "Leiden University Medical Center Flow Cytometry Core Facility" ;
NIFRID:synonym "Flow Cytometry Core Facility" ;
NIFRID:abbrev "LUMC FCF" ;
definition: "Provides flow cytometers for users from the LUMC, Leiden University and external companies.Instruments include conventional and spectral analyzers, cell sorters and mass cytometers. These instruments allow analysis and sorting up to biohazard level ML-II, while one analyzer is available for ML-III material. Provides support for all aspects of cytometry, including experimental design, instrument setup, data acquisition and data analysis." .
SCR:023904 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SunChrom | SunTissuePrep Tissue Section Preparation System" ;
NIFRID:synonym "SunTissuePrep" ;
definition: "System automates all tissue section preparation steps that were previously performed manually. Deparaffinization, rehydration, antigen-retrieval and pH-adjustment steps are performed efficiently, reliably and fully automated." .
SCR:023905 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SunChrom | SunDigest Incubator" ;
definition: """SunDigest incubation device provides fully software controlled and highly reproducible digestion process under standardized conditions. Feature includes Temperatures precisely adjustable between 4 °C and 50 °C; On-Tissue digestion process under optimal humidity;
Preservation of spatial resolution; High performance digestion at 50 °C; Full digestion process control.Essential for reproducible results.""" .
SCR:023906 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SunChrom | SunCollect CF Spotter" ;
NIFRID:synonym "CF-Spotter for MALDI-TOF Microbial Identification" ;
definition: "CF-Spotter for MALDI-TOF microbial identification. Enables fast, efficient and reproducible sample preparation for MALDI-TOF microbial identification system and relieves your laboratory staff from tedious and time-consuming pipetting. Due to the non-contact application of the solutions, there is no carryover of the samples and the costs for consumables such as pipette tips are eliminated." .
SCR:023907 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SunCollect MALDI Sprayer" ;
NIFRID:synonym "SunCollect Sprayer" ;
definition: """For tissue preparation for Imaging MALDI. The sprayer can handle fresh-frozen or FFPE tissue sections. Enzymes such as trypsin can be applied to the tissue for in situ digestion.
Sprayer offers the following key features: Automated delivery of matrix, enzyme or derivatization solutions; 6 port PEEK valve with low dead-volume to minimise liquid usage;
Automatic self-cleaning function at end of matrix application; 100 % biocompatible;
Compact unit 36 x 49 x 40 cm (w,d,h);Preprogrammed spray protocols;Up to 8 sample slides can be sprayed simultaneously;Easy to use software.""" .
SCR:023908 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "SunChrom" ;
NIFRID:synonym "SunChrom Wissenschaftliche Geräte GmbH" ;
definition: "Develops and manufactures scientific instruments. Specialists for system solutions in liquid chromatography, development and optimization of front-end applications and sample preparation systems for MALDI and MALDI-MSI." .
SCR:023909 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoString | CosMx Spatial Molecular Imager" ;
NIFRID:synonym "CosMx Spatial Molecular Imager",
"NanoString CosMx Spatial Molecular Imager" ;
definition: "Integrated system with mature cyclic fluorescent in situ hybridization chemistry, resolution imaging readout, interactive data analysis and visualization software. Analysis platform to provide spatial multiomics with formalin-fixed paraffin-embedded and fresh frozen tissue samples at cellular and subcellular resolution. CosMx SMI enables rapid quantification and visualization of up to 1,000 RNA and 64 validated protein analytes. Spatial single-cell imaging platform that drives deeper insights for cell atlasing, tissue phenotyping, cell-cell interactions, cellular processes, and biomarker discovery." .
SCR:023910 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "10x Genomics | Xenium Analyzer" ;
NIFRID:synonym "Xenium Analyzer" ;
definition: "Xenium Analyzer offers subcellular profiling of 100s to 1,000s of RNA targets alongside multiplexed protein, in fresh, frozen or FFPE tissue." .
SCR:023911 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Resolve Biosciences" ;
NIFRID:synonym "Resolve Biosciences GmbH" ;
definition: "Biotechnology research company for molecular cartography. Applys the power of Molecular Cartography to enable scientists to gain new insights based on the highest-resolution view of single-cell spatial biology." .
SCR:023912 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "NanoString Technologies" ;
NIFRID:synonym "NanoString" ;
definition: "Publicly held biotech company offering discovery and translational research solutions. NanoString's products include the nCounter® Gene Expression System, the GeoMx® Digital Spatial Profiler, the CosMx™ Spatial Molecular Imager, and the AtoMx™ Spatial Informatics Platform." .
SCR:023913 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "epialleleR" ;
definition: "Software R package for calling hypermethylated variant epiallele frequencies at level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map files as input. Used for sensitive allele specific methylation analysis in next generation sequencing data. Used for sensitive detection, quantification and visualisation of mosaic epimutations in methylation sequencing data." .
SCR:023914 a NLX:63400,
owl:NamedIndividual .
SCR:023916 a NLX:63400,
owl:NamedIndividual .
SCR:023917 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_53" ;
definition: "Scientific Instrument Services provides technical support functions including repair and maintenance of lab equipment; custom design and fabrication of new fixtures and devices using CAD, 3-D printing, and traditional machining; protocol development and performance optimization of wide variety of automated liquid handlers deployed in many of our institutions core services.Services are provided for JAX faculty." .
SCR:023918 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Freibox" .
SCR:023919 a owl:NamedIndividual ;
rdfs:label "commutator" ;
definition: """Affordable commutator that is equipped with novel sensing system that improves online tracking of cable rotations without impairing the 1-photon calcium imaging via Miniscope.
Commutator to allow freely moving behaviors while recording neural activity from platforms such as Miniscope V4 and OpenEphys. Used to perform calcium imaging.""" .
SCR:023920 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Molecular Devices | SpectraMax iD3 multi-mode microplate reader" ;
NIFRID:synonym "Molecular Devices SpectraMax iD3 multi-mode microplate reader",
"SpectraMax® iD3 multi-mode microplate reader" ;
definition: "Microplate reader to measure absorbance, fluorescence and luminescence." .
SCR:023921 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mONiTor" ;
definition: "Software tool monitors metrics available in sequencer, state of the computer to which the sequencer is connected, and the contents of the fast5 and fastq files. Real-time monitoring of Oxford Nanopore Technology sequencing run. Used for monitoring nanopore sequencing process." .
SCR:023922 a NLX:63400,
owl:NamedIndividual .
SCR:023923 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Collaborative Research Network Cloud" ;
NIFRID:abbrev "CRN Cloud" ;
definition: "MJFF in partnership with Aligning Science Across Parkinson’s are in the process of establishing data platform, CRN Cloud, leveraging Verily Workbench to share data generated by researcher labs funded through ASAP Collaborative Research Network. The data types include mainly raw and processed single cell RNA-seq, single nucleus RNA-seq, and bulk RNA-seq from both PD and healthy control samples." .
SCR:023924 a NLX:63400,
owl:NamedIndividual ;
definition: "Curated data resource of protein carbonylation sites.Manually curated data resource of experimentally confirmed carbonylated proteins and sites.Provides information on other related resources such as list of other oxidative protein modification databases, list of protein oxidation and carbonylation prediction tools." .
SCR:023925 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PKD Genome Browser" ;
NIFRID:synonym "Polycystic Kidney Disease Genome Browser" .
SCR:023928 a owl:NamedIndividual ;
NIFRID:synonym "confgen" .
SCR:023929 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chemyx | Fusion 4000-X Dual Independent Channels syringe pump system" ;
NIFRID:synonym "Chemyx Fusion 4000-X",
"Chemyx Fusion 4000-X Dual Independent Channels syringe pump",
"Fusion 4000-X independent dual-channel infuse and withdraw syringe pump" ;
definition: "Syringe pump is built with 2 separate pump drives capable of independent pulseless, reproducible rates and movement. Programmable multi-step and cycle mode allows users to input complex flow profiles or perform flow cycling from computer Labview or the pump itself. This multi-channel syringe infusion pump system also can be expanded with 2-syringe push and pull rack attachment to increase the total syringe capacity to four." .
SCR:023930 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iPRECIO | Programmable Infusion Pump" ;
definition: "Advanced infusion device for drug delivery applications in mice, rats and larger animals. With versatile programmable functions and refillable reservoir, this implantable infusion pump enables full control over dosing studies and empowers researchers to execute even the most complex dosing protocols, including multiple bolus dosing, variable/constant delivery, escalating drug administration, and more." .
SCR:023931 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012961" ;
rdfs:label "CancerModels.Org" ;
NIFRID:synonym "PDCM Finder",
"PDX Finder" ;
definition: "Cancer research platform that aggregates clinical, genomic and functional data from various types of patient derived cancer models, xenographs, organoids and cell lines. Open catalog of harmonised patient-derived cancer models. Standardises, harmonises and integrates clinical metadata, molecular and treatment-based data from academic and commercial providers worldwide. Data is FAIR and underpins generation and testing of new hypotheses in cancer mechanisms and personalised medicine development. PDCM Finder have expanded to organoids and cell lines and is now called CancerModels.Org. PDCM Finder was launched in April 2022 as successor of PDX Finder portal, which focused solely on patient-derived xenograft models." .
SCR:023932 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Molecular Operating Environment" ;
NIFRID:synonym "Chemical Computing Group ULC Molecular Operating Environment",
"Molecular Operating Environment (MOE)" ;
NIFRID:abbrev "MOE" .
SCR:023934 a NLX:63400,
owl:NamedIndividual ;
NIFRID:abbrev "OAT" .
SCR:023935 a owl:NamedIndividual ;
rdfs:label "NamSor" ;
definition: "A software tool useful for finding the name origin, ethnicity of a name. It can infer gender, translate Chinese names and Japanese names, format a phone number, and split a full name via user interface and an API." .
SCR:023936 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "BioNovoGene Mzkit" .
SCR:023937 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | 6495 Triple Quadrupole LC/MS" ;
NIFRID:synonym "Agilent 6495 Triple Quadrupole LC/MS system",
"Stanford Agilent 6495 Triple Quadrupole LC/MS system" ;
definition: "Agilent 6495C triple quadrupole LC/MS system increases capacity and sensitivity for targeted quantitation applications. Used to investigate more diverse and biologically relevant groups of targeted peptides, small molecules and metabolites in single experiment without compromising sensitivity, quantitative accuracy, or linearity." .
SCR:023938 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Waters | Select Series MRT" ;
NIFRID:synonym "Waters Select Series Multi Reflecting Time-of-Flight" ;
definition: "Multi Reflecting Time-of-Flight features routine ppb mass accuracy and ultra-high resolution by extending the flight path via gridless electrostatic mirrors in mass analyzer. It is equipped with DESI and MALDI sources for imaging mass spectrometry." .
SCR:023939 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Waters | Select Series Cyclic IMS" ;
NIFRID:synonym "Stanford Waters Select Series Cyclic IMS" ;
definition: "Cyclic IMS pairs unique cyclic ion mobility separation which enables separation based on shape, with time-of-flight separation based on mass to charge ratio (m/z). It is equipped with DESI and electrospray sources for surface and solution analyses." .
SCR:023940 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bacmapping" ;
definition: "Software set of tools used in production and exploration of bacterial artificial chromosome restriction maps." .
SCR:023941 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Customized Guide Cannulas" ;
definition: "Open source modular apparatus to produce guide cannulas exploiting 3D printing technology. Step by step procedure to realize hippocampal guide cannulas. 3D-printed guide cannula implant, as well as rotary tool based cutting station for fabrication of cannulae. Useful to conduct research in all the fields where access to brain areas is needed." .
SCR:023942 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EBSCO SPORTDiscus" ;
NIFRID:synonym "SPORTDiscus" ;
definition: "Bibliographic database for sports and sports medicine research. Includes records from leading sports medicine journals. Includes rigorous curation and indexing of open access journals. Once validated and certified for inclusion, these journals are treated with subject indexing and full text linking." .
SCR:023943 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Health Information National Trends Survey" ;
NIFRID:synonym "Health Information National Trends Survey (HINTS)",
"The Health Information National Trends Survey (HINTS)" ;
NIFRID:abbrev "HINTS" ;
definition: "Regularly collects nationally representative data about American public’s knowledge of, attitudes toward, and use of cancer and health related information. HINTS data are used to monitor changes in fields of health communication and health information technology and to create more effective health communication strategies across different populations. Weighted, nationally representative probability based survey of civilian, non-institutionalized adults administered by National Cancer Institute on knowledge of and attitudes toward cancer relevant information." .
SCR:023944 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "CDC HPV and Cancer HPV-Associated Cancer",
"CDC HPV-Associated Cancer" .
SCR:023945 a owl:NamedIndividual ;
NIFRID:synonym "Linked-Read ToolKit",
"Linked-Read ToolKit (LRTK)" .
SCR:023946 a NLX:63400,
owl:NamedIndividual .
SCR:023947 a NLX:63400,
owl:NamedIndividual ;
definition: "Comprehensive DNA methylation database. Provides genome wide mapping of methylation sites to target genes through integrating a large number of DNA methylation and gene expression profiles in human diseases, and to annotate methylation sites to abundant regulatory elements and TFs." .
SCR:023948 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MAP Client" ;
NIFRID:synonym "MAP Client mapping tools",
"MAP Client mapping tools v0.19.1",
"MAP Client v0.19.1",
"Musculoskeletal Atlas Project Client" ;
definition: "Software Python cross platform framework for creating, managing, and sharing workflows. Workflow consists of number of connected workflow steps. Framework is plugin-based application where the plugins are workflow steps. Can be used for visualising and mapping anatomical structures." .
SCR:023949 a NLX:63400,
owl:NamedIndividual .
SCR:023950 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SM2010 R" ;
rdfs:label "Leica | SM2010 R Sliding Microtome" ;
NIFRID:synonym "Leica SM 2000R",
"SM2010 R Sliding Microtome" ;
definition: "Sliding microtome produces sections for human paraffin sectioning applications.Microtome has enclosed micrometer feeding system with ergonomically positioned object head close to the user. Running sledge can be locked in 11 positions by using sledge brake." .
SCR:023951 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1822" ;
rdfs:label "University of Missouri Bioinformatics and Analytics Core Facility" ;
NIFRID:synonym "MU Bioinformatics and Analytics",
"University of Missouri MU Bioinformatics and Analytics Core" ;
definition: "Provides expert bioinformatics, analytical, and data science consulting and analysis solutions. Offers support for the management and analysis of large scale biological datasets." .
SCR:023952 a owl:NamedIndividual ;
rdfs:label "University of Wisconsin-Madison Biochemistry Optical Core Facility" ;
definition: "Core provides instrumentation for light and fluorescence based microscopy, including epifluorescence, confocal, and super-resolution imaging.Provides access to and training on basic and advanced light microscopy techniques. Expertise and advice is available for the design of experiments involving these techniques." .
SCR:023953 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneHancer" ;
definition: "Database of human regulatory elements like enhancers and promoters, and their inferred target genes which is embedded in GeneCards, human gene compendium. Associations between regulatory elements and target genes were based on multiple sources of linking molecular data, along with distance." .
SCR:023956 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "simulation of Adaptive Immune Receptor Repertoire data" .
SCR:023957 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ST5010 XL" ;
rdfs:label "Leica | Autostainer ST5010 XL" ;
definition: "Leica ST5010 Autostainer XL provides reproducible, consistent high quality staining, and increased workload throughput compared to manual staining." .
SCR:023959 a owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1825" ;
rdfs:label "South Dakota State University Genomics Sequencing Core Facility" ;
NIFRID:synonym "SDState-Genomics Sequencing Facility",
"South Dakota State University SDState-Genomics Sequencing Facility" ;
definition: "Facility offers custom sequencing services from DNA/RNA extractions to sequencing using Illumina and Oxford Nanopore platforms. Projects examples include bulk RNAseq, 3\\'RNASeq, Single Cell transcriptomics (10X Genomics), Genome sequencing, and amplicon sequencing (ie 16SRNA, genotyping). Services include experimental design and bioinformatics data analysis." .
SCR:023960 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aeskulap" ;
NIFRID:synonym "aeskulap",
"Aeskulap - DICOM Viewer" ;
definition: "Software application as medical image viewer.Able to load series of special images stored in DICOM format for review. Able to query and fetch DICOM images from archive nodes (also called PACS) over the network. Designed to run under Linux." .
SCR:023961 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "alleleCount" ;
NIFRID:synonym "allelecount" ;
definition: "Software package to prevent code duplication. Support code for NGS copy number algorithms. Generates count of coverage of each allele ACGT at that location given any filter settings." .
SCR:023962 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_20869" ;
rdfs:label "Atropos" ;
NIFRID:synonym "atropos" ;
definition: "Software tool for specific, sensitive, and speedy trimming of NGS reads." .
SCR:023963 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "assembly-stats" ;
definition: "Software to get assembly statistics from FASTA and FASTQ files." .
SCR:023964 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Augur" ;
NIFRID:synonym "augur" ;
definition: "Software package to track evolution from sequence and serological data. Provides collection of commands which are designed to be composable into larger processing pipelines." .
SCR:023965 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Aghermann" ;
NIFRID:synonym "aghermann" ;
definition: "Sotware tool designed to run Process S simulations on Slow Wave Activity profiles from human EEG recordings.Produces set of sleep homeostat parameters which can be used to describe and differentiate individual sleepers, such as short vs long sleepers, early vs late, etc.Sleep research experiment manager, with facility for reading, displaying, and manual and semi-automatic scoring EEG recordings in edf format; conventional PSD and EEG Microcontinuity profiles; artifact detection; Independent Component Analysis; basic sleep analysis NREM-REM cycle detection." .
SCR:023966 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Auspice" ;
NIFRID:synonym "auspice" ;
definition: "Web application for visualizing pathogen evolution.Interactive web app for visualizing phylogenomic data." .
SCR:023967 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11402" ;
rdfs:label "Assemblytics" ;
NIFRID:synonym "assemblytics" ;
definition: "Web analytics tool for detection of variants from assembly. Used to detect and analyze structural variants from genome assembly by comparing it to reference genome." .
SCR:023968 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AxParafit" ;
NIFRID:synonym "Accelerated Parafit",
"axparafit" ;
definition: "Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Allows for rapid and much more thorough computation and analyses of large co-phylogenetic datasets." .
SCR:023969 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bamkit" ;
definition: "Software tools for common BAM file manipulations." .
SCR:023970 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bambamc" ;
definition: "Software package contains lightweight C implementation of name collating BAM file input and BAM file output." .
SCR:023971 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AxPcoords" ;
NIFRID:synonym "Accelerated DistPCoA",
"axpcoords" ;
definition: "Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Faster than DistPCoA and numerically stable on large datasets." .
SCR:023972 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BBHash" ;
NIFRID:synonym "bbhash" ;
definition: "Software library for building minimal perfect hash function. Designed to handle large scale datasets." .
SCR:023973 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biber" ;
NIFRID:synonym "biber" ;
definition: "Software bibliography processing backend for LaTeX biblatex package. Supports unsurpassed feature set for automated conformance to complex bibliography style requirements such as labelling, sorting and name handling. BibTeX replacement for users of BibLaTeX." .
SCR:023974 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bibus" ;
NIFRID:synonym "bibus" ;
definition: "Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records." .
SCR:023975 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_12164" ;
rdfs:label "BCALM 2" ;
NIFRID:synonym "bcalm" ;
definition: "Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution." .
SCR:023976 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_03734" ;
rdfs:label "BAli-Phy" ;
NIFRID:synonym "bali-phy",
"BAli-Phy version 3" ;
definition: "Software application as simultaneous Bayesian inference of alignment and phylogeny. Used to estimate multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. to explore the joint space of alignment and phylogeny given molecular sequence data. BAli-Phy version 3 is model based co-estimation of alignment and phylogeny. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models and other new models. Implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously." .
SCR:023977 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19790" ;
rdfs:label "BioCocoa" ;
NIFRID:synonym "biococoa" ;
definition: "Open source framework for bioinformatics written in Objective-C. Provides Cocoa and GNUstep programmers with full suite of APIs for handling and manipulating biological sequences." .
SCR:023978 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_13504" ;
rdfs:label "BOLT-LMM" ;
NIFRID:synonym "bolt-lmm" ;
definition: "Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts." .
SCR:023979 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioImageXD" ;
NIFRID:synonym "bioimagexd" ;
definition: "Software package for analyzing, processing and visualizing multi-dimensional microscopy images. Multipurpose postprocessing tool for bioimaging. Can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once." .
SCR:023980 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CLI for BioMAJ" ;
NIFRID:synonym "biomaj3-cli",
"biomaj-cli" ;
definition: "Software package to use BioMAJ providing biomaj-cli." .
SCR:023981 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CAMP" ;
NIFRID:synonym "camp" ;
definition: """Software multi-purpose reflection library developped by Technogerma Systems France and then by Tegesoft. Provides extra layer of
flexibility to programs, and allows them to fully expose their data structures at runtime.""" .
SCR:023982 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_24974" ;
rdfs:label "caftools" ;
definition: "Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site." .
SCR:023983 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21717" ;
rdfs:label "BioMAJ" ;
NIFRID:synonym "BIOlogie Mise A Jour",
"BioMAJ3",
"biomaj3" ;
definition: "Software workflow engine dedicated to data synchronization and processing. Software automates the update cycle and the supervision of the locally mirrored databank repository." .
SCR:023984 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CamiTK" ;
NIFRID:synonym "camitk",
"Computer Assisted Medical Intervention Tool Kit" ;
definition: "Software Computer Assisted Medical Intervention Tool Kit helps researchers and clinicians to easily and rapidly collaborate in order to prototype CAMI applications, that feature medical images, surgical navigation and biomechanical simulations.Open source, cross-platform generic tool, written in C++, which can handle medical images, surgical navigations and biomechanical simulations." .
SCR:023985 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CDK" ;
NIFRID:synonym "cdk",
"Chemistry Development Kit" ;
definition: "Open Source software modular Java libraries for cheminformatics." .
SCR:023986 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_08874" ;
rdfs:label "Change-O" ;
NIFRID:synonym "changeo" ;
definition: "Collection of software tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin Ig sequences, and reconstructing germline sequences." .
SCR:023987 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CHIME" ;
NIFRID:synonym "chime",
"COVID-19 Hospital Impact Model for Epidemics" ;
definition: "Software designed to assist hospitals and public health officials with understanding hospital capacity needs as they relate to the COVID pandemic. CHIME enables capacity planning by providing estimates of total daily and running totals of inpatient hospitalizations, ICU admissions, and patients requiring ventilation." .
SCR:023988 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CAT and BAT" ;
NIFRID:synonym "BAT",
"Bin Annotation Tool",
"CAT",
"cat-bat",
"CAT/BAT",
"Contig Annotation Tool" ;
definition: "Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies." .
SCR:023989 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_08756" ;
rdfs:label "CodonW" ;
NIFRID:synonym "codonw" ;
definition: "Software tool designed to simplify Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage." .
SCR:023990 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11185" ;
rdfs:label "ChromImpute" ;
NIFRID:synonym "chromimpute" ;
definition: "Software tool for large scale systematic epigenome imputation. ChromImpute takes existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally." .
SCR:023991 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "conda-package-handling" ;
definition: "Software to create and extract conda packages of various formats." .
SCR:023992 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chemtool" ;
NIFRID:synonym "chemtool" ;
definition: "Software tool for drawing organic molecules. Runs under the X Window System using the GTK widget set. Used for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11." .
SCR:023993 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Conquest DICOM" ;
NIFRID:synonym "conquest-common",
"conquest-dbase",
"conquest-dicom-server",
"conquest-mysql",
"conquest-postgres",
"conquest-sqlite" ;
definition: "Software for DICOM training and testing,Demonstration and research image archives,Image format conversion from scanner with DICOM network access,DICOM image viewing and slide making, DICOM image selection, (limited) editing, and splitting and merging of series, Advanced scriptable image modification, filtering, forwarding and conversion, DICOM caching and archive merging, DICOM web access for viewing and data management (scriptable),Connection to Lua IDE for all sorts of DICOM manipulation." .
SCR:023994 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_03452" ;
rdfs:label "CONTRAfold" ;
NIFRID:synonym "CONditional TRAining for RNA Secondary Structure Prediction",
"contrafold" ;
definition: "Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction." .
SCR:023995 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012727" ;
rdfs:label "CARD" ;
NIFRID:synonym "card-rgi",
"Comprehensive Antibiotic Resistance Database",
"The Comprehensive Antibiotic Resistance Database" ;
definition: "Comprehensive antibiotic resistance database. Bioinformatic database of resistance genes, their products and associated phenotypes." .
SCR:023996 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CiftiLib" ;
NIFRID:synonym "ciftilib" ;
definition: "Software C++ Library for reading and writing CIFTI-2 and CIFTI-1 files." .
SCR:023997 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CTDopts" ;
NIFRID:synonym "ctdopts" ;
definition: "Software gives your command-line tools a CTD-compatible interface. Module for enabling tools with CTD reading/writing, argument parsing, validating and manipulating capabilities." .
SCR:023998 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "covtobed" ;
definition: "Software tool to generate BED coverage tracks from BAM files." .
SCR:023999 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "C Thread Pool" ;
NIFRID:synonym "C-Thread-Pool",
"cthreadpool" ;
definition: "Software for minimal but powerful thread pool in ANSI C." .
SCR:024000 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_20006" ;
rdfs:label "cyvcf2" ;
definition: "Software Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. Used for variant analysis." .
SCR:024001 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_30643" ;
rdfs:label "Deepbinner" ;
NIFRID:synonym "deepbinner" ;
definition: "Software tool for demultiplexing barcoded Oxford Nanopore sequencing reads.Signal level demultiplexer for Oxford Nanopore reads." .
SCR:024002 a owl:NamedIndividual ;
rdfs:label "CTK" ;
NIFRID:synonym "ctk",
"CTK - The Common Tool Kit" ;
definition: "Software to support biomedical image computing." .
SCR:024003 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_04266" ;
rdfs:label "Dendroscope3" ;
NIFRID:synonym "dendroscope",
"dendroscope3" ;
definition: "Software Java program for analyzing and visualizing rooted phylogenetic trees and networks." .
SCR:024004 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CTSim" ;
NIFRID:synonym "ctsim",
"Open Source Computed Tomography Simulator" ;
definition: "Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions." .
SCR:024005 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DEXTRACTOR" ;
NIFRID:synonym "dextractor",
"Dextractor and Compression Command Library" ;
definition: "Software as Bax file decoder and data compressor." .
SCR:024006 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dicompyler" ;
definition: "Software extensible open source radiation therapy research platform based on the DICOM standard. It also functions as a cross-platform DICOM RT viewer." .
SCR:024007 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CTDConverter" ;
NIFRID:synonym "ctdconverter" ;
definition: "Software Python scripts to convert CTD files into other formats such as Galaxy, CWL." .
SCR:024008 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dicom3tools" ;
NIFRID:synonym "dicom3tools" ;
definition: "Software package provides DICOM medical image files manipulation and conversion tools. Command line utilities for creating, modifying, dumping and validating DICOM files." .
SCR:024009 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_13264" ;
rdfs:label "DNApi" ;
NIFRID:synonym "dnapi" ;
definition: "Software de novo adapter prediction algorithm for small RNA sequencing data." .
SCR:024010 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EDFlib" ;
NIFRID:synonym "edflib" ;
definition: "Software programming library for C/C++ to read/write EDF+/BDF+ files.It also reads old-type EDF/BDF files." .
SCR:024011 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_24617" ;
rdfs:label "ELPH" ;
NIFRID:synonym "elph",
"Estimated Locations of Pattern Hits" ;
definition: "Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs)." .
SCR:024012 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_08871" ;
rdfs:label "EMMAX" ;
NIFRID:synonym "Efficient Mixed-Model Association eXpedited",
"emmax" ;
definition: "Software statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model." .
SCR:024013 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EMPeror" ;
NIFRID:synonym "EMPEROR",
"Emperor",
"emperor" ;
definition: "Web browser enabled tool with versatile command line interface to perform exploratory investigations of 3D visualizations of microbial community data, such as principal coordinates plots. EMPeror includes set of controllers to modify features as function of metadata. Web interactive next generation tool for analysis, visualization and understanding of high throughput microbial ecology datasets." .
SCR:024014 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EMBOSS explorer" ;
NIFRID:synonym "emboss-explorer" ;
definition: "Web based graphical user interface to the EMBOSS suite of bioinformatics tools." .
SCR:024015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Entangle" ;
NIFRID:synonym "entangle" ;
definition: "Software tool provides graphical interface for tethered shooting, aka taking photographs with digital camera completely controlled from the computer." .
SCR:024016 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19988" ;
rdfs:label "Epigrass" ;
NIFRID:synonym "Epidemiological Geo-referenced Analysis and Simulation system",
"epigrass" ;
definition: "Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior." .
SCR:024017 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_23387" ;
rdfs:label "EpiFire" ;
NIFRID:synonym "epifire" ;
definition: "Open source C++ library and application for contact network epidemiology. Application programming interface that models the spread of infectious disease in population and generates and manipulates networks of nodes and edges." .
SCR:024018 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FFP" ;
NIFRID:synonym "Feature Frequency Profile Phylogeny",
"ffp" ;
definition: "Softwaare alignment free comparison tool for phylogenetic analysis and text comparison. Can be applied to nucleotide sequences, complete genomes, proteomes and for text comparison." .
SCR:024019 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_10303" ;
rdfs:label "ExaBayes" ;
NIFRID:synonym "exabayes" ;
definition: "Software package for Bayesian tree inference. Used for large-scale analyses on computer clusters." .
SCR:024020 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Filtlong" ;
NIFRID:synonym "filtlong" ;
definition: "Software tool for filtering long reads by quality.Can take set of long reads and produce smaller, better subset. Uses both read length and read identity when choosing which reads pass the filter." .
SCR:024021 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EDFbrowser" ;
NIFRID:synonym "edfbrowser" ;
definition: "Open source, multiplatform, universal viewer, annotator and toolbox intended for time-series storage files like EEG, EMG, ECG, BioImpedance, etc." .
SCR:024022 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FreeImage" ;
NIFRID:synonym "freeimage" ;
definition: "Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications." .
SCR:024023 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_29589" ;
rdfs:label "Fast5 Library" ;
NIFRID:synonym "Fast5",
"fast5" ;
definition: "Software C++ library for accessing Oxford Nanopore Technologies sequencing data." .
SCR:024024 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_04834" ;
rdfs:label "GATB" ;
NIFRID:synonym "GATB-CORE",
"gatb-core",
"GATB-TOOLS",
"The Genome Analysis Toolbox with de-Bruijn graph" ;
definition: "Software genome analysis toolbox with de-Bruijn graph. Library dedicated to genome assembly and analysis." .
SCR:024025 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "foreign" ;
NIFRID:synonym "r-cran-foreign" ;
definition: "Software tool for reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files." .
SCR:024026 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_02363w" ;
rdfs:label "GenomeTester4" ;
NIFRID:synonym "genometester" ;
definition: "Software toolkit for performing set operations - union, intersection and complement on k-mer lists." .
SCR:024027 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GDCM" ;
NIFRID:synonym "gdcm",
"Grassroots DICOM library" ;
definition: "GDCM includes file format definition and network communications protocol, both of which should be extended to provide full set of tools for researcher or small medical imaging vendor to interface with existing medical database.Implementation of DICOM standard designed to be open source so that researchers may access clinical data directly." .
SCR:024028 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GCLib" ;
NIFRID:synonym "gclib",
"genome-code-lib" ;
definition: "Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time." .
SCR:024029 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GNUmed" ;
NIFRID:synonym "gnumed",
"gnumed-client",
"gnumed-server" ;
definition: "Software to build Electronic Medical Record in multiple languages to assist and improve longitudinal care specifically in ambulatory settings.Useful to anyone documenting the health of patients including,doctors, physical therapists, occupational therapists,acupuncturists, nurses, psychologists." .
SCR:024030 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19577" ;
rdfs:label "GfaPy" ;
NIFRID:synonym "Gfapy",
"gfapy" ;
definition: "Software library for handling sequence graphs in Python." .
SCR:024031 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ginkgo CADx" ;
NIFRID:synonym "ginkgocadx" ;
definition: "Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files." .
SCR:024032 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_05314" ;
rdfs:label "GramAlign" ;
NIFRID:synonym "gramalign" ;
definition: "Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences." .
SCR:024033 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IDeFIX" ;
NIFRID:synonym "idefix" ;
definition: "Software tool for demultiplexing Illumina NGS data. Reports inconsistencies between the raw data and the Sample Sheet, checks for duplicates of indices/ index combinations in the latter and removes unwanted characters from it. Creates an IDeFIX_Report.csv containing the indices/ index combinations from the raw data and their abundance as well as their count in the Sample Sheet and the corresponding Index ID(s)." .
SCR:024034 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Htscodecs" ;
NIFRID:synonym "htscodecs" ;
definition: "Software repository implements the custom CRAM codecs used for \"EXTERNAL\" block types.Custom compression for CRAM custom algorithm written to compress the BAM file format for DNA sequencing data." .
SCR:024035 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GraphMap2" ;
NIFRID:synonym "graphmap2" ;
definition: "Software tool as splice aware RNA-seq mapper for long reads produced by Pacific Biosciences and Oxford Nanopore devices" .
SCR:024036 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HTSJDK" ;
NIFRID:synonym "htsjdk" ;
definition: "Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data." .
SCR:024037 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_16456" ;
rdfs:label "IgDiscover" ;
NIFRID:synonym "igdiscover" ;
definition: "Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:024038 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_02397" ;
rdfs:label "InsPecT" ;
NIFRID:synonym "Inspect",
"inspect" ;
definition: "Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed." .
SCR:024039 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ImageTooth" ;
NIFRID:synonym "imagetooth" ;
definition: "Software library to generate images for odontograms.Allows to choose between png or jpg images." .
SCR:024040 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Insight Toolkit" ;
NIFRID:synonym "insighttoolkit4",
"ITK" ;
definition: "Open source, software cross-platform library that provides suite of software tools for image analysis.ITK builds on proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions." .
SCR:024041 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_31218" ;
rdfs:label "InSilicoSeq" ;
NIFRID:synonym "insilicoseq",
"InSilicoSeq- A sequencing simulator" ;
definition: "Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome." .
SCR:024042 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Intake" ;
NIFRID:synonym "intake",
"Intake: A general interface for loading data" ;
definition: "Software package for finding, investigating, loading and disseminating data." .
SCR:024043 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ISMRMRD" ;
NIFRID:synonym "ISMRM Raw Data Format",
"ismrmrd" ;
definition: "Prerequisite for sharing magnetic resonance imaging reconstruction algorithms and code is a common raw data format. This repository describes such common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. The repository also contains a C/C++ library for working with the format." .
SCR:024044 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_08188" ;
rdfs:label "IVA" ;
NIFRID:synonym "Iterative Virus Assembler - de novo virus assembler of Illumina paired reads.",
"iva" ;
definition: "Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth." .
SCR:024045 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iVar" ;
NIFRID:synonym "ivar" ;
definition: "Software package for viral amplicon based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.Contains intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates.Following functions are implemented in iVar: trimming of primers and low-quality bases; consensus calling; variant calling both iSNVs and insertions/deletions; identifying mismatches to primer sequences and excluding the corresponding reads from alignment files." .
SCR:024046 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_27932" ;
rdfs:label "Kaptive" ;
NIFRID:synonym "kaptive" ;
definition: "Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies." .
SCR:024047 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JabRef" ;
NIFRID:synonym "jabref",
"JabRef Bibliography Management" ;
definition: "Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research." .
SCR:024048 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KBibTeX" ;
NIFRID:synonym "kbibtex" ;
definition: "Software tool as bibliography editor for KDE. Used in conjunction with Kile. BibTeX editor for KDE. KBibTeX's primary file format is BibTeX as known from LaTeX, but other formats such as RIS, PDF, or RTF can be imported and exported." .
SCR:024049 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_18309" ;
rdfs:label "kineticsTools" ;
NIFRID:synonym "kineticstools" ;
definition: "Software tools for detecting DNA modifications from single molecule, real-time sequencing data. This tool implements the P_ModificationDetection module in SMRT� Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol." .
SCR:024050 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_20021" ;
rdfs:label "JAligner" ;
NIFRID:synonym "jaligner" ;
definition: "Open source software Java implementation of the Needleman�Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model." .
SCR:024051 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kleborate" ;
NIFRID:synonym "KLEBORATE",
"kleborate" ;
definition: "Software tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for MLST sequence type, species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), ICEKp associated virulence loci (yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)), virulence plasmid associated loci (salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)), antimicrobial resistance determinants (acquired genes, SNPs, gene truncations and intrinsic ?-lactamases), and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive." .
SCR:024052 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_08009" ;
rdfs:label "Lambda" ;
NIFRID:synonym "LAMBDA",
"lambda-align",
"Lambda: the Local Aligner for Massive Biological DatA" ;
definition: "Software tool as local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools." .
SCR:024053 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_18534" ;
rdfs:label "IGoR" ;
NIFRID:synonym "igor",
"Inference and Generation Of Repertoires" ;
definition: "C++ software designed to infer V(D)J recombination related processes from sequencing data." .
SCR:024054 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_31606" ;
rdfs:label "KMA" ;
NIFRID:synonym "kma" ;
definition: "Software mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.Used for aligning high quality reads against highly redundant databases, where unique matches often does not exist. Works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the \"ConClave\" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, based on users demands." .
SCR:024055 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "kempbasu" ;
definition: "Software package implements two significance tests for comparing digital gene expression profiles. They provide two programs: Kemp for the frequentist test and Basu for the Bayesian test, and some auxiliary scripts." .
SCR:024056 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-ASN1-EntrezGene" ;
NIFRID:synonym "Bio-ASN1-EntrezGene - Regular expression-based Perl Parser for NCBI Entrez Gene",
"libbio-asn1-entrezgene-perl" ;
definition: "Software regular expression based Perl Parser for NCBI Entrez Gene genome databases. Parses ASN.1-formatted Entrez Gene record and returns data structure that contains all data items from gene record." .
SCR:024057 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AcePerl" ;
NIFRID:synonym "ACE",
"Ace",
"Ace - Object-Oriented Access to ACEDB Databases",
"Ace-Perl",
"ace-perl",
"libace-perl" ;
definition: "Software provides an interface to the ACEDB object-oriented database. Both read and write access is provided, and ACE objects are returned as similarly-structured Perl objects. Multiple databases can be opened simultaneously." .
SCR:024058 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KmerResistance" ;
NIFRID:synonym "kmerresistance" ;
definition: "Software tool to correlate mapped genes with the predicted species of WGS samples, where this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available." .
SCR:024059 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Chado-Schema" ;
NIFRID:synonym "Bio-Chado-Schema - A standard DBIx-Class layer for the Chado database schema",
"libbio-chado-schema-perl" ;
definition: "Standard object-relational mapping layer for use with GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of DBIx::Class::Schema::Loader module." .
SCR:024060 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AI-FANN" ;
NIFRID:synonym "AI-FANN - Perl wrapper for the Fast Artificial Neural Network library",
"libai-fann-perl" ;
definition: "Software Perl wrapper for the Fast Artificial Neural Network library" .
SCR:024061 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Graphics" ;
NIFRID:synonym "Bio-Graphics - Generate GD images of Bio-Seq objects",
"libbio-graphics-perl" ;
definition: "Software package to generate GD images of Bio::Seq objects." .
SCR:024062 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_20057" ;
rdfs:label "BioD" ;
definition: "Software memory efficient bioinformatics library written in D programming language whose aim is to provide platform for developing high performance computational biology applications using the D programming language through automatic parallelization of tasks where possible and by avoiding unnecessary memory allocations." .
SCR:024063 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Coordinate" ;
NIFRID:synonym "Bio-Coordinate - Modules for working with biological coordinates",
"libbio-coordinate-perl" ;
definition: """Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.
""" .
SCR:024064 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-EUtilities" ;
NIFRID:synonym "Bio-EUtilities - BioPerl low-level API for retrieving and storing data from NCBI eUtils",
"libbio-eutilities-perl" ;
definition: "Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic." .
SCR:024065 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bioparser" ;
NIFRID:synonym "bioparser",
"libbioparser-dev" ;
definition: "Software C++ library for parsing several formats in bioinformatics. C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files." .
SCR:024066 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-SamTools" ;
NIFRID:synonym "libbio-samtools-perl" ;
definition: "Software Perl interface to SamTools library for DNA sequencing." .
SCR:024067 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Tools-Run-Alignment-Clustalw" ;
NIFRID:synonym "Bio-Tools-Run-Alignment-Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program",
"libbio-tools-run-alignment-clustalw-perl" ;
definition: "Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program." .
SCR:024068 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-SCF" ;
NIFRID:synonym "Bio-SCF - Perl extension for reading and writting SCF sequence files",
"libbio-scf-perl" ;
definition: "Software Perl extension for reading and writting SCF sequence files.This module provides Perl interface to SCF DNA sequencing files. It has both tied hash and an object-oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify them and write them back." .
SCR:024069 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Tools-Phylo-PAML" ;
NIFRID:synonym "baseml",
"basemlg",
"Bio-Tools-Phylo-PAML - Parses output from the PAML programs codeml",
"codemlsites and yn00",
"libbio-tools-phylo-paml-perl" ;
definition: "Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output." .
SCR:024070 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Tools-Run-Alignment-TCoffee" ;
NIFRID:synonym "libbio-tools-run-alignment-tcoffee-perl" ;
definition: "Software object for calculation of multiple sequence alignment from set of unaligned sequences or alignments using the TCoffee program." .
SCR:024071 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Libchipcard" ;
NIFRID:synonym "libchipcard",
"libchipcard-dev",
"libchipcard-tools" ;
definition: "Software library for generic access to chipcard readers and cards" .
SCR:024072 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "libdisorder" ;
definition: "Software C library for entropy measurement of byte streams and other data." .
SCR:024073 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chado" ;
NIFRID:synonym "libchado-perl" ;
definition: "Relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals." .
SCR:024074 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FAST Analysis of Sequences Toolbox" ;
NIFRID:synonym "fast",
"FAST - FAST Analysis of Sequences Toolbox",
"Fast Analysis of Sequences Toolbox",
"libfast-perl" ;
NIFRID:abbrev "FAST" ;
definition: "Software Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX utilities (for example fasgrep, fascut, fashead and fastr) that extends the UNIX toolbox paradigm to bioinformatic sequence records.FAST workflows are designed for serial processing of flatfile biological sequence record databases per-sequence, rather than per-line, through UNIX pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FASTQ format is supported. FAST is designed for learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, and reproducibility. FAST tools expose the power of Perl and BioPerl to users in an easy-to-learn command-line paradigm." .
SCR:024075 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "libGDF" ;
NIFRID:synonym "gdf-tools",
"libgdf",
"libgdf-dev",
"octave-gdf" ;
definition: "Software library for processing of biomedical signals. Provides generic storage for biosignals, such as EEG, ECG, MEG. C++ implementation of GDF - \" general dataformat for biosignals\" version V2.20." .
SCR:024076 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JLODA" ;
NIFRID:synonym "jloda",
"libjloda-java" ;
definition: "Software Java library of data structures and algorithms.Provides some basic data structures and algorithms used by SplitsTree, Dendroscope and MEGAN." .
SCR:024077 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "libmaus2" ;
definition: "Software collection of data structures and algorithms. Contains I/O classes (single byte and UTF-8), bitio classes (input, output and various forms of bit level manipulation), text indexing classes (suffix and LCP array, fulltext and minute (FM), ...), BAM sequence alignment files input/output (simple and collating) and many lower level support classes." .
SCR:024078 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_15611" ;
rdfs:label "Edlib" ;
NIFRID:synonym "Edib: A lightweight and super fast C/C++ library for sequence alignment using edit distance.",
"libedlib" ;
definition: "Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance." .
SCR:024079 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "libdivsufsort" ;
NIFRID:synonym "libdivsufsort: A lightweight suffix-sorting library" ;
definition: "Software library that implements lightweight suffix array construction algorithm. Provides C API to construct suffix array and Burrows-Wheeler transformed string from given string over constant size alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) bytes of memory space, where n is the length of the string." .
SCR:024080 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_20523" ;
rdfs:label "libncl" ;
NIFRID:synonym "NCL",
"ncl",
"NCL - the NEXUS Class Library" ;
definition: "Software C++ class library for interpreting data files in NEXUS format. NEXUS Class Library software package is collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses.NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored." .
SCR:024081 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MIA" ;
NIFRID:synonym "libmia-2.4-dev",
"libmialm",
"libmialm-dev",
"libmiaviewit-dev",
"libvistaio-dev",
"mia-tools",
"mia-viewit",
"mialmpick",
"python3-mia" ;
definition: "Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality." .
SCR:024082 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-PrimerDesigner" ;
NIFRID:synonym "Bio-PrimerDesigner - Design PCR Primers using primer3 and epcr",
"libbio-primerdesigner-perl" ;
definition: "Software package provides low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio-PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported." .
SCR:024083 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_20524" ;
rdfs:label "libqes" ;
definition: "Software C library with bioinformatic focus optimised for speed and clean API." .
SCR:024084 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Java NeXML libraries and tools" ;
NIFRID:synonym "libnexml-java",
"nexml.java" ;
definition: "Software repository contains java code for NeXML processing." .
SCR:024085 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "libics" ;
NIFRID:synonym "libics- Image Cytometry Standard file reading and writing" ;
definition: "Software reference library for Image Cytometry Standard, an open standard for writing images of any dimensionality and data type to file, together with associated information regarding the recording equipment or recorded subject.Image Cytometry Standard file reading and writing." .
SCR:024086 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "libminc" ;
NIFRID:synonym "Medical Image NetCDF library" ;
definition: "Software core library and API of the Medical Image NetCDF toolkit." .
SCR:024087 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Core Wrapper" ;
NIFRID:synonym "CORE-WRAPPER",
"core-wrapper" ;
definition: "Software library that exports C++ mmCIF accessors to Python." .
SCR:024088 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "libqc++" ;
NIFRID:synonym "libqcpp" ;
definition: "Software C++11 library for next-gen sequence quality control and assessment." .
SCR:024089 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_20525" ;
rdfs:label "SSW Library" ;
NIFRID:synonym "Complete-Striped-Smith-Waterman-Library",
"libssw",
"SIMD Smith-Waterman Library" ;
definition: "SIMD Smith-Waterman C/C++ library for use in genomic applications. SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages." .
SCR:024090 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TaxonomyTree" ;
NIFRID:synonym "librdp-taxonomy-tree-java" ;
definition: "Software library used by other RDP tools.TaxonomyTree building and traversal utility classes." .
SCR:024091 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14682" ;
rdfs:label "SeqLib" ;
NIFRID:synonym "libseqlib" ;
definition: "Software C++ htslib/bwa-mem/fermi interface for interrogating sequence data" .
SCR:024092 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sort-Key-Top" ;
NIFRID:synonym "libsort-key-top-perl",
"Sort-Key-Top - select and sort top n elements" ;
definition: "Functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures." .
SCR:024093 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "libStatGen" ;
NIFRID:synonym "C++ Library: libStatGen",
"libstatgen" ;
definition: "Software library as set of classes for creating statistical genetic programs." .
SCR:024094 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ThreadPool" ;
NIFRID:synonym "libthread-pool",
"Thread pool" ;
definition: "Software C++ thread pool library." .
SCR:024095 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lighter" ;
NIFRID:synonym "lighter" ;
definition: "Software tool as kmer-based error correction method for whole genome sequencing data. Lighter uses sampling rather than counting to obtain set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors." .
SCR:024096 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Libxdf" ;
NIFRID:synonym "libxdf",
"Libxdf � a C++ library for loading XDF files" ;
definition: "Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications." .
SCR:024097 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "limereg" ;
definition: "Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image." .
SCR:024098 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11266" ;
rdfs:label "LTRsift" ;
NIFRID:synonym "LTRSIFT",
"ltrsift" ;
definition: "Software graphical desktop tool for semi-automatic postprocessing of de novopredicted LTR retrotransposon annotations, such as the ones generated by LTRharvestand LTRdigest. Interface displays LTR retrotransposon candidates, their putative families and their internal structure in a hierarchical fashion allowing the user to \"sift\" through results of de novo prediction software. It also offers customizable filtering and classification functionality." .
SCR:024099 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14823" ;
rdfs:label "Lucy" ;
NIFRID:synonym "lucy",
"Lucy DNA sequence quality and vector trimming tool" ;
definition: "Software tool to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses." .
SCR:024100 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VIGRA" ;
NIFRID:synonym "libvigraimpex",
"The VIGRA Computer Vision Library",
"Vision with Generic Algorithms" ;
definition: "Software image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, without thereby giving up execution speed. As of version 1.7.1, VIGRA also provides extensive Python bindings on the basis of the popular numpy framework." .
SCR:024101 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tab2MAGE" ;
NIFRID:synonym "ArrayExpress Tab2MAGE",
"mage2tab" ;
definition: "Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange." .
SCR:024102 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_18310" ;
rdfs:label "Mapsembler2" ;
NIFRID:synonym "Mapsembler",
"mapsembler2" ;
definition: "Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants." .
SCR:024103 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MAXFLOW" ;
NIFRID:synonym "maxflow" ;
definition: "Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph." .
SCR:024104 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_20118" ;
rdfs:label "Logol" ;
NIFRID:synonym "logol" ;
definition: "Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic." .
SCR:024105 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_06743" ;
rdfs:label "MafFilter" ;
NIFRID:synonym "maffilter",
"MafFilter a genome alignment processor" ;
definition: "Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc." .
SCR:024106 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_20116" ;
rdfs:label "MacSyFinder" ;
NIFRID:synonym "macsyfinder" ;
definition: "Software tool to mine genomes for molecular systems with Application to CRISPR-Cas Systems. Detection of macromolecular systems in protein datasets using systems modelling and similarity search." .
SCR:024107 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tabixpp" ;
NIFRID:synonym "libtabixpp" ;
definition: "Software C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.Wrapper to tabix indexer" .
SCR:024108 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Maude" ;
NIFRID:synonym "maude" ;
definition: "Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation." .
SCR:024109 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCL" ;
NIFRID:synonym "Markov Cluster Algorithm",
"mcl" ;
definition: "Software tool as general purpose cluster algorithm for both weighted and unweighted networks. Unsupervised cluster algorithm for graphs based on simulation of stochastic flow in graphs. Cluster algorithm for graphs." .
SCR:024110 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_20187" ;
rdfs:label "Metastudent" ;
NIFRID:synonym "metastudent",
"metastudent-data" ;
definition: "Software tool to predict gene ontology terms for protein sequences through homology." .
SCR:024111 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "metaBIT" ;
NIFRID:synonym "metabit" ;
definition: "Software pipeline for metagenomic and taxonomical analysis from shotgun sequencing." .
SCR:024112 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_17085" ;
rdfs:label "MicrobeGPS" ;
NIFRID:synonym "microbegps" ;
definition: "Software tool for analysis of metagenomic sequencing data.Used to profile composition of metagenomic communities. Calculates quality metrics for estimated candidates and allows the user to identify false candidates." .
SCR:024113 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_13515" ;
rdfs:label "MHAP" ;
NIFRID:synonym "mhap",
"MinHash Alignment Process" ;
definition: "Software tool as reference implementation of probabilistic sequence overlapping algorithm. Used to detect overlaps between noisy long-read sequence data." .
SCR:024114 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11366" ;
rdfs:label "Miniasm" ;
NIFRID:synonym "miniasm" ;
definition: "Software OLC-based de novo assembler for noisy long reads." .
SCR:024115 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_05472" ;
rdfs:label "MindTheGap" ;
NIFRID:synonym "mindthegap" ;
definition: "Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome." .
SCR:024116 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_31718" ;
rdfs:label "mirtop" ;
definition: "Command lines tool to annotate miRNAs with standard mirna/isomir naming." .
SCR:024117 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "medicalterms" ;
NIFRID:synonym "hunspell-de-med",
"wgerman-medical" ;
definition: "Software package to create specialized dictionaries for medical terms used in various languages.German medical dictionary words." .
SCR:024118 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_33146" ;
rdfs:label "mPSQed" ;
NIFRID:synonym "mpsqed" ;
definition: "Software tool for the design of multiplex pyrosequencing assays." .
SCR:024119 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_20188" ;
rdfs:label "SMILE" ;
NIFRID:synonym "mlv-smile" ;
definition: "Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths." .
SCR:024120 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mmtf-python" ;
definition: "Software Python implementation of MacroMolecular Transmission Format API, decoder and encoder. Repository holds the Python 2 and 3 compatible API, encoding and decoding libraries." .
SCR:024121 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_15264" ;
rdfs:label "mPTP" ;
NIFRID:synonym "mptp",
"multi-rate Poisson Tree Processes" ;
definition: "Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets." .
SCR:024122 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Molekel" ;
NIFRID:synonym "molekel" ;
definition: "Open source multi platform molecular visualization program." .
SCR:024123 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRtrix3" ;
NIFRID:synonym "mrtrix3" ;
definition: "Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses." .
SCR:024124 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11495" ;
rdfs:label "Nanocall" ;
NIFRID:synonym "nanocall" ;
definition: "Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller." .
SCR:024125 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoLyse" ;
NIFRID:synonym "nanolyse" ;
definition: "Software package to remove reads mapping to the lambda phage genome from a fastq file." .
SCR:024126 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_03642" ;
rdfs:label "Mustang" ;
NIFRID:synonym "MUltiple (protein) STructural AligNment alGorithm",
"MUSTANG",
"mustang" ;
definition: "Software tool for structural alignment of multiple protein structures. Used to produce sequence alignment. Reports multiple sequence alignment and corresponding superposition of structures." .
SCR:024127 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_29732" ;
rdfs:label "NanoSV" ;
NIFRID:synonym "nanosv" ;
definition: "Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers." .
SCR:024128 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoPlot" ;
NIFRID:synonym "nanoplot" ;
definition: "Software package as plotting tool for long read sequencing data and alignments." .
SCR:024129 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_15907" ;
rdfs:label "MView" ;
NIFRID:synonym "mview" ;
definition: "Web-compatible database search or multiple alignment viewer, Software tool as command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats." .
SCR:024130 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCBI accession download script" ;
NIFRID:synonym "ncbi-acc-download" ;
definition: "Software tool as partner script to the popular ncbi-genome-download script. Allows to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API." .
SCR:024131 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21450" ;
rdfs:label "NeoBio" ;
NIFRID:synonym "neobio" ;
definition: "Software library of sequence alignment algorithms implemented in Java." .
SCR:024132 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11714" ;
rdfs:label "Murasaki" ;
NIFRID:synonym "murasaki" ;
definition: "Software language-theory based homology detection tool across multiple large genomes." .
SCR:024133 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_03695" ;
rdfs:label "Ngila" ;
NIFRID:synonym "ngila" ;
definition: "Software alignment program that can align pairs of sequences using logarithmic and affine gap penalties." .
SCR:024134 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_30332" ;
rdfs:label "NextSV" ;
NIFRID:synonym "nextsv",
"NextSV3" ;
definition: "Software tool for automated structrual variation detection from long-read sequencing using state-of-the-art tools. NextSV3 uses Minimap2 to do read mapping and uses two state-of-the-art SV callers (Sniffles and cuteSV) to do SV calling." .
SCR:024135 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nextflow" ;
NIFRID:synonym "nextflow" ;
definition: "Software workflow manager that enables development of portable and reproducible workflows.Supports deploying workflows on variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Provides support to manage workflow dependencies through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more." .
SCR:024136 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Entrez Direct" ;
NIFRID:synonym "EDirect",
"Entrez Direct: E-utilities on the Unix Command Line",
"ncbi-entrez-direct" ;
definition: "Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats." .
SCR:024137 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_04815" ;
rdfs:label "NJplot" ;
NIFRID:synonym "njplot" ;
definition: "Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods." .
SCR:024138 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NW-align" ;
NIFRID:synonym "nw-align" ;
definition: "Software tool as alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm." .
SCR:024139 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21452" ;
rdfs:label "NORSp" ;
NIFRID:synonym "NOn-Regular Secondary Structure predictor",
"norsp",
"NORSp - predictor of NOn-Regular Secondary Structure" ;
definition: "Online predictor of NOn-Regular Secondary Structure for disordered regions in protein. Used to predict long regions with no regular secondary structure. Upon user submission of protein sequence, NORSp will analyse the protein about its secondary structure, and presence of transmembrane helices and coiled-coil then return e-mail to user about the presence and position of disordered regions." .
SCR:024140 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Odil" ;
NIFRID:synonym "odil" ;
definition: "Software DICOM library which provides user-friendly C++11 and Python API for different parts of the DICOM standard." .
SCR:024141 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_32696" ;
rdfs:label "OBITools" ;
NIFRID:synonym "obitools" ;
definition: "Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses." .
SCR:024142 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14951" ;
rdfs:label "OpenCFU" ;
NIFRID:synonym "opencfu" ;
definition: "Software to count cell colonies and other circular objects. Used to facilitate enumeration of colony forming unit." .
SCR:024143 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_31719" ;
rdfs:label "omegaMap" ;
NIFRID:synonym "omegamap" ;
definition: "Software tool for detecting natural selection and recombination in DNA or RNA sequences." .
SCR:024144 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenEMR" ;
NIFRID:synonym "openemr" ;
definition: "Open source software for electronic health records and medical practice management solution." .
SCR:024145 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Orthanc" ;
NIFRID:synonym "orthanc" ;
definition: "Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases." .
SCR:024146 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_16034" ;
rdfs:label "NORSnet" ;
NIFRID:synonym "Norsnet",
"norsnet" ;
definition: "Software as neural network based method that focuses on identification of unstructured loops. Trained to distinguish between very long contiguous segments with non-regular secondary structure and well-folded proteins. Trained on predicted information rather than on experimental data." .
SCR:024147 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenSurgSim" ;
NIFRID:synonym "opensurgsim" ;
definition: "Open source software framework that includes the necessary building blocks for surgical simulations, such as native device support, haptic feedback, graphics, discrete collision detection and physics simulation. Developers can refactor the physics engine, swap models, ODE solvers, or linear system solvers." .
SCR:024148 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenIGTLink" ;
NIFRID:synonym "Open Network Interface for Image-Guided Therapy Link",
"openigtlink" ;
definition: "Open source software network communication interface for image guided interventions.Provides plug-and-play unified real-time communications in operating rooms for image-guided interventions, where imagers, sensors, surgical robots,and computers from different vendors work cooperatively to ensure seamless data flow among those components and enable a closed loop process of planning, control, delivery, and feedback." .
SCR:024149 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_33123" ;
rdfs:label "OptimiR" ;
NIFRID:synonym "optimir" ;
definition: "Software miRSeq data alignment workflow. Used to integrate genetic information to assess the impact of variants on miRNA expression. Used for integrating genome wide genotype data into miRNA sequence alignment analysis." .
SCR:024150 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "parallel-fastq-dump" ;
definition: "Software wrapper to speed up downloading process by dividing the work into multiple threads." .
SCR:024151 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PAIPline" ;
definition: "Software Python program to search for pathogen nucleic acid sequences in NGS datasets.Used for pathogen identification in metagenomic and clinical next generation sequencing samples." .
SCR:024152 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pbcopper" ;
definition: "Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications." .
SCR:024153 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21461" ;
rdfs:label "Parsnp" ;
NIFRID:synonym "parsnp" ;
definition: "Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction." .
SCR:024154 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Patristic" ;
NIFRID:synonym "patristic" ;
definition: "Software Java program for calculating patristic distances and graphically comparing the components of genetic change." .
SCR:024155 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14370" ;
rdfs:label "PDB2PQR" ;
NIFRID:synonym "pdb2pqr" ;
definition: "Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files." .
SCR:024156 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14997" ;
rdfs:label "PCMA" ;
NIFRID:synonym "pcma",
"Profile Consistency Multiple Sequence Alignment" ;
definition: "Software tool for multiple sequence alignment based on profile consistency. Used to construct multiple sequence alignment given set of protein sequences." .
SCR:024157 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PartitionFinder" ;
NIFRID:synonym "partitionfinder",
"PartitionFinder 2" ;
definition: "Software Python program to discover optimal partitioning schemes for DNA sequences.Used for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data." .
SCR:024158 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_29588" ;
rdfs:label "PfTools" ;
NIFRID:synonym "pftools" ;
definition: "Software suite of tools to build and search generalized profiles." .
SCR:024159 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21686" ;
rdfs:label "PhySamp" ;
NIFRID:synonym "physamp" ;
definition: "Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree." .
SCR:024160 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_33677" ;
rdfs:label "PiGx-RNAseq" ;
NIFRID:synonym "pigx-rnaseq" ;
definition: "Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables." .
SCR:024161 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "picopore" ;
definition: "Software tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality." .
SCR:024162 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PHYLOViZ" ;
definition: "Platform independent JAVA software for analysis of sequence based typing methods that generate allelic profiles and their associated epidemiological data.Phylogenetic inference and data visualization for sequence based typing methods." .
SCR:024163 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21460" ;
rdfs:label "ParsInsert" ;
NIFRID:synonym "parsinsert" ;
definition: "Software C++ implementation of Parsimonious Insertion algorithm. Used to produce phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis." .
SCR:024164 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phyx" ;
definition: "Software phylogenetic tools for unix. Used to perform phylogenetics analyses on trees and sequences. Collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects." .
SCR:024165 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pipasic" ;
definition: "Software tool for similarity and expression correction for strain level identification and quantification in metaproteomics. Peptide intensity weighted proteome abundance similarity correction tool to correct identification and spectral counting based quantification results. Pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor." .
SCR:024166 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PlasmidID" ;
NIFRID:synonym "plasmidid" ;
definition: "Software mapping based, assembly assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. Computational pipeline implemented in BASH that maps Illumina reads over plasmid database sequences." .
SCR:024167 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_28371" ;
rdfs:label "PlasmidSeeker" ;
NIFRID:synonym "plasmidseeker" ;
definition: "Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads." .
SCR:024168 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Plastimatch" ;
definition: "Open source software for image computation with main focus on high performance volumetric registration, segmentation, and image processing of volumetric medical images." .
SCR:024169 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pngquant" ;
definition: "Software command line utility and library for lossy compression of PNG images. The conversion reduces file sizes significantly and preserves full alpha transparency. Generated images are compatible with all web browsers and operating systems." .
SCR:024170 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_06498" ;
rdfs:label "PLAST" ;
NIFRID:synonym "parallel local alignment search tool",
"plast" ;
definition: "Software parallel local alignment search tool for database comparison. NGS sequence similarity search tool providing significant accelerations of seeds based heuristic comparison methods." .
SCR:024171 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21692" ;
rdfs:label "ProDA" ;
NIFRID:synonym "proda" ;
definition: "Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures." .
SCR:024172 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14254" ;
rdfs:label "POA" ;
NIFRID:synonym "Partial Order Alignment",
"poa" ;
definition: "Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment." .
SCR:024173 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_08028" ;
rdfs:label "PLIP" ;
NIFRID:synonym "plip",
"Protein-Ligand Interaction Profiler" ;
definition: "Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures." .
SCR:024175 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_29592" ;
rdfs:label "Populations" ;
NIFRID:synonym "populations" ;
definition: "Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions." .
SCR:024176 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11487" ;
rdfs:label "Placnet" ;
NIFRID:synonym "placnet",
"plasmid constellation networks" ;
definition: "Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools." .
SCR:024177 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_05355" ;
rdfs:label "Proteinortho" ;
definition: "Software tool to detect orthologous genes within different species. Stand-alone tool for large datasets for orthology analysis." .
SCR:024178 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRINSEQ" ;
NIFRID:synonym "prinseq-lite" ;
definition: "Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format." .
SCR:024179 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_13706" ;
rdfs:label "PROFisis" ;
NIFRID:synonym "profisis" ;
definition: "Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures." .
SCR:024181 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pssh2" ;
definition: "Software tools for creating the sequence-to-structure alignment database PSSH2." .
SCR:024182 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyepl" ;
NIFRID:synonym "Python Experiment-Programming Library" ;
definition: "Software library for coding psychology experiments in Python.Supports presentation of both visual and auditory stimuli, and supports both manual and sound input as responses." .
SCR:024183 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "purple" ;
NIFRID:synonym "Picking Unique Relevant Peptides for viraL Experiments" ;
definition: "Software tool for selecting target specific peptide candidates directly from given proteome sequence data." .
SCR:024184 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pufferfish" ;
definition: "Software tool implementing novel indexing data structure for compacted de Bruijn graph and colored compacted de Bruijn graph." .
SCR:024185 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pycoqc" ;
definition: "Software application to compute metrics and generate interactive QC plots for Oxford Nanopore technologies sequencing data." .
SCR:024186 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyFAI" ;
NIFRID:synonym "pyFai",
"pyfai" ;
definition: "Open source Python software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments." .
SCR:024187 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "python-airr" ;
definition: "Software airr reference library provides basic functions and classes for interacting with AIRR Community Data Representation Standards, including tools for read, write and validation." .
SCR:024188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyomo" ;
definition: "Open source Python-based optimization modeling language with diverse set of optimization capabilities." .
SCR:024189 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_15419" ;
rdfs:label "pynast" ;
NIFRID:synonym "Python Nearest Alignment Space Termination tool" ;
definition: "Software tool for aligning sequences to template alignment." .
SCR:024190 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21694" ;
rdfs:label "pyscanfcs" ;
definition: "Software application for perpendicular line scanning fluorescence correlation spectroscopy." .
SCR:024191 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyranges" ;
definition: "Software application for efficient comparison of genomic intervals in Python." .
SCR:024192 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14006" ;
rdfs:label "PyCogent" ;
NIFRID:synonym "COmparative GENomic Toolkit",
"python-cogent" ;
definition: "Software Python library for analysis of genomic sequence data. Framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics." .
SCR:024193 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "python-biom-format" ;
definition: "Software provides command line interface and Python API for working with Biological Observation Matrix files." .
SCR:024194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cooler" ;
NIFRID:synonym "python-cooler" ;
definition: "Software library for sparse, compressed, binary persistent storage format used to store genomic interaction data, such as Hi-C contact matrices.Scalable storage for Hi-C data and other genomically labeled arrays." .
SCR:024195 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "qcat" ;
definition: "Software Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files." .
SCR:024196 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "psignifit" ;
definition: "Software toolbox to fit psychometric functions and to test hypotheses about psychometric data." .
SCR:024197 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_08877" ;
rdfs:label "DendroPy" ;
NIFRID:synonym "python-dendropy" ;
definition: "Software Python library for phylogenetic computing. Provides classes and functions for simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:024198 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_10013" ;
rdfs:label "rambo-k" ;
definition: "Software tool for rapid and sensitive removal of background sequences from Next Generation Sequencing data." .
SCR:024199 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "qtlreaper" ;
definition: "Software, written in C and compiled as Python module, for rapidly scanning microarray expression data for Quantitative Trait Locies. Searches for association between each expression trait and all genotypes and evaluates that association by permutation test. Performs bootstrap resampling to estimate confidence region for location of putative QTL." .
SCR:024200 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_18457" ;
rdfs:label "qtltools" ;
definition: "Software tool set for molecular Quantitative Trait Loci discovery and analysis. Allows to go from raw sequence data to collection of molecular Quantitative Trait Loci in few easy-to-perform steps." .
SCR:024201 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21300" ;
rdfs:label "raccoon" ;
definition: "Software graphical interface for preparing AutoDock virtual screenings.Automates some of the most common operations performed when preparing virtual screening." .
SCR:024202 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_18239" ;
rdfs:label "python-bx" ;
definition: "Software Python library and associated set of scripts for rapid implementation of genome scale analyses." .
SCR:024203 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "qcumber" ;
definition: "Software for quality control, quality trimming, adapter removal and sequence content check of NGS data." .
SCR:024204 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_10349" ;
rdfs:label "rapmap" ;
NIFRID:synonym "RapMap" ;
definition: "Software tool for mapping RNA-seq reads to transcriptomes. Used for rapid sensitive and accurate read mapping via quasi-mapping" .
SCR:024205 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "quicktree" ;
definition: "Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments." .
SCR:024206 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_07883" ;
rdfs:label "ragout" ;
NIFRID:synonym "Reference-Assisted Genome Ordering UTility" ;
definition: "Software tool for chromosome level scaffolding using multiple references. Given initial assembly fragments and one or multiple related references it produces chromosome scale assembly." .
SCR:024207 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_33016" ;
rdfs:label "rampler" ;
definition: "Standalone software for sampling genomic sequences.Supports two modes, random subsampling of sequencing data to desired depth and file splitting to desired size in bytes." .
SCR:024208 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_05076" ;
rdfs:label "rasmol" ;
NIFRID:synonym "RasMol" ;
definition: "Software package for molecular graphics visualisation.Used for visualisation of molecules." .
SCR:024209 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Moodle LMS" ;
NIFRID:synonym "Moodle",
"moodle",
"moodle (LMS)" ;
definition: "Open source learning platform to provide educators, administrators and learners with integrated system to create personalised learning environments. Designed to help educators create online courses based on pedagogical principles." .
SCR:024210 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MorePower" ;
NIFRID:synonym "MorePower 6.0",
"MorePower calculator" ;
definition: "Software tool as flexible freeware statistical calculator that computes sample size, effect size, and power statistics for factorial ANOVA designs." .
SCR:024211 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Epworth Sleepiness Scale" ;
NIFRID:abbrev "ESS" ;
definition: "New method for measuring daytime sleepiness. Self administered questionnaire to provide measurement of subject's general level of daytime sleepiness. Subjects are to rate the chances that they would doze off or fall asleep when in eight different situations commonly encountered in daily life.Used to give valid measurements of sleep propensity in adults." .
SCR:024212 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Karolinska Sleepiness Scale" ;
definition: "The scale measures subjective level of sleepiness at particular time during the day. On this scale subjects indicate which level best reflects the psycho-physical sate experienced in the last 10 min.KSS is measure of situational sleepiness." .
SCR:024213 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ambulatory Monitoring | Psychomotor Vigilance Task system" ;
NIFRID:synonym "Psychomotor Vigilance Task",
"PVT-192 Psychomotor Vigilance Task Monitor" ;
definition: "System includes PVT-192 monitor and REACT software. Used for reaction time testing for long-term, large-scale testing of vigilance, effects of sleep deprivation, and drug effects. Used for PVT test wherever measures of performance or sleepiness effects are needed." .
SCR:024214 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenomeMUSter" ;
definition: "Web and programmatically accessible data service comprising allelic data covering strains at segregating sites. Mouse genetic variation service enables multi-trait, multi-population data integration and analyses. Interoperation with phenotype databases, analytic tools and other resources enable wealth of applications including multi-trait, multi-population meta-analysis. Mouse genetic resource that includes typed, sequenced, and imputed allelic states of 657 inbred mouse strains and their derivatives at 106.8M sites." .
SCR:024215 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rocker " ;
definition: """Software suite of Docker images with customized R environments for particular tasks.
Docker containers for R to create, distribute, deploy, and run software applications
using containers.""" .
SCR:024216 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ensemblQueryR" ;
definition: "Software R package allowing integration of Ensembl querying with R workflow. Used to seemlessly integrate querying of Ensembl databases into your R workflow." .
SCR:024217 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multiome Pipeline" ;
NIFRID:synonym "Multiome GEX and scATAC Pipeline" ;
definition: "Software open-source, cloud-optimized pipeline developed in collaboration with members of the BRAIN Initiative (BICCN and BICAN Sequencing Working Group) and SCORCH. It supports the processing of 10x 3' single-cell and single-nucleus gene expression (GEX) and chromatin accessibility (ATAC) data generated with the 10x Genomics Multiome assay." .
SCR:024220 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_05054" ;
rdfs:label "Raster3D" ;
NIFRID:synonym "raster3d" ;
definition: "Software tools for generating high quality raster images of proteins or other molecules. Photorealistic molecular graphics. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing." .
SCR:024221 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "annotate" ;
definition: "Software R package for using R enviroments for annotation." .
SCR:024222 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_06940" ;
rdfs:label "Rate4Site" ;
NIFRID:synonym "rate4site" ;
definition: "Software tool for detecting conserved amino-acid sites by computing relative evolutionary rate for each site in multiple sequence alignment. Used for identification of functional regions in proteins." .
SCR:024223 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_29381" ;
rdfs:label "affyio" ;
definition: "Software R package as routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing CEL and CDF file formats." .
SCR:024224 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biobase" ;
definition: "Software R package provides functions that are needed by many other packages or which replace R functions. Base functions for Bioconductor." .
SCR:024225 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "altcdfenvs" ;
NIFRID:synonym "alternative CDF environments" ;
definition: "Software R package contains convenience data structures and functions to handle cdfenvs." .
SCR:024226 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BiocGenerics" ;
definition: "Software R package defines many S4 generic functions used in Bioconductor." .
SCR:024227 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_29380" ;
rdfs:label "AnnotationHub" ;
definition: "Software R package to provide a client for the Bioconductor AnnotationHub web resource. AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered." .
SCR:024228 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "biomformat" ;
definition: "Software R package for interfacing with BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, limited support for writing biom-object back to biom-format file." .
SCR:024229 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "biovizBase" ;
definition: "Software R package to provide set of utilities, color schemes and conventions for genomic data. Used for various high-level packages for biological data visualization." .
SCR:024230 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bsgenome" ;
definition: "Software R package provides infrastructure shared by all the Biostrings-based genome data packages." .
SCR:024231 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bridgedbr" ;
definition: "Software R pacakge provides functions and load identifier mapping databases in R. Uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files." .
SCR:024232 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ctc" ;
definition: "Software R package for export and import classification trees and clusters to other programs." .
SCR:024233 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_33013" ;
rdfs:label "CNEr" ;
definition: "Software R package provides large scale identification and advanced visualization of sets of conserved noncoding elements." .
SCR:024234 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_15854" ;
rdfs:label "geneplotter" ;
definition: "Software R package provides functions for plotting genomic data" .
SCR:024235 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "genomeinfodb" ;
definition: "Software R package contains data and functions that define and allow translation between different chromosome sequence naming conventions, including function that attempts to place sequence names in their natural, rather than lexicographic order." .
SCR:024236 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "genomicalignments" ;
definition: "Software R package provides efficient containers for storing and manipulating short genomic alignments. This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments." .
SCR:024237 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_07953" ;
rdfs:label "groHMM" ;
NIFRID:synonym "grohmm" ;
definition: "Software R package for analysis of GRO-seq data. Used for identifying unannotated and cell type-specific transcription units from global run-on sequencing data" .
SCR:024238 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_29382" ;
rdfs:label "genefilter" ;
definition: "Software R package provides some basic functions for filtering genes." .
SCR:024239 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_17191" ;
rdfs:label "gviz" ;
definition: "Software R package to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package." .
SCR:024240 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hypergraph" ;
definition: "Software R package that implements some simple capabilities for representing and manipulating hypergraphs." .
SCR:024241 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_22608" ;
rdfs:label "go.db" ;
definition: "Software R package provides set of annotation maps describing entire Gene Ontology assembled using data from GO." .
SCR:024242 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "htsfilter" ;
definition: "Software R package implements filtering procedure for replicated transcriptome sequencing data based on global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions." .
SCR:024243 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "impute" ;
definition: "Software R package for imputation for microarray data." .
SCR:024244 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_12862" ;
rdfs:label "mergeomics" ;
definition: "Software R pacakage for multidimensional data integration to identify pathogenic perturbations to biological systems. Used for integrating multidimensional omics disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. Includes Marker set enrichment analysis and Weighted Key Driver Analysis parts." .
SCR:024245 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19308" ;
rdfs:label "multiassayexperiment" ;
definition: "Software R package to harmonize data management of multiple experimental assays performed on overlapping set of specimens.Provides user experience by extending concepts from SummarizedExperiment, supporting open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis." .
SCR:024246 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_07813" ;
rdfs:label "metagenomeseq" ;
definition: "Software R package to determine features that are differentially abundant between two or more groups of multiple samples. Used to address the effects of both normalization and under-sampling of microbial communities on disease association detection and testing of feature correlations." .
SCR:024247 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mutationalpatterns" ;
definition: "Software R package provides set of flexible functions to evaluate and visualize multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells." .
SCR:024248 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "makecdfenv" ;
definition: "Software R package has two functions. One reads Affymetrix chip description file and creates hash table environment containing location/probe set membership mapping. The other creates package that automatically loads that environment." .
SCR:024249 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pwmenrich" ;
definition: "Software toolkit of high level functions for DNA motif scanning and enrichment analysis built upon Biostrings. Used for PWM enrichment analysis of already known PWMs. Also implements high-level functions for PWM scanning and visualisation." .
SCR:024250 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nanostringqcpro" ;
definition: "Software R package to assess quality of NanoString mRNA gene expression data, to identify outlier probes and outlier samples. Provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and easily sharable html quality control output." .
SCR:024251 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rbgl" ;
definition: "Software R package as interface to the graph algorithms contained in the BOOST library." .
SCR:024252 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14344" ;
rdfs:label "pcaMethods" ;
NIFRID:synonym "pcamethods" ;
definition: "Software R package providing PCA methods for incomplete data. Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and conventional SVD PCA. Cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation." .
SCR:024253 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rcpi" ;
definition: "Software R package as molecular informatics toolkit with integration of bioinformatics and chemoinformatics tools for drug discovery." .
SCR:024254 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "preprocesscore" ;
definition: "Software library of core preprocessing routines." .
SCR:024255 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "qusage" ;
NIFRID:synonym "Quantitative Set Analysis for Gene Expression" ;
definition: "Software R package is implementation Quantitative Set Analysis for Gene Expression method. Used to provide faster, more accurate, and easier to understand test for gene expression studies." .
SCR:024256 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rgsepd" ;
definition: "Software R package to help disambiguate transcriptome samples by automating differential expression, then gene set enrichment, and finally N-dimensional projection to quantify in which ways each sample is like either treatment group." .
SCR:024257 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rsamtools" ;
definition: "Software R package provides interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating Sequence Alignment Map, FASTA, binary variant call and compressed indexed tab-delimited files." .
SCR:024258 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_15992" ;
rdfs:label "savr" ;
definition: "Software R package to parse Illumina Sequence Analysis Viewer files, access data, and generate QC plots." .
SCR:024259 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ade4" ;
definition: "Software R package for multivariate data analysis. Used for analysis of one-table, two-table, three-table and K-table." .
SCR:024260 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11082" ;
rdfs:label "tfbstools" ;
NIFRID:synonym "TFBSTools" ;
definition: "Software R package for analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software." .
SCR:024261 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21399" ;
rdfs:label "alakazam" ;
definition: "Software R package for high-throughput adaptive immune receptor repertoire sequencing analysis. In particular, immunoglobulin sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage." .
SCR:024262 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "beeswarm" ;
NIFRID:synonym "an Alternative to Stripchart",
"beeswarm: The Bee Swarm Plot",
"r-cran-beeswarm",
"The Bee Swarm Plot" ;
definition: "Software R package implementing bee swarm plots. Bee swarm plot is one-dimensional scatter plot like \"stripchart\", but with closely packed, non overlapping points." .
SCR:024263 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xvector" ;
definition: "Software R package provides memory efficient S4 classes for storing sequences externally." .
SCR:024264 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_06963" ;
rdfs:label "BoolNet" ;
NIFRID:synonym "BoolNet: Construction",
"r-cran-boolnet",
"Simulation and Analysis of Boolean Networks" ;
definition: "Software R package provides functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks." .
SCR:024265 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cmprsk" ;
NIFRID:synonym "cmprsk: Subdistribution Analysis of Competing Risks",
"r-cran-cmprsk" ;
definition: "Software R package for estimation, testing and regression modeling of subdistribution functions in competing risks." .
SCR:024266 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_12577" ;
rdfs:label "bio3d" ;
NIFRID:synonym "bio3d: Biological Structure Analysis",
"r-cran-bio3d" ;
definition: "Softwar R package for comparative analysis of protein structures. Used to process, organize and explore protein structure, sequence and dynamics data. Used to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. Enables statistical and graphical power of R environment to work with biological sequence and structural data." .
SCR:024267 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_08682" ;
rdfs:label "adephylo" ;
definition: "Software R package provides multivariate tools to analyze comparative data. Analysis of comparative evolutionary data. Used for investigating phylogenetic signal in biological traits." .
SCR:024268 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DoseFinding" ;
NIFRID:synonym "DoseFinding: Planning and Analyzing Dose Finding Experiments",
"r-cran-dosefinding" ;
definition: "Software R package provides functions for design and analysis of dose finding experiments. Used for multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and implementation of MCPMod methodology." .
SCR:024269 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_33012" ;
rdfs:label "distory" ;
NIFRID:synonym "distory: Distance Between Phylogenetic Histories",
"r-cran-distory" ;
definition: "Software R package for geodesic distance between phylogenetic trees and associated functions." .
SCR:024270 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DT" ;
NIFRID:synonym "DataTables",
"DT: A Wrapper of the JavaScript Library 'DataTables'",
"r-cran-dt" ;
definition: "Software R package for data objects in R to render as HTML tables using JavaScript library DataTables. DataTables library has been included in this R package." .
SCR:024271 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "biwt" ;
NIFRID:synonym "biwt: Compute the Biweight Mean Vector and Covariance & Correlation Matrice",
"r-cran-biwt" ;
definition: "Software R package for compute multivariate location, scale, and correlation estimates based on Tukey's biweight M-estimator." .
SCR:024272 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Epi" ;
NIFRID:synonym "Epi: Statistical Analysis in Epidemiology",
"r-cran-epi" ;
definition: "Software R package provides functions for demographic and epidemiological analysis in Lexis diagram, i.e. register and cohort follow-up data. In particular representation, manipulation, rate estimation and simulation for multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Contains functions for Age-Period-Cohort and Lee-Carter modeling and function for interval censored data and some useful functions for tabulation and plotting, as well as number of epidemiological data sets." .
SCR:024273 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fitbitscraper" ;
definition: "Software R package to scrape data from Fitbit to generate graphs." .
SCR:024274 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fitdistrplus" ;
definition: "Software R package extends fitdistr function to help the fit of parametric distribution to non-censored or censored data." .
SCR:024275 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "epibasix" ;
NIFRID:synonym "epibasix: Elementary Epidemiological Functions for Epidemiology and Biostatistics",
"r-cran-epibasix" ;
definition: "Software R package for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement." .
SCR:024276 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "incidence" ;
definition: "Software R package provides functions and classes to compute, handle and visualise incidence from dated events for defined time interval. Dates can be provided in various standard formats." .
SCR:024277 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "forecast" ;
definition: "Software R package for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling." .
SCR:024278 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lexrankr" ;
definition: "Software R package as implementation of LexRank algorithm. Used for computing sentence importance based on concept of eigenvector centrality in graph representation of sentences." .
SCR:024279 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "genetics" ;
definition: "Software R package for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium." .
SCR:024280 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_23803" ;
rdfs:label "dynamicTreeCut" ;
NIFRID:synonym "dynamicTreeCut: Methods for Detection of Clusters in Hierarchical Clustering Dendrograms",
"r-cran-dynamictreecut" ;
definition: "Software R package contains methods for detection of clusters in hierarchical clustering dendrograms." .
SCR:024281 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mediana" ;
definition: "Software R package for clinical trial simulations based on Clinical Scenario Evaluation approach. The package supports broad class of data models, analysis strategies and commonly used evaluation criteria." .
SCR:024282 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "itertools" ;
definition: "Software R package for creating iterators, many patterned after functions in the Python itertools module, and others patterned after functions in the 'snow' package." .
SCR:024283 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "optimalcutpoints" ;
definition: "Software R package to compute optimal cutpoints for diagnostic tests or continuous markers.Used for selecting optimal cutoffs, analysis and diagnostic test accuracy measures." .
SCR:024284 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nmf" ;
definition: "Software R package provides framework to perform Non-negative Matrix Factorization.Used for nonnegative matrix factorization.Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines." .
SCR:024285 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_16887" ;
rdfs:label "parmigene" ;
NIFRID:synonym "Parallel Mutual Information Estimation for Gene Network Reconstruction" ;
definition: "Software R package for parallel estimation of mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for reconstruction of gene regulatory networks." .
SCR:024286 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_17528" ;
rdfs:label "proc" ;
definition: "Software R tools for visualizing, smoothing and comparing receiver operating characteristic. Partial area under curve AUC can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves." .
SCR:024287 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pcapp" ;
definition: "Software R package provides functions for principal component analysis by projection pursuit." .
SCR:024288 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "psychotree" ;
definition: "Software R package for recursive partitioning based on psychometric models, employing general MOB algorithm to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial credit models." .
SCR:024289 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "psyphy" ;
definition: "Software R package useful in analyzing data from psychophysical experiments.Includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice data to be used with binomial family in glm and self-Start functions for estimating gamma values for CRT screen calibrations." .
SCR:024290 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rncl" ;
definition: "Software R package provides interface to Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. Provides elements of file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'." .
SCR:024291 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rnexml" ;
definition: "Software R package provides access to phyloinformatic data in 'NeXML' format." .
SCR:024292 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "phylobase" ;
definition: "Software R package provides base S4 class for comparative methods, incorporating one or more trees and trait data. Used for phylogenetic analysis." .
SCR:024293 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_12451" ;
rdfs:label "qqman" ;
definition: "Software R package to create Q-Q and manhattan plots for GWAS data from PLINK output files." .
SCR:024294 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hms" ;
definition: "Software R package implements S3 class for storing and formatting time-of-day values, based on the 'difftime' class." .
SCR:024295 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "psychometric" ;
NIFRID:synonym "Applied Psychometric Theory" ;
definition: "Software R package for measurement theory, meta-analysis, reliability, item analysis, inter-rater reliability, classical utility, and correlation" .
SCR:024296 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rniftilib" ;
definition: "Software R package provides R-interface to the NIfTI reference implementation the niftilib C-library." .
SCR:024297 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rann" ;
definition: "Software R package finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3)." .
SCR:024298 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rook" ;
definition: "Web server for R with documented API to interface between R and the server. The documentation contains the Rook specification and details for building and running Rook applications." .
SCR:024299 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "robustrankaggreg" ;
NIFRID:synonym "Robust Rank Aggregation" ;
NIFRID:abbrev "RRA" ;
definition: "Software R package for aggregating ranked lists, especially lists of genes. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking." .
SCR:024300 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rpact" ;
definition: "Software R package for design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints." .
SCR:024301 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_29370" ;
rdfs:label "shazam" ;
definition: "Software R package provides computational framework for analyzing mutations in immunoglobulin sequences. Immunoglobulin Somatic Hypermutation Analysis." .
SCR:024302 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rwave" ;
definition: "Software R package provides environment for Time-Frequency analysis of 1-D signals." .
SCR:024303 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rsvd" ;
NIFRID:synonym "randomized singular value decomposition" ;
definition: "Software R package used to compute near optimal low-rank singular value decomposition of massive data sets with high accuracy. Provides several randomized matrix algorithms such as randomized singular value decomposition (rsvd), randomized principal component analysis (rpca), randomized robust principal component analysis (rrpca), randomized interpolative decomposition (rid), and the randomized CUR decomposition (rcur). In addition several plot functions are provided." .
SCR:024304 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "surveillance" ;
definition: "Software R package for modeling and monitoring of time series of counts, proportions and categorical data, as well as for modeling of continuous-time point processes of epidemic phenomena." .
SCR:024305 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tsne" ;
definition: "Softare R package as implementation of the t-SNE algorithm." .
SCR:024306 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_28401" ;
rdfs:label "rotl" ;
definition: "Software R package provides interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling comprehensive phylogenetic tree for all named species." .
SCR:024307 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sjplot" ;
definition: "Software R package as collection of plotting and table output functions for data visualization. Results of various statistical analyses that are commonly used in social sciences can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, generalized linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models including interaction terms. This package supports labelled data." .
SCR:024308 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "waveslim" ;
definition: "Software R package for basic wavelet routines for time series 1D, image 2D and array 3D analysis." .
SCR:024309 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "snowfall" ;
definition: "Software R package usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it." .
SCR:024310 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_07533" ;
rdfs:label "tigger" ;
definition: "Software R package infers V genotype of individual from immunoglobulin repertoire sequencing data like AIRR-Seq, Rep-Seq. Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among sample sequences." .
SCR:024311 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "wavethresh" ;
definition: "Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation." .
SCR:024312 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "webgestaltr" ;
NIFRID:synonym "WebGestaltR" ;
definition: "Software R package to support gene set enrichment analysis, network topology analysis.Can be integrated into other pipeline or simultaneously analyze multiple gene lists. The user-friendly output report allows interactive and efficient exploration of enrichment results." .
SCR:024313 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "readseq" ;
definition: "Software package as Java based common sequence file format reader and sequence file manipulation." .
SCR:024314 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "resfinder" ;
NIFRID:synonym "ResFinder" ;
definition: "Software tool identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria. Used for identification of acquired antimicrobial resistance genes in whole-genome data." .
SCR:024315 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "readucks" ;
definition: "Software package as Nanopore read de-multiplexer." .
SCR:024316 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "roguenarok" ;
definition: "Software tool as versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index." .
SCR:024317 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "recan" ;
definition: "Software tool as genetic distance plotting for recombination events analysis." .
SCR:024318 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21698" ;
rdfs:label "roadtrips" ;
NIFRID:synonym "ROADTRIPS 2.0" ;
definition: "Software C program that performs single SNP, case control association testing in samples with partially or completely unknown population and pedigree structure." .
SCR:024319 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "stringi" ;
definition: "Software R package as collection of character string/text/natural language processing tools for pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing." .
SCR:024320 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_28979" ;
rdfs:label "rtax" ;
definition: "Software tool for rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene." .
SCR:024321 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "runcircos-gui" ;
definition: "GUI tool to run circos" .
SCR:024322 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ruby-bio" ;
definition: "Software tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO." .
SCR:024323 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19578" ;
rdfs:label "rgfa" ;
definition: "Ruby library for handling GFA files." .
SCR:024324 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_16243" ;
rdfs:label "saint" ;
NIFRID:synonym "Significance Analysis of INTeractome" ;
NIFRID:abbrev "SAINT" ;
definition: "Software package for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments." .
SCR:024325 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "crb-blast" ;
NIFRID:synonym "Conditional Reciprocal Best Blast" ;
definition: "Software tool for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation." .
SCR:024326 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_03939" ;
rdfs:label "sailfish" ;
definition: "Software tool that implements novel, alignment free algorithm for estimation of isoform abundances directly from set of reference sequences and RNA-seq reads." .
SCR:024327 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sepp" ;
definition: "Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem." .
SCR:024328 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_07586" ;
rdfs:label "sambamba" ;
definition: "Software tools for working with SAM/BAM data" .
SCR:024329 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_06013" ;
rdfs:label "sbmltoolbox" ;
definition: "Software toolbox provides set of basic functions allowing SBML models to be used in both MATLAB and Octave." .
SCR:024330 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "samclip" ;
definition: "Software tool to filter SAM file for soft and hard clipped alignments" .
SCR:024331 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11290" ;
rdfs:label "seqmagick" ;
definition: "Software application to expose file format conversion in BioPython in convenient way. Imagemagick like frontend to Biopython SeqIO." .
SCR:024332 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "seqwish" ;
definition: "Software tool for alignment to variation graph inducer." .
SCR:024333 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21700" ;
rdfs:label "seqsero" ;
definition: "Software pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies." .
SCR:024334 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "shiny-server" ;
definition: "Open Source platform to host multiple Shiny applications on single server." .
SCR:024335 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "shapeit4" ;
NIFRID:synonym "SHAPEIT",
"SHAPEIT4" ;
definition: "Software tool for estimation of haplotypes aka phasing for SNP array and high coverage sequencing data. The version 4 is refactored and improved version of SHAPEIT algorithm with multiple key additional features." .
SCR:024336 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11719" ;
rdfs:label "sibelia" ;
definition: "Software comparative genomics tool to assist biologists in analysing genomic variations that correlate with pathogens, or genomic changes that help microorganisms adapt in different environments. Used for evolutionary and genome rearrangement studies for multiple strains of microorganisms." .
SCR:024337 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_29594" ;
rdfs:label "sigma-align" ;
NIFRID:synonym "Simple greedy multiple alignment" ;
definition: "Software alignment program with new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step." .
SCR:024338 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21290" ;
rdfs:label "sibsim4" ;
definition: "Software tool designed to align expressed DNA sequence with genomic sequence, allowing for introns." .
SCR:024339 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "signalalign" ;
definition: "Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments," .
SCR:024340 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sigviewer" ;
definition: "Software viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information such as annotations or artifact selections." .
SCR:024341 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "skesa" ;
NIFRID:synonym "SKESA" ;
definition: "Software de-novo sequence read assembler for microbial genomes.Designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.SKESA contigs could be connected into GFA graph using GFA connector." .
SCR:024342 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_12011" ;
rdfs:label "sistr" ;
NIFRID:synonym "Salmonella In Silico Typing Resource" ;
NIFRID:abbrev "SISTR" ;
definition: "SISTR command-line tool. Open web accessible tool for rapidly typing and subtyping draft salmonella genome assemblies." .
SCR:024343 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "seq-seq-pan" ;
definition: "Software workflow for SEQuential alignment of SEQuences to build PAN-genome data structure and whole-genome-alignment." .
SCR:024344 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sitplus" ;
NIFRID:synonym "SITPLUS" ;
definition: "Software framework to provide ludic-therapeutic activities for people with disabilities.Offers new forms of interaction based on computer vision, voice and other peripherals to produce result in form of image and sound. Used for continuous and remote interaction, attainable to majority of people with cognitive, sensory and physical disabilities." .
SCR:024345 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_05427" ;
rdfs:label "spaced" ;
definition: "Software for alignment free sequence comparison. Uses pattern of care and don't care positions. Compares frequencies of spaced words according to pre-defined pattern." .
SCR:024346 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sofa-apps" ;
NIFRID:synonym "SOFA" ;
definition: "Open source software framework targeting at real-time simulation, with emphasis on medical simulation." .
SCR:024347 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21832" ;
rdfs:label "sourmash" ;
definition: "Software library for MinHash sketching of DNAsearch. Used to compare and analyze genomic and metagenomic data sets." .
SCR:024348 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_15114" ;
rdfs:label "snpomatic" ;
NIFRID:synonym "SNP-o-matic" ;
definition: "Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping," .
SCR:024349 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sparta" ;
NIFRID:synonym "SPARTA" ;
definition: "Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms." .
SCR:024350 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_03771" ;
rdfs:label "sra-toolkit" ;
NIFRID:synonym "NCBI SRA Toolkit" ;
definition: "Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces." .
SCR:024351 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "strap-base" ;
definition: "Software tool as Intuitive Editor for annotated multiple Sequence and Structure Alignments." .
SCR:024352 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_19112" ;
rdfs:label "sumaclust" ;
definition: "Software tool aims to cluster sequences in a way that is fast and exact at the same time." .
SCR:024353 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21293" ;
rdfs:label "sprai" ;
NIFRID:synonym "single pass read accuracy improver" ;
definition: "Software tool to correct sequencing errors in single pass reads for de novo assembly." .
SCR:024354 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "streamlit" ;
definition: "Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps." .
SCR:024355 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_09480" ;
rdfs:label "surankco" ;
definition: "Machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet." .
SCR:024356 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "libswiss-perl" ;
definition: "Software object oriented Perl library to handle Swiss-Prot entries" .
SCR:024357 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_08598" ;
rdfs:label "sweed" ;
definition: "Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps." .
SCR:024358 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14578" ;
rdfs:label "swarm" ;
definition: "Software tool as clustering method for amplicon-based studies." .
SCR:024359 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tab2mage" ;
NIFRID:synonym "Tab2MAGE" ;
definition: "Software package written and supported by ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets to our public repository database." .
SCR:024360 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_21299" ;
rdfs:label "zAlign" ;
NIFRID:synonym "zalign" ;
definition: "Software tool as local sequence aligner intended for use with large biological DNA sequences, with more than 1 Millions of base pairs." .
SCR:024361 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tiddit" ;
NIFRID:synonym "TIDDIT" ;
definition: "Software tool as structural variant calling." .
SCR:024362 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yanagiba" ;
NIFRID:synonym "yanagiba" ;
definition: "Software tool to filter and slice Nanopore reads which have been basecalled with Albacore." .
SCR:024363 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yanosim" ;
NIFRID:synonym "yanosim",
"yet another nanopore simulator" ;
definition: "Software tool as read simulator for nanopore DRS datasets." .
SCR:024364 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Workrave" ;
NIFRID:synonym "workrave" ;
definition: "Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage." .
SCR:024365 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_04675" ;
rdfs:label "yaha" ;
NIFRID:synonym "YAHA" ;
definition: "Software tool as fast and flexible long read alignment with optimal breakpoint detection." .
SCR:024366 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XMedCon" ;
NIFRID:synonym "xmedcon" ;
definition: "Open source software toolkit for medical image conversion." .
SCR:024367 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VolPack" ;
NIFRID:synonym "volpack" ;
definition: "Portable software library for volume rendering." .
SCR:024368 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VMD" ;
NIFRID:synonym "vmd" ;
definition: "Software tool as 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." .
SCR:024369 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "variation graph" ;
NIFRID:synonym "variationgraph" ;
NIFRID:abbrev "vg" ;
definition: "Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes." .
SCR:024370 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VisIt" ;
NIFRID:synonym "visit" ;
definition: "Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations." .
SCR:024371 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_17862" ;
rdfs:label "VirulenceFinder" ;
NIFRID:synonym "virulencefinder" ;
definition: "Software tool for detection of E. coli virulence genes. Used to identify viruelnce genes in total or partial sequenced isolates of bacteria. E. coli, Enterococcus, S. aureus and Listeria are available.for detection of E. coli virulence genes." .
SCR:024372 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11863" ;
rdfs:label "vcfanno" ;
definition: "Software tool for flexible annotation of genetic variants.Extracts and summarizes attributes from multiple annotation files and integrates annotations within INFO column of the original VCF file." .
SCR:024373 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_04455" ;
rdfs:label "VARNA" ;
NIFRID:synonym "varna",
"Visualization Applet for RNA" ;
definition: "Software tool for automated drawing, visualization and annotation of secondary structure of RNA, designed as companion software for web servers and databases.Allows manual modification and structural annotation of resulting drawing using either interactive point and click approach, within web server or through command-line arguments." .
SCR:024374 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tacg" ;
definition: "Software tool as command line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms core of the program, it has been expanded to fill more roles, sort of 'grep' for DNA." .
SCR:024375 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14435" ;
rdfs:label "VarMatch" ;
NIFRID:synonym "varmatch" ;
definition: "Software tool for variant matching problem.Used for robust matching of small variant datasets using flexible scoring schemes" .
SCR:024376 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14601" ;
rdfs:label "VelvetOptimiser" ;
NIFRID:synonym "perl-velvetoptimiser",
"velvetoptimiser" ;
definition: "Software tool to run as wrapper script for Velvet assembler and to assist with optimising the assembly.Used to search supplied hash value range for optimum, estimates expected coverage and then searches for optimum coverage cutoff. Estimates insert lengths for paired end libraries. Can optimise assemblies by default optimisation condition or by user supplied one. It outputs the results to subdirectory and records all its operations in logfile." .
SCR:024377 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VADR" ;
NIFRID:synonym "ushahidi" ;
definition: "Software suite of tools for classifying and analyzing sequences homologous to set of reference models of viral genomes or gene families." .
SCR:024378 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_11724" ;
rdfs:label "FISH" ;
definition: "Software tool for identifying regions of common ancestry between genome maps. Used for identification and statistical evaluation of segmental homologies in comparative maps." .
SCR:024379 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_26281" ;
rdfs:label "CCS" ;
NIFRID:synonym "ccs ; unanimity" ;
definition: "Software to generate highly accurate single molecule consensus reads." .
SCR:024380 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_14591" ;
rdfs:label "Unicycler" ;
NIFRID:synonym "unicycler" ;
definition: "Software assembly pipeline for bacterial genomes. Used for resolving bacterial genome assemblies from short and long sequencing reads. Can assemble Illumina only read sets where it functions as SPAdes-optimiser. Can assembly long read only sets for PacBio or Nanopore where it runs miniasm+Racon pipeline." .
SCR:024381 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_12783" ;
rdfs:label "umis" ;
definition: "Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias." .
SCR:024382 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_18458" ;
rdfs:label "TREE-PUZZLE" ;
NIFRID:synonym "tree-puzzle" ;
definition: "Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set." .
SCR:024383 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TopHat-Recondition" ;
definition: "Software tool as post-processor for TopHat unmapped reads that restores read information in the proper format.Enables downstream software to process plethora of BAM files written by TopHat." .
SCR:024384 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Trinculo" ;
NIFRID:synonym "trinculo" ;
definition: "Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping." .
SCR:024385 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_07268" ;
rdfs:label "toppred" ;
definition: "Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins." .
SCR:024386 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_33039" ;
rdfs:label "trace2dbEST" ;
definition: "Software tool to process raw sequenceing chromatograph trace files from EST projects into quality checked sequences, ready for submission to dbEST." .
SCR:024387 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tn-seq explorer" ;
NIFRID:synonym "Tn-seq Explorer",
"tn-seqexplorer" ;
definition: "Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions." .
SCR:024388 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tombo" ;
NIFRID:synonym "ont-tombo" ;
definition: "Software suite of tools for identification of modified nucleotides from nanopore sequencing data.Used also for analysis and visualization of raw nanopore signal." .
SCR:024389 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_10215" ;
rdfs:label "TRANSIT" ;
NIFRID:synonym "tnseq-transit" ;
definition: "Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions." .
SCR:024390 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_03646" ;
rdfs:label "TM-align" ;
definition: "Software tool for protein structure alignment based on TM-score.Used to identify structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming. Used for sequence independent protein structure comparisons." .
SCR:024391 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "OMICS_25666" ;
rdfs:label "toil" ;
definition: "Software pipeline management system, written in Python. Enables reproducible, open source, big biomedical data analyses." .
SCR:024392 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FTA32" ;
NIFRID:synonym "First Ten Angstrom FTA32",
"FTA32 2.0" ;
definition: "Software tool for tensiometry measurements and contact angle hysteresis." .
SCR:024393 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Galileo | Tissue Microarray CK Series" ;
NIFRID:synonym "Galileo computer assisted tissue microarray",
"Galileo Fully Automated Tissue Microarray",
"Galileo Tissue Microarray",
"Galileo TMA CK",
"Galileo TMA CK Series" ;
definition: "Galileo computer assisted Tissue Microarray instrument allows TMA preparation with different paraffin block sizes, producing digital excel format reporting and possibility of data transfer to several Digital TMA Slide Scanners for complete tracking of Tissue Microarray process." .
SCR:024394 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gate" ;
NIFRID:synonym "GATE",
"GATE V6",
"Geant4 Application for Tomographic Emission" ;
definition: "Software toolkit for PET and SPECT. Simulation platform for medical imaging and radiotherapy. Used for modelling of planar scintigraphy, single photon emission computed tomography (SPECT) and positron emission tomography (PET) acquisitions, this platform is widely used to assist PET and SPECT research. Extension of this platform, released by OpenGATE collaboration as GATE V6, enables modelling of x-ray computed tomography and radiation therapy experiments." .
SCR:024395 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scNTImpute" ;
NIFRID:synonym "single-cell Neural Topic Imputation" ;
definition: "Software imputation model for scRNA-seq data. Used to accurately and efficiently identify dropout values and impute them precisely, which helps to improve downstream analyses of single-cell RNA sequencing data." .
SCR:024396 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BrainWAVE" ;
NIFRID:synonym "Brain Wide-spectrum Audio/Visual Exposure",
"BrainWAVE: Noninvasive Rhythm Stimulation" ;
definition: "Code to program and run flicker stimulation on BrainWAVE stimulator device. This brain oscillation stimulating software can be adapted across subjects and integrated into variety of experimental designs like electrophysiology, neuroimaging, EEG, MRI. Flexible method for noninvasive stimulation of brain rhythms across species. Used to measure effects of rhythmic brain activity on behavior." .
SCR:024397 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChrAccR" ;
NIFRID:synonym "Chromatin Accessibility data in R" ;
definition: "Software R package for comprehensive analysis chromatin accessibility data. Analyzing chromatin accessibility data in R. Used for data quality control, exploratory analyses including unsupervised methods for dimension reduction, clustering and quantifying transcription factor activities, and identification and characterization of differentially accessible regions. Used for analysis of large bulk datasets comprising hundreds of samples as well as for single cell datasets." .
SCR:024398 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2832" ;
rdfs:label "Indiana University Bloomington Flow Cytometry Core Facility" ;
NIFRID:synonym "IUB Flow Cytometry Core Facility" ;
NIFRID:abbrev "FCCF" ;
definition: "Core offers flow cytometry analysis and cell sorting services. It houses FACS Aria II 5-laser, 14-color sorter, SH800 2-laser, 6-color user-run cell sorter, COPAS Select, Drosophila embryo and large particle sorter, LSRII, 4-laser, 14-color analyzer, MACSQuant VYB 3-laser, 8-color analyzer with 96-well plate option, as well as Moxi Z cell counter technology used for determining cell concentration and size distribution and Miltenyi QuadroMACS separator. Services include technician assisted sorting, as well as training for analyzers, SH800 and Moxi instruments. Help with experimental design is available.Facility maintains workstation with flow cytometry data analysis software, and has copy of this software as well as site license for use outside of facility." .
SCR:024399 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Efficient and Adaptive Gaussian Smoothing" ;
NIFRID:abbrev "EAGS" ;
definition: "Software tool for high resolved spatial transcriptomics. Smoothing approach for spatial transcriptome data with ultrahigh resolution. Used to determine neighborhood relationship of cells, to calculate smoothing contribution to recalculate the gene expression of each cell." .
SCR:024400 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1826" ;
rdfs:label "National Autonomous University of Mexico Materials Research Institute Electron Microscopy University Laboratory Core Facility" ;
NIFRID:synonym "National Autonomous University of Mexico Materials Research Institute Electron Microscopy University Laboratory",
"Universidad Nacional Autonoma de Mexico LUME" ;
NIFRID:abbrev "LUME" ;
definition: "Core covers main techniques of electron microscopy, from scanning electron microscopy to scanning transmission electron microscopy, for characterization of morphology and structure of materials at micrometer and nanometer scale.Provides equipment for preparing samples for analysis by different electron microscopy techniques." .
SCR:024401 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Learning Locker" ;
NIFRID:synonym "Learning Record Store" ;
NIFRID:abbrev "LRS" ;
definition: "Open source software Learning Record Store implementing the xAPI (Tin Can API) e-learning standard.Type of data repository designed to store learning activity statements generated by xAPI (Tin Can) compliant learning activities." .
SCR:024402 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brainways" ;
definition: """Open source software that automatically registers coronal slices and quantifies fluorescent markers. Python based, AI registration algorithm for slice matching to the Waxholm rat
atlas. Slice quantification can be trained on any atlas, which allows use for other subjects such as mice, zebrafish, and humans. AI-based software for registration and analysis of fluorescent markers on coronal brain slices.""" .
SCR:024403 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FindTelomeres" ;
definition: "Software Python tool for finding telomeric repeats (TTAGGG/CCCTAA) in FASTA files." .
SCR:024404 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2446" ;
rdfs:label "University of British Columbia Advanced Research Computing Core Facility" ;
NIFRID:synonym "UBC Advanced Research Computing",
"University of British Columbia Advanced Research Computing" ;
definition: "Core supports high performance computing and data management needs of UBC researchers by providing consultation, expertise, and access to digital research infrastructure such as high performance computing clusters and storage." .
SCR:024405 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_1827" ;
rdfs:label "Jackson Laboratory JAX Scientific Research Services Microscopy Services Core Facility" ;
NIFRID:synonym "JAX Microscopy Services",
"The Jackson Laboratory JAX Microscopy Services" ;
definition: "Jackson Laboratory Microscopy Services, located in Bar Harbor, Maine and Farmington, Connecticut, provides essential support to their faculty labs. Service includes standard widefield microscopy; advanced fluorescent microscopy, including confocal and spinning disk; 2-photon and fluorescence lifetime microscopy ; longitudinal observation or live cell imaging, including imaging of iPS and ES cells under various environmental conditions; laser capture microdissection, image analysis and 3D visualization; high throughput cell based screening; brightfield slide scanning; automated fluorescence slide scanning." .
SCR:024406 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RiboToolkit" ;
definition: "Integrated web server developed for Ribo-seq data analysis. Platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.Web based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs." .
SCR:024407 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Acute Kidney Injury Data Portal" ;
definition: "UK Renal Registry collection of data from acute kidney injury patients in England." .
SCR:024408 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ramr" ;
NIFRID:synonym "rare aberrantly methylated regions" ;
definition: "Software R package for detection of low frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. Provides functions to visualize found aberrantly methylated regions, to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms." .
SCR:024409 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "BioImaging North America" ;
NIFRID:abbrev "BINA" ;
definition: "US-based non-profit engaging bioimaging scientists across Canada, Mexico, the US and its territories by creating inclusive and supportive community to support bioimaging scientists through on-line events, registration assistance for professional development opportunities and the chance to visit peer imaging facilities to learn new techniques, develop or expand management skills, and/or image data management and analysis skills., through Exchange of Experience program." .
SCR:024410 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Healthcare Cost and Utilization Project" ;
NIFRID:abbrev "HCUP" ;
definition: "Family of healthcare databases and related software tools and products developed through Federal-State-Industry partnership. Databases bring together data collection of State data organizations, hospital associations, private data organizations, and Federal government to create national information resource of encounter-level healthcare data. HCUP includes largest collection of longitudinal hospital care data in the United States, with all-payer, encounter-level information beginning in 1988. These databases enable research on broad range of health policy issues, including cost and quality of health services, medical practice patterns, access to healthcare programs, and outcomes of treatments at the national, State, and local market levels." .
SCR:024411 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SoftCite" ;
NIFRID:synonym "Software Citation" ;
definition: "Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale." .
SCR:024412 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ctregistries" ;
definition: "Software R package to facilitate detection and analysis of clinical trial registration numbers. Data package of regular expressions and provides some R functions for implementing the regexes. Data Package and R Functions for Clinical Trial Registries and other MEDLINE Databanks." .
SCR:024413 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRIcroGL" ;
definition: "Medical image viewer that allows to load overlays and draw regions of interest. Runs on Windows, Linux and OSX. Allows to view 2D slices and renderings of your brain imaging data. It can display many image formats and includes graphical interface for dcm2nii to convert DICOM images to NIfTI format. Allows to draw regions of interest which can aid lesion mapping and fMRI analysis." .
SCR:024414 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProteinPilot" ;
definition: "Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems." .
SCR:024415 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "survivalROC" ;
NIFRID:synonym "survival Receiver Operating Characteristic" ;
definition: "Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data." .
SCR:024417 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pRRophetic" ;
definition: "Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data," .
SCR:024418 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RNALocate" ;
NIFRID:synonym "RNALOCATE",
"RNALocate v2.0" ;
definition: "Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation." .
SCR:024419 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GOplot" ;
NIFRID:synonym "R GOplot" ;
definition: "Software R package for visually combining expression data with functional analysis." .
SCR:024420 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ROCit" ;
NIFRID:synonym "Receiver Operating Characteristic it" ;
definition: "Software R package for assessing overall diagnostic ability of binary classifier. Used to evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot." .
SCR:024421 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyWavelets" ;
definition: "Software Python package for wavelet analysis." .
SCR:024422 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rgdal" ;
NIFRID:synonym "R geospatial data abstraction library",
"rgdal" ;
definition: "Software R package provides bindings for the Geospatial Data Abstraction Library. Translator library for raster and vector geospatial data formats." .
SCR:024423 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyPCcazip" ;
definition: "Software PCA-based toolkit for compression and analysis of molecular simulation data. Used for compression and analysis of molecular dynamics (MD) simulation data." .
SCR:024424 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "riskRegression" ;
definition: "Software R package provides risk regression models and prediction scores for survival analysis with competing risks." .
SCR:024425 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ScanProsite" ;
NIFRID:abbrev "PMID:16845026" ;
definition: "Web tool for detecting PROSITE signature matches in protein sequences." .
SCR:024426 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RapGreen" ;
NIFRID:abbrev "PMID:34568824" ;
definition: "Software phylogenetic tree analysis package. Phylogenetic tree management, exploration and display package." .
SCR:024427 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RNAfold" ;
definition: "Web server predict secondary structures of single stranded RNA or DNA sequences." .
SCR:024428 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LFP Monitoring" ;
NIFRID:synonym "Local Field Potential video Monitoring" ;
definition: "Low cost platform for multianimal chronic Local Field Potential video monitoring with Graphical User Interface for seizure detection and behavioral scoring. Enables chronic monitoring of several animals simultaneously, synchronizes bilateral local field potential and video streams in real time, and parses recorded data into manageable file sizes. Hardware solution leverages Intan and Open Ephys acquisition systems and software solution is implemented in Bonsai. Data are synchronized and parsed in Bonsai, allowing for flexibility and scalability of up to 128 channels per animal. The use of Intan adapter board for LFP video recordings allows compatibility with large variety of recording devices. Custom made electrodes and cables were components for the chronic LFP recordings. Used as acquisition system for long term video neurophysiology recordings." .
SCR:024429 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NutritionQuest Questionnaires and Screeners" ;
definition: "NutritionQuest provides questionnaires and screeners for assessment of diet and physical activity. Questionnaires are derived from and based on Dr. Block's landmark research into the development of valid, user-friendly assessment methods. Questionnaires and dietary analysis services are available to nutritional epidemiologists and public health researchers." .
SCR:024430 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ecocyte Bioscience Xenopus laevis oocytes delivery service" ;
NIFRID:synonym "Ecocyte Bioscience Xenopus laevis defolliculated oocytes",
"Xenopus laevis defolliculated oocytes",
"Xenopus laevis oocytes delivery service" ;
definition: "Ecocyte Bioscience offers weekly delivery service of Xenopus laevis oocytes for expression studies. Products include defolliculated and ready to use Xenopus Laevis oocytes used for mRNA or cDNA injections or other electrophysiological experiments." .
SCR:024431 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rockd" ;
definition: "Map database allows to record your geological observations and uses your location to provide spatially informed suggestions for nearby geologic units, time intervals, and fossils." .
SCR:024432 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sparrow-data" ;
definition: "Software for managing geochemical data created by individual geochronology laboratory. Designed for flexibility and extensibility, so that it can be tailored to the needs of individual analytical labs that manage wide variety of data. Database set up for metadata tracking." .
SCR:024433 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Olympus FV10-ASW Viewer" ;
NIFRID:synonym "FV10-ASW Viewer software v4.2b" ;
definition: "Software for image processing. Reads data captured by FV1200/FV1000/FV500/FV300 microscopes. Images saved with FV file format (OIF, OIB, FV Multi-Tiff) can be read." .
SCR:024434 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XDD" ;
definition: "Software digital library and cyberinfrastructure facilitating discovery and utilization of data and knowledge in published documents." .
SCR:024435 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Cerner Enviza" ;
definition: "American healthcare company that provides data, analytics, and research to the life sciences industry, with particular focus on oncology and rare diseases." .
SCR:024437 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Cancer Institute Cancer Statistics Cancer Stat Facts" ;
definition: "Collection of statistical summaries for number of common cancer types. They were developed to provide quick overview of frequently requested cancer statistics. Available statistics may include incidence, mortality, survival, stage, prevalence, and lifetime risk. Links to additional resources from NCI including risk factors, treatment, and clinical trials are also provided. The statistics will be updated annually to coincide with the SEER data release." .
SCR:024438 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StereoCell v2.0" ;
NIFRID:synonym "StereoCell" ;
definition: "Enhanced application on generating single cell gene expression profile for high resolution spatial transcriptomics. Registers spatial gene expression map and cell membrane/wall staining image with nuclei staining image as intermediary, thus cell membrane/wall outlines can be directly segmented from cell membrane/wall staining image without correcting nuclei boundaries." .
SCR:024439 a NLX:63400,
owl:NamedIndividual ;
NIFRID:abbrev "MLme" ;
definition: "Software toolkit for Machine Learning Driven Data Analysis. Simplifies machine learning for data exploration, visualization and analysis." .
SCR:024440 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Allen Brain Cell Atlas" ;
NIFRID:synonym "ABC Atlas",
"Allen Brain Cell (ABC) Atlas",
"The Allen Brain Cell Atlas" ;
definition: "Provides platform for visualizing multimodal single cell data across mammalian brain and aims to empower researchers to explore and analyze multiple whole brain datasets simultaneously. Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas. Atlas as part of Brain Knowledge Platform will enable neuroscience community to identify more cell types in brain; Investigate spatial location of cell types; Investigate gene expression and co-expression patterns in cell types; Refine boundaries and knowledge of brain regions defined by gene expression." .
SCR:024441 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCKAN Composer" ;
NIFRID:synonym "SPARC Connectivity Knowledge Base of the Autonomic Nervous system Composer" ;
definition: "Web application authoring interface that permits users to display, inspect, survey, and formulate knowledge statements to be added to SCKAN, as well as the ability to query and augment knowledge information within SCKAN, the SPARC Connectivity Knowledge Base of the Autonomic Nervous system." .
SCR:024443 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Metabox" ;
NIFRID:synonym "metabox",
"metabox2",
"Metabox 2.0" ;
definition: "Software R toolbox for thorough metabolomic data analysis, integration and interpretation. Metabox 2.0 is updated version of R package Metabox and includes several methods for data processing, statistical analysis, biomarker analysis, integrative analysis and data interpretation." .
SCR:024444 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "INFRAFRONTIER" ;
NIFRID:synonym "European Research Infrastructure for Modelling Human Diseases" ;
definition: "Non-profit organisation dedicated to advancing disease, understanding and treatment through cutting-edge models. Provides mouse model resources for modelling human diseases. Provides research infrastructure for generation, phenotyping, archiving, and distribution of mouse models in Europe. Through collaboration with other infrastructures, it fosters global data sharing and contributes to tackling significant health challenges." .
SCR:024445 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cancer Information Service" ;
NIFRID:synonym "Cancer Information Service in Japan" ;
definition: "Portal provides information on Cancer Statistics in Japan. Official website operated by National Cancer Center for cancer information." .
SCR:024446 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Scientific Maps Software" ;
NIFRID:synonym "Maps Software" ;
definition: "Correlative electron microscopy and cross-platform imaging automation software. Imaging and correlative workflow software suite compatible with full line of Thermo Scientific SEM, DualBeam (FIB SEM) and TEM platforms." .
SCR:024447 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OsteoMetrics OsteoMeasure" ;
NIFRID:synonym "OsteoMeasure",
"OsteoMetrics Osteomeasure" ;
definition: "Software for semi-automatic bone histomorphometry. Used for manual tracing of bone surfaces." .
SCR:024448 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss | Lightsheet 7" ;
NIFRID:synonym "ZEISS Lightsheet 7 imaging system" ;
definition: "System for imaging of living and cleared specimens. Used to image large optically cleared specimens in toto with subcellular resolution. Dedicated optics, sample chambers and holders allow adaption to the refractive index of your chosen clearing method." .
SCR:024449 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Resolve Biosciences Molecular Cartography" ;
NIFRID:synonym "Molecular Cartography",
"Resolve Biosciences Molecular Cartography platform" ;
definition: "Platform is multi-analyte, multiplex spatial analysis technology that enables scientists to resolve complex biological challenges in areas such as oncology, neuroscience, and infectious disease. Platform produces contextual data sets that illuminate molecular interactions at subcellular resolution, while preserving the sample tissue." .
SCR:024450 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "vhlab-microscopyimageanalysis-matlab" ;
definition: "Software Matlab app for analysis of high density imaging data like that from Array Tomography." .
SCR:024451 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MOBFinder" ;
NIFRID:synonym "Mobilization Finder" ;
definition: "Software tool for MOB typing for plasmid metagenomic fragments based on language model." .
SCR:024453 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyMouseTracks" ;
NIFRID:abbrev "PMT" ;
definition: "Open source, adaptable tracking system for multiple rodents. Scalable and customizable system for tracking and behavior assessment consists of Raspberry Pi based video and RFID acquisition. Maximum of six rodents of any coat color can be tracked simultaneously in any user defined arena with few restrictions. For pose estimation and travel trajectory analysis, PyMouseTracks supports interfacing with open source packages such as DeepLabCut and Traja." .
SCR:024456 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2448" ;
rdfs:label "Pennsylvania State University Huck Institutes Cryo-Electron Microscopy Core Facility" ;
NIFRID:synonym "Huck Institutes' Cryo-Electron Microscopy Facility" ;
definition: "Cryo-Electron Microscopy Facility houses FEI Titan Krios microscope that offers data collection for life sciences while incorporating materials science applications. Used for creating super high definition 3D images of atoms and molecules. Facility allows for fully automated atomic resolution single particle and high contrast tomography tilt-series data collection. Additional microscopy components permit a full range of materials science applications, including EELS, STEM, and DPC. Facility also houses ThermoFisher Arctica G2." .
SCR:024457 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2449" ;
rdfs:label "Pennsylvania State University Huck Institutes Microscopy Core Facility" ;
NIFRID:synonym "Huck Institutes' Microscopy Facility" ;
definition: "Microscopy facility specializes in areas of optical microscopy, electron microscopy, and histology. Facility is equipped with confocal microscopes, research fluorescence microscopes, and transmission and scanning electron microscopes. Research staff engage in experimentation, training, project collaboration, and consultation." .
SCR:024458 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2450" ;
rdfs:label "Pennsylvania State University Huck Institutes Automated Biological Calorimetry Core Facility" ;
NIFRID:synonym "Huck Institutes' Automated Biological Calorimetry Facility" ;
definition: "Automated Biological Calorimetry Facility provides infrastructure and support for individual investigators to undertake studies of macromolecule binding and folding, as well as protein and lipid quantification. Our calorimetry instruments are fully automated and require the least amount of sample of any commercially available instruments.Provides instrumentation and collaborative assistance for Isothermal titration calorimetry for studying ligand-macromolecule binding; Differential scanning calorimetry for investigating stability and folding thermodynamics. Staff is available to assist with project development and research." .
SCR:024459 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2451" ;
rdfs:label "Pennsylvania State University Huck Institutes CSL Behring Fermentation Core Facility" ;
NIFRID:synonym "Huck Institutes CSL Behring Fermentation Facility" ;
definition: "Biotechnology pilot plant capable of research and pilot scale production of microbial cells, recombinant proteins, and other microbial products over wide range of controlled conditions. Facility provides equipment and expertise to university affiliated and independent government and industry researchers interested in fermentation and related technologies, including cell separation and disruption, biomolecule production and purification, and process monitoring." .
SCR:024460 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2452" ;
rdfs:label "Pennsylvania State University Huck Institutes Flow Cytometry Core Facility" ;
NIFRID:synonym "Huck Institutes' Flow Cytometry Facility" ;
definition: "Facility is equipped with flow cytometers and cell sorters to examine cell samples within range of micron. Staff engage in experimentation, training, project collaboration, and consultation." .
SCR:024461 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2453" ;
rdfs:label "Pennsylvania State University Huck Institutes High Field Magnetic Resonance Imaging Core Facility" ;
NIFRID:synonym "Huck Institutes' High-Field Magnetic Resonance Imaging Facility" ;
definition: "Facility for investigating samples at micrometer scale using in vivo imaging and magnetic resonance microscopy. Facility houses Bruker BioSpec 70/30 horizontal magnet and Agilent 14.1 Tesla vertical magnet." .
SCR:024462 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2454" ;
rdfs:label "Pennsylvania State University Huck Institutes Proteomics and Mass Spectrometry Core Facility" ;
NIFRID:synonym "Huck Institutes' Proteomics and Mass Spectrometry Core Facility" ;
definition: "Facility offers highly sensitive and accurate mass spectrometry analysis, including identification and quantitation of proteins by liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS-MS) or by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-TOF-MS)." .
SCR:024463 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2455" ;
rdfs:label "Pennsylvania State University Huck Institutes Sartorius Cell Culture Core Facility" ;
NIFRID:synonym "Huck Institutes Sartorius Cell Culture Facility" ;
definition: "Sartorius Cell Culture Facility delivers hands-on training in cell culture to students, faculty, staff, and external personnel, while providing researchers across numerous Penn State disciplines access to the lab environment." .
SCR:024464 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2456" ;
rdfs:label "Pennsylvania State University Huck Institutes X-Ray Crystallography Core Facility" ;
NIFRID:synonym "Huck Institutes' X-Ray Crystallography Facility" ;
definition: """Facility provides infrastructure and support for investigators to undertake single crystal X-ray structural studies. Provides instrumentation, training, and collaboration for Protein characterization, including dynamic light scattering, differential scanning calorimetry, bio-layer interferometry, and circular dichroism; Binding studies using isothermal titration calorimetry; Robotic crystallization, incubators, UV, and digital microscopes;Robotic imaging;
Diffraction data collection and processing; Structure determination and analysis; Molecular modeling; Small angle X-ray scattering. Staff is available to train researchers to use equipment and to assist with project development and research.""" .
SCR:024465 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CURTAIN" ;
definition: """Web tool for exploration and sharing of mass spectrometry based proteomics data.
Used for analysis and sharing of proteomics data, data visualization, export of plots in SVG format, assessment of experimental quality by correlation matrix and profile plot. User can analyze domain structure, AlphaFold predicted structure, reported interactors, relative expression, disease and pharmaceutical links, and mutagenesis information on all selected hits.""" .
SCR:024466 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SIMA" ;
definition: "Software Python package for analysis of dynamic fluorescence microscopy data." .
SCR:024467 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ocular" ;
NIFRID:synonym "Teledyne Photometrics Ocular" ;
definition: "Photometrics acquisition software to capture, save and publish images and movies. Allows users of color and monochrome cameras to capture high quality images and videos from their microscope or lens system." .
SCR:024468 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pattern Health Digital Research Platform" ;
definition: "Platform for researchers to economically create and manage digital health programs. Platform built for research management and digital interventions. Helps researchers collect data and engage participants." .
SCR:024469 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FAIRassist.org" ;
NIFRID:synonym "FAIR Assist",
"FAIRassist" ;
definition: "Portal that aggregates tools that assist users ascertain FAIR-ness. Offers guidance to discover standards and repositories in FAIRsharing, which should be used to make data FAIR, as well as signpost other resources that enable FAIRness." .
SCR:024470 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2457" ;
rdfs:label "Karolinska Institute Biomedicum Flow Cytometry Core Facility" ;
NIFRID:synonym "Biomedicum Flow Cytometry (BFC) Core Facility",
"Biomedicum Flow Cytometry Core Facility Karolinska Institutet" ;
NIFRID:abbrev "BFC" ;
definition: "Facility is shared resource laboratory providing comprehensive suite of services to support research needs in flow cytometry. Offers conventional and full spectral cytometry for multi-parametric analysis, as well as multiparameter fluorescence activated cell sorting." .
SCR:024471 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Science-Metrix" ;
definition: "Independent research evaluation firm, based in the U.S. and Canada. Provider of research analytics services and data. Provides science research evaluation and analytics to assess science and technology activities. Headquartered in Montréal, Canada, Science-Metrix is known for independent bibliometric analysis and research evaluation and bibliometric and informetrics expertise. Science-Metrix was an early adopter of Elsevier’s abstract database Scopus and has worked closely with Elsevier. Elsevier has acquired Science-Metrix Inc. in 2018." .
SCR:024472 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyEulerCurves" ;
definition: "Software Python package to compute Euler Characteristic Curves of point cloud or image data." .
SCR:024473 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AIA-900" ;
rdfs:label "Tosoh | AIA-900 Automated Immunoassay Analyzer" ;
definition: """AIA immunoassay analyzer offers automation for immunoassay testing with flexible expansion capabilities. AIA-900 features: 90 tests/hour throughput; Load 10 racks on board;
Load up to 5 tests/patient; First result in 18 minutes; Random access; Continuous processing; Simple touch screen operation; Bar coded primary tube sampling; Clot detection; Unit Dose Test Cup; Automated pretreatment; Automated dilution from 2 to 1000.""" .
SCR:024474 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CARGO" ;
NIFRID:synonym "Cellular Autophagy Regulation and GOlgiphagy" ;
definition: "Web browser for analysis of proteomic data. ShinyApp interface generated in R and RStudio." .
SCR:024475 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "CNS Vital Signs" ;
NIFRID:synonym "CNS Vital Signs LLC" ;
definition: "Designs and develops neurocognitive and behavioral assessment tools and technologies. Provides clinicians and researchers with leading-edge technologies for improved neurocognitive and behavioral evaluation and management capabilities. Provides CNS Vital Signs which is reimbursable assessment procedure that utilizes scientifically validated, objective, and reliable computerized neuropsychological tests to evaluate neurocognitive status of patients and covers a range of mental processes from simple motor performance, attention, memory, to executive functions. CNS Vital Signs is available as both web/cloud platform and local platform." .
SCR:024478 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Planet Microbe" ;
definition: "Web based platform that enables data discovery from curated historical and on going oceanographic sequencing efforts. Enables discovery and integration of oceanographic ‘omics, environmental and physiochemical data layers. Used to centralize and standardize contextual data associated with major marine 'omic datasets. Used for marine microbiology to discover and analyze interconnected 'omics and environmental data." .
SCR:024479 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2458" ;
rdfs:label "University of Arizona Molecular Clinical Core Facility" ;
NIFRID:synonym "Arizona Molecular Clinical Core",
"UA-Arizona Molecular Clinical Core",
"University of Arizona UA-Arizona Molecular Clinical Core" ;
NIFRID:abbrev "AZClinCore" ;
definition: "Core is CLIA certified/CAP accredited laboratory specializing in high complexity genetic and serological clinical testing and research. Provides inpatient and outpatient diagnostic testing services as well as support for clinical trial and clinical research activities for physicians, researchers and industry clients. The AZClinCore has aided in development of novel genetic testing and clinical trial protocols as well as providing evaluations for new technology and testing platforms. Supports end-to-end clinical testing as well as reference lab services." .
SCR:024480 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lightning Pose" ;
definition: "Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools." .
SCR:024481 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DNA Amplicon" ;
NIFRID:synonym "Illumina DNA Amplicon" ;
definition: "Local Run Manager DNA Amplicon analysis module aligns amplicon reads against reference specified in the manifest file. Variants are called for the targeted regions." .
SCR:024482 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2459" ;
rdfs:label "Florida State University Innovation Hub Core Facility" ;
NIFRID:synonym "Florida State University Innovation Hub",
"FSU-Innovation Hub" ;
definition: "Hosts makerspaces, labs, and promotes design based frameworks toward iteration and innovation. Acts as open intersection of university departmental collaboration and provides access to low barrier prototyping tools. Supports FSU student, staff, and faculty research initiatives." .
SCR:024483 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NGmerge" ;
definition: "Software tool for merging paired-end reads via novel empirically derived models of sequencing errors. Used for merging paired-end reads and removing adapters. Corrects errors and ambiguous bases and assigns quality scores for merged bases that accurately reflect the error rates." .
SCR:024484 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NOTUNG" ;
NIFRID:synonym "Notung 2.9" ;
definition: "Software package to facilitate large scale analysis, using both rooted and unrooted trees.Used for dating gene duplications and optimizing gene family trees.Used for inferring duplication dates from gene trees automatically and can also be used as exploratory analysis tool for evaluating alternative hypotheses." .
SCR:024485 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OMNISEC" ;
definition: "Software for OMNISEC instrument control, data acquisition, analysis and reporting. Used for advanced analysis of proteins and polymers by GPC/SEC, and is specifically designed for control of OMNISEC RESOLVE and OMNISEC REVEAL." .
SCR:024486 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Optimization Toolbox" ;
definition: "Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations." .
SCR:024487 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PHYLDOG" ;
definition: "Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously." .
SCR:024488 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenBUGS" ;
NIFRID:synonym "Open Bayesian inference Using Gibbs Sampling" ;
definition: "Software for analysing complex statistical models using Markov chain Monte Carlo methods." .
SCR:024489 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProgRes Capture Pro" ;
NIFRID:synonym "Jenoptic ProgRes Capture Pro" ;
definition: "Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras." .
SCR:024490 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ocular" ;
NIFRID:synonym "Teledyne Photometrics Ocular" ;
definition: "Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system." .
SCR:024491 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent Seahorse Wave" ;
NIFRID:synonym "Seahorse Wave" ;
definition: "Instrument control and data acquisition software for Agilent Seahorse XFe96 and XFe24 analyzers with Windows 10 64-bit OS only. Experiment design, instrument control, data analysis, and file management software. Software provides intuitive interface with predefined assay templates and streamlined experimental design for simplified metabolic analysis." .
SCR:024492 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Umediation" ;
definition: "Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding." .
SCR:024493 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nano Measurer" ;
definition: "Software tool to process micrograph images for particle size." .
SCR:024494 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VSEARCH" ;
definition: "Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data." .
SCR:024495 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WHONET" ;
definition: "Software free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance at the Brigham and Women's Hospital in Boston, Massachusetts. WHONET, available in 44 languages, supports local, national, regional, and global surveillance efforts in over 2,300 hospital, public health, animal health, and food laboratories in over 130 countries worldwide." .
SCR:024496 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ToposPro" ;
definition: "Software package for analysis of geometrical and topological properties of periodic structures including crystals, networks, tilings.ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters." .
SCR:024497 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Treerecs" ;
definition: "Open source, species and gene tree reconciliation software. Software integrated phylogenetic tool, from sequences to reconciliations. Used to correct, rearrange and reroot gene trees with regard to given species tree." .
SCR:024498 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TomoStudio" ;
definition: "Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data." .
SCR:024499 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stem" ;
NIFRID:synonym "Short Time-series Expression Miner" ;
definition: "Software tool for analysis of short time series gene expression data. Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments. Allows to identify significant temporal expression profiles and genes associated with these profiles and to compare behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology." .
SCR:024500 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SRAMP" ;
NIFRID:synonym "Sequence-based Rna Adenosine Methylation site Predictor" ;
definition: "Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features." .
SCR:024501 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SimPhy" ;
definition: "Software package for simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, all three potentially leading to species tree/gene tree discordance and gene conversion. Used for phylogenomic simulation of gene, locus, and species trees." .
SCR:024502 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mutation Assessor" ;
definition: "Web server predicts functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. Functional impact is assessed based on evolutionary conservation of affected amino acid in protein homologs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:024503 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CRISPResso2" ;
definition: "Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments." .
SCR:024504 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WinNonlin" ;
NIFRID:synonym "Phoenix WinNonlin" ;
definition: "Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool." .
SCR:024505 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FastMulRFS" ;
definition: "Software pipeline for estimating species trees from multi copy gene trees." .
SCR:024506 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Evalue" ;
definition: "Web application as E-value calculator that compute E-values for variety of outcome measures, including risk ratios, odds ratios, rate ratios, risk differences, hazard ratios, and standardized mean differences." .
SCR:024507 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gamm4" ;
definition: "Software R package to estimate generalized additive mixed models." .
SCR:024508 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Inference of CRISPR Edits" ;
NIFRID:synonym "Synthego Inference of CRISPR Edits" ;
NIFRID:abbrev "ICE" ;
definition: "Software tool that offers analysis of CRISPR editing data. Used for inference of CRISPR edits from Sanger trace data." .
SCR:024509 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DAGitty" ;
definition: "Software R package provides access to all of the capabilities of DAGitty web application for drawing and analysing Directed Acyclic Graphs within the R platform for statistical computing. Used for graphical analysis of structural causal models." .
SCR:024510 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "geepack" ;
NIFRID:synonym "generalized estimating equations pack" ;
definition: "Software R package implements generalized estimating equations for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can handle clustered categorical responses. Used for fitting marginal generalized linear models to clustered data." .
SCR:024511 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggridges" ;
definition: "Software R package enables creation of Ridgeline plots in 'ggplot2'" .
SCR:024512 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CopyKAT" ;
NIFRID:synonym "Copynumber Karyotyping of Aneuploid Tumors" ;
definition: "Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data." .
SCR:024513 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoRT" ;
definition: "Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides." .
SCR:024514 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CMplot" ;
NIFRID:synonym "Circle Manhattan Plot" ;
definition: "Software drawing R package designed for Manhattan plot of genomic analysis." .
SCR:024515 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "classInt" ;
NIFRID:synonym "Class Intervals" ;
definition: "Software R package for choosing univariate class intervals for mapping or other graphics purposes." .
SCR:024516 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mitml" ;
definition: "Software R package for multiple imputation of missing data in multilevel modeling." .
SCR:024517 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaPSICOV" ;
definition: "Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins." .
SCR:024518 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ModFOLD" ;
NIFRID:synonym "ModFOLD6",
"ModFOLD8" ;
definition: "Web server for the global and local quality estimation of 3D protein models" .
SCR:024519 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "maftools" ;
definition: "Software R package offers multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses. Maftools requires somatic variants in Mutation Annotation Format (MAF) and is independent of larger alignment files." .
SCR:024520 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ASTRAL-Pro" ;
NIFRID:synonym "ASTRAL for PaRalogs and Orthologs",
"ASTRAL-Pro 2" ;
definition: "Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy." .
SCR:024521 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kaplan Meier Plotter" ;
NIFRID:synonym "Kaplan-Meier Plotter",
"KM Plotter" ;
definition: "Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma." .
SCR:024522 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MADOKA" ;
definition: "Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library." .
SCR:024523 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IntFOLD" ;
definition: "Web integrated protein structure and function prediction server. Integrated server for modelling protein structures and functions from amino acid sequences." .
SCR:024524 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lDDT" ;
NIFRID:synonym "Local Distance Difference Test" ;
definition: "Web server for local superposition free score for comparing protein structures and models using distance difference tests. Superposition free score that evaluates local distance differences of all atoms in model, including validation of stereochemical plausibility." .
SCR:024525 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LaCyTools" ;
definition: "Software high throughput data extraction package for LC-MS data.Targeted Liquid Chromatography-Mass Spectrometry data processing package for relative quantitation of glycopeptides." .
SCR:024526 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bedr" ;
definition: "Software R package for genomic interval processing.Genomic regions processing using open-source command line tools to perform genome arithmetic e.g indexing, formatting and merging." .
SCR:024527 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2510" ;
rdfs:label "Stanford University Microfluidics Foundry Core Facility" ;
NIFRID:synonym "Stanford Microfluidics Foundry",
"Stanford University Stanford Microfluidics Foundry" ;
NIFRID:abbrev "SMF" ;
definition: "Core in part of Bioengineering Department at Stanford University and is the main service provider of integrated microfluidic devices on Stanford campus servicing universities and academic institutions." .
SCR:024528 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2512" ;
rdfs:label "Stanford University Koret Human Neurosciences Community Laboratory Core Facility" ;
NIFRID:synonym "Koret Human Neurosciences Community Laboratory",
"Stanford University Koret Human Neurosciences Community Laboratory" ;
NIFRID:abbrev "HNCL" ;
definition: "Core for collaborative human neuroscience research provides access to technology and expertise to high density electroencephalography recording and transcranial magnetic stimulation studies in human subjects." .
SCR:024529 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2511" ;
rdfs:label "Stanford University Additive Manufacturing and Printing Core Facility" ;
NIFRID:synonym "Additive Manufacturing and Printing Facility",
"Stanford University Additive Manufacturing and Printing Facility" ;
NIFRID:abbrev "AMPF" ;
definition: "Advanced 3D printing facility enables digital design, prototyping, and small scale production as integrated innovation hub and shared use facility for innovation and commercialization for investigators spanning the Stanford campus and Silicon Valley." .
SCR:024530 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2513" ;
rdfs:label "Pennsylvania State University Huck Institutes Genomics Research Incubator Core Facility" ;
NIFRID:synonym "Pennsylvania State University Huck Institutes Genomics Research Incubator" ;
NIFRID:abbrev "GRI" ;
definition: """Provides access to highly specialized and custom genomics and epigenomics assays that Genomics Core Facility does not currently support. Examples include ATAC sequencing;
RUN sequencing;Tag sequencing;Chromatin immunoprecipitation;Custom assays. Offers hands-on experiences and training for researchers in genomic technologies, methodologies, and instrumentation.""" .
SCR:024531 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ms-variability-analysis" ;
definition: "Variability analysis of proteomics data used for deep learning." .
SCR:024532 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Splice AI" ;
definition: "Software package annotates genetic variants with their predicted effect on splicing. Used to identify splice variants." .
SCR:024533 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MediBeacon | Transdermal GFR Monitor" ;
definition: "Transdermal Glomerular Filtration Rate monitor used to assess renal function in mouse and rat models of acute kidney injury and chronic kidney disease." .
SCR:024534 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D ImageJ Suite" ;
definition: "Software suite provides plugins to enhance 3D capabilities of ImageJ." .
SCR:024535 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TP1020" ;
rdfs:label "Leica | TP1020 Automatic Benchtop Tissue Processor Semi Enclosed" ;
NIFRID:synonym "Leica TP1020 tissue processor" ;
definition: "Leica TP1020 tissue processor is available in four configurations: basic instrument, basic instrument with vacuum, basic instrument with fume control system and basic instrument with both vacuum and fume control. Used for gentle specimen processing and high level of specimen safety at all stages of processing run." .
SCR:024536 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "10x Genomics | Chromium iX Single Cell Analyzer" ;
NIFRID:synonym "Chromium iX",
"Chromium iX Single Cell Analyzer" ;
definition: "Chromium iX offers cost effective, lower throughput single cell analysis, and can be upgraded to the high throughput full-range Chromium X.Chromium iX does not run high-throughput (HT) assays." .
SCR:024537 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "10x Genomics | Chromium X Single Cell Analyzer" ;
NIFRID:synonym "10X Genomics Chromium X",
"Chromium X",
"Chromium X Single Cell Analyzer" ;
definition: "Analyzer used for high throughput full range single cell analysis. Chromium X runs high-throughput assays. It runs all single cell assays, including high-throughput assays for Single Cell Immune Profiling and Single Cell Gene Expression." .
SCR:024538 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TADA-A" ;
NIFRID:synonym "TADA-Annotations" ;
definition: "Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies." .
SCR:024539 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioThings API" ;
definition: "FAIR API ecosystem for inter-connected biomedical knowledge. Provides three components in its API development ecosystem: family of high-performance APIs for accessing up-to-date annotations for genes, genetic variants, chemicals and drugs; provides BioThings API packages its API-development best practice into reusable Software Development Kit to help other bioinformaticians to build same high-quality API to distribute their own specific knowledge; BioThings API provides platform to foster findability and interoperability across community developed biomedical APIs. Provides tools for authoring API metadata following community supported OpenAPI standard and hosts standardized interactive API documentation. Defines set of OpenAPI extensions to provide biomedical specific semantic annotations." .
SCR:024540 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Playbook Workflow Builder" ;
definition: "Web based platform that facilitates knowledge resolution by enabling users to traverse growing network of input datasets, semantically annotated API endpoints, and data visualization tools contributed by the ecosystem. Via user friendly web based user interface, workflows can be constructed from these building blocks without technical expertise." .
SCR:024541 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Luna" ;
definition: "Software package for analysis of sleep signal data. Open source C/C++ software for manipulating and analyzing polysomnographic recordings, with focus on sleep EEG." .
SCR:024542 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Moonlight" ;
definition: "Web Luna based interactive viewer for EDF signal and annotations, specifically designed for polysomnographic data. Supports visualization, analyses and manipulation of sleep signals, range of summary statistics and hypnogram based analyses including automated staging." .
SCR:024543 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ImageTwin" ;
definition: "AI based software for detecting integrity issues in figures of scientific articles. Used for detecting integrity issues in life science articles. Detects inappropriate manipulation and duplication in many figure types, including blots, microscopy images, and light photography." .
SCR:024544 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2469" ;
rdfs:label "University of California at Berkeley Electron Microscope Laboratory Core Facility" ;
NIFRID:synonym "Electron Microscope Laboratory",
"UC Berkeley Electron Microscope Laboratory",
"University of California at Berkeley Electron Microscope Laboratory",
"University of California Berkeley UC Berkeley Electron Microscope Laboratory" ;
NIFRID:abbrev "EML" ;
definition: "Imaging core and shared resource facility. Provides electron microscopy services, education, and training. Equipped with high resolution transmission electron microscopes, scanning electron microscopes, high pressure freezer and ancillary sample preparation equipment. The equipment can provide nanometer scale analysis for biological, chemical and materials science. Offers Project consultation, Education and training for new users, Equipment for trained users who anticipate having long term EM projects, Full service microscopy." .
SCR:024545 a owl:NamedIndividual ;
rdfs:label "Molecular Property Diagnostic Suite Covid-19" ;
NIFRID:synonym "Galaxy MPDS COVID-19" ;
NIFRID:abbrev "MPDS-Covid19" ;
definition: "Galaxy based disease specific web portal for drug discovery research of COVID-19. Open access disease specific drug discovery portal." .
SCR:024546 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BatchEval" ;
definition: "Software tool for evaluating batch effects in data integration. Tool to improve accuracy and reliability of experimental results. Used to evaluate batch effect of dataset integration and output comprehensive report." .
SCR:024547 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Franklin by Genoox" ;
definition: "Platform as clinical knowledge base to search information to answer genomic questions. Connects clinicians, genetic counselors, and healthcare organizations by sharing genetic insights, enabling platform users to make impactful discoveries providing better patient care." .
SCR:024548 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kassandra" ;
definition: "Software bulk RNA-seq cellular deconvolution tool. Used for analysis of healthy tissue and tumor biopsies. Based on RNA-seq NGS data of biological sample, Kassandra predicts cellular composition including stromal and immune elements by analyzing gene expression." .
SCR:024549 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OSS Research and Community Activity" ;
NIFRID:synonym "Emerging Technology Observatory Open Source Software Research and Community Activity",
"Open Source Software Research and Community Activity" ;
NIFRID:abbrev "ORCA" ;
definition: "Platform for data on open source software (OSS) used in science and technology research. Drawing on Github Archive, ETO’s Merged Academic Corpus, and many other data sources, ORCA tracks OSS usage, health, development activity, and community engagement across software projects and research subjects. Use ORCA to compare OSS projects in particular research area, track trends over time, and sort and filter projects by different metrics." .
SCR:024551 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Customizable Multielectrode Array" ;
NIFRID:synonym "16-channel customizable multielectrode array",
"CMEA: Customizable Multielectrode Arrays" ;
NIFRID:abbrev "CMEA" ;
definition: "Simple, lightweight, and low cost customizable multielectrode array for Local Field Potential recordings. Used to collect LFP data from different brain regions simultaneously in rats. Can be modified to record single unit and multiunit activity in addition to LFP activity using both wired and wireless neural data acquisition systems." .
SCR:024552 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Berkeley Seismological Laboratory" ;
NIFRID:synonym "Berkeley Seismological Lab" ;
definition: "Acts as part of statewide earthquake monitoring system, the California Integrated Seismic Network. Conducts essential research on earthquakes and solid earth processes while collecting and delivering high quality geophysical data. Data from these geophysical networks are recorded digitally and are archived at the Northern California Earthquake Data Center, which is located at the Berkeley Seismological Lab." .
SCR:024553 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biocode Commons" ;
definition: "Platform provides resources for genomic observations from collection to analysis and publication. Works with standards community to ensure clear vocabularies and useful ontologies for biological resources and related assets. Biocode Commons is also collaborating on development of Biological Collections Ontology, working to better integrate ontologies, vocabularies, and relevant standards that are related to BCO." .
SCR:024554 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "California Coastal Atlas" ;
definition: "Resource designed to publish information and data about California coast reflecting current scientific understanding and data for the purpose of informing public policy and advancing the understanding of coastal processes." .
SCR:024555 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2472" ;
rdfs:label "University of Florida Scripps Institute for Biomedical Innovation and Technology Structural Biology Cryo Electron Microscopy Core Facility" ;
NIFRID:synonym "Structural Biology Cryo-Electron Microscopy Core",
"The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology Structural Biology Cryo Electron Microscopy Core",
"UF Scripps Institute for Biomedical Innovation and Technology Structural Biology Cryo Electron Microscopy Core" ;
definition: "Provides scientists with cryo-electron microscopy utilization, skills and knowledge to aid in their research." .
SCR:024556 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2514" ;
rdfs:label "Yale University Wu Tsai Institute BrainWorks Core Facility" ;
NIFRID:synonym "Wu Tsai Institute-BrainWorks" ;
definition: "Service core arm of Center for Neurocognition and Behavior. Used for measuring healthy human brain and behavior in action. Facility houses equipment, including MRI, SQUID and triaxial OPM MEG, EEG, NIRS, TMS, VR, eye-tracking, and body motion tracking." .
SCR:024557 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Comprehensive Everglades Restoration Plan" ;
NIFRID:synonym "South Florida Water Management District Comprehensive Everglades Restoration Plan" ;
NIFRID:abbrev "CERP" ;
definition: "Platform provides framework for restoring, protecting and preserving the greater Everglades ecosystem. The plan is partnership between State of Florida and federal government." .
SCR:024558 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_B15" ;
rdfs:label "Heraeus | B 15 Compact Incubator" ;
definition: "Compact incubator total volume is 15 litres and it operates at temperatures from 5 °C above ambient to 50 °C. Temperature is displayed in increments of 0.2 °C. Air circulation system ensures heat distribution and minimizes the drying out of samples. Incubator can be set up directly on any counter top or work bench and is made of plastic that can be sterilised with standard disinfectants. Small opening on the housing can be used to accommodate cables for electrical devices placed inside the incubator. Reservoir for collecting spilled liquids is provided for additional safety." .
SCR:024559 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cobas_C311" ;
rdfs:label "Roche | Cobas C311" ;
definition: "Autoanalyzer is standalone system that provides consolidated testing from range of clinical chemistry applications. Allows determination of sodium, potassium and chloride in serum, plasma and urine using ion selective electrodes. Measurement of HbA1c levels in whole blood can also be performed." .
SCR:024560 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Infinite_M200" ;
rdfs:label "Tecan | Infinite M200" ;
NIFRID:synonym "Infinite M200",
"TECAN Infinite M200" ;
definition: "TECAN Infinite M200 is laboratory device and accessory for multiplex luminescence and fluorescence applications. Device features automated robotic arm for dispensing samples or reagents onto cuvettes or microplates, as well as range of high speed and throughput sample injection capabilities. Infinite M200 is integrated with TECAN's proven laser-based multi-channel detection technology, to measure multiple biological responses simultaneously. System features graphical user interface to configure instrument for single or multiple sample injection processes. Accommodates range of different cuvette and microplate vessels, suitable for both 1.5ml and 0.2ml tubes as well as plates up to 384 wells. Multichannel optical detector can detect up to four different signals in parallel, with wide range of detection wavelengths. Designed for high-throughput applications with sensitive fluorescence and luminescence. Features automated sample injection unit that enables hands-free operation of 96 or 1,536 up to eight-channel multipoint experiments, providing maximum flexibility. Comes with range of software, including intuitive data collection and analysis interface. Designed with automated calibration settings, providing reliable, accurate and reproducible results." .
SCR:024561 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NanoQuantPlate" ;
rdfs:label "Tecan | NanoQuantPlate" ;
definition: "Device designed for simultaneous measurement of multiple low volume samples. Consists of 16 precision manufactured quartz optics in user friendly format, offering precise, straightforward absorbance and fluorescence based measurements from sample volumes as low as 2 µl. Combined with Tecan’s Infinite series readers – the Infinite 200 PRO, Infinite F500 and Infinite M1000 PRO – the NanoQuant Plate provides solution for DNA or RNA quantification, allowing detection of concentrations down to 1 ng/µl for wide variety of applications." .
SCR:024562 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tecan i-Control" ;
NIFRID:synonym "i-Control",
"Tecan i-Control software" ;
definition: "Microplate reader software as user friendly interface for control of Tecan's Infinite series of microplate readers designed for professional use." .
SCR:024563 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | TCS SP8 DLS LightSheet microscope" ;
NIFRID:synonym "Leica DLS TCS SP8" ;
definition: "Digital LightSheet full confocal with gentle single plane illumination microscope for easy light sheet imaging. TwinFlect mirror deflects illuminating light sheet at 90° angle, which allows integration of illumination and detection beam path into vertical axis of every inverted, Leica TCS SP8 confocal." .
SCR:024564 a NLX:63400,
owl:NamedIndividual ;
definition: "Software R package to predict drug functional similarity to drug repurposing." .
SCR:024565 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2516" ;
rdfs:label "Griffith University Compounds Australia Core Facility" ;
NIFRID:synonym "Compounds Australia - Griffith University" ;
definition: "Core for compound management and logistics. Through specialist infrastructure and expertise, we enable health researchers worldwide to outsource their sample logistics. Securely stores and curates suite of compound libraries (>1.5 million compounds), which are provided to researchers in flexible, assay-ready formats." .
SCR:024566 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 501100001791",
"GRID grid.1022.1",
"ISNI 0000 0004 0437 5432",
"Wikidata Q1202292" ;
rdfs:label "Griffith University; Brisbane; Australia" ;
definition: "Griffith University, Brisbane, Queensland, Australia is public research university in South East Queensland on the east coast of Australia. One of Australia's leading universities. The university offers undergraduate, postgraduate, and research programs across range of disciplines, including business, law, science, health, education, engineering, and arts." .
SCR:024567 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miRNet" ;
NIFRID:synonym "miRNet 2.0" ;
definition: "Web based tool that offers statistical, visual and network based approaches to understand miRNAs functions and regulatory mechanisms. Used for dissecting miRNA-target interactions and functional associations through network-based visual analysis.miRNet 2.0 is network based visual analytics for miRNA functional analysis and systems biology." .
SCR:024568 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Illumina | NovaSeq X Plus" ;
NIFRID:synonym "NovaSeq X Plus",
"NovaSeq X Plus Sequencing System" ;
definition: """NovaSeq X Plus Sequencing System has ability to sequence more than 128 genomes per run. Provides faster run times, and the ability to process data directly on the instrument.
Uses dual flow cells. Production scale sequencing system can also perform broad range of data intensive applications, from single-cell analysis to exome and circulating tumor DNA sequencing.""" .
SCR:024569 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Illumina | NovaSeq X" ;
NIFRID:synonym "NovaSeq X",
"NovaSeq X Sequencing System" ;
definition: "Updated NovaSeq to NovaSeq X. NovaSeq X Sequencing System achieves lower cost per genome by packing more genomes per flowcell, and that is because each flowcell has more wells for more fragments. NovaSeq X uses single flow cell." .
SCR:024570 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "10x Genomics | Visium CytAssist" ;
NIFRID:synonym "Visium CytAssist" ;
definition: """Compact, benchtop instrument that enables transfer of transcriptomic probes from
standard glass slides to Visium slides, enabling spatial profiling insights to be gained from even more samples. Enables whole transcriptomic spatial profiling insights across entire tissue section, and expanded compatibility with FFPE and/or FF samples.""" .
SCR:024571 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lubridate" ;
definition: "Software R package to work with date-times and time-spans. Used for fast and user friendly parsing of date-time data, extraction and updating of components of date-time, algebraic manipulation on date-time and time-span objects." .
SCR:024573 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2517" ;
rdfs:label "University of Pennsylvania Institute for RNA Innovation Targeting Core Facility" ;
NIFRID:synonym "Targeting Core",
"University of Pennsylvania Institute for RNA InnovationTargeting Core",
"University of Pennsylvania Targeting Core" ;
definition: "Core to support advancement of RNA biotherapeutics via enabling swift and low failure solutions of targeting related aspects. Provides methodologies, equipment, reagents, expertise and support in identification of epitopes and ligands, molecular design and testing of targeting RNA to diverse multitudes of desirable addresses in the body." .
SCR:024574 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2518" ;
rdfs:label "University of Pennsylvania Institute for Immunology and Immune Health I3H Core Facility" ;
NIFRID:synonym "Immune Health Platforms",
"PennMedicine Immune Health" ;
NIFRID:abbrev "I3H" ;
definition: "Core provides infrastructure and technical support for scaling clinical immune profiling of large scale clinical cohorts. Provides biospecimen processing, sample storage, high dimensional immune assays, computational analysis, and project management. Services are only available to investigators and teams whose cohorts have been approved by the Immune Health leadership." .
SCR:024575 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DataMares " ;
definition: "Open source, and interactive platform to resolve trans disciplinary problems related to coastal and marine ecosystem. Data sharing and science communication portal holds amounts of fishery, reef, and mangrove data pertaining to Gulf of California and Mexico specific oceans, and delivers this information in interactive and easily digestible manner. Consistently expands library of datasets while improving functionality and overall usability of the platform. Facilitate access to scientific knowledge and data to promote transparency, education, and deeper understanding of Mexico’s ecosystems and their biodiversity to bridge gap between science and design process of conservation and resource management programs." .
SCR:024576 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EarthCube" ;
definition: "Platform provides tools, data, services, apps and community resources for geoscience researchers. EarthCube community works together to influence how data will be collected accessed, analyzed, visualized, shared and archived; participate in interdisciplinary and collaborative research; and contribute to transformation of geoscience research through emerging practices of digital scholarship, data and software stewardship, and open science." .
SCR:024577 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EarthRef" ;
definition: "Platform for Earth reference data and models supported by San Diego Supercomputer Center and Scripps Institution of Oceanography. Provides webservices and database." .
SCR:024578 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Engineering Biology Research Consortium" ;
NIFRID:synonym "The Engineering Biology Research Consortium (EBRC)" ;
NIFRID:abbrev "EBRC" ;
definition: "Non-profit, public-private partnership dedicated to bringing together inclusive community committed to advancing engineering biology to address national and global needs. We showcase cutting-edge research in engineering biology, identify pressing challenges and opportunities in research and application, articulate compelling research roadmaps and programs to address them, and provide timely access to other key developments in engineering biology." .
SCR:024579 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Geotechnical Extreme Events Reconnaissance" ;
NIFRID:abbrev "GEER" ;
definition: "Leading global organization for investigation and collection of highly valuable and perishable geotechnical insights and data and timely distillation and provision of that information to public through reports." .
SCR:024580 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kavli Institute for Theoretical Physics Online Talks" ;
NIFRID:synonym "KITP Online Talks" ;
NIFRID:abbrev "KITP" ;
definition: "Most seminars, conferences, colloquia, and lectures at KITP since late 1997 have been archived on this website, in the form of slides, audio, video, and podcasts. Portal to foster scientific communication, education, and outreach." .
SCR:024581 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LBNL OpenMSI" ;
NIFRID:synonym "Open Mass Spectrometry Imaging",
"OpenMSI" ;
definition: "Web-based platform for mass spectrometry imaging. Used for visualization, analysis and management of mass spectrometry imaging data. Used for management and storage of MSI data, visualization of hyper-dimensional contents of data, and statistical analysis." .
SCR:024583 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biobank@VITO" ;
definition: "Population biobank hosts heterogeneous collection of samples from general population spread across Flanders and over time and covers different ages. Biobank in which bio-specimen including human peripheral blood, cord blood, serum, plasma, cells, RNA, DNA), urine, hair, nails, exhaled breath condensate, saliva DNA, and human breast milk collected from non-diseased populations are preserved. These biospecimen were collected since 2002 in different human biomonitoring studies comprising European (e.g., DEMOCOPHES, HBM4EU), national (e.g., WHO human breastmilk studies), Flemish (Flemish Environment and Health Study (FLEHS) campaigns), and local (e.g., hotspots, 3xG project) well-defined and ethically approved research projects." .
SCR:024584 a owl:NamedIndividual ;
rdfs:label "ProPlot" ;
definition: "Software tool as succinct matplotlib wrapper for making publication quality graphics." .
SCR:024585 a "Oganization",
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100007058",
"GRID grid.261128.e",
"ISNI 0000 0000 9003 8934",
"Wikidata Q1191344" ;
rdfs:label "Northern Illinois University; DeKalb; USA" ;
definition: "Northern Illinois University is a public research university in DeKalb, Illinois. It was founded as Northern Illinois State Normal School in 1895 by Illinois Governor John P. Altgeld to provide the state with college-educated teachers." .
SCR:024586 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2551" ;
rdfs:label "Northern Illinois University Molecular Analysis Core Facility" ;
NIFRID:synonym "Molecular Analysis Core Facility",
"Northern Illinois University MAC core facility",
"Northern Illinois University MAC facility" ;
NIFRID:abbrev "NIU MAC" ;
definition: "Molecular Analysis Core offers analytical and instructional expertise in mass spectrometry. Provides instruments for spectroscopy, chromatography, and thermal analysis. Located in La Tourette Hall 304 and managed and supported by the Division of Research and Innovation Partnerships" .
SCR:024587 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cartopy" ;
definition: "Software Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses. Cartographic library with matplotlib support." .
SCR:024588 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bayesplot" ;
definition: "Software R package providing extensive library of plotting functions for use after fitting Bayesian models.Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow." .
SCR:024589 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Waters" ;
NIFRID:synonym "Waters Corporation" ;
definition: "Publicly traded analytical laboratory instrument and software company headquartered in Milford, Massachusetts. Leading provider of lab equipment, supplies and software. Has pioneered chromatography, mass spectrometry, and thermal analysis innovations." .
SCR:024590 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Evosep" ;
definition: "Business Services and Biotechnology Research company in Odense, Denmark." .
SCR:024591 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2519" ;
rdfs:label "Weill Cornell Medical College Department of Pathology and Laboratory Medicine Multiparametric In Situ Imaging Laboratory Core Facility" ;
NIFRID:synonym "Weill Cornell Medical College MISI WCM" ;
NIFRID:abbrev "MISI WCM" ;
definition: "Core focuses on providing immunohistochemistry, multiplex immunofluorescence and high-plex histological imaging.Provides in situ-based profiling of cellular microenvironments at single cell resolution, in tumor and non-tumor tissues." .
SCR:024592 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Live Mouse Tracker Toolkit Analysis" ;
NIFRID:synonym "Live Mouse Tracker Toolkit",
"LMT Toolkit",
"LMT toolkit analysis",
"lmt toolkit analysis",
"LMT-toolkit",
"LMT-Toolkit Analysis" ;
definition: "Open source web application created to analyze Live Mouse Tracker data easily and intuitively. Used to check reliability and to make some analysis of data from Live Mouse Tracker experiments. LMT stores data in SQLite files that requires some computer skills, but LMT-toolkit makes it easy to compute and extract behavioral profiles for each animal tested following step-by-step process." .
SCR:024593 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "IonOpticks" ;
definition: "Innovative Australian company that develops, manufactures and distributes advanced proteomics tools. Produces high performance nanoflow chromatography solutions for global research community." .
SCR:024594 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "windrose" ;
definition: "Software Python library to manage wind data, draw windroses also known as polar rose plots, and fit Weibull probability density functions." .
SCR:024595 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scikit-learn-intelex" ;
definition: "Software tool as Intel(R) Extension for Scikit-learn to speed up Scikit-learn application. Used to accelerate existing scikit-learn code. Accelerates Scikit-learn applications and still have full conformance with all Scikit-Learn APIs and algorithms. Software AI accelerator brings over 10-100X acceleration across variety of applications." .
SCR:024596 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.462422.4",
"ISNI 0000 0001 2109 9028",
"Wikidata Q6291683" ;
rdfs:label "Marine and Coastal Research Institute of Columbia; Santa Marta; Colombia" ;
NIFRID:abbrev "INVEMAR" ;
definition: "Nonprofit marine and coastal research institute of Colombia linked to Ministry of Environment and Sustainable Development. Provides basic and applied scientific research on marine and coastal issues related to biodiversity, geosciences, resource use assessment, environmental quality and management of marine and coastal information. Coordinates Environmental Information System in marine and coastal aspects. Infrastructure has specialized laboratories with cutting-edge technology and Museum of Marine Natural History of Colombia. INVEMAR is recognized nationally and internationally for quality and leadership in its basic and applied research activities and its commitment to sustainable use of marine and coastal resources." .
SCR:024597 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100014585",
"GRID grid.507579.9",
"ISNI 0000 0001 2190 7056",
"Wikidata Q6971323" ;
rdfs:label "National Center for Ecological Analysis and Synthesis" ;
NIFRID:abbrev "NCEAS" ;
definition: "Synthesis science center to help to transform ecology and environmental science to generate bigger insights. Leader in environmental data science, has led development of technological solutions to improve data access and management and efficiency of analyses, and helped set scientific standards in data ethics." .
SCR:024598 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Nightingale" ;
NIFRID:abbrev "NGSCI" .
SCR:024599 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011973" ;
rdfs:label "Arctic Data Center" ;
NIFRID:synonym "NSF Arctic Data Center" ;
definition: "Data and software repository for Arctic section of National Science Foundation’s Office of Polar Programs. Repository has CoreTrustSeal certification so that the data can be used, shared, and preserved over long timespan. Helps research community reproducibly preserve and discover all products of NSF funded science in Arctic, including data, metadata, software, documents, and provenance that link these in coherent knowledge model. Initiative is the partnership between National Center for Ecological Analysis and Synthesis at UC Santa Barbara, DataONE, and National Centers for Environmental Information." .
SCR:024600 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ocean Protection Council" ;
NIFRID:abbrev "OPC" ;
definition: "Cabinet level state body that works jointly with state and federal agencies, NGOs, tribes and public to ensure that California maintains healthy, resilient, and productive ocean and coastal ecosystems. The mission is to protect California’s coast and ocean by advancing innovative, science based policy and management, making strategic investments, and catalyzing action through partnerships and collaboration. Provides global model for ecosystem based protection and conservation." .
SCR:024601 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CodeMeta Generator" ;
definition: "Web application that creates CodeMeta files." .
SCR:024602 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Software Heritage" ;
definition: "Software Heritage provides service for archiving and referencing historical and contemporary software with focus on human readable source code. The site was unveiled in 2016 by Inria and is supported by UNESCO. The project itself is structured as non‑profit multi‑stakeholder initiative." .
SCR:024603 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Tree of Life" ;
definition: "Project aims to construct comprehensive, dynamic and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data." .
SCR:024604 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Context" ;
definition: "Publishes documentation and data to make them discoverable and searchable on the Web. Publishing service archives data by integrating analyses, maps, media, and journals together. Open Context editors clean data and organize content. Every item receives unique identifier that allows citation of individual items. Your data publication receives DOI. Creative Commons licenses facilitate reuse. All Open Context data publications are preserved with California Digital Library." .
SCR:024605 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rstanarm" ;
definition: "Software R package for Bayesian applied regression modeling via Stan." .
SCR:024606 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2521" ;
rdfs:label "Tulane University TNBRC Anatomic Pathology Core Facility" ;
NIFRID:synonym "TNBRC Anatomic Pathology Core",
"Tulane University TNBRC Anatomic Pathology Core" ;
NIFRID:abbrev "APC" ;
definition: "Anatomic Pathology Core is responsible for post-mortem examinations, tissue collection and distribution, fixation, processing, slide preparation, routine and special staining, and diagnostic gross and histologic pathology services. Processes and interprets biopsy specimens for both research and diagnostic purposes and provides tissue trimming, paraffin processing, sectioning, and routine and special staining for clinical and research staff and faculty. APC works closely with clinical veterinarians, and through diagnostic pathology on biopsies and necropsies, plays major role in monitoring and maintaining health of animals in breeding colonies." .
SCR:024607 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2522" ;
rdfs:label "Tulane University TNBRC Immunology Assay Core Facility" ;
NIFRID:synonym "TNBRC Immunology Assay Core",
"Tulane University TNBRC Immunology Assay Core" ;
NIFRID:abbrev "IAC" ;
definition: "Immunology Assay Core provides several immunology services to core and affiliate investigators. Offers multicolor staining for flow cytometry, access to inventory of commonly used antibodies, reagent compounding, sample processing such as cell isolation, automated cell separation through RoboSep, and irradiation of biological samples.Offers multiplex assays using MESO QuickPlex SQ 120 Imager to investigators." .
SCR:024608 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2523" ;
rdfs:label "Tulane University TNBRC Infectious Disease Aerobiology Core Facility" ;
NIFRID:synonym "TNPRC Infectious Disease Aerobiology Core",
"Tulane University TNBRC Infectious Disease Aerobiology Core" ;
definition: "Core focuses on infectious disease aerobiology. Core facilitates biomedical research efforts that require unique demands of aerosol and aerobiology in their respective performance." .
SCR:024609 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2526" ;
rdfs:label "Tulane University TNBRC Clinical Pathology Core Facility" ;
NIFRID:synonym "TNBRC Clinical Pathology Core",
"Tulane University TNBRC Clinical Pathology Core" ;
NIFRID:abbrev "CPC" ;
definition: "Clinical Pathology Core performs clinical diagnostic testing for all research and colony animals. This includes complete blood counts, routine chemistry panels, and microbial culture workups. The lab is equipped with Sysmex XN1000v veterinary hematology analyzer, Beckman AU480 chemistry analyzer, and Matrix assisted laser desorption ionization time of flight MALDI-TOF instrument for microbe identification. CPC is staff with American Society of Clinical Pathologist certified licensed Medical Technologists." .
SCR:024610 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2525" ;
rdfs:label "Tulane University TNBRC Unit of Collaborative Research Core Facility" ;
NIFRID:synonym "TNBRC Unit of Collaborative Research",
"Tulane University TNBRC Unit of Collaborative Research" ;
NIFRID:abbrev "UCR" ;
definition: "Core serves as regional and national resource and center of excellence for biomedical research using Nonhuman Primate Models. Unit is staffed by personnel with expertise in veterinary medicine, research study design, budgeting, database management, IACUC issues, sample acquisition, processing, performing laboratory base assays and shipping." .
SCR:024611 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2528" ;
rdfs:label "Tulane University TNBRC Flow Cytometry Core Facility" ;
NIFRID:synonym "TNBRC Flow Cytometry",
"Tulane University TNBRC Flow Cytometry" ;
definition: "Core provides analytical flow cytometry services and live cell sorting under enhanced Biosafety Level 2 conditions. Instruments available include six analyzers ranging from 4-30 color acquisition and three sorters using 1-,2-,4-way, and plate sorting between 6-18 colors. Provides experimental and panel design consultation. Provides continued education in seminar format and one-on-one sessions with user." .
SCR:024612 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2531" ;
rdfs:label "Tulane University TNBRC High Containment Research Performance Core Facility" ;
NIFRID:synonym "TNBRC High Containment Research Performance Core",
"Tulane University TNBRC High Containment Research Performance Core" ;
NIFRID:abbrev "HCRPC" ;
definition: "Provides full or partial support for researchers seeking to perform BSL3 and BSL2/BSL3 Select Agent studies and provides services for bacterial/viral culture and propagation, sample preparation, and processing of blood, BAL, single cell isolation, flow cytometry, and more. Offers project management assistance in study design, budgeting, and IACUC and IBC preparation. Our standard operating procedures have been tested to ensure consistent practices and have undergone rigorous quality assurance processes to ensure reproducibility. Offers assay services for qPCR, O ink Q100, Biorad Bioplex 200, Meso QuickPlex SQ120 Imager and Microscope Axio Observer." .
SCR:024613 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2527" ;
rdfs:label "Tulane University TNBRC Confocal Microscopy and Molecular Pathology Core Facility" ;
NIFRID:synonym "TNBRC Confocal Microscopy and Molecular Pathology Core",
"Tulane University TNBRC Confocal Microscopy and Molecular Pathology Core" ;
NIFRID:abbrev "CMMPC" ;
definition: "Core provides research support and training with molecular pathology skills, confocal microscopy, image analysis, and multicolor immunohistochemistry and in-situ hybridization techniques for internal and affiliate scientists. Services include assistance with experimental design, antibody selection, molecular probe selection, fixation and staining protocols, operating fluorescent and confocal microscopes, acquiring and storing imaging data, interpretation of results, and generation of publication-quality images. Image analysis services include assistance with capturing images for evaluation and with use of various image analysis software." .
SCR:024614 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2524" ;
rdfs:label "Tulane University TNPRC Pathogen Detection and Quantification Core Facility" ;
NIFRID:synonym "TNPRC Pathogen Detection and Quantification Core",
"Tulane University TNPRC Pathogen Detection and Quantification Core" ;
NIFRID:abbrev "PDQC" ;
definition: "THIS RESOURCE IS NO LONGER AVAILABLE. SAME SERVICES ARE AVAILABLE IN Molecular Virology and Sequencing Core. Documented on January 28,2025. Core provides services for maintaining Specific Pathogen Free status in macaque breeding colonies. Services include antibody detection in serum or plasma by Luminex-based assays and /or ELISA for SPF-agents like SIV, SRV, STLV, B virus, SFV. CMV, RRV, SVV, SV40, and LCV, and non-SPF infectious agents like measles, Burkholderia pseudomallei, Tripanosoma cruzi, Mycobacterium tuberculosis, and SARS-CoV-2. Offers services of cytokines quantification, and molecular assays for detection of SRV, CMV, SFV, and RRV.Performs nucleic acid purification from blood and tissue samples as well as qPRC for SIV viral load in plasma, cells, or tissue." .
SCR:024615 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2529" ;
rdfs:label "Tulane University TNBRC Genetics and Genome Banking Core Facility" ;
NIFRID:synonym "TNBRC Genetics and Genome Banking",
"Tulane University TNBRC Genetics and Genome Banking" ;
definition: "Core assists in design of breeding groups and monitors genetic diversity among colony breeding animals. Core is responsible for maintaining genome bank including DNA and cryopreserved primary fibroblast cell lines, including cell lines and DNA samples representing nearly 9,000 animals. Genotype data using NPRC standardized SNP array is available and whole genome sequence is available for over 520 animals. Genomic data is available via mGAP and can be integrated with physical resource and records by contacting the core. Targeted genotyping for new model development and specialized breeding is also available." .
SCR:024626 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRECISE Traumatic Brain Injury Model Catalog" ;
NIFRID:synonym "PRE Clinical Interagency reSearch resourcE Traumatic Brain Injury Model Catalog",
"PRECISE catalog",
"PRECISE TBI Model Catalog",
"PRECISE-TBI",
"PRECISE-TBI Model Catalog" ;
definition: "Platform for preclinical Traumatic Brain Injury model literature metadata. Model catalog to enhance reproducibility of preclinical TBI research by increasing ability to find and access preclinical TBI model papers." .
SCR:024627 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WebProtege" ;
NIFRID:synonym "WebProtégé" ;
definition: "Web based platform for editing biomedical ontologies. Web application for editing OWL 2 ontologies. Open source, lightweight, web based ontology editor implemented in Java and JavaScript using OWL API and Google Web Toolkit. For users who do not wish to host their ontologies on Stanford servers, WebProtégé is available as Web app that can be run locally using Servlet container such as Tomcat." .
SCR:024628 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Injury Knowledge Ontology" ;
NIFRID:synonym "BIKO TBI",
"BIKO Traumatic Brain Injury",
"BIKO-TBI",
"Brain Injury Knowledge Ontology Traumatic Brain Injury" ;
NIFRID:abbrev "BIKO" ;
definition: "Application ontology to formalize concepts and methods used in translational traumatic brain injury research. Multi species translational traumatic brain injury ontology to assist in formalizing concepts and methods used in traumatic brain injury research." .
SCR:024629 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RDFLib" ;
NIFRID:synonym "Resource Description Framework Library" ;
definition: "Software Python library for working with Resource Description Framework. Used for working with RDF which is standard model for data interchange on the Web." .
SCR:024630 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MMV Im2Im" ;
NIFRID:synonym "MMV_Im2Im" ;
definition: "Software Python package for image to image transformation in bioimaging applications. Can be used for semantic segmentation, instance segmentation, image restoration, image generation, and more." .
SCR:024631 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Dementias Platform UK" ;
NIFRID:abbrev "DPUK" ;
definition: "Public-private partnership of universities, charities, and pharmaceutical and technology companies with core funding from Medical Research Council. Based at Oxford University, in the Department of Psychiatry, and have project sites at Swansea University and Cambridge University, we bring together expertise to enable breakthroughs in dementia research." .
SCR:024632 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_465" ;
rdfs:label "Mayo Clinic Medical Genome Core Facility" ;
NIFRID:synonym "Mayo Clinic Medical Genome Facility",
"Medical Genome Facility" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 23,2026. Medical Genome Facility includes Cytogenetics Core, Genome Analysis Core and Proteomics Core. Available services include Sanger DNA sequencing, genotyping, gene expression and cytogenetic analysis, biospecimens accessioning and processing, tissue and cell molecular analysis, RNA interference, and oligonucleotide synthesis. Provides Illumina HiSeq2000 platforms and Pacific Biosciences RS single molecule real-time sequencer.Offers applied research services for development of innovative, personalized tests and treatments, especially with regard to biomarkers." .
SCR:024633 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2534" ;
rdfs:label "State University of Campinas Institute of Chemistry Microscopy Core Facility" ;
NIFRID:synonym "UNICAMP - Institute of Chemistry - Microscopy Core Facility",
"UNICAMP Institute of Chemistry Microscopy Core Facility" ;
definition: "Core offers services in advancing scientific research in the field of chemistry. Provides Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), Confocal Laser Scanning Microscopy (CLSM), and Optical Microscopy. Offers sample preparation techniques, including ultramicrotome, ultracryomicrotome, and sputter coating,training and technical support." .
SCR:024637 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Partnership for Interdisciplinary Studies of Coastal Oceans" ;
NIFRID:synonym "Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO)" ;
NIFRID:abbrev "PISCO" ;
definition: "Academic consortium that conducts research to advance understanding of the coastal ocean within the California Current Large Marine Ecosystem and inform management and policy." .
SCR:024638 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SDSC Center for Applied Internet Data Analysis" ;
NIFRID:synonym "San Diego Supercomputer Center CAIDA" ;
NIFRID:abbrev "SDSC CAIDA" ;
definition: "Center aimes at promoting greater cooperation in engineering and maintenance of global Internet infrastructure, better manage ever increasing volume of digitally based information including security and network data analysis. Provides open access data and tools. " .
SCR:024639 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Center for Effective Global Action" ;
NIFRID:abbrev "CEGA" ;
definition: "Network of world class researchers and innovators to improve lives of people living in poverty by generating insights and tools for decision makers backed by rigorous, inclusive, and transparent research. Hub for research, training and innovation headquartered at University of California, Berkeley." .
SCR:024640 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Triton Shared Computing Cluster" ;
NIFRID:abbrev "TSCC" ;
definition: "Provides advanced computing resources and services to support needs of UC San Diego research community. In addition, researchers from other academic institutions and industries can also participate in this research computing program. TSCC operates on two different computing models – Condo (a system purchase model) and Hotel (a pay-as-you-go model) to support broad range of research computing workloads including traditional HPC, HTC, and emerging big data pipelines." .
SCR:024641 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Project Production Systems Laboratory" ;
NIFRID:synonym "The Project Production Systems Laboratory",
"UC Berkeley Project Production Systems Laboratory" ;
NIFRID:abbrev "P2SL" ;
definition: "Research institute dedicated to developing and deploying knowledge and tools for project management. Projects are temporary production systems. Dedicated to developing and deploying knowledge and tools for management of project production systems and the management of organizations that produce and deliver goods and services through such systems." .
SCR:024642 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UC Berkeley Research IT" ;
definition: "Provides research data and computing technologies, consulting, and community for the UC Berkeley campus to advance research through IT innovation. " .
SCR:024643 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UC Davis eScholarship" ;
definition: "Provides scholarly publishing and repository services that enable departments, research units, publishing programs, and individual scholars associated with University of California to have direct control over creation and dissemination of the full range of their scholarship." .
SCR:024644 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UC Davis Social Science Data Service" ;
NIFRID:synonym "UC Davis Social Science Data Resources" ;
definition: "Portal provides information about social science data." .
SCR:024645 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UC Medical Humanities Consortium" ;
NIFRID:synonym "University of California Medical Humanities Consortium" ;
definition: "Faculty directors from UC Berkeley, UC Davis, UC Irvine, and UCSF support collaborative student research projects, publications, and resources with the aim to have substantial record of achievement and innovation pursued through allocated research funding to support humanism in medicine and health science education." .
SCR:024646 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UC Natural Reserve System" ;
NIFRID:abbrev "UCNRS" ;
definition: "Library of ecosystems throughout California. Most of the state’s major habitat types are represented, from coastal tidepools to inland deserts, and lush wetlands to redwood forests." .
SCR:024647 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "University of California Press" ;
NIFRID:synonym "UC Press" ;
definition: "Publishing house associated with University of California that engages in academic publishing. UC Press Foundation raises funds to uphold vital role as independent, nonprofit publisher, and receives philanthropic support." .
SCR:024648 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCSC Library" ;
NIFRID:synonym "University of California Santa Cruz Library" ;
definition: "Library shares with other academic libraries commitment to intellectual freedom and access to information. This commitment is reflected in open stacks, active interlibrary loan service, online catalog, and Web site linked efficiently to other sites and databases. Has partnerships with libraries at other University of California campuses, local California State Universities, community colleges, and public libraries. Has active participation in California Digital Library." .
SCR:024649 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100000020" ;
rdfs:label "Coastal Data Information Program" ;
NIFRID:synonym "UCSD CDIP" ;
NIFRID:abbrev "CDIP" ;
definition: "Network for monitoring waves and beaches and prediction of waves and shoreline change along coastlines of United States. Since 1975 program has produced database of publicly accessible environmental data for use by coastal engineers and planners, scientists, mariners, and marine enthusiasts. Forefront of coastal monitoring, developing numerous innovations in instrumentation, system control and management, computer hardware and software, field equipment, and installation techniques. Operated by Ocean Engineering Research Group, part of Integrative Oceanography Division at Scripps Institution of Oceanography. CDIP measures, analyzes, archives and disseminates coastal environment data for use by coastal engineers, planners and managers, as well as scientists and mariners." .
SCR:024650 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCSD WIFIRE" ;
NIFRID:synonym "UCSD WIFIRE Lab",
"WIFIRE Lab" ;
definition: "Consortium of UC San Diego organizations and number of partnerships including university collaborators, industry partners, fire departments, utilities, State’s CalOES and CPUC. Develops science driven technologies with fire management community using collaborative workflows integrating science and AI. Provides real time fire modeling and predictions for firefighters. Harnesses emerging AI techniques to offer novel way to approach spatial heterogeneity and upgrading of data." .
SCR:024651 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UC Davis Library" ;
NIFRID:synonym "University of California Davis Library" ;
definition: "Collections include print and ebooks, newspapers, maps, photographs, art, historical archives, and other materials in physical and digital formats. Provides campuswide subscriptions to wide range of licensed resources, from journals and library databases to streaming media, clinical apps, and lab experiment videos. Offers access to UC collection as part of University of California." .
SCR:024652 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2535" ;
rdfs:label "New York Institute of Technology NYIT Visualization Center Core Facility" ;
NIFRID:synonym "New York Institute of Technology NYIT Visualization Center",
"NYIT Visualization Center" ;
definition: "Core provides instruments including micro-computed tomography scanner, non-contact 3D optical profiler , and high powered workstations." .
SCR:024653 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2536" ;
rdfs:label "Broad Institute Imaging Platform Core Facility" ;
NIFRID:synonym "Broad Institute Broad Institute Imaging Platform",
"Broad Institute Imaging Platform" ;
definition: "Core to help users turn images into answers by offering assistance and training with open source image analysis tools, creating custom image analysis workflows, and creating custom software for image analysis when needed." .
SCR:024654 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyEGA" ;
NIFRID:synonym "Python European Genome-phenome Archive" ;
definition: "Software Python tool for viewing and downloading files from authorized European Genome-phenome Archive datasets. Python based EGA download client." .
SCR:024655 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2537" ;
rdfs:label "University of Connecticut Health Center for Cell Analysis and Modeling Microscopy Core Facility" ;
NIFRID:synonym "CCAM Microscopy Facility",
"CCAM-Microscopy",
"UConn Health CCAM Microscopy Facility",
"University of Connecticut Health Center CCAM-Microscopy" ;
definition: "CCAM Microscopy Facility provides access to equipment for quantitative fluorescence imaging applications. Instruments include laser scanning confocal microscopes equipped with 34 channel highefficiency QUASAR detectors. One of these microscopes supports nonlinear optical excitation, fluorescence correlation spectroscopy, and fluorescence lifetime imaging microscopy. Additionally, there is a light sheet microscope available for micro/mesoscale 3D imaging. The Zeiss Elyra 7 microscope is capable of total internal reflection fluorescence microscopy and supports several super resolution techniques such as lattice structured illumination microscopy, stochastic optical reconstruction microscopy, 3D photoactivated localization microscopy, and DNA points accumulation for imaging in nanoscale topography." .
SCR:024656 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ATAC Pipeline" ;
NIFRID:synonym "ATAC",
"atac",
"atac pipeline" ;
definition: "Software open-source, cloud-optimized pipeline developed in collaboration with members of the BRAIN Initiative (BICCN and BICAN Sequencing Working Group) and SCORCH. It supports the processing of 10x single-nucleus data generated with 10x Multiome ATAC-seq (Assay for Transposase-Accessible Chromatin), a technique used in molecular biology to assess genome-wide chromatin accessibility." .
SCR:024657 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LMD7" ;
rdfs:label "Leica | LMD7 Laser Microdissection microscope" ;
NIFRID:synonym "Leica LMD7" ;
definition: "Laser Microdissection system enables users to isolate specific single cells or entire areas of tissue. Powered by unique laser design and dynamic software, Leica LMD systems allow users to easily isolate Regions of Interest from entire areas of tissue down to single cells or even subcellular structures such as chromosomes. LMD7 provides higher laser power. Suited to dissect any kind of tissue independent of its size or shape." .
SCR:024658 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LMD6" ;
rdfs:label "Leica | LMD6 Laser Microdissection microscope" ;
NIFRID:synonym "Leica LMD6" ;
definition: "Laser Microdissection system enables users to isolate specific single cells or entire areas of tissue. Powered by unique laser design and dynamic software, Leica LMD systems allow users to easily isolate Regions of Interest from entire areas of tissue down to single cells or even subcellular structures such as chromosomes. Leica LMD6 is for standard tissue dissection. Used for standard applications dissecting soft tissues such as brain, liver, or kidney." .
SCR:024659 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_STELLARIS 8 DIVE" ;
rdfs:label "Leica | STELLARIS 8 DIVE multiphoton microscope" ;
NIFRID:synonym "Leica STELLARIS 8 DIVE" ;
definition: "Multiphoton microscope provides flexible multicolor imaging beyond 1 mm in depth with spectrally tunable non-descanned detector to define up to four detection bands simultaneously or unlimited number when imaged sequentially. Possible fluorophore combinations to study complex processes, such as neuronal connectivity, organ structure, dynamic interactions, or spatial relationships of cells and proteins in much more detail." .
SCR:024660 a "Microscope, functional imaging, investigate cellular physiology,dynamics in living cells, video rate lifetime imaging acquisition,",
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ STELLARIS 8 FALCON FLIM" ;
rdfs:label "Leica | STELLARIS 8 FALCON FLIM microscope" ;
NIFRID:synonym "STELLARIS 8 FALCON FLIM Microscope",
"STELLARIS 8 FAst Lifetime CONtrast Fluorescence Lifetime Imaging Microscope" ;
definition: "Microscope for functional imaging. Used to investigate cellular physiology and to explore dynamics in living cells. Enables video rate lifetime imaging acquisition for rapid kinetic studies in live cells. Adds new dimension of contrast to imaging for biosensing and tracking of interactions between proteins." .
SCR:024661 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_STELLARIS 8 CRS" ;
rdfs:label "Leica | STELLARIS 8 CRS microscope" ;
NIFRID:synonym "Leica STELLARIS 8 CRS Coherent Raman Scattering microscope",
"STELLARIS 8 CRS Coherent Raman Scattering microscope" ;
definition: "Microscope enables to implement label free chemical imaging. Used to study structures that cannot be visualized with traditional fluorescent microscopy methods." .
SCR:024662 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_STELLARIS 8 STED" ;
rdfs:label "Leica | STELLARIS 8 STED microscope" ;
NIFRID:synonym "Leica STELLARIS 8 Stimulated Emission Depletion microscope" ;
definition: "Microscope for imaging beyond the diffraction limit to obtain 2D and 3D nanoscopy results in no time with astounding image quality and resolution, while protecting sample. STED super resolution allows you to study multiple dynamic events simultaneously." .
SCR:024663 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_STELLARIS 5" ;
rdfs:label "Leica | STELLARIS 5 microscope" ;
definition: "STELLARIS 5 microscope has core system with integrated WLL, combined with proprietary Acousto-Optical Beam Splitter and Power HyD S detectors. Together with the TauSense technology, STELLARIS 5 sets a new standard for the quality of images and quantity of information generated. Imaging with user interface, ImageCompass." .
SCR:024664 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_STELLARIS 8" ;
rdfs:label "Leica | STELLARIS 8 microscope" ;
definition: "STELLARIS 8 microscope with core system addition of spectrum WLL and specialized detector options of Power HyD family to expand range of confocal applications. Can be combined with all Leica Microsystems modalities, including FAst Lifetime CONtrast (FALCON), Deep In Vivo Explorer (DIVE), STED, Digital Light Sheet (DLS) and CARS. STELLARIS 8 new features maximize the potential of these modalities." .
SCR:024665 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Noraxon myoMuscle" ;
NIFRID:synonym "myoMuscle",
"Noraxon myoMuscle software" ;
definition: "Software tool for analyzing kinesiological data obtained from Noraxon Ultium EMG system, as well as older Noraxon legacy electromyography systems. Enables detailed insight for performance enhancement, injury prevention, and neuromuscular biofeedback." .
SCR:024666 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Artinis Medical Systems Oxysoft" ;
definition: "Software application used to collect, store, view, and analyse all necessary data from the Brite Family devices, PortaMon, PortaLite, OctaMon and OxyMon developed by Artinis Medical Systems and highly customisable to individual requirements." .
SCR:024667 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Wattbike Expert" ;
definition: "Software to scientifically analyse Wattbike sessions on Windows PC or Laptop, while Power Cycling is perfect for group training in health clubs and gyms." .
SCR:024668 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multitron | Incubation Shaker" ;
NIFRID:synonym "Multitron Standard Incubation Shaker" ;
definition: "Shaker for cultivation of microorganisms and cell cultures provides homogeneous conditions for cultivation up to 63 liters or 23 000 batches in parallel in less than square meter of space." .
SCR:024669 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Climate engine" ;
definition: "Climate Engine App is no-code solution for on-demand cloud computing and visualization of climate and satellite Earth Observation data. Provides rainfall, maximum and minimum temperature daily data." .
SCR:024670 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Franklin" ;
definition: "Connectivity hub across medical genetics domain. Network of genomic information. Supports all vendors and workflows and thus enables any genetic professional to deliver more accurate, more actionable data insights." .
SCR:024671 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_STELLARIS 5 Cryo" ;
rdfs:label "Leica | STELLARIS 5 Cryo Confocal Light Microscope" ;
NIFRID:synonym "STELLARIS 5 Cryo",
"STELLARIS 5 Cryo Confocal Light Microscope" ;
definition: "Confocal light microscope system to target area of interest for cryo-electron tomography." .
SCR:024672 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MapMyCells" ;
NIFRID:synonym "Allen MapMyCells",
"Map My Cells" ;
definition: "MapMyCells maps single cell and spatial transcriptomics data sets to massive, high-quality, and high-resolution cell type taxonomies. It enables speeding up the creation of brain reference atlases by facilitating the integration of datasets from the scientific community with a shared reference. MapMyCells is part of the growing Brain Knowledge Platform. Its key advantage is scale: researchers can provide up to 327 million cell-gene pairs from their own data, a huge leap forward for working with whole-brain datasets. Allen Institute and its collaborators continue to add new reference taxonomies and algorithms to MapMyCells." .
SCR:024673 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Instant Clue" ;
definition: "Software suite for interactive data visualization and analysis. Python based desktop application using PyQt6 library for data visualization and analysis." .
SCR:024674 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SlicerMorph" ;
definition: "Open and extensible platform to retrieve, visualize and analyse 3D morphology.Extension to import microCT data and conduct 3D morphometrics in Slicer. Used for data import, visualization, measurement, annotation, and geometric morphometric analysis on 3D data, including volumetric scans (CTs and MRs) and 3D surface scans, all within the 3D Slicer application." .
SCR:024675 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scCustomize" ;
definition: "Software R package for custom visualizations and functions for streamlined analyses of single cell sequencing." .
SCR:024676 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NovoExpress" ;
NIFRID:synonym "Agilent NovoExpress",
"NovoExpress flow cytometry software",
"NovoExpress version 1.6.2" ;
definition: "NovoExpress software enables sample acquisition and analysis. User hands-on time is minimized with the walk-away autosampler functionality as well as batch analysis, statistics, and reporting." .
SCR:024677 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2540" ;
rdfs:label "University of Massachusetts Lowell Microscopy Core Facility" ;
NIFRID:synonym "UML - Microscopy Core Lab",
"University of Massachusetts Lowell UML - Microscopy Core Lab" ;
NIFRID:abbrev "MCL" ;
definition: "Core offers micro-imaging and micro-analysis solutions by providing access to several photon-, scanned probe-, ion beam-, and electron beam-based imaging and analytical instruments, services, and technical expertise for characterization of materials including nano-engineered materials, microelectronics, photonics, biomaterials, and others with applications in life sciences, drug discovery, environmental and energy research. Consultative services are also available." .
SCR:024678 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2541" ;
rdfs:label "Seattle Children's Research Institute Micro Computed Tomography Imaging and Visualization Lab Core Facility" ;
NIFRID:synonym "SCRI Micro Computed Tomography Imaging and Visualization Lab" ;
definition: "Shared instrument facility that has a Bruker Skyscan 1272 ex-vivo microCT that is capable of X-ray imaging at sub-microb resolution. The instrument can optionally be equipped with a 16-sample sample changer to automate the scanning queue. Core provides visualization and image analysis support for researchers, using open-source 3D Slicer biomedical imaging suite." .
SCR:024679 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2543" ;
rdfs:label "Tulane University TNPRC Virus Characterization, Isolation, Production and Sequencing Core Facility" ;
NIFRID:synonym "Isolation",
"Production and Sequencing Core",
"TNPRC Virus Characterization",
"Tulane University TNPRC Virus Characterization" ;
definition: "THIS RESOURCE IS NO LONGER AVAILABLE. SAME SERVICES ARE AVAILABLE IN Molecular Virology and Sequencing Core. Documented on January 28, 2025. Core is divided into virus characterization, isolation, and production part and next generation sequencing part. Virus Characterization, Isolation and Production component provides virus expansion and characterization, viral titer by plaque and TCID50 assays, live virus neutralization and inhibition assays at both BSL-2 and -3 level including SARS-CoV-2. Next Generation Sequencing component provides expertise in next generation sequencing and genomic services including whole genome, epigenetics, targeted amplicons, and 16S metagenomics." .
SCR:024680 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2542" ;
rdfs:label "Tulane University TNBRC Vector Borne Infectious Disease and Diagnostic Parasitology Core Facility" ;
NIFRID:synonym "TNBRC Vector-Borne Infectious Disease and Diagnostic Parasitology Core",
"Tulane University TNPRC Vector Borne Infectious Disease and Diagnostic Parasitology Core",
"Tulane University TNPRC Vector-Borne Infectious Disease and Diagnostic Parasitology Core",
"Tulane University Tulane National Biomedical Research Center Vector Borne Infectious Disease and Diagnostic Parasitology Core",
"Vector-Borne Infectious Disease and Diagnostic Parasitology" ;
NIFRID:abbrev "VIDDP" ;
definition: "Vector Borne Infectious Disease core produces tick vectors for research on Lyme disease and other tick borne diseases. Diagnostic Parasitology component provides diagnostic services to clinical veterinarians and core and affiliate investigators when parasitic diseases are suspected in resident nonhuman primates. Services for affiliate investigators include blood parasite detection via microscopic examination of prepared blood smears and quantitative buffy-coat analysis, and intestinal parasite detection via microscopic examination of direct wet mounts, zinc sulfate flotation prepared slides, or parasite specific assays." .
SCR:024681 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyPOLAR" ;
definition: "Software Python based app for analyzing polarization resolved microscopy data to measure molecular orientation and order in biological samples." .
SCR:024682 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PERFect" ;
NIFRID:synonym "Permutation Filtering Package in R" ;
definition: "Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering." .
SCR:024683 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "corrplot" ;
definition: "Software R package as visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.Used for graphical display of correlation matrix, confidence interval. Contains some algorithms to do matrix reordering. Good at details, including choosing color, text labels, color labels, layout, etc." .
SCR:024684 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIMP: Neuroanatomy-anchored Information Management Platform for Collaborative BICAN Data Generation" ;
NIFRID:synonym "BICAN Specimen Portal" ;
NIFRID:abbrev "NIMP" ;
definition: """Web application that tracks the status of the BICAN consortium tissue samples and related data.NIMP is developed under NIH BRAIN Initiative's BICAN U24MH130988 award as a part of the coordinating unit for biostatistics, informatics, and engagement (CUBIE) for the BRAIN Initiative Cell Atlas Network (BICAN) program.NIMP consists of two portals for BICAN collaborative data generation: the Specimen Portal and the Sequence Library (SeqLib) Portal. The Specimen Portal focuses on tissue management from donors to brain slabs and annotated brain samples. The SeqLib Portal manages the workflow starting from tissue, all the way downstream to track data deposition to assay-dependent, data-modality-specific archives. Both portals work in tandem to generate multimodal genomic data that can be traced back to their anatomical origins using the Allen Brain Atlas.
The portals provide multiple types of data interfaces through dashboards, APIs, faceted queries, and batch data ingestion and exporting. All of the underlying functionalities are achieved through a robust agile development strategy using NHash resource identifiers, metadata standardization, active combinatorial dashboarding, resource provenance linkage and rendering (e.g. Sankey diagrams), and dedicated interfaces with NIH Neuro Biobank, sequencing centers, NeMO, and the larger BICAN data ecosystem.""" .
SCR:024685 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCI SEER Cancer Statistics Review" ;
NIFRID:synonym "and End Results Cancer Statistics Review",
"Epidemiology",
"National Cancer Institute SEER Cancer Statistics Review",
"NIH NCI SEER Cancer Statistics Review",
"NIH NCI Surveillance",
"SEER Cancer Statistics Review" ;
definition: "Platform to report outlining trends in cancer statistics and methods to derive various cancer statistics from the Surveillance, Epidemiology, and End Results (SEER) program. Authoritative source for cancer statistics in the United States." .
SCR:024686 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCI Lymphoid Neoplasm Recode 2020 Revision Definition" ;
NIFRID:synonym "Lymphoid Neoplasm Recode 2020 Revision Definition",
"National Cancer Institute Lymphoid Neoplasm Recode 2020 Revision Definition",
"NIH NCI Lymphoid Neoplasm Recode 2020 Revision Definition" ;
definition: "Website describing International Classification of Diseases codes that corresponds to lymphomas in the Surveillance, Epidemiology, and End Results (SEER) registry." .
SCR:024687 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCI Site Recode ICD-O-3/WHO 2008 Definition" ;
NIFRID:synonym "National Cancer Institute Site Recode ICD-O-3/WHO 2008 Definition" ;
definition: "Website describing International Classification of Diseases-Oncology codes that corresponds to different cancer sites in the Surveillance, Epidemiology, and End Results (SEER) registry." .
SCR:024688 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MEBOCOST" ;
definition: "Software Python package to predict metabolite mediated cell-cell communications by single-cell RNA-seq data. Used for inferring metabolite, such as lipid, mediated cell-cell communication events using single-cell RNA-seq data." .
SCR:024689 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Planet Labs PBC API" ;
NIFRID:synonym "PLANET APIS" ;
definition: "Portal provides everything needed to start using Planet services. Planet Application Program Interface to retrieve Planet Labs PBC's satellite images and products." .
SCR:024690 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepGOPlus " ;
definition: "Software application for predicting protein functions from protein sequences using deep neural networks combined with sequence similarity based predictions." .
SCR:024691 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "getorf" ;
NIFRID:synonym "EMBOSS getorf" ;
definition: "Web application to find and extract open reading frames (ORFs). Used to find and output sequences of open reading frames in one or more nucleotide sequences." .
SCR:024692 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dbEMT 2" ;
NIFRID:synonym "dbEMT2.0",
"Epithelial Mesenchymal Transition Gene database" ;
definition: "Database to establish comprehnsive gene resource for epithelial-mesenchymal transition." .
SCR:024693 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SimpleITK" ;
NIFRID:synonym "Simple Insight Segmentation and Registration Toolkit" ;
definition: "Open source software library for multi dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++. New interface to Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. Provides easy to use and simplified interface to ITK's algorithms." .
SCR:024694 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "qmazda" ;
definition: "Software package for digital image analysis. Used to search for optimal methods for image classification and segmentation. Computes shape, color and texture descriptors of arbitrary regions of interest. Color analysis includes RGB, CMY, HSY, YIQ, YUV, CIELab and CIEXYZ models. Texture feature extraction algorithms include co-occurrence matrix, run-length matrix, autoregression model, brightness distribution statistics, local binary patterns, histogram of oriented gradients, Haar and Gabor transforms. Enables calculation of morphological features such as moments of inertia, Feret diameters, ratios of Danielson, Blair-Bliss or Malinowska, and many others. Implements algorithms of discriminant analysis and data classification such as linear discriminant analysis, mutual information, convex decision boundary and support vector machines." .
SCR:024695 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Noldus | Erasmus Ladder" ;
NIFRID:synonym "Erasmus Ladder" ;
definition: "System consists of hardware and software for assessment of motor performance and motor learning in mice. Hardware includes two goal boxes with horizontal ladder in between. Touch sensitive rungs of the ladder make it possible to measure step durations and step types. ErasmusLadder software controls experiments by sending protocol and start command to apparatus. Sessions are performed automatically, and afterwards, data is sent back to software for storage and analysis." .
SCR:024696 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Noldus | PhenoTyper" ;
NIFRID:synonym "PhenoTyper" ;
definition: """System designed to facilitate behavioral observations in home cage environment. Instrumented observation cage to measure and test behavior of laboratory rodents.
Device comes with PhenoTyper top unit which included lighting and camera, both powered by EthoVision XT, and range of optional sensors and stimuli.""" .
SCR:024697 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Focinator" ;
NIFRID:synonym "Focinator V2" ;
definition: "Open source software tool providing automated analysis of foci images including foci counting and colocalization of foci. Focinator v2-0 is able to perform multi channel analysis of four channels and evaluation of protein-protein colocalization by comparison of up to three foci channels. This enables for example the quantification of foci in cells of specific cell cycle phase." .
SCR:024698 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pyradigm" ;
definition: "Software Python package to arbitrarily combine and subset datasets, while ensuring dataset integrity and automatically updating their description and other provenance for neuroscience and neuroimaging applications where each sample needs to be uniquely identified . Container data structure to encapsulate machine learning dataset with all the key info necessary." .
SCR:024699 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "microbiome" ;
definition: "Software R package for use in microbiome analysis. Used to provide comprehensive collection of tools and tutorials, with particular focus on amplicon sequencing data." .
SCR:024700 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Center for Sudden Unexpected Death in Epilepsy Research",
"Center for SUDEP Research" ;
definition: "NIH funded center to provide system for sharing multimodal epilepsy data for Sudden Unexpected Death in Epilepsy. Modality Epilepsy Data Capture and Integration System (MEDCIS) is cross cohort query interface for SUDEP (Sudden Unexpected Death in EPilepsy) research." .
SCR:024701 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rpy2" ;
definition: "Software interface to use R from Python." .
SCR:024702 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "httk" ;
NIFRID:abbrev "high throughput toxicokinetics" ;
definition: "Software R package for high-throughput toxicokinetics. Pre-made models that can be rapidly tailored to various chemicals and species using chemical specific in vitro data and physiological information. Used for prediction toxicokinetics (chemical absorption, distribution, metabolism, and excretion by the body)." .
SCR:024703 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Expasy Translate " ;
NIFRID:synonym "Translate" ;
definition: "Web tool for translation of nucleotide sequence to protein sequence." .
SCR:024704 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ensembl Covid-19" ;
definition: "Ensembl SARS-Cov2 data portal." .
SCR:024706 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss | Axio Imager M2" ;
NIFRID:synonym "Axio Imager M2" ;
definition: "Upright microscope platform for Life Science Research. System platform tailored to materials analysis tasks. System features include Universal stand transmitted-light; Motorized: luminous field stop; Light manager;Contrast manager; Motorized z-drive with 25nm step size; Reflected-light beam path; ACR for objectives; Apotome 3; 2- und 3-plate scanning stages; 2 TV tube motorized; Automatic image acquisition and analysis; 3D Imaging; Medium sample throughput; Multi-user environment." .
SCR:024707 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Narishige_IM-300" ;
rdfs:label "Narishige | IM-300 Microinjector" ;
NIFRID:synonym "IM-300 Microinjector" ;
definition: "Electrically controlled pneumatic microinjector designed to deliver and aspirate extremely small, precise volumes of liquid or gas (picoliters to microliters). It is primarily used in biological and medical research labs for microinjection into cells, transgenic organism creation, and patchingMulti-functional, motor-driven injector for precise control of small volumes." .
SCR:024708 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | Angle Two Computer Assisted Stereotaxic System" ;
NIFRID:synonym "Angle Two™ system",
"Leica Angle Two™ Computer-Assisted Stereotaxic System" ;
definition: "System used for stereotaxic surgery on small animals (mice and rats)." .
SCR:024709 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CM120" ;
rdfs:label "Philips | FEI CM120 BioTwin Transmission Electron Microscope" ;
NIFRID:synonym "FEI CM120 Biotwin",
"FEI/PHILIPS CM120 TEM",
"Philips CM120 Biotwin Lens",
"Philips/FEI CM120 Bio Twin Transmission Electron Microscope" ;
definition: "Transmission electron microscope with maximum acceleration voltage of 120 kv.Microscope primarily used for sample screening." .
SCR:024710 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SFX250" ;
rdfs:label "Emerson | Branson Digital Sonifier SFX250" ;
NIFRID:synonym "Branson Digital Sonifier" ;
definition: "Branson Sonifier ultrasonic cell disruptor / homogenizers are versatile laboratory units suitable for broad range of liquid processing applications. Digital sonifier to disrupt cells, bacteria, spores, or tissue. Ideal for initiating and accelerating chemical, biochemical, and physical reactions, and for degassing liquids. Used to prepare emulsion to 0.01 micron, homogenize immiscible liquids, polymerize some materials, and depolymerize others." .
SCR:024711 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2545" ;
rdfs:label "University of Nebraska Lincoln Flow Cytometry Core Facility" ;
NIFRID:synonym "Flow Cytometry Core Facility" ;
definition: "Provides flow cytometry services. Instruments include Beckman Coulter CytoFLEX SRT sorter and CytoFLEX LX, as well as NanoAnalyzer from NanoFCM. Facility staff are able to assist with everything from experimental design, instrument training, sample collection, and data analysis." .
SCR:024712 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sample specific miRNA regulation" ;
NIFRID:synonym "Sample-specific miRNA regulation (Scan)" ;
NIFRID:abbrev "Scan" ;
definition: "Software application for scanning sample specific miRNA regulation from bulk and single cell RNA sequencing data." .
SCR:024713 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "microbeMASST" ;
definition: "Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns." .
SCR:024715 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SwinT-fairSIM" ;
definition: "This repository contain the source code for the denoising of SR-SIM images." .
SCR:024716 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Machine Learning Cumulative Performance Score for Classification Problems" ;
NIFRID:synonym "MLcps: Machine Learning Cumulative Performance Score for Classification Problems" ;
NIFRID:abbrev "MLcps" ;
definition: "Machine Learning Cumulative Performance Score (MLcps), a novel evaluation metric for classification problems. MLcps integrates several pre-computed evaluation metrics into a unified score, enabling a comprehensive assessment of the trained model's strengths and weaknesses. We tested MLcps on four publicly available datasets, and the results demonstrate that MLcps provides a holistic evaluation of the model's robustness, ensuring a thorough understanding of its overall performance." .
SCR:024718 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ToxCodAn-Genome" ;
definition: "ToxCodAn-Genome is a computational tool designed to annotate toxin genes in genomes of venomous lineages." .
SCR:024719 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "X-omics ACTION demonstrator multi-omics analysis workflow" ;
definition: "Software application as multi-omics data analysis workflow. Comprises genome-wide DNA methylation, targeted metabolomics and behaviour data pre-processing, and integrative analysis methods. Individuals of a cohort are clustered using Similarity Network Fusion (SNF), latent feature dimensions are uncovered using different unsupervised methods including Multi-Omics Factor Analysis (MOFA) and Multiple Correspondence Analysis (MCA), and correlations between -omics and phenotype dimensions are determined in downstream analyses including results visualisation." .
SCR:024720 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vulture" ;
definition: "Software scalable cloud based pipeline that performs microbial calling for single cell RNA sequencing data, enabling meta analysis of the single cell host microbial studies from AWS Open Data and other public domain." .
SCR:024721 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pep2TCR" ;
definition: "Web tool for CD4 TCR specificity prediction and biology applications. Used for accurate prediction of CD4 T cell receptor binding specificity through transfer learning and ensemble approach. Repository comprises codes of Pep2TCR, providing comprehensive guidance for researchers interested in Pep2TCR." .
SCR:024722 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TheBehaviourForum.org" ;
definition: "Portal for discussion of scientific matters relating to use of home cages to behavioural research in laboratory animals, including experimental procedures, use of equipment, problem solving, ethical considerations, job offers and advertisement of community events." .
SCR:024723 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2553" ;
rdfs:label "University of Chicago MRI Research Center Core Facility" ;
NIFRID:synonym "University of Chicago MRI Research Center" ;
definition: "MRI Research Center houses magnetic resonance scanners and highly qualified experienced staff for support of research projects with MR imaging component." .
SCR:024724 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DSCompare" ;
definition: "Software tool that analyzes, compares and validates analysis and reanalysis datasets with observed dataset using statistical tests such as Mann Whitney (U-test), t-test, F-test, Root Mean Square Error (RMSE), correlation coefficient, BIAS, normalized BIAS, trend, scatter index and maximum anomalies." .
SCR:024725 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Early Postnatal Developmental Mouse Brain Atlas" ;
NIFRID:abbrev "epDevAtlas" ;
definition: "Suite of open access resources including 3D atlases of early postnatally developing mouse brain and mapped cell type density growth charts, which can be used as standalone resources or to implement data integration. Web platform can be utilized to analyze and visualize the spatiotemporal growth of GABAergic, microglial, and cortical layer-specific cell type densities in 3D. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system with an isotropic resolution of 20 μm (XYZ in coronal plane). Average transformations were conducted at 20 μm voxel resolution by interpolating high resolution serial two photon tomography images from primarily Vip-IRES-Cre;Ai14 mice at postnatal (P) ages P4, P6, P8, P10, P12, and P14. For all ages, anatomical labels from the P56 Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) were iteratively down registered to each early postnatal time point in a non-linear manner, aided by manual parcellations of landmarks in 3D, consistent with the Allen Mouse Reference Atlas Ontology." .
SCR:024726 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IKA | MTS 2/4 digital microtiter shaker" ;
NIFRID:synonym "MTS 2/4 digital microtiter shaker" ;
definition: "Special orbital shaker for shaking two or four microtiter plates." .
SCR:024727 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "American Community Survey" ;
NIFRID:abbrev "ACS" ;
definition: "American Community Survey is annual demographics survey program conducted by the U.S. Census Bureau. American Community Survey releases new data every year through variety of data tables. Provides information about other special datasets, such as the ACS Experimental Data, ACS Summary File, and ACS Public Use Microdata Sample files." .
SCR:024728 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hematological Malignancy Research Network" ;
NIFRID:abbrev "HMRN" ;
definition: "Network provides information about leukaemias, lymphomas, myelomas, and related blood disorders. The statistics are based on data from the UK, and use the World Health Organization’s Classification for Oncology (ICD-O-3) which currently recognises over 100 different haematological malignancy subtypes." .
SCR:024729 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dynamic Functional Connectivity" ;
NIFRID:abbrev "dFC",
"pydfc" ;
definition: "Open source Python toolbox that facilitates the implementation of multi analysis dynamic Functional Connectivity assessment using MRI data." .
SCR:024730 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.184764.8; ISNI 0000 0001 0670 228X; Crossref Funder ID 100007233; Wikidata Q891082;" ;
rdfs:label "Boise State University; Idaho; USA" ;
definition: "Public research university in Boise, Idaho. Founded in 1932 by the Episcopal Church, it became independent junior college in 1934 and has been awarding baccalaureate and masters degrees since 1965. It became public institution in 1969." .
SCR:024731 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tractor" ;
NIFRID:synonym "Tractor - Local Ancestry Aware GWAS" ;
definition: "Software tool to enhance Genome Wide Association Studies for diverse cohorts by addressing challenges associated with analyzing admixed populations. Admixed populations are often excluded from genomic studies due to concerns about how to properly account for their complex ancestry.Tractor facilitates the inclusion of admixed individuals in association studies by leveraging local ancestry, allowing for finer resolution in controlling for ancestry in GWAS, and empowering identification of ancestry-specific loci." .
SCR:024732 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rare and Atypical Diabetes Network" ;
NIFRID:synonym "Rare and Atypical DIAbetes NeTwork" ;
NIFRID:abbrev "RADIANT" ;
definition: "Portal dedicated to characterizing, discovering and defining rare and atypical forms of diabetes. Network of universities, hospitals and clinics across the United States dedicated to better understanding atypical diabetes. Team of academic institutions and scientists collaborates with physicians and healthcare groups to identify those with atypical diabetes and learn more about their health." .
SCR:024733 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2547" ;
rdfs:label "Boise State University Fabrication, Characterization, and Testing Core Facility" ;
NIFRID:synonym "Boise State University BSU FaCT Core",
"BSU FaCT Core" ;
NIFRID:abbrev "FaCT" ;
definition: "Core contains instrumentation and expertise for fabrication, characterization, and testing of biomedical devices, sensors, and systems. Core administratively combines 4 existing engineering cores: the Idaho Microfabrication Laboratory (IML); Boise State Center for Materials Characterization (BSCMC); Research Machining and Engineering (RME) center; and Biomechanics and Mechanobiology (BMMB) facility.Offers variety of instruments including 3D printers, deposition and photolithography tools, profilometers, SEM, TEM, light microscopy, confocal microscopy, cell culture. Offers services including design, machining, imaging, etc." .
SCR:024734 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2548" ;
rdfs:label "University of Massachusetts Lowell Nanofabrication Lab Core Facility" ;
NIFRID:synonym "UML - Nanofabrication Lab",
"University of Massachusetts Lowell UML - Nanofabrication Lab" ;
definition: "Core features 4,200 ft2 Class 100 clean room equipped with over 40 pieces of process and analytical instrumentation for complex research projects that require micro and nano scale fabrication." .
SCR:024735 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2549" ;
rdfs:label "University of Pennsylvania Bollinger Digital Fabrication Laboratory Core Facility" ;
NIFRID:synonym "Bollinger Digital Fabrication Lab",
"University of Pennsylvania UPenn-Bollinger Digital Fabrication Laboratory",
"UPenn-Bollinger Digital Fabrication Laboratory" ;
definition: "Provides fabrication services and consultations contributing to innovation in teaching, learning, research, and clinical care at the University of Pennsylvania." .
SCR:024736 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford Cryo-Electron Microscopy Center Core Facility" ;
NIFRID:synonym "Stanford Cryo-Electron Microscopy Center",
"Stanford Cryo-Electron Microscopy Center (cEMc)" ;
NIFRID:abbrev "cEMc" ;
definition: "Core enables macromolecular structure determination, mechanistic investigations, and drug discovery through cryo-electron microscopy. Services include High-resolution data collection for single-particle analysis (SPA), soft-matter research, and tomography; High-throughput cryo sample screening and collection of diagnostic small data sets; Screening negatively stained samples; Training and various levels of assistance for diverse experimental designs, including sample preparation, negative stain screening, and equipment operation; Full-service option for screening and data collection." .
SCR:024737 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NuAire | Laminar Flow Hood" ;
NIFRID:synonym "Laminar Flow Hood" ;
definition: """Laminar Flow Hood offer ISO Class 5 clean air product protection for USP 797 sterile non-hazardous drug compounding applications in pharmacy, microbiology labs, and agricultural research. Hood can be used where clean airflow per ISO 14644-1 is required to prepare injectable drugs, IV solutions, tissue culture, optics, microelectronics, and more.
All workstations use ultra high efficiency motor to provide robust 90 FPM (0,46 m/s) laminar flow of HEPA filtered air to work zone composed of stainless steel walls and work surface made of stainless steel on PVC core.""" .
SCR:024739 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "org.Hs.eg.db" ;
definition: "Software R package as object for simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to all possible GenBank accession numbers." .
SCR:024740 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Orthology.eg.db" ;
definition: "Software R package to provide orthology mappings between species, based on NCBI Gene IDs and NCBI orthology mappings." .
SCR:024741 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LinearSVC" ;
NIFRID:synonym "Linear Support Vector Classification" ;
definition: "Software application for linear support vector classification. Used in classification problems." .
SCR:024742 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SingleCellNet" ;
definition: "Software tool to classify single cell RNA-Seq data across platforms and across species." .
SCR:024743 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciBet" ;
definition: "Software tool as supervised cell type identifier that accurately predicts cell identity for newly sequenced single cells." .
SCR:024744 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Parsnip" ;
definition: "Software R package to create and manipulate functions commonly used during modeling e.g. fitting the model, making predictions, etc." .
SCR:024745 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IFNepitope" ;
definition: "Web server for predicting and designing interferon gamma inducing epitopes. Users are allowed to paste or upload file with multiple peptide sequences and each sequence would be predicted according to model selected. Used to predict IFN-gamma inducing peptide/epitope in set of peptides or peptide library." .
SCR:024746 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IL-10Pred" ;
definition: "Web server to predict IL-10 inducing peptides, where users are allowed to paste or upload file with multiple peptide sequences and each sequence would be predicted according to model selected. Used to design, discover and mapping of peptides that may induce IL-10." .
SCR:024747 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Deep Learning Toolbox" ;
definition: "Software application provides simple MATLAB commands for creating and interconnecting layers of deep neural network." .
SCR:024748 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2554" ;
rdfs:label "University of Calgary Live Cell Imaging Laboratory Core Facility" ;
NIFRID:synonym "Snyder Institute- Live Cell Imaging Laboratory",
"University of Calgary Snyder Institute- Live Cell Imaging Laboratory" ;
NIFRID:abbrev "LCI" ;
definition: "Offers advanced imaging technology, as well as training and support personalized to their imaging goals and experience. Provides Technology access and training; Assisted imaging and coaching at every step of the imaging workflow, from sample preparation to data analysis; Pilot experiments and feasibility testing; Developing custom image analysis pipelines; Image analysis consultation and training; Developing and testing new instruments and devices; Full scientific and technological collaborations and partnerships; Offsite coaching, assistance and consulting ; Collaborative projects in academic, health and allied industrial sectors;" .
SCR:024749 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2550" ;
rdfs:label "University of Maryland School of Medicine Translational Genomics Laboratory Core Facility" ;
NIFRID:synonym "UMSOM-Translational Genomics Laboratory (TGL)",
"University of Maryland Medical Center Midtown Campus Translational Genomics Laboratory",
"University of Maryland Medical Center Midtown Campus Translational Genomics Laboratory Core Facility",
"University of Maryland Medical Center Midtown Campus UMSOM-Translational Genomics Laboratory (TGL)",
"University of Maryland Medical Center Translational Genomics Laboratory" ;
NIFRID:abbrev "TGL" ;
definition: "Core provides range of genomics technologies to support basic, translational, and clinical research.Services support basic research. Clinical assays offered are similar to those offered to support basic research, except that these assays are validated under CLIA, enabling them to be used in clinical decision making process in research protocols and for routine patient care." .
SCR:024750 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Minerva" ;
NIFRID:synonym "Minerva Author",
"Minerva Story" ;
definition: "Software tools for interactive viewing and fast sharing of large image data. Comprises Minerva Author, a tool to create and annotate images, and Minerva Story, a narrative image viewer for web hosting. Used for interpreting and interacting with complex images, organized around guided analysis approach. Enables fast sharing of large image data that is stored on Amazon S3 and viewed using zoomable image viewer implemented using OpenSeadragon, making it ideal for integration into multi-omic browsers for data dissemination of tissue atlases." .
SCR:024751 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scimap" ;
definition: "Software toolkit for analyzing spatial molecular data. Underlying framework is generalizable to spatial datasets mapped to XY coordinates. Package uses anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. Python based implementation efficiently deals with large datasets of millions of cells." .
SCR:024752 a NLX:63400,
owl:NamedIndividual ;
definition: "Software C toolkit for alignment free and spatial temporal analysis of multi-FASTA data. Used for entangling presence of multiple sequences from epidemic and pandemic events." .
SCR:024753 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nutil To Useable" ;
NIFRID:abbrev "N2U" ;
definition: "Web application to transform Nutil outputs and plots it on mouse anatomical heatmap." .
SCR:024754 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2562" ;
rdfs:label "NCI Center for Cancer Research Genomics Core Facility" ;
NIFRID:synonym "National Cancer Institute Center for Cancer Research Genomics Core",
"NCI CCR Genomics Core",
"NCI Center for Cancer Research Genomics Core" ;
definition: "Core provides access to genomic technologies and Next-Generation Sequencing. Provides DNA and RNA quality control services, user accessible instrumentation, training, consultation services, bioinformatics support, and secure data delivery management." .
SCR:024755 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "jMORP" ;
definition: "Japanese multi omics reference panel. Provides multidimensional approach to diversity of Japanese population. Public database for plasma metabolome and proteome analyses. Updated to metabolome, genome, transcriptome, metagenome, number of samples, analysis methods of each dataset, expanding links between each layer and links between hierarchies." .
SCR:024756 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JOSA" ;
NIFRID:synonym "JOint Spherical registration and Atlas building" ;
definition: "Software tool for joint surface based registration and atlas construction of brain geometry and function.Cortical registration framework that jointly models mismatch between geometry and function while simultaneously learning unbiased population specific atlas." .
SCR:024757 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FindPlantNLRs" ;
definition: "Software pipeline for annotating predicted Nucleotide binding and leucine rich repeat genes from non-masked genome fasta file input." .
SCR:024758 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PEPATAC" ;
definition: "Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats." .
SCR:024759 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scNAT" ;
definition: "Software application to integrate scRNA-seq and scTCR-seq data to allow for more comprehensive analysis that leverages the strengths of both data types.Repository contains code and information of data used in the paper “scNAT: A deep learning method for integrating paired single cell RNA and T cell receptor sequencing profiles”. Source code for scNAT are in the scNAT folder, the tutorial is in the tutorials folder." .
SCR:024760 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2563" ;
rdfs:label "American Museum of Natural History Microscopy and Imaging Core Facility" ;
NIFRID:synonym "American Museum of Natural History Microscopy and Imaging Facility" ;
definition: "Shared instrumentation facility at the American Museum of Natural History with tools for X-ray tomography, electron microscopy, confocal microscopy, light microscopy and image analysis. Provides expert assistance in the use of all lab equipment." .
SCR:024761 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2564" ;
rdfs:label "University of Manchester Mass Spectrometry and Separations Core Facility" ;
NIFRID:synonym "Mass Spectrometry and Separations",
"MS and Sep Facility" ;
definition: "Core is part of the University of Manchester Faculty of Science and Engineering. Facility offers support and services in chemistry, biology and materials. Mass spectrometers including Orbitraps, Ion Mobility, MALDI, DESI, hyphenated LC-MS and GC-MS apparatuses. Other instruments are HPLC systems, UHPLC systems and GC systems." .
SCR:024762 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2558" ;
rdfs:label "Van Andel Institute Bioinformatics and Biostatistics Core Facility" ;
NIFRID:synonym "VAI Bioinformatics and Biostatistics Core",
"Van Andel Institute VAI Bioinformatics and Biostatistics Core" ;
definition: "Core provides bioinformatics and statistics expertise. Core develops and maintains automated and customizable workflows for processing and analyzing many types of genomic data; supports design of rigorous, robust and reproducible experiments and proposals; assists in preparation of manuscripts, grants and presentations; and provides education and training in use of software and analysis methods.Core can contribute to many types of bioinformatics or statistical projects." .
SCR:024763 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2565" ;
rdfs:label "University of Chicago PaleoCT Core Facility" ;
NIFRID:synonym "UChicago PaleoCT",
"University of Chicago PaleoCT Lab" ;
definition: "Core utilizes dual tube micro X-ray computed tomography scanner for imaging specimens in fields of paleontology, comparative anatomy, evolution and development, basic biomedical studies, and research in geology and material sciences.It is equipped with 180 kV nano-focus and high power 240 kV micro-focus CT tube. This setup allows to scan very small specimens with high resolution using nano tube or dense fossils using high power tube." .
SCR:024764 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Opencast" ;
definition: "Open source platform to support management of educational audio and video content. Institutions can use Opencast to produce lecture recordings, manage existing video, serve designated distribution channels, and provide user interfaces to engage students with educational videos." .
SCR:024765 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MSIsensor-pro" ;
definition: "Software tool for microsatellite instability detection using high throughput sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region sequencing data as input. Introduces multinomial distribution model to quantify polymerase slippages for each tumor sample and discriminative sites selection method to enable MSI detection without matched normal samples." .
SCR:024766 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRDetect" ;
definition: "Software application to estimate presence of MRD in plasma cfDNA WGS through evaluation of matched tumour-derived mutations (SNVs or CNVs)." .
SCR:024767 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FusionAnnotator" ;
definition: "Software tool for annotating fusion transcripts, incorporated into Trinity Cancer Transcriptome Analysis Toolkit utilities, and leveraging databases including CTAT Human Fusion Lib." .
SCR:024768 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ichorCNA" ;
definition: "Software tool that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. Used to simultaneously segment genome, predict large scale copy number alterations, and estimate tumor fraction of ultra low pass whole genome sequencing sample." .
SCR:024769 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2560" ;
rdfs:label "University of Luxembourg LCSB Metabolomics, Lipidomics and Proteomics Platform Core Facility" ;
NIFRID:synonym "LCSB Metabolomics and Lipidomics Platform",
"LCSB Metabolomics Lipidomics and Proteomics Platform Core Facility",
"LCSB Metabolomics Platform" ;
definition: "The Metabolomics, Lipidomics, and Proteomics Platform facilitates metabolism-related and molecular research, serving researchers from academia and industry in Luxembourg and beyond. We specialize in the comprehensive analysis of small molecules and proteins within complex biological matrices. Our advanced analytical infrastructure and broad method portfolio accelerate scientific discoveries across biology, biomedicine, and systems biology." .
SCR:024771 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CalculiX" ;
definition: "Software finite element analysis package. Used to solve field problems." .
SCR:024772 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Feature-specific Information Transfer scripts" ;
definition: "Software application as MATLAB scripts to compute measures of Feature-specific Information Transfer (FIT) and conditional FIT (cFIT). FIT quantifies direction and magnitude of information flow about specific feature S (such as feature of sensory stimulus) between simultaneously recorded brain regions X and Y. cFIT quantifies amount of directed feature information transmitted between regions X and Y that cannot be potentially routed through region Z." .
SCR:024773 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LemkeCelottoEtAl_codes_repo" ;
definition: "Software code package associated to the paper: Lemke et al. Information flow between motor cortex and striatum reverses during skill learning. 2023. Quantifies information theoretic quantities used in the associated study." .
SCR:024774 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bioinformatics platform" ;
definition: "Web service for online data drawing and analysis, personalized data analysis, scientific research mapping, online page/database development and hosting. Used for high throughput sequencing data analysis including eccDNA-seq, MeRIP-seq, circRNA-seq, miRNA-seq, mRNA-seq, LncRNA-seq, piRNA-seq, ChIP-seq, etc." .
SCR:024775 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2566" ;
rdfs:label "Louisiana State University in Shreveport Research Core Facility" ;
NIFRID:synonym "Research Core Facility" ;
NIFRID:abbrev "RCF" ;
definition: "Core provides access to research services, educational and training opportunities, and technologies including cellular metabolism, flow cytometry, fluorescence, confocal, super resolution confocal microscopy, next generation sequencing, and real-time PCR. Provides assistance with all aspects of these technologies, including experimental design, protocol optimization, instrument operation, and data analysis." .
SCR:024776 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2568" ;
rdfs:label "Louisiana State University in Shreveport Animal Models and Histology Core Facility" ;
NIFRID:synonym "Animal Models and Histology Core",
"Louisiana State University in Shreveport Animal Models and Histology Core" ;
definition: "Core provides services for mouse genotyping and tissue histology, access to tools for analyzing cardiovascular function, data analysis, expertise and training. Services include genotyping using PCR or RT PCR, histology services with tissue processing, paraffin-embedding and sectioning, along with several cardiovascular relevant histological stains such as Picrosirius Red and Masson Trichrome." .
SCR:024777 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2567" ;
rdfs:label "Louisiana State University in Shreveport Small Animal Imaging Core Facility" ;
NIFRID:synonym "Louisiana State University in Shreveport Small Animal Imaging Facility",
"Small Animal Imaging Facility" ;
NIFRID:abbrev "SAIF" ;
definition: "Core provides imaging support to investigators who use small animal models in their research. Offers bioluminescence and fluorescence imaging, X-ray imaging, computed tomography, and positron emission tomography. Core provides imaging support services for investigators, including assistance in experimental design, conducting animal studies including anesthetization and imaging acquisition, and processing and interpreting imaging data." .
SCR:024778 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2569" ;
rdfs:label "Louisiana State University in Shreveport Redox Molecular Signaling Core Facility" ;
NIFRID:synonym "CoBRE Redox Molecular Signaling Core",
"Redox Molecular Signaling Core" ;
definition: "Facility includes Analytic Redox Biology and Molecular Signaling Sub-Cores. Provided services include measurements of reactive oxygen species, reactive nitrogen species, reactive sulfide species, protein, peptides, metabolites, and lipids in cell culture and tissue samples. High-performance liquid chromatography systems, coupled with UV-vis and fluorescence detectors to quantify cellular and mitochondrial superoxide production, hydrogen sulfide pools (free sulfide, sulfide bound to transitional metals, and sulfane sulfur), and thiols (glutathione, GSH/GSSG, cysteine, cystine, homocysteine, persulfides, and glutathionylation).Instruments include Sievers NO Analyzer (NOA 280i, GE), Agilent 8890 GC and 8335 sulfur chemiluminescence detector ,Thermo Scientific Orbitrap Exploris 480 and SCIEX Triple Quad 7500 mass spectrometer. Molecular Signaling Sub-Core offers services for molecular cloning and site-directed mutagenesis, design and production of vectors for CRISPR/Cas9 modification of vascular cells, services for endothelial, smooth muscle, and cardiac myocyte cell isolation, for generation of vascular cell lines, and for lentivirus production for transient or stable modification of cardiovascular cells, access to equipment and expertise for studying cellular effects of hypoxia/reoxygenation injury (Coy Hypoxic Chamber, CLARIOstar Spectrofluorometer), for automated capillary Western blot analysis (ProteinSimple Jess Simple Western), and for high-resolution fluo-respirometry to study mitochondrial function (Oroboros O2k modular system)." .
SCR:024779 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2571" ;
rdfs:label "Louisiana State University in Shreveport CAIPP Bioinformatics and Modeling Core Facility" ;
NIFRID:synonym "CAIPP Bioinformatics and Modeling Core" ;
definition: "Core supports data analysis, network modeling, and data science research. Provides training and education opportunities." .
SCR:024780 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2572" ;
rdfs:label "Cincinnati Children's Hospital Bionutrition Research Core Facility" ;
NIFRID:synonym "Bionutrition Research Facility",
"Cincinnati Children's Hospital Bionutrition Research Facility" ;
definition: "Facility works with investigators to obtain and analyze high-quality nutrition and body composition data from study participants. Staff and facilities are located in the Schubert Research Clinic at Cincinnati Childrens Hospital. Core provides diet assessment services." .
SCR:024781 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2570" ;
rdfs:label "Louisiana State University in Shreveport CAIPP Immunophenotyping Core Facility" ;
NIFRID:synonym "CAIPP Immunophenotyping Core" ;
definition: "Immunophenotyping core provides services for isolation of cellular populations from tissues, automated quantification of cell numbers, quantification of GFP, DAPI, RFP, Cy5 or Cy7 positive populations, automated quantification of cytokine concentration in supernatants and biological samples, and flow cytometric and microscopic assay development and execution.Provides training and education opportunities." .
SCR:024782 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Evident" ;
NIFRID:synonym "Evident Scientific",
"Olympus Scientific Solutions" ;
definition: "Company for development, manufacture, sale and provision of solutions for biological microscopes, industrial microscopes, industrial endoscopes, non-destructive inspection equipment, X-ray analyzers, etc." .
SCR:024783 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VS200" ;
rdfs:label "Olympus | VS200 Slide Scanner" ;
NIFRID:synonym "SLIDEVIEW VS200 research slide scanner",
"VS200 Slide Scanner" ;
NIFRID:abbrev "VS200" ;
definition: "Flexible system that supports various slide sizes, different objectives, SILA optical sectioning device, oil dispenser, cameras, loaders, and LED/laser light sources with multiple filter sets. VS200 supports brightfield, darkfield, polarization, phase contrast, and fluorescence, with possibility to scan sample using multiple techniques at the same time. VS200 software supports offline analysis, deep learning, 3D deconvolution, and batch conversion to standard file formats. It also supports the NIS-SQL database for data management and the DICOM format for easy integration into lab information management system." .
SCR:024784 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2589" ;
rdfs:label "University of Manchester Services and Equipment Core Facility" ;
NIFRID:synonym "UoMaH Services and Equipment" ;
definition: "Core to build partnerships with government, National Facilities, industrial and academic stakeholders at Harwell and beyond, to jointly address challenges set by UK’s Industrial Strategy through research and to discover and develop innovative techniques and technologies to enhance facility science, data analytics and workplace safety." .
SCR:024785 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2590" ;
rdfs:label "University of Manchester X-ray Diffraction Platform Core Facility" ;
NIFRID:synonym "University of Manchester X-ray Diffraction Platform" ;
definition: "Core to bring together community of knowledge and best practise from three Faculty of Science and Engineering Departments: Chemistry, EES and Materials. Provided equipment is housed across numerous parts of campus with bulk being operated from Engineering Building A and Chemistry. Offers technical expertise in techniques such as residual stress analysis, texture analysis, phase identification in crystalline and semi crystalline powders and solid materials, single crystal and small angle scattering. Machines are available for examination of both small specimens and large components, and for wide range of materials." .
SCR:024786 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2591" ;
rdfs:label "University of Manchester Magnetic Resonance and Related Technology Platform Core Facility" ;
NIFRID:synonym "University of Manchester Magnetic Resonance and Related Technology Platform" ;
definition: "Core is equipped with instrumentation supporting areas of NMR, EPR and related techniques." .
SCR:024787 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2592" ;
rdfs:label "University of Manchester Corrosion and Materials for Demanding Environments Core Facility" ;
NIFRID:synonym "Corrosion and Materials for Demanding Environments" ;
definition: "Core includes facilities and techniques, supporting exploration of this unique research space. Provides expertise and services for advanced materials and interdisciplinary research activity." .
SCR:024788 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2593" ;
rdfs:label "University of Manchester Biochemical and Biophysical Sciences Technology Platform Core Facility" ;
NIFRID:synonym "University of Manchester Biochemical and Biophysical Sciences Technology Platform" ;
definition: "Core includes range of facilities that support all biological related activity in Faculty of Science and Engineering. We work at the interface of physical sciences, engineering and biology and provide major link to facilities in Faculty of Biology, Medicine and Health. Supports research activities in areas that include physical understanding of biological systems, engineering biomolecules and biological processes, biomaterials and environmental sciences." .
SCR:024789 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2594" ;
rdfs:label "University of Manchester Surface Characterisation Core Facility" ;
definition: "Core includes range of surface analysis techniques and supportive instruments across three research institutes: Henry Royce Institute, Photon Science Institute, and National Graphene Institute." .
SCR:024790 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2595" ;
rdfs:label "University of Manchester Advanced Manufacturing Platform Core Facility" ;
definition: "Core offers services, teaching and collaboration between Laser Processing Research Laboratory, Manufacturing Technology Research Laboratory and Bioenergy laboratory." .
SCR:024791 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Recentrifuge" ;
definition: "Software application for robust comparative analysis and contamination removal for metagenomics. Implements robust method for removal of negative control and crossover taxa from the rest of samples. Analyzes results from taxonomic classifiers using interactive charts with emphasis on confidence level of classifications. In addition to contamination subtracted samples, provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." .
SCR:024792 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCFLIRT" ;
NIFRID:synonym "MC FMRIB's Linear Image Registration Tool",
"Motion Correction FMRIB's Linear Image Registration Tool" ;
definition: "Software intra-modal motion correction tool designed for use on fMRI time series for linear (affine) inter- and inter-modal brain image registration." .
SCR:024793 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2596" ;
rdfs:label "University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility" ;
NIFRID:synonym "University of Nevada High Spatial and Temporal Resolution Imaging Core" ;
NIFRID:abbrev "HSTRI Core" ;
definition: "Core provides high spatial and temporal resolution imaging methodologies and instrumentation for studying cellular structure, signaling pathways, and function in health and disease. Offers education, training and expertise in advising investigators in the use of the new technologies." .
SCR:024794 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.266826.e",
"ISNI 0000 0000 9216 5478",
"Wikidata Q8215036" ;
rdfs:label "University of New England; Biddeford; USA" ;
definition: "Private research university in Maine with campuses in Portland and Biddeford, as well as study abroad campus in Tangier, Morocco. " .
SCR:024795 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FB11201" ;
rdfs:label "Thermo Fisher | 112xx Series Advanced Ultrasonic Cleaner" ;
NIFRID:synonym "Fisher Advanced Ultrasonic Cleaners" ;
definition: "Dual frequency sonicating water bath with temperature control." .
SCR:024796 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Benchmark Scientific | Orbi-Shaker MP4 orbital shaker" ;
NIFRID:synonym "Orbi-Shaker MP4",
"Orbi-shaker MP microplate shaker with 4 position platform" ;
definition: "Orbital shaker for up to 4 microplates with digital speed control.Designed with 3mm mixing orbit, optimized for thorough mixing of microplates and/or PCR plates. Up to four plates can be placed on the included platform." .
SCR:024797 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2588" ;
rdfs:label "University of Wisconsin Madison Biotechnology Center Animal Models Core Facility" ;
NIFRID:synonym "University of Wisconsin Madison Biotechnology Center Animal Models Core",
"UW Biotechnology Center-Animal Models Core" ;
definition: "Core provides support for generation of novel animals including mice, rats and swine models using CRISPR or transgenic technology, cryopreservation, rederivation, and IVF recovery of rodent animal models." .
SCR:024798 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bulkGAN" ;
definition: "Software tool for scRNA and spatial transcriptomics.Used to generate RNA data close to real bulk RNA-seq with constraints of scRNA-seq data, based on keras and tensflow framework." .
SCR:024799 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HDOCK server" ;
NIFRID:synonym "HDOCK" ;
definition: "Web server for protein-protein and protein-DNA/RNA docking based on hybrid strategy. With input information for receptor and ligand molecules either amino acid sequences or Protein Data Bank structures, the server automatically predicts their interaction through hybrid algorithm of template-based and template-free docking." .
SCR:024800 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2576" ;
rdfs:label "University of Manchester National X-ray Computed Tomography Core Facility" ;
NIFRID:synonym "University of Manchester UoM-FSE-Section of The National X-ray Computed Tomography Facility",
"UoM-FSE-Section of The National X-ray Computed Tomography Facility" ;
NIFRID:abbrev "NXCT" ;
definition: "Provides access and expert support to run cutting-edge 3D and 3D time-lapse imaging experiments.Provides access to X-ray instruments, technical support for new and existing users, expertise to design complex experiments, infrastructure and resources to analyse 3D and 4D data.Funded by the Engineering and Physical Sciences Research Council (EPSRC)." .
SCR:024801 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2584" ;
rdfs:label "University of Manchester Design, Fabrication and Testing Core Facility" ;
NIFRID:synonym "Fabrication & Testing",
"University of Manchester UoM-FSE-Platform of Design",
"UoM-FSE-Platform of Design" ;
definition: "Core supports areas of research from Heavy Structures and Concrete design, fabrication and testing to Non-Destructive Testing, development and construction of novel fibre, polymers and composite materials." .
SCR:024802 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XSwap" ;
definition: "Software Python library (C++ backend) for degree preserving network randomization." .
SCR:024803 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SGAE" ;
NIFRID:synonym "Siamese Graph Autoencoder" ;
definition: "Software graph neural network based tool for spatial domain deciphering. Used for deciphering spatial domains from spatially resolved transcriptomics." .
SCR:024804 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SAIBR" ;
NIFRID:synonym "Spectral Autofluorescence Image Correction By Regression" ;
definition: "Software application as platform independent protocol and FIJI plug-in to correct for autofluorescence using standard filter sets and illumination conditions. Spectral autofluorescence correction method based on simple 2- or 3-Channel images implemented in Python and Fiji. Used for performing spectral autofluorescence correction on biological images." .
SCR:024805 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Enformer" ;
definition: "Software package provides implementation of the Enformer model and examples on running the model." .
SCR:024806 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChromBPNet " ;
definition: "Software application as bias factorized, base-resolution deep learning models of chromatin accessibility." .
SCR:024807 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyBigWig" ;
definition: "Software application as Python extension for quick access to bigWig and bigBed files." .
SCR:024808 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cisTarget" ;
definition: "Web application to download database for motif enrichment, motif annotations,cluster-buster implementation, precomputed regions for creating gene-based databases and to download lists of transcription factors for human, mouse and fly, chip-seq tracks annotations." .
SCR:024809 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tomtom" ;
definition: "Software motif comparison tool. Compares one or more motifs against database of known motifs, ranks motifs in database and produces alignment for each significant match." .
SCR:024810 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cluster-Buster" ;
definition: "Software application for detection of sequences that regulate gene transcription, such as enhancers and silencers, but other types of biological regulation may be mediated by motif clusters too." .
SCR:024811 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TF-Modisco " ;
NIFRID:synonym "TF MOtif Discovery from Importance SCOres",
"Transcription-Factor Motif Discovery from Importance Scores" ;
definition: "Software application as algorithm for identifying motifs from basepair-level importance scores computed on genomic sequence data." .
SCR:024812 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "h5py " ;
definition: "Software package provides interface to HDF5 library from Python. The low-level interface is intended to be complete wrapping of the HDF5 API, while the high-level component supports access to HDF5 files, datasets and groups using established Python and NumPy concepts." .
SCR:024813 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ipykernel" ;
definition: "Software package provides IPython kernel for Jupyter." .
SCR:024814 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EazyDraw" ;
definition: "Software vector based drawing application for desk top publishing with Apple's macOS operating system. Illustration or drawing software application that offers vector-based graphics editing and creation capabilities for creating simple not-photographic drawings, technical diagrams and illustrations such as logos, icons, buttons and stylized art." .
SCR:024815 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoTube" ;
definition: "Software that quantifies vascular morphometry parameters like area covered by vessels, vessel width, skeleton length and branching or crossing points of vascular networks in tissues and in vitro assays." .
SCR:024816 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2597" ;
rdfs:label "Creighton University Innovative Genomics and Bioinformatics Core Facility" ;
NIFRID:synonym "Creighton University Innovative Genomics and Bioinformatics Core",
"Innovative Genomics and Bioinformatics Core" ;
NIFRID:abbrev "IGBC" ;
definition: "Provides services for genomics research that range from sequencing to data analysis. Instruments available include Illumina NextSeq 2000, 10x Genomics Chromium iX Controller, Agilent TapeStation 4200, and Qubit Flex Fluorometer." .
SCR:024817 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2600" ;
rdfs:label "Creighton University Drug Discovery and Delivery Core Facility" ;
NIFRID:synonym "Creighton University CU-DDD Core - Drug Design",
"CU-DDD Core - Drug Design",
"Synthesis and Validation Subcore" ;
NIFRID:abbrev "DDDC" ;
definition: "Core subcores include Drug Design, Synthesis and Validation Laboratory, ADMETox Laboratory,Zebrafish Laboratory. Offers experts and technologies to provide services tailored to drug development needs. Can assist with drug screening and design from small molecules to peptides, development and applying methodologies to synthesize drug candidate, and validate its chemical structure and purity. Offers services to detect and quantify drugs in biological samples. Follow-up studies can be conducted using services of ADMETox subcore to characterize drug candidate toxicity, efficacy, and pharmacokinetic and pharmacodynamic profiles, and assist in developing appropriate formulation and delivery approaches." .
SCR:024818 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2599" ;
rdfs:label "Beth Israel Deaconess Medical Center Glycomics Core Facility" ;
NIFRID:synonym "Beth Israel Deaconess Medical Center Glycomics Core",
"Glycomics Core" ;
definition: "Glycomics Core provides services, instrumentation and expertise in glycomics. Services include Glycan Microarrays,Glycan analysis by Mass Spectrometry, Distribution of specific reagents,Trainings." .
SCR:024819 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2598" ;
rdfs:label "Beth Israel Deaconess Medical Center Precision RNA Medicine Detection Unit Core Facility," ;
NIFRID:synonym "Beth Israel Deaconess Medical Center Detection Unit Precision RNA Medicine Core",
"BIDMC Detection Unit Precision RNA Medicine Core",
"Detection Unit Precision RNA Medicine Core" ;
definition: "Detection Unit of ncRNA Core can perform highly sensitive microRNA detection platform for diverse biospecimens.Technology is based on qPCR and uses single plate panel for simultaneous detection of 384 miRNAs using MIRXES technology. Services offered by unit include Detection of miRNA, Analysis of dysregulated miRNA,Consultation and support for non-coding RNA biology and research." .
SCR:024820 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ExperimentHub" ;
definition: "Software R package provides central location where curated data from experiments, publications or training courses can be accessed." .
SCR:024821 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Drugmonizome" ;
definition: "Database with search engine for querying annotated sets of drugs and small molecules for performing drug set enrichment analysis." .
SCR:024822 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GREP" ;
NIFRID:synonym "Genome for REPositioning drugs",
"GREP: Genome for REPositioning drugs" ;
definition: "Standalone Python software to quantify enrichment of user-defined set of genes in target of clinical indication categories and to capture potentially repositionable drugs targeting gene set." .
SCR:024824 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggbreak" ;
definition: "Software package provides several scale functions to break down ‘gg’ plot into pieces and align them together with gap plot or without (wrap plot or cut plot) ignoring subplots. Package was first designed to set breakpoints for truncating plot to shrink outlier long branch of phylogenetic tree. Set Axis Break for ggplot2." .
SCR:024825 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggrastr" ;
definition: "Software R package to Rasterize Layers for ggplot2." .
SCR:024826 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "patchwork" ;
definition: "Software R package to combine separate ggplots into same graphic. Composer of Plots." .
SCR:024827 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Colorectal cancer detection" ;
NIFRID:synonym "ColoPola: Colorectal cancer polarimetric image",
"Polarimetric imaging" ;
definition: "Software application to classify colorectal cancer using ColoPola dataset." .
SCR:024828 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "spatiAlign" ;
definition: "Software tool as unsupervised contrastive learning model that employs expression of all measured genes and spatial location of cells, to integrate multiple tissue sections. Enables joint downstream analysis of multiple datasets in low-dimensional embeddings and also in reconstructed full expression space. Used for integrative analysis of time-series brain sections, including spatial clustering, differential expression analysis, and particularly trajectory inference that requires corrected gene expression matrix." .
SCR:024829 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NHT3" ;
rdfs:label "Anton Paar | NHT3 Nanoindentation Tester" ;
NIFRID:synonym "NHT³ Nanoindentation Tester" ;
definition: "Used for testing hardness, elastic modulus, creep and other surface properties at nanometer to micrometer scale. Its range is from 0.1 mN to 500mN with no need to wait to reach thermal stable state, and instrument indentation test can be performed immediately after startup.NHT3 is a versatile, research-grade platform suited for highly customizable mechanical surface testing." .
SCR:024830 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FACSymphony_A1" ;
rdfs:label "BD Biosciences | FACSymphony A1 Cell Analyzer" ;
NIFRID:synonym "BD FACSymphony A1" ;
definition: """Analyzer applies BD FACSymphony instrument technology to reduce background noise and increase detection sensitivity. Features low-noise electronics, high-powered lasers and tight beam spot to support immunophenotyping up to 16 colors. Enables independent analysis of large and small particles on single instrument. Optional small particle detector enables detection of small particles such as extracellular vesicles, viral particle and more.
Compatible with broad portfolio of catalog and custom BD Horizon Brilliant Reagents and BD FACSDiva Software. Permits easy placement on standard lab bench with its compact format.""" .
SCR:024831 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpikeHunter" ;
definition: "Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins." .
SCR:024832 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BioFlux_1000z" ;
rdfs:label "Fluxion Biosciences | BioFlux 1000z" ;
NIFRID:synonym "BIOFLUX 1000Z",
"BioFlux 1000z" ;
definition: "Gives ability to introduce flow to research and drug discovery experiments with in vivo conditions. Microfluidic well plate format opens up multitude of experiments. Customizable BioFlux solutionon for ultimate imaging flexibility. Additional Standard Features to those in BioFlux 200 include Custom automated microscope configuration, User defined camera and Fully integrated control and analysis software." .
SCR:024833 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TS420" ;
rdfs:label "Transonic | TS420 Perivascular Flow Module" ;
NIFRID:synonym "TS420 Perivascular Flow Module" ;
definition: "TS420 Perivascular Flow Module with Flowprobes to fit every vessel in research models from mice to sheep and even giraffes, provides high resolution blood flow wave forms and arterial/venous flow measurements in mL/min or L/min. Gold Standard for blood flow measurement in cardiovascular research with outputs analog signals compatible with most data acquisition systems. Features plug and play set up routines to calibrate/scale/test and measure. Fit into 400-Series Instrumentation Consoles and compatible to mix and match with other 400-Series Modules. Perivascular Flowprobes are available for small and large vessel sizes, and for acute use and chronic implantation." .
SCR:024834 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3DHISTECH |PANNORAMIC MIDI II scanner" ;
NIFRID:synonym "3D HISTECH PANNORAMIC MIDI II",
"PANNORAMIC MIDI II" ;
definition: "Automatic digital slide scanner with 12 slide capacity in one run, fluorescence scanning, 9 physical filter cubes and 45 logical fluorescence channels. Powered by PANNORAMIC Scanner Software. Supports Carl Zeiss objectives, achieving up to 43x or 86x magnification and 0.087 µm/pixel resolution within the same instrument, along with advanced FISH scanning technique." .
SCR:024835 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ECLIPSE_Ni-U" ;
rdfs:label "Nikon | ECLIPSE Ni-U Microscope" ;
definition: "Manual model using halogen light source, manual focus, motorized nosepiece and motorized fluorescence cube turret. Standard model suitable for brightfield observation of pathological specimens and digital imaging." .
SCR:024836 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2606" ;
rdfs:label "University of Washington I-LABS MEG Brain Imaging Center Core Facility" ;
NIFRID:synonym "I-LABS MEG Brain Imaging Center",
"Institute for Learning and Brain Sciences (I-LABS) MEG Brain Imaging Center",
"MagnetoEncephaloGraphy Brain Imaging",
"MEG Brain Imaging" ;
definition: "Magnetoencephalography facility focusing on children. Equipped with MEGIN TRIUX Neo system with helium recycler, MAGSTIM EEG data acquisition system, Tucker-Davis Technologies RZ6 for stimulus generation, Epson Home Cinema 3200 for video projection, custom video recording system with 4 cameras, Eyelink eyetracker, and Polhemus 3D digitizer." .
SCR:024837 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenomeSpy" ;
definition: "Software visualization grammar and GPU-accelerated toolkit for genomic data. Visualization grammar and GPU-accelerated rendering engine for genomic data. Grammar based toolkit for authoring tailored, interactive visualizations for genomic data analysis." .
SCR:024838 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NAVIP" ;
NIFRID:synonym "Neighborhood-Aware Variant Impact Predictor",
"Neighborhood-Aware Variant Impact Predictor (NAVIP)" ;
definition: "Software tool for functional impact prediction for sequence variants. Neighborhood-Aware Variant Impact Predictor (NAVIP) considers all variants within a given protein coding sequence when predicting the functional consequences." .
SCR:024839 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Primate Research Center Consortium" ;
NIFRID:synonym "NPRC Consortium",
"The National Primate Research Center (NPRC) Consortium",
"The National Primate Research Center Consortium" ;
definition: "NPRC Consortium is collaboration across seven Centers to increase access and promote sharing of NonHuman Primate related resources among biomedical researchers. NPRCs advance missions of NIH Institutes, Centers, and Offices by providing animals, facilities, expertise, and resources required by investigators in disease specific areas. Each Center provides expertise on the use of various NHP species as models of human disease to address specific research projects in major research fields such as infectious diseases, aging, cardiovascular disease, diabetes and metabolic disorders, neuroscience, pediatrics, regenerative medicine, reproductive health, and women’s health. ORIP supports Specific Pathogen Free rhesus macaque colonies at the California,Oregon, Southwest, Yerkes, and Tulane NPRCs and the Caribbean Primate Research Center in Puerto Rico. Additionally, SPF pigtail macaque colonies are maintained at the Washington NPRC and at the Johns Hopkins University School of Medicine." .
SCR:024840 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepDraw" ;
definition: "Software application for creating scalable muscle spindles dataset based on kinematic data and define action recognition task as benchmark. Training and analysis of hierarchical neural networks to solve recognition task from muscle spindle inputs." .
SCR:024841 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "World Health Organization Health Action International project on medicine prices and availability" ;
NIFRID:synonym "WHO/Health Action International project on medicine prices and availability" ;
definition: "Project on Medicine Prices and Availability collaborative partnership between WHO and international non-governmental organization Health Action International. Through project, standardized survey methodology for measuring medicine prices, availability, affordability and price components was developed." .
SCR:024842 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Statistics Sweden" ;
definition: "Organization responsible for official statistics and for other government statistics. Used to develop, produce and disseminate statistics, coordinate system for official statistics in Sweden, conduct long term cooperation projects with statistical offices in developing countries, which are financed by Sida." .
SCR:024843 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StatFin database" ;
NIFRID:synonym "StatFin" ;
definition: "Finland's statistical database contains collection of statistical tables on Finnish society and population of Finland including economy, housing, transport, tourism, consumption, prices, wages and salaries, energy, enterprises and other topics." .
SCR:024844 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Prostate Cancer Register of Sweden" ;
NIFRID:synonym "National Prostate Cancer Register (NPCR) of Sweden" ;
NIFRID:abbrev "NPCR of Sweden" ;
definition: "National Prostate Cancer Register of Sweden database." .
SCR:024845 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RATTEN" ;
NIFRID:synonym "Interactive On Line Report from National Prostate Cancer Register (NPCR) of Sweden" ;
definition: "Online report from NPCR that contains data on prostate cancer care from all healthcare providers in Sweden. Source of knowledge about Swedish prostate cancer healthcare for all stakeholders, patients, healthcare professionals, researchers, administrators and decision makers." .
SCR:024846 a NLX:63400,
owl:NamedIndividual .
SCR:024847 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DNBSEQ-T7" ;
rdfs:label "MGI | DNBSEQ-T7 Genetic Sequencer" ;
NIFRID:synonym "DNBSEQ-T7 Sequencer" ;
definition: "Instrument features include High Speed: 22 hrs to 24 hrs for PE150 sequencing; High Flexibility: 4 Flow Cells, PE150, and PE100 at the same time; Ultra-high Throughput: 7 Tb per day; high quality data around the clock." .
SCR:024848 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "BGI Genomics" ;
definition: "Provider of precision medicine serving customers in more than 100 countries, involving over 2,300 medical institutions. Relying on sequencing and bioinformatics technology, provides clinical molecular diagnostic solutions and high-throughput sequencing research services." .
SCR:024849 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Innomics Inc." ;
definition: "Provides expertise in multi-omics (Genomics, Transcriptomics, Epigenomics, Proteomics and Metabolomics), offering end-to-end next-generation sequencing and mass spectrometry solutions to researchers and healthcare professionals." .
SCR:024850 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Motic | MoticEasyScan One-FS" ;
NIFRID:synonym "MoticEasyScan One-FS scanning system" ;
definition: "Compact scanner for any digital slide application. Scanning system with FS-Live software suite, optimized for frozen section, cytology, ROSE, and FNA adequacy evaluation, places control into hands of remote pathologist to pilot the system and provide diagnosis without travel time." .
SCR:024851 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Motic | MoticEasyScan Pro 6-FS" ;
NIFRID:synonym "MoticEasyScan Pro 6-FS Scanner System" ;
definition: "MoticEasyScan Pro scanner system scans up to 6 slides in one click and uploads digital slides to your slide management server. Ideal for any application that requires glass slide digitization." .
SCR:024852 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Motic | MoticEasyScan Infinity 102" ;
NIFRID:synonym "MoticEasyScan Infinity 102 Scanning System" ;
definition: "Scanning solution for high volume scanning. Scanner system scans up to 60 slides in one click, providing scanning at 20X and40X magnifications. With Infinity Scanning design, slides can be added to the system without interrupting the scanning process." .
SCR:024853 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Motic | MoticEasyScan Infinity 60" ;
NIFRID:synonym "MoticEasyScan Infinity 60 Scanning System" ;
definition: "Scanning solution for high volume scanning. Scanner system scans up to 60 slides in just one click, providing scanning at 20X and40X magnifications with Infinity Scanning design, slides can be added to the system at any time, without interrupting the scanning process." .
SCR:024854 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Motic | MoticEasyScan Pro 6" ;
NIFRID:synonym "MoticEasyScan Pro 6 Scanning System" ;
definition: "Scanner system scans up to 6 slides in just one click. It scans and uploads high-quality digital slides to your slide management server. Multipurpose scanner for any application that requires glass slide digitization." .
SCR:024855 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Motic | MoticEasyScan One" ;
NIFRID:synonym "MoticEasyScan One Scanner" ;
definition: "Compact scanner for any digital slide application. This scanning system with FS-Live software suite, optimized for frozen section, cytology, ROSE, and FNA adequacy evaluation, for remote pathologist to pilot the system and provide diagnosis without travel time." .
SCR:024856 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Motic" ;
definition: "Company provides innovative microscope and microscopy solutions designed for education, medical, clinical, and industrial needs. Motic Microscopes specializes in designing and manufacturing conventional and digital microscopy solutions. Motic Digital Pathology drives adoption of digital medicine by making whole slide imaging, AI, and software technologies approachable for hospitals and labs everywhere.Motic Electric designs, develops and manufactures High Voltage insulation components for transmission and distribution systems in the electric power industry.Motic Energy strives to lead in smart energy technology through our next-gen management platform, using big data, AI, and cloud technology to create networked energy ecosystem for the world." .
SCR:024857 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DM6_B" ;
rdfs:label "Leica | DM6 B Upright Microscope" ;
NIFRID:synonym "Leica DM6 B Automated Upright Microscope System" ;
definition: "Leica DM6 B Upright Microscope includes the Leica DFC7000 T Camera and LAS X Software." .
SCR:024858 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DM4_B" ;
rdfs:label "Leica | DM4 B Upright Microscope" ;
NIFRID:synonym "Leica DM4 B Automated Upright Microscope System" ;
definition: "Leica DM4 B Upright Microscopes are designed specifically for use in clinical and life science research applications. These microscopes simplify your workflow with automated functions and easy-to-use software. The DM4 features 19-mm sCMOS camera imaging port to capture publication quality images and LAS X Navigator Software. Variety of optional accessories are available." .
SCR:024859 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cell2location " ;
definition: "Software tool that can resolve fine grained cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues. Used for comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics." .
SCR:024860 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RcisTarget" ;
definition: "Software R package to identify transcription factor binding motifs over represented on gene list. RcisTarget selects DNA motifs that are significantly over represented in surroundings of transcription start site of genes in gene-set, then annotates to TFs and those that have high Normalized Enrichment Score are retained and than candidate target genes are predicted. Used to identify transcription factor binding motifs enriched on list of genes or genomic regions." .
SCR:024861 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TISSUEGNOSTICS | StrataQuest" ;
NIFRID:synonym "StrataQuest tissue flow cytometry quantitative analysis system" ;
definition: "Tissue flow cytometry quantitative analysis platform integrates precise quantitative analysis solution at single cell level in tissue provided by HistoQuest/TissueQuest software. Software is compatible with multiple types of tissue and cell samples, enabling quantitative analysis in different biological research fields." .
SCR:024862 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2603" ;
rdfs:label "Beth Israel Deaconess Medical Center Precision RNA Medicine Delivery Unit Core Facility" ;
NIFRID:synonym "Beth Israel Deaconess Medical Center Precision RNA Medicine Core - Delivery Unit",
"Precision RNA Medicine Core - Delivery Unit" ;
definition: "Delivery Unit offers training and services on the NanoAssemblr Spark, NanoAssemblr Ignite+, and Malvern Zetasizer for the purpose of synthesis and characterisation of Lipid Nanoparticles (LNPs). The Zetasizer is able to read zeta potential and size of particles, including exosomes, liposomes, and LNPs." .
SCR:024863 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CLASTR" ;
NIFRID:synonym "Cellosaurus Short Tandem Repeat search tool" ;
definition: "Web tool to seach for similarity between cell line Short Tandem Repeat markers and those stored in Cellosaurus knowledge resource.Cellosaurus STR similarity search tool for cell line authentication." .
SCR:024864 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HFOApp" ;
NIFRID:synonym "High Frequency Oscillation App" ;
definition: "Software for detecting and identifying high frequency oscillations observed in EEG recordings. MATLAB based graphical user interface for High Frequency Oscillation marking." .
SCR:024865 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciLifeLab Data Platform" ;
definition: "Platform collates tools, databases, information, and other resources that can be useful to researchers and data producing facilities working in the area of data driven life science. Hub for data driven life science research in Sweden." .
SCR:024866 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Swedish Pathogens Portal" ;
definition: "Portal provides information, guidelines, data, services, and other resources aimed at supporting Swedish research community to share data related to pathogens and pandemic preparedness." .
SCR:024867 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "neuTube" ;
definition: "Software for reconstructing neurons from fluorescence microscope images. Used to generate neuron structure from 3D image with user interaction, which mainly consists of mouse clicks. It can also load SWC files from any other source for visualization or further editing." .
SCR:024868 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_2500" ;
rdfs:label "Neuorscience Tools | NeuroPactor" ;
NIFRID:synonym "NeuroPact TBI Instrument",
"Neuropactor",
"The NeuroPactor" ;
definition: "Electromagnetic instrument to mount on stereotaxic device, that delivers accurate reproducible contact with small laboratory animals for preclinical research." .
SCR:024869 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "RWD-68094 (Mice) & Model RWD-68095 (Rats)" ;
rdfs:label "Conduct Science | Stereotaxic Impactor" ;
NIFRID:synonym "Precise Spinal Impactor",
"Stereotaxic Impactor" ;
definition: "Precise spinal impactor used for reproducible impact on laboratory animals to generate neurotrauma injury for preclinical research." .
SCR:024870 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model FP301 & Model FP302" ;
rdfs:label "AmScien Instruments | Fluid Percussion Device" ;
NIFRID:synonym "Basic Fluid Percussion Device",
"Fluid Percussion Device w/ a PC-Based Pressure Measurement Unit" ;
definition: "Device creates controlled and measurable fluid percussion in small to medium sized animals for preclinical research." .
SCR:024871 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HPD-1700" ;
rdfs:label "Dragonfly | HPD-1700" ;
definition: "FP device consisting of falling pendulum that generates reproducible, hydraulic pulses to replicate closed TBI for neurological research." .
SCR:024872 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CS-WDTBIM" ;
rdfs:label "Conduct Science | Weight Drop TBI apparatus" ;
NIFRID:synonym "Weight Drop TBI Apparatus" ;
definition: "Weight drop device that allows for angled impact to the head of free-roaming laboratory animal for preclinical research." .
SCR:024873 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AMS_ 201" ;
rdfs:label "AmScien Instruments | Pneumatic Cortical Impact Device" ;
NIFRID:synonym "Cortical Impact Device",
"Pneumatic Cortical Impact Device" ;
definition: "Pneumatic impact device designed to reproduce controlled cortical impact to laboratory animals for preclinical research." .
SCR:024874 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TBI-0310" ;
rdfs:label "Precision Systems and Instrumentation | Head Impactor TBI-0310" ;
NIFRID:synonym "Head Impactor" ;
definition: "Computer controlled device with accurate and reproducible detection of cortical surface prior to initiating injury sequence, designed for preclinical research." .
SCR:024875 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Custom Design and Fabrication | Fluid Percussion Injury Device" ;
definition: "Fluid percussion device to be used on laboratory animals for neurologic research." .
SCR:024877 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2604" ;
rdfs:label "Beth Israel Deaconess Medical Center Functional Genomics and Bioinformatics Core Facility" ;
NIFRID:synonym "Functional Genomics and Bioinformatics Core" ;
definition: "Core provides consultative, laboratory, and bioinformatic services for next generation sequencing based applications.Core services include Pre- and post-experimental consultation to determine proper experimental approach, design, and interpretation; Standalone RNA preparation, RNA and DNA Bioanalyzer analyses, chromatin shearing/shear checks; Sample quality assessment of DNA and RNA using the BioAnalyzer and Qubit assays; Library preparation, sequencing, and analysis of transcriptomes (RNA-seq), cistromes (ChIP-seq), chromatin accessibility (ATAC-seq); Standalone sequencing on NextSeq500; Multiplexed 10x Single Cell/Nucleus Library RNA-seq Droplet generation, Library Preparation; Basic data analysis: quality assessment and normalization, genomic alignment, differential expression/enrichment, functional enrichment analysis (overrepresentation and GSEA), sample clustering, and motif enrichment; Bespoke data analysis, including integration of complex ChIP-seq and RNA-seq data sets, single-cell sequencing analyses.Core is located on the 7th floor of the Center for Life Sciences building in the Longwood Medical area (3 Blackfan Circle, CLS-728)." .
SCR:024878 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TDT | RZ5P Fiber Photometry Processor" ;
definition: "Optimized processor for fiber photometry.RZ5P is intended for use with TDT’s Synapse software." .
SCR:024879 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Med Associates | Wireless Running Wheel" ;
definition: "Allows monitoring of wireless wheel running activity without running wires." .
SCR:024880 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DIG-807" ;
rdfs:label "Med Associates | Wireless Running Wheel Hub" ;
definition: "Device connects wireless running wheels to data acquisition computer via a USB cable.All wheels must be set to the same address as the hub with which they communicate.Hub relays data to Wheel Manager Software." .
SCR:024881 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Julearn" ;
definition: "Software library of easy testing ML models directly from pandas DataFrames, while keeping the flexibility of using scikit-learn’s models." .
SCR:024882 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "San Diego Instruments | Rotor Rod System" ;
NIFRID:synonym "Rotor Rod",
"Rotor Rod System",
"ROTOR-ROD System" ;
definition: "System to study motor coordination using natural fear of falling response with reliability and accuracy. System measures motor function, motor learning, coordination, and equilibrium in both rats and mice." .
SCR:024883 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Qt Creator" ;
definition: "Cross-platform, complete Integrated Development Environment for application developers to create applications for multiple desktop, embedded, and mobile device platforms, such as Android and iOS. It is available for Linux, macOS and Windows operating systems. In addition, you can use the experimental WebAssembly plugin to build applications in web format and run them in web browsers." .
SCR:024884 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Arduino IDE 1.x",
"Arduino IDE 2.0",
"Arduino IDE 2.2.",
"Arduino IDE 2.x",
"Arduino Integrated Development Environment" .
SCR:024885 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3DHISTECH SlideViewer" ;
NIFRID:synonym "SlideViewer" ;
definition: "Software tool for working with whole slide images. Digital microscope application for supporting histopathological diagnostic workflow and microscope examination process. Advanced slide viewing software used in clinical pathology and research." .
SCR:024887 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adobe Fresco" ;
definition: "Software digital painting and drawing application. Used to create figures. Built for the latest stylus and touch devices, now including iPhones. Collection of vector and raster brushes, live brushes, to deliver natural painting and drawing experience.Vector and raster graphics editor developed by Adobe primarily for digital painting. Originally designed for the Apple iPad with Pencil support." .
SCR:024888 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggfortify" ;
definition: """Software tool as unified interface to visualize statistical results of popular R packages.
Provides unified interface that enables users to use one line of code to visualize statistical results of many R packages using ggplot2 idioms. Allows ggplot2 to handle some popular R packages.""" .
SCR:024889 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tidybayes" ;
definition: "Software R package to integrate popular Bayesian modeling methods into tidy data plus ggplot workflow." .
SCR:024890 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Octopus" ;
definition: "Software tool as mapping based variant caller that implements several calling models within unified haplotype aware framework. Variant caller that uses polymorphic Bayesian genotyping model capable of modeling sequencing data from range of experimental designs within unified haplotype aware framework. Bayesian haplotype based mutation calling." .
SCR:024891 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SomaticSeq" ;
definition: "Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification." .
SCR:024892 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PEPhub" ;
NIFRID:synonym "Portable Encapsulated Projects hub" ;
definition: "Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end." .
SCR:024893 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellTypist" ;
definition: "Web application for automated cell type annotation for scRNA-seq datasets. Allows for cell prediction using either built-in or custom models, in order to assist in accurate classification of different cell types and subtypes." .
SCR:024894 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CZ CELLxGENE Discover" ;
NIFRID:synonym "Chan Zuckerberg CELL by GENE Discover" ;
definition: "Portal used to find and download any of data sets published on CELLxGENE. Allows to download and visually explore data to understand functionality of human tissues at cellular level. Optimized for finding, exploring, and reusing single cell data. Collections Page lists collections hosted on CELLxGENE Discover and metadata that define tissue, assay, disease, organism, and cell count for each collection. Once you find published dataset of interest on CELLxGENE Discover, you can click on the explore button below the dataset description to explore the cells of that dataset using the CELLxGENE Explorer." .
SCR:024895 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Epi-Retro-Seq" ;
NIFRID:synonym "Epi-Retro-Seq web application" ;
definition: "Web application to link single-cell epigenomes and cell types." .
SCR:024896 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "United States Cancer Statistics Public Information Data" ;
definition: "United States Cancer Statistics public information data provided by Centers for Disease Control and Prevention." .
SCR:024897 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "score-assemblies" ;
definition: "Software Snakemake workflow for scoring and comparing multiple bacterial genome assemblies from Illumina and Nanopore to reference genomes." .
SCR:024898 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ont-assembly-snake" ;
definition: "Software Snakemake workflow for bacterial genome assembly plus polishing for Oxford Nanopore sequencing using multiple tools." .
SCR:024899 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lifelines" ;
definition: "Software survival analysis library written in Python." .
SCR:024900 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "table1" ;
definition: "Software R package to create HTML tables of descriptive statistics, as one would expect to see as the first table in medical epidemiological journal article. Used for generating tables of descriptive statistics in HTML." .
SCR:024901 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ANCOM-BC2" ;
NIFRID:synonym "Analysis of Compositions of Microbiomes with Bias Correction 2" ;
definition: "Software R package for differential abundance of microbiome. Used for performing differential abundance analysis of microbiome count data. Microbiome differential abudance and correlation analyses with bias correction." .
SCR:024902 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2607" ;
rdfs:label "Donald Danforth Plant Science Center Plant Growth Core Facility" ;
NIFRID:synonym "DDPSC Plant Growth Facility",
"Donald Danforth Plant Science Center DDPSC Plant Growth Facility" ;
definition: "Core offers scientists variety of advanced plant growth spaces and expert horticultural services.This includes Greenhouse Complex,Growth Chamber facility and Headhouse space. Greenhouses are designed for cultivation and containment of research crops, including regulated and protected plant materials.All greenhouses are environmentally controlled for temperature, humidity and light levels, and have automated irrigation and nutrient delivery capability using Argus Control Systems. Many houses have 14 to 20 ft sidewalls for growing taller crops, as well as in-floor heating, height-adjustable light canopies and automated irrigation capabilities. Over 95% of the greenhouse complex utilizes high intensity, energy-efficient horticultural LED lighting. Plant Growth Facility has multiple special-use work spaces including potting areas, seed processing, seed storage coolers, plant dry-down and soil handling rooms, autoclave, fertigation/utility rooms, as well as general storage space.Core is also responsible for managing Seed Storage coolers housing Danforth Center Institutional Seed Collection." .
SCR:024903 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2610" ;
rdfs:label "Van Andel Institute Mass Spectrometry Core Facility" ;
NIFRID:synonym "Mass Spectrometry Core",
"VAI Mass Spectrometry Core",
"VAI Mass Spectrometry Core (MSC)",
"Van Andel Institute Mass Spectrometry Core" ;
definition: "Core is committed to developing scientific partnerships with research labs to develop and deploy LC/MS and GC/MS methods specifically tailored to meet the needs of every project. Provides suite of technologies, experimental design support and staff expertise to deliver metabolomics, lipidomics, and proteomics capabilities to VARI scientists and collaborators. Analytical capabilities are combined with custom informatics and statistics solutions.Specific capabilities include: Metabolomics and Lipidomics liquid chromatography mass spectrometry (LC/MS) systems (Thermo Orbitrap ID-X, Thermo Orbitrap Exploris 240, and Agilent 6470 QQQ) and gas chromatography (GC)/MS systems (Agilent 5977b (2), Thermo 7610 ISQ) dedicated to small molecule analysis;Proteomics nano LC/MS systems (Orbitrap Eclipse and Orbitrap Exploris 480) for protein analysis; Bioinformatics for developing and maintaining informatics pipelines for mass spectrometry data analysis and visualization.Major equipment in the facility includes Thermo Scientific Orbitrap ID-X LC/MS,Thermo Scientific Orbitrap Exploris 240 LC/MS,Thermo Scientific Orbitrap Eclipse nanoLC/MS,Thermo Scientific Orbitrap Exploris 4800 LC/MS,Agilent 6470 Triple Quadrupole LC/MS ,Agilent Infinity 1290II UPLC,Agilent 5977B GC/MS,Thermo Scientific ISQ7610 EI/CI enabled GC/M." .
SCR:024904 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2609" ;
rdfs:label "University of Victoria Genome BC Proteomics Centre Core Facility" ;
NIFRID:synonym "University of Victoria Genome BC Proteomics Centre",
"University of Victoria Proteomics Centre" ;
definition: "Core for proteomics technology development and service. Provides mass spectrometry analytical services to academic, industrial, and government laboratories." .
SCR:024905 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2608" ;
rdfs:label "Beth Israel Deaconess Medical Center Spatial Technologies Unit Core Facility" ;
NIFRID:synonym "Spatial Technologies Unit" ;
definition: "Core for spatial and single cell technologies provides expertise, training, education and equipment. Supports projects, starting from consultation with matching right technologies to project needs, budget, and timeline. Provided services include single cell and spatial assays, tissue preparations, staining, sequencing, bioinformatic analyses.Equipment include 10x Genomics Visium,10x Genomics Xenium,Akoya PhenoImager HT whole slide scanner, Akoya Phenocycler Fusion,Bruker Vutara VXL,Nanostring GeoMX DSP, Vizgen MERSCOPE, Epredia TMA Grandmaster and more." .
SCR:024906 a owl:NamedIndividual ;
rdfs:label "HBio: Multichallel Systems | Roboinject" ;
NIFRID:synonym "Resource" ;
definition: "Fully automated robot for compound injection into oocytes, eggs, and embryos. Uses industry standard 96, 384, as well as custom well plates." .
SCR:024907 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HBio: Multichallel Systems | Roboocyte2" ;
NIFRID:synonym "Roboocyte" ;
definition: "Roboocyte provides automated cDNA/mRNA injection and subsequent TEVC recording on Xenopus oocytes in 96-well microtiter plates. Roboocyte2 was designed not only for Xenopus oocyte expression system, but to also for drug discovery. Provides sequential two electrode voltage clamp recording in oocytes and classical perfusion of compounds." .
SCR:024908 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "SolidWorks" ;
definition: "Brand within Dassault Systèmes that develops and markets solid modeling computer-aided design, computer-aided engineering, 3D CAD design and collaboration, analysis, and product data management software." .
SCR:024909 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Single Cell Pathway Analysis" ;
NIFRID:synonym "Single Cell Pathway Analysis (SCPA)" ;
NIFRID:abbrev "SCPA" ;
definition: "Software R package for pathway analysis in scRNA-seq data. It’s a different approach to pathway analysis that defines pathway activity as a change in multivariate distribution of a given pathway across conditions, rather than enrichment or over representation of genes." .
SCR:024910 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Synaptic Vesicles Detection" ;
definition: "Software tool as Python based synaptic vesicle classifier algorithm to identify neurotransmitter vesicles in electron microscopy images using Pytorch." .
SCR:024911 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2631" ;
rdfs:label "Tulane University TNBRC Animal Resources" ;
NIFRID:synonym "Tulane University TNBRC Animal Resources Core Facility",
"Tulane University Tulane National Biomedical Research Center Animal Resources Core Facility" ;
definition: "Unit is part of Tulane National Primate Research Center. Provides services including routine husbandry care for animal colonies, reporting of animals abnormal clinical signs or activities to veterinary medical staff and faculty. Animal Care Technicians provide support during diagnostic and therapeutic procedures and administration of preventive medicine program. Coordinates its activities with research personnel to provide assistance, equipment and support for their work. After hours care includes administration of treatments, collection of biologic samples for research activities and observation of animals. TNPRC facilities are accredited by Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC)." .
SCR:024912 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PS:Power and Sample Size Calculation" ;
NIFRID:abbrev "PS" ;
definition: "Software application as interactive program for performing power and sample size calculations. Can determine the sample size needed to detect specified alternative hypothesis with required power, the power with which specific alternative hypothesis can be detected with given sample size, or the specific alternative hypotheses that can be detected with given power and sample size." .
SCR:024913 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Daphnia Atlas" ;
definition: "Whole organism atlas utilizing 2D and 3D imaging. Atlas at cellular resolution serves as foundation for characterization of tissue and cellular change in Daphnia." .
SCR:024914 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2614" ;
rdfs:label "University of California Los Angeles Broad Stem Cell Research Center Microscopy Core Facility" ;
NIFRID:synonym "Los Angeles UCLA-Broad Stem Cell Research Center Microscopy Core",
"UCLA-Broad Stem Cell Research Center Microscopy Core",
"University of California" ;
definition: "Microscopy Core is collaboration of Broad Stem Cell Research Center and Department of Molecular, Cell and Developmental Biology at UCLA. Provides high resolution technologies for imaging and analyzing molecular and structural organization of cells and tissue as well as bioengineered materials. Services include confocal, wide field fluorescence and live cell imaging, as well as image analysis software." .
SCR:024915 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FMRI Expert Analysis Tool" ;
NIFRID:abbrev "FEAT" ;
definition: "Software tool for high quality model based FMRI data analysis. Used for preprocessing and statistical analysis of FMRI data." .
SCR:024916 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multivariate Exploratory Linear Optimized Decomposition into Independent Components" ;
NIFRID:synonym "MELODIC:Multivariate Exploratory Linear Optimized Decomposition into Independent Components" ;
NIFRID:abbrev "MELODIC" ;
definition: "Software tool to use at both the subject and group level to decompose FMRI data into time courses and spatial maps using Independent Component Analysis. Used to decompose single or multiple 4D data sets into different spatial and temporal components." .
SCR:024917 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FABBER" ;
definition: "Software command-line tool for approximate Bayesian inference using generative signal models." .
SCR:024918 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BASIL" ;
NIFRID:synonym "BASIL:Bayesian Inference for Arterial Spin Labeling MRI",
"Bayesian Inference for Arterial Spin Labeling MRI" ;
definition: "Software toolbox for kinetic model inversion to the data using Bayesian algorithm. Performs kinetic model inversion on ASL label control difference data." .
SCR:024919 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VERBENA" ;
NIFRID:synonym "VERBENA:Vascular Model Based Perfusion Quantification for DSC-MRI" ;
definition: "Software tool for quantification of perfusion and other haemodynamic parameters from Dynamic Susceptibility Contrast perfusion MRI of the brain." .
SCR:024920 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FMRIB's Automated Segmentation Tool" ;
NIFRID:synonym "FAST:FMRIB's Automated Segmentation Tool",
"Functional Magnetic Resonance Imaging of the Brain's Automated Segmentation Tool" ;
NIFRID:abbrev "FAST" ;
definition: "Software tool to segment 3D image of brain into different tissue types like Grey Matter, White Matter, CSF, etc., whilst also correcting for spatial intensity variations also known as bias field or RF inhomogeneities. Used to perform tissue type segmentation and bias field correction." .
SCR:024921 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FMRIB’s Integrated Registration and Segmentation Tool" ;
NIFRID:synonym "Functional Magnetic Resonance Imaging of the Brain's Integrated Registration and Segmentation Tool" ;
NIFRID:abbrev "FIRST" ;
definition: "Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences." .
SCR:024922 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FMRIB's Linear Image Registration Tool" ;
NIFRID:abbrev "FLIRT" ;
definition: "Sotware automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration." .
SCR:024923 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FNIRT" ;
definition: "Software tool to perform linear registration, meaning that it will translate, rotate, zoom and shear one image to match it with another." .
SCR:024924 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FSLVBM" ;
NIFRID:synonym "FSL Voxel Based Morphometry" ;
definition: "Software tool to analyse structural data. Voxel based morphometry style analysis carried out with FSL tools." .
SCR:024925 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SIENA " ;
definition: "Software package for both single-time-point and two-time-point analysis of brain change. Used to estimate percentage brain volume change between two input images, taken of the same subject, at different points in time." .
SCR:024926 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SIENAX" ;
definition: "Software tool to estimate total brain tissue volume, from single image, normalized for skull size." .
SCR:024927 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multimodal Image Segmentation Tool" ;
NIFRID:abbrev "MIST" ;
definition: "Software flexible tool for subcortical segmentation. It differs from FIRST in that it can use complementary information in different MRI modalities and is less reliant on manual segmentations." .
SCR:024928 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Intensity AbNormality Classification Algorithm" ;
NIFRID:synonym "BIANKA:Brain Intensity AbNormality Classification Algorithm" ;
NIFRID:abbrev "BIANCA" ;
definition: "Software tool for automated segmentation of white matter hyperintensities. Classifies image’s voxels based on their intensity and spatial features, and the output image represents the probability per voxel of being WMH. Flexible in terms of MRI modalities to use and offers different options for weighting spatial information, local spatial intensity averaging, and different options for choice of number and location of training points." .
SCR:024929 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multimodal Surface Matching" ;
NIFRID:synonym "MSM:Multimodal Surface Matching" ;
NIFRID:abbrev "MSM" ;
definition: "Software tool for registering cortical surfaces. Capable of driving alignment using wide variety of descriptors of brain architecture, function and connectivity." .
SCR:024930 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fsl_anat" ;
NIFRID:synonym "Anatomical Processing Script: fsl_anat" ;
definition: "Software tool provides general pipeline for processing anatomical images." .
SCR:024931 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FMRIB's Diffusion Toolbox" ;
NIFRID:synonym "Functional Magnetic Resonance Imaging of the Brain Diffusion Toolbox" ;
NIFRID:abbrev "FDT" ;
definition: "Software toolbox for analysis of diffusion weighted images." .
SCR:024932 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "TBSS:Tract-Based Spatial Statistics",
"Tract-Based Spatial Statistics" ;
NIFRID:abbrev "TBSS" .
SCR:024933 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XTRACT" ;
definition: "Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain." .
SCR:024934 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eddy" ;
definition: "Software tool for correcting eddy currents and movements in diffusion data. Used to predict undistorted data, to which actual observed images can be aligned, to estimate and to correct for volume-to-volume movement and off-resonance fields, to signal dropout caused by movement during diffusion encoding, within-volume movement and movement-induced changes of susceptibility-induced off-resonance field. In addition to correcting for these effects, the output from this framework offers description of off resonance and subject movement effects present in uncorrected data." .
SCR:024935 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "topup " ;
definition: "Software tool for estimating and correcting susceptibility induced distortions." .
SCR:024936 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eddyqc" ;
definition: "Software tool allows to assess dMRI data both at single subject and group levels.Calculates average SNR across all voxels within brain mask to give summary measure of overall quality of dataset. Used to generate single subject and study wise reports and databases." .
SCR:024937 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "randomise" ;
definition: "Software tool for nonparametric permutation inference on neuroimaging data." .
SCR:024938 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fsl-cluster" ;
NIFRID:synonym "cluster" ;
definition: "Software application used to form clusters, report information about clusters and/or perform cluster based inference." .
SCR:024939 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FDR" ;
NIFRID:synonym "False Discovery Rate" ;
definition: "Software program which takes in p-value image and uses False Discovery Rate theory to carry out multiple comparison correction." .
SCR:024940 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DualRegression" ;
definition: "Software application used as part of group level resting state analysis to identify subject specific contributions to group level Independent Component Analysis." .
SCR:024941 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "FLOBS:FMRIB's Linear Optimal Basis Sets",
"FMRIB's Linear Optimal Basis Sets" ;
NIFRID:abbrev "FLOBS" .
SCR:024942 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FSLeyes" ;
definition: "Web application as FSL image viewer for visualising neuroimaging data." .
SCR:024943 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fslutils" ;
NIFRID:synonym "FSLUTILS" ;
definition: "Software application set of useful command line utilities which allow conversion, processing etc. of Analyze and Nifti format data sets." .
SCR:024944 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atlasquery" ;
definition: "Software tool designed to allow command line interrogation of atlas images supplied with FSL. It takes as input the name of one of FSL atlases together with either coordinate of interest or mask." .
SCR:024945 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Rice Post-GWAS/QTL Analysis" ;
definition: "Web app for post-GWAS/QTL analysis that performs slew of novel bioinformatics analyses to cross GWAS/QTL mapping results with host of publicly available rice databases." .
SCR:024946 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mammalian Stress Granules Proteome" ;
NIFRID:abbrev "MSGP" ;
definition: "Database of protein components of mammalian stress granules." .
SCR:024947 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SUSAN" ;
NIFRID:synonym "Smallest Univalue Segment Assimilating Nucleus" ;
definition: "Software tool to cover image noise filtering, edge finding and corner finding." .
SCR:024948 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FUGUE" ;
definition: "Software tools for Echo Planar Imaging distortion correction used in diffusion imaging, functional MRI and perfusion imaging." .
SCR:024949 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Miscvis" ;
definition: "Software tool to combine background image (raw FMRI or high resolution MRI) with one or two statistics images. Statistics images must be in registration with the background image." .
SCR:024950 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "POSSUM" ;
NIFRID:synonym "Physics-Oriented Simulated Scanner for Understanding MRI" ;
definition: "Software tool that produces realistic simulated MRI and FMRI images or time series." .
SCR:024951 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BayCEST" ;
NIFRID:synonym "Bayesian Chemical Exchange Saturation Transfer" ;
definition: "Software tool for Bayesian analysis for chemical exchange saturation transfer z-spectra." .
SCR:024952 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ICA-PNM" ;
definition: "Software de-noising pipeline combines noise regressors identified by tools such as PNM and ICA (and FIX) and effectively prepares them for entry into single FEAT model, thus allowing the user to clean data in single step." .
SCR:024953 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FSL-MRS" ;
NIFRID:synonym "FSL Magnetic Resonance Spectroscopy" ;
definition: "Software spectroscopy analysis package includes tools for preprocessing of raw spectroscopy data, including coil combination, frequency and phase alignment, and filtering. Spectroscopy processing package that incorporates Bayesian fitting of spectra." .
SCR:024954 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PlayMolecule" ;
definition: "Virtual environment for drug discovery where simulations, AI and data are integrated to discover new opportunities. Online platform for drug discovery applications." .
SCR:024955 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2617" ;
rdfs:label "University of South Carolina Instrumentation Resource Core Facility" ;
NIFRID:synonym "Instrumentation Resource Facility (IRF)",
"USC Instrumentation Resource Facility (IRF)",
"USC School of Medicine Columbia Instrumentation Resource Facility (IRF)" ;
NIFRID:abbrev "IRF" ;
definition: "IRF houses biotechnological equipment that provide investigation ranging from single cell and molecular level analysis to whole animal imaging. Additionally, the IRF maintains a full range of ancillary equipment available for sample preparation, image enhancement, and data analysis." .
SCR:024957 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder: ID 501100002712",
"GRID: grid.412414.6",
"ISNI: 0000 0000 9151 4445",
"Wikidata: Q47249304" ;
rdfs:label "Oslo Metropolitan University" ;
NIFRID:synonym "OsloMet – Oslo Metropolitan University" ;
NIFRID:abbrev "OsloMet" ;
definition: "State university in Oslo and Kjeller in Norway. It is the result of the merger of many former vocational colleges in the Greater Oslo Region." .
SCR:024958 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RNAPhaSep " ;
definition: "Database that collects phase separation related RNAs manually curated from publication and public databases." .
SCR:024959 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RNA Granule Database " ;
NIFRID:synonym "RNAgranuleDB",
"RNAgranuleDB v2.0" ;
definition: "Created to collate literature evidence that support gene or protein association with the stress granules (SGs) and P-bodies (PBs), with the goal of consolidating high-confidence proteomes of SG and PB. Protein database for mammalian SGs and processing bodies (PBs), which are related condensates." .
SCR:024960 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RPS" ;
definition: "Comprehensive database of RNAs involved in liquid-liquid phase separation." .
SCR:024961 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ESpritz " ;
definition: "Web server to detect disordered regions from primary sequence." .
SCR:024962 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DisPhaseDB" ;
definition: "Database of mutations found in proteins involved in membrane-less organelles and liquid-liquid phase separation in human diseases." .
SCR:024963 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhaSeDis" ;
NIFRID:synonym "MloDisDB" ;
definition: "Manually curated database of relations between phase separation and diseases." .
SCR:024964 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhaSepDB" ;
definition: "Provides a collection of manually curated phase separation (PS) proteins and Membraneless organelles (MLOs) related proteins. Annotated phase separation-related proteins with droplet states, co-phase separation partners and other experimental information." .
SCR:024965 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhaSePro" ;
definition: "Database of proteins driving liquid–liquid phase separation. Stores over one hundred proteins that are able to drive LLPS, all curated and supported by literature references." .
SCR:024966 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LLPSDB" ;
NIFRID:synonym "Liquid Liquid Phase Separation DataBase" ;
definition: "Database of proteins undergoing liquid–liquid phase separation in vitro. Contains LLPS related proteins together with the corresponding phase separation conditions validated by experiments." .
SCR:024967 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DrLLSP" ;
definition: "Integrative database for proteins involved in liquid-liquid phase separation. Data resource of liquid–liquid phase separation in eukaryotes." .
SCR:024968 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dSCOPE" ;
definition: "Web server developed for detecting sequences critical for phase separation related proteins. Software to detect sequences critical for liquid-liquid phase separation. Deep learning based prediction tool for detecting sequences critical for phase separation related proteins." .
SCR:024969 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhaSePred" ;
definition: "Web server as meta-predictor for phase-separating proteins. Displays proteome-level quantiles of different features, thus profiling PS propensity and providing crucial information for identification of candidate proteins." .
SCR:024970 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CD-CODE " ;
NIFRID:synonym "CrowDsourcing COndensate Database and Encyclopedia" ;
definition: "Comprehensive, semi-manually curated crowdsourcing database of biomolecular condensates and their constituents as well as encyclopedia for scientific terms used to describe them." .
SCR:024971 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "D2P2" ;
NIFRID:synonym "Database of Disordered Protein Predictions" ;
definition: "Database of disordered protein predictions. Community resource for pre-computed disorder predictions on a large library of proteins from completely-sequenced genomes." .
SCR:024972 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PlaToLoCo" ;
NIFRID:synonym "PLAtform of TOols for LOw COmplexity" ;
definition: "Web meta-server for visualization and annotation of low complexity regions in proteins. Used for discovering LCRs and provides functional annotations such as domain detection, transmembrane segment prediction, and calculation of amino acid frequencies." .
SCR:024973 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PLAAC" ;
NIFRID:synonym "Prion Like Amino Acid Composition" ;
definition: "Web and command-line application to identify proteins with prion-like amino acid composition. Searches protein sequences to identify probable prion subsequences using hidden-Markov model algorithm." .
SCR:024974 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SGnn" ;
definition: "Web server for prediction of prion-like domains recruitment to stress granules upon heat stress." .
SCR:024975 a "Resoruce",
owl:NamedIndividual ;
rdfs:label "catGRANULE" ;
definition: "Algorithm for prediction of granules formation in yeast." .
SCR:024976 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cornell Veterinary Biobank" ;
NIFRID:synonym "Cornell University College of Veterinary Medicine Cornell Veterinary Biobank" ;
NIFRID:abbrev "CVB" ;
definition: "Biobank for collecting biological samples from both ill and healthy animals. Samples are processed and cataloged with the appropriate clinical information. Biobank has ISO 20387 accreditation." .
SCR:024977 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ncbi-genome-download" ;
definition: "Scripts to download genomes from the NCBI FTP servers." .
SCR:024978 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_352" ;
rdfs:label "Wistar Institute Molecular Screening and Protein Expression Core Facility" ;
NIFRID:synonym "Molecular Screening and Protein Expression",
"The Wistar Institute Molecular Screening and Protein Expression" ;
definition: "Facility enables to discover molecular, genetic, and small molecule compounds suitable to study functions of poorly understood proteins, signaling pathways, and cells in complex biological processes relevant to human physiology and disease; provides technical assistance with viral vector preparation and expression and purification of recombinant proteins; fosters collaborations. Staff will also develop and implement new technology as needed. Education and training is also available. Provides opportunities to develop new innovative basic and translational research, preliminary data for hypothesis driven research grant applications, and public-private partnerships." .
SCR:024979 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2618" ;
rdfs:label "University of Massachusetts Lowell Nuclear Magnetic Resonance Spectroscopy Lab Core Facility" ;
NIFRID:synonym "Nuclear Magnetic Resonance Spectroscopy Lab",
"UML - Nuclear Magnetic Resonance & Spectroscopy",
"University of Massachusetts Lowell UML - Nuclear Magnetic Resonance & Spectroscopy" ;
definition: "Core provides JEOL 400 MHz NMR equipped with auto sampling and automatic tuning and matching. Instrument can perform temperature and kinetic studies as well as x-nuclei and 2D experiments." .
SCR:024980 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2619" ;
rdfs:label "University of Massachusetts Lowell Thermal and Mechanical Properties Lab Core Facility" ;
NIFRID:synonym "UML - Thermal & Mechanical Properties Lab",
"University of Massachusetts Lowell UML - Thermal & Mechanical Properties Lab" ;
definition: "Core houses thermal analysis suite. Researchers are able to investigate behavior of material under stress and temperature change. Service level work and technical expertise are provided." .
SCR:024981 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2620" ;
rdfs:label "University of Massachusetts Lowell Next Generation Sequencing and Genomics Core Facility" ;
NIFRID:synonym "UML - Next Generation Sequencing & Genomics",
"University of Massachusetts Lowell UML - Next Generation Sequencing & Genomics" ;
definition: "Core provides Next-Generation DNA and RNA sequencing services and technical expertise including NGS library prep, DNA and RNA quality assessment, Fluorometric quantification of DNA/RNA/Protein, DNA and RNA isolation, PCR/qPCR, Qubit fluorometry, gene expression and drug development studies. Consultative services are available." .
SCR:024982 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Development of Immunological Reagents for the Identification of New World Monkey Biomarkers" ;
definition: "Project portal for generating recombinant NWM proteins, producing mouse monoclonal antibodies against New World Monkeys, validating immunological assays using these reagents, and distributing reagents and related scientific information to interested investigators." .
SCR:024983 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hybrid Rat Diversity Program" ;
definition: "Portal for Hybrid Rat Diversity Program with goal to extend the use of rat models for clinical translation through establishing animal resource and genomic dataset to facilitate the translation of laboratory research to clinical relevance. Specifically, the Hybrid Rat Diversity Panel resource provides the research community with foundation for systems genetics and tool for forward genetics." .
SCR:024984 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Center for Neuroanatomy with Neurotropic Viruses" ;
NIFRID:abbrev "CNNV" ;
definition: "This national resource was created to provide neuroscience community with access to reagents, training and facilities that are necessary to use neurotropic viruses as transneuronal tracers." .
SCR:024985 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EukRep" ;
definition: "Software tool as classifier that utilizes k-mer composition of assembled sequences to identify eukaryotic genome fragments prior to gene prediction. Used for eukaryotic sequence identification. Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets." .
SCR:024986 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "combi" ;
NIFRID:synonym "Compositional Omics Model-Based Integration" ;
definition: "Software R package for simultaneous exploration of multiple datasets. Compositional omics model based visual integration.Used to integrate omics data for visualization, with special focus on compositionality." .
SCR:024987 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Unipept" ;
NIFRID:synonym "Unipept 4.0" ;
definition: "Web application for metaproteome data analysis, with initial focus on tryptic-peptide-based biodiversity analysis of MS/MS samples.Designed for metaproteomics data analysis with focus on interactive data visualizations. Unipept 4.0 introduces complementary functional analysis based on GO terms and EC numbers." .
SCR:024988 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pyteomics" ;
NIFRID:synonym "Pyteomics 4.0" ;
definition: "Software library providing Python interfaces to proteomic data. Provides set of modules to facilitate the most common tasks in proteomics data analysis." .
SCR:024989 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Snellius supercomputer system" ;
NIFRID:synonym "Dutch National supercomputer system" ;
NIFRID:abbrev "Snellius" ;
definition: "Dutch National supercomputer system facilitates scientific research carried out in many Universities, independent research institutes, governmental organizations, and private companies in the Netherlands. Cluster of heterogeneous nodes built by Lenovo, containing predominantly AMD technology, with capabilities for high performance computing (parallel, symmetric multiprocessing), data-processing, and machine learning. Has several system specific storage resources, that are geared towards supporting the various types of computing. System has peak performance of 14 petaflop/s, making it the most powerful high-performance computing system in the Netherlands." .
SCR:024990 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2623" ;
rdfs:label "Louisiana State University Health Sciences Shreveport INLET High Throughput Screening Core Facility" ;
NIFRID:synonym "High Throughput Screening - INLET",
"Innovative North Louisiana Experimental Therapeutics program (INLET)" ;
definition: "Facility focused on discovery and development of drugs and genetic targets that affect human diseases including cancer, fungal, bacterial and viral infection, neurological disorders and cardiovascular disorders. Both live and fixed high throughput microscopy is performed using Incucyte S3, Incucyte SX5 and Cellomics ArrayScan VTI HCS Reader. Provides expertise and protocol design for variety of assays including: Cell proliferation, Cell viability, Phagocytosis, Chemotaxis, Cell migration/invasion, 3D spheroid growth. INLET Core provides cutting edge, multiplexed functional imaging platforms to perform multi-well high-throughput live-cell imaging and analysis assays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:024991 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GastroPlus" ;
definition: "Software modeling and simulation package for pharmacodynamics and pharmacokinetics." .
SCR:024992 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pipette Finding CNN" ;
NIFRID:synonym "Pipette Finding Convolutional Neural Network" ;
definition: "Software application for convolutional neural network that assesses pipette positioning before patch clamp is begun to minimize patch clamping errors in electrophysiology experiments. Used for detecting pipette positioning and making patch clamping procedures." .
SCR:024993 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Variable Neighborhood Search" ;
NIFRID:abbrev "VNS" ;
definition: "Algorithm to organize cells into clusters, utilizing information from both gene expression matrices and spatial coordinates. Comprehensive solution for cell clustering problem in spatial transcriptomics." .
SCR:024994 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ntsm" ;
NIFRID:synonym "ntsm: nucleotide sequence sample matcher" ;
definition: "Software alignment free, ultra low coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection. Used to count number of specific k-mers within sequence data. The counts can then be compare to other counts to determine to compute the probability that sample are of the same origin to discover incongruent samples or sample swaps." .
SCR:024995 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TissueScope LE" ;
rdfs:label "Huron Technologies | TissueScope LE Slide Scanner" ;
NIFRID:synonym "Huron Digital Pathology TissueScope LE Slide Scanner",
"TissueScope LE scanner" ;
definition: "Scanner for versatility, throughput, and ease of use. Scan up to twelve 1” x 3” brightfield slides, up to six 2” x 3” slides, or any size slide up to 6”x 8”." .
SCR:024996 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Huron Digital Pathology" ;
definition: "Manufacturer in St. Jacobs, Ontario, Canada. Provides whole slide scanners to clinical and research institutions. Offers slide scanning services. Each customer is given secured access to view and download their images. After scanning is complete, the glass specimens are returned if requested by the customer." .
SCR:024997 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Abaqus FEA" ;
NIFRID:synonym "Simulia Abaqus FEA" ;
definition: "Software suite for finite element analysis and computer aided engineering." .
SCR:024998 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2626" ;
rdfs:label "University of Rochester Medical Center Metabolomics Resource Core Facility" ;
NIFRID:synonym "Metabolomics Resource",
"University of Rochester Medical Center Metabolomics Resource" ;
definition: "Core specializes in metabolomic analysis. Provides Orbitrap Exploris 240 mass spectrometer, as well as dedicated staff for consultation and the analysis of biological samples." .
SCR:024999 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2627" ;
rdfs:label "University of Pennsylvania Penn Genomics and Sequencing Core Facility" ;
NIFRID:synonym "Penn Genomics and Sequencing Core",
"University of Pennsylvania Penn Genomics and Sequencing Core" ;
definition: "Provided services include molecular profiling of DNA and RNA on different platforms, Sanger sequencing, full service Next Generation Sequencing with different applications and bioinformatics, fragment analysis including human cell line authentication., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:025000 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2630" ;
rdfs:label "Stanford Geomicrobiology Shared Laboratories Core Facility" ;
NIFRID:synonym ;
definition: "Geomicrobiology analytical facilities consist of four different labs in the Green Earth Sciences Building. Main areas of study are: molecular, bio(geo)chemical, and ecological aspects of microbial cycling of nitrogen, carbon, and metals in environment diversity, distribution, and activity of microorganisms driving greenhouse gas cycling in ocean and beyond molecular biomarkers in modern organisms to refine our interpretations of microbial fossil record." .
SCR:025001 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stereo-seq Analysis Workflow" ;
NIFRID:synonym "SAW: Stereo-seq Analysis Workflow" ;
NIFRID:abbrev "SAW" ;
definition: "Software set of pipelines bundled to map sequenced reads to their spatial location on tissue section, quantify corresponding gene expression levels and visually present spatial gene expression distribution." .
SCR:025002 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hecatomb" ;
definition: "Software virome analysis pipeline for analysis of Illumina sequence data. Integrated software platform for viral metagenomics." .
SCR:025003 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Affiniti 50" ;
rdfs:label "Philips | Affiniti 50 Ultrasound System" ;
NIFRID:synonym "PHILIPS AFFINITI 50G version 1.5.8.916" ;
definition: "Portable ultrasound system that provides high rich image quality. User friendly for fast and critical clinical applications. Ultrasounds with Doppler." .
SCR:025004 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GE: Healthcare | Lunar Prodigy Advance system" ;
NIFRID:synonym "GE Healthcare Lunar Prodigy Advance version ENCORE 18",
"GE Lunar Prodigy Advance" ;
definition: "System offers dual energy X-ray absorptiometry assessment. Bone densitometry scan with enCORE v18 software platform. Meets International Society for Clinical Densitometry testing guidelines. Used to take measurements to work out the strength of bones in advanced bone and metabolic health clinical applications." .
SCR:025005 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Data LMU" ;
NIFRID:synonym "Open Data Ludwig-Maximillians University" ;
definition: "Data publication platform for publication and hosting of research data. Data repository contains open access journals published at Ludwig-Maximillians University, Munich, Germany. Server provides direct access to research data sets produced by projects at LMU. Open Journals LMU. Open Data LMU." .
SCR:025006 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LABRAT" ;
NIFRID:synonym "Lightweight Alignment Based Resolution of Alternative Three prime ends" ;
definition: "Software application to quantify usage of alternative polyadenylation and cleavage sites in RNAseq data and identify genes whose usage of these sites varies across experimental conditions." .
SCR:025007 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciLifeLab Research Data Management Guidelines " ;
definition: "Research Data Management guidelines to serve as information resource to life science researchers in Sweden regarding research data management committed to principles of FAIR (Findable, Accessible, Interoperable and Reusable) research data." .
SCR:025008 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CRAPome" ;
NIFRID:synonym "CRAPome:Contaminant Repository for Affinity Purification" ;
definition: "Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions." .
SCR:025009 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cytoscape StringApp" ;
NIFRID:synonym "stringApp" ;
definition: "Software application for network analysis and visualization of proteomics data. Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains appearance and many of features of STRING, and integrates data from associated databases." .
SCR:025010 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3DP Gustometer" ;
NIFRID:synonym "3D Printed Gustometer" ;
definition: "3D printed pacifier shaped mouthpiece for fMRI compatible gustometers to deliver up to eight liquids during fMRI task. Can be utilized to study flavor, taste reactivity, reward or punishment with food, conditioning, and neurodegenerative conditions such as Alzheimers and Parkinsons, since taste and smell senses diminish early into disease acquisition." .
SCR:025011 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2632" ;
rdfs:label "University of Nebraska Lincoln Bioinformatics Core Facility" ;
NIFRID:synonym "University of Nebraska�Lincoln UNL-Bioinformatics Core Research Facility",
"UNL-Bioinformatics Core Research Facility" ;
NIFRID:abbrev "BCRF" ;
definition: "Core offers education, analysis, and computational services in the area of bioinformatics and computational biology. Offers initial consultations to help with experimental design and power analysis of 'omics data for grant submissions and bioinformatics needs for current projects." .
SCR:025012 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2633" ;
rdfs:label "University of Nebraska Lincoln CryoEM Core Facility" ;
NIFRID:synonym "CryoEM Core Facility" ;
definition: "Core facility is dedicated to structural characterization of biological samples and microcrystals using cryo-electron microscopy. CryoEM workflows including, single-particle CryoEM, Cryo-electron tomography , and Micro crystal electron diffraction. Instrumentation includes TFS 200kV Glacios CryoTEM, equipped with zero-loss Selectris Energy Filter, Flacon 4i Direct Electron Detector, and Ceta-D camera, Pelco Easy Glow Discharger, TFS Vitrobot Mark IV, and Leica EM GP2. We also present all the capacities for storing and shipping samples. Facility has Data storage Server and Live processing workstation for our users� convenience, including data processing suites RELION and CryoSPARC available at our campus supercomputer Swan cluster at the Holland Computer Center." .
SCR:025013 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GROMACS topology editors" ;
NIFRID:abbrev "gmxtras" ;
definition: "Software tool as set of Python scripts to modify GROMACS topology files, by adding content from different topology files and other GROMACS input files. Useful, particularly when system components are assembled outside of GROMACS, or in different steps within GROMACS. This helps prevent users from having to copy and paste significantly large blocks of text within topology files." .
SCR:025014 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StemChecker" ;
definition: "Web server to check whether given list of genes can be associated with stemness. Used to identify sets of genes considered essential to define stem cells. Used to explore presence of stemness signatures in user-defined gene sets. Analysis tool, based on curation of published stemness signatures defined by gene expression, RNAi screens, Transcription Factor binding sites, literature reviews and computational approaches." .
SCR:025015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Louisiana State University Health Shreveport Library" ;
NIFRID:synonym "LSU Health Shreveport Library" ;
definition: "Provides systematic review literature searching services, writing review services, and resources in print and electronic format to faculty, students, and researchers in the schools of the health sciences. The Library also manages the SPSS and EndNote licenses for the campus." .
SCR:025016 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MAGeCK" ;
NIFRID:synonym "Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout" ;
definition: "Software tool to identify important genes from genome-scale CRISPR-Cas9 screens. Used for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens." .
SCR:025017 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "2FAST2Q" ;
definition: "Software package for general purpose sequence search and counting program for FASTQ files. Python3 program that counts sequence occurrences in raw FASTQ files. Used for CRISPRi-Seq, and for extracting and counting any kind of information from Illumina reads, such as barcodes." .
SCR:025018 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JStor Global Plants" ;
NIFRID:synonym "Global Plants" ;
definition: "Database of digitized plant specimens. Used for finding plant name, type, specimens and their label data.The collection also includes partner contributed reference works and primary sources. Used for research and teaching in botany, ecology, and conservation studies." .
SCR:025019 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012002" ;
rdfs:label "International Plant Name Index" ;
NIFRID:abbrev "IPNI" ;
definition: "Global repository for all plant names with citation of its place of origin. Provides nomenclatural data, including spelling, author, types and first place/date of publication, for scientific names of vascular plants from family to infraspecific ranks." .
SCR:025020 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QSBB Digital Pathology Resource" ;
NIFRID:synonym "Queen Square Brain Bank Digital Pathology Resource",
"University College London Queen’s Square Brain Bank Digital Pathology Resource" ;
definition: "Platform for archival digital glass slide collection containing digital whole slide images from Lewy body disorders: Parkinson’s Disease, Parkinson’s Disease with Dementia and Dementia with Lewy Bodies, and control cases.E stained post-mortem brain tissues from patients with neurodegenerative diseases and controls." .
SCR:025021 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | ST5020 Multistainer Slide Stainer" ;
NIFRID:synonym "Leica ST5020 Multistainer" ;
definition: "Histology multistainer produces results for both routine and special stains and can perform single or multiple protocols at the same time. Contains 12 slide racks and 34 reagent stations." .
SCR:025022 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WaybackMachine" ;
NIFRID:synonym "Internet Archive WaybackMachine" ;
definition: "Digital library of Internet sites and other cultural artifacts in digital form. Web history is accessible through Wayback Machine and they work with 1,200+ library and other partners through Archive-It program to identify more important web pages." .
SCR:025023 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Guided Sparse Factor Analysis" ;
NIFRID:abbrev "GSFA" ;
definition: "Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data." .
SCR:025024 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FLUOstar_Omega" ;
rdfs:label "BMG Labtech | FLUOstar Omega" ;
NIFRID:synonym "BMG Labtech FLUOstar Omega plate reader",
"FLUOstar Omega",
"FLUOstar Omega plate reader" ;
definition: "Multi-mode microplate reader with three detection modes.Utilises ultra-fast UV/vis spectrometer or filters for absorbance as well as highly sensitive filters for all other detection modes." .
SCR:025025 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CKX53" ;
rdfs:label "Olympus | CKX53 Inverted Microscope" ;
NIFRID:synonym "CKX53 Inverted Microscope" ;
definition: "Inverted microscpe for visualization of live cell culture." .
SCR:025026 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Social Deprivation Index" ;
NIFRID:abbrev "SDI" ;
definition: "SDI is composite measure of area level deprivation based on seven demographic characteristics collected in the American Community Survey and used to quantify the socio-economic variation in health outcomes." .
SCR:025027 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AccPbFRET" ;
NIFRID:synonym "Acceptor Photobleaching Fluorescence Resonance Energy Transfer" ;
definition: "Software tool for analysis of acceptor photobleaching FRET images. Allows fully corrected, pixel-wise calculation and detailed, region of interest based analysis of FRET efficiencies in microscopic images." .
SCR:025028 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RiFRET" ;
NIFRID:synonym "Ratiometric Fluorescence Resonance Energy Transfer" ;
definition: "Software tool used to calculate FRET efficiency on pixel-by-pixel basis from ratiometric FRET images. Allows to correct for channel cross-talk and to calculate FRET from image stacks, i.e., from 3D data sets. ImageJ plugin for intensity-based three-filter set (ratiometric) FRET." .
SCR:025029 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OrthoIntegrate" ;
definition: "Software R package for Orthologue assignment and Integration of single cell data. Functions for Orthologue Assignment and Integration of Single Cell Data between species." .
SCR:025031 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "moseq2-app" ;
NIFRID:synonym "MoSeq2 Jupyter Notebook platform" ;
definition: "Software application as starting point to MoSeq2 package suite. Unsupervised machine learning method which takes inputs from depth cameras in 3D and transforms them into different behavioral motifs which called syllables. Used to extract mouse pose from depth video and model how pose evolves over time." .
SCR:025032 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Keypoint MoSeq" ;
definition: "Software application as machine learning-based platform for identifying behavioral modules from keypoint data without human supervision. Package provides tools for fitting MoSeq model to keypoint tracking data. Used to infer pose dynamics with keypoint data in addition to behavioral syllables." .
SCR:025033 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NextDenovo" ;
definition: "Software error correction and accurate assembly tool for noisy long reads. De novo assembler for long reads. String graph-based de novo assembler for long reads like CLR, HiFi and ONT." .
SCR:025034 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2665" ;
rdfs:label "University of Colorado Boulder Geomicrobiology Lab Core Facility" ;
NIFRID:synonym "Geomicrobial Physiology and Evolution Lab",
"University of Colorado Boulder GeoMicrobial Co-Culturing Lab" ;
NIFRID:abbrev "GEOM" ;
definition: "Microbial culturing facility focused on growing microorganisms with diverse physiologies from photosynthesis to methanogenesis." .
SCR:025035 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gplots" ;
definition: "Software R package to create figures." .
SCR:025036 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sorting long Reads of Y or other sex-limited chromosome" ;
NIFRID:abbrev "SRY" ;
definition: "Software application for sorting long-read of sex-limited (Y or W) chromosome. Used to identify male specific k-mers based on population data." .
SCR:025037 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CHARMM-GUI" ;
definition: "Web-based platform to interactively build complex systems and prepare their inputs with well established and reproducible simulation protocols for molecular simulations." .
SCR:025038 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QMeanDisco" ;
NIFRID:synonym "distance constraints" ;
definition: "Web server for accurate local and global model quality estimates. Composite scoring function to derive entire structure and residue absolute quality estimates on basis of one single model." .
SCR:025039 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepTMHMM" ;
definition: "Web application for prediction of topology of both alpha-helical and beta-barrel transmembrane proteins. Used to predict alpha and beta transmembrane proteins using deep neural networks." .
SCR:025040 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Axio_Examiner" ;
rdfs:label "Zeiss | Axio Examiner microscope" ;
NIFRID:synonym "ZEISS Axio Examiner" ;
definition: "Fixed stage microscope for patch-clamp experiments on nerve cells and brain slices. With its design optimized for low vibration and generous room for micromanipulation and patch clamp accessories, Axio Examiner enables undisturbed low-noise single-channel recordings." .
SCR:025041 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "snm3C Pipeline" ;
NIFRID:synonym "Single Nucleus Methly-Seq and Chromatin Capture",
"Single Nucleus Methly-Seq and Chromatin Capture (snM3C)",
"single-nucleus Methylome and Chromatin Contact" ;
NIFRID:abbrev "snM3C" ;
definition: "Software open-source, cloud-optimized computational workflow for processing single-nucleus methylome and chromatin contact (snm3C) sequencing data. The workflow is designed to demultiplex and align raw sequencing reads, call chromatin contacts, and generate summary metrics." .
SCR:025042 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Paired-Tag Pipeline" ;
NIFRID:synonym "Paired-Tag",
"paired_tag" ;
definition: "Software open-source, cloud-optimized pipeline developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN). It supports the processing of 3' single-nucleus histone modification data (generated with the paired-tag protocol]) and 10x gene expression (GEX) data generated with the 10x Chromium Multiome assay." .
SCR:025043 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ML Commons" ;
definition: "Artificial Intelligence engineering consortium, built on philosophy of open collaboration to improve AI systems to measure and improve accuracy, safety, speed and efficiency of AI technologies helping companies and universities around the world. Community-driven and community-funded effort." .
SCR:025044 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LJPcalc" ;
NIFRID:synonym "Liquid Junction Potential calculator" ;
definition: "Web application for calculating liquid junction potential between two solutions according to the stationary Nernst-Planck equation." .
SCR:025045 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggsurvfit" ;
definition: "Software R package for flexible time-to-event figures creation. Used to create figures ready for publication." .
SCR:025046 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "zellkonverter" ;
definition: "Software package for converting between SingleCellExperiment objects and alternative objects for storing single-cell RNA-sequencing data. Used for conversion between scRNA-seq objects." .
SCR:025047 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Find My Understudied Genes " ;
NIFRID:abbrev "FMUG" ;
definition: """Software data-driven tool to identify understudied genes and characterize their tractability. Users submit list of human genes and can filter these genes down based on list of factors.
Code to generate Find My Understudied Genes app for Windows, iOS and macOS platforms.""" .
SCR:025048 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LSM 980" ;
rdfs:label "Zeiss | LSM 980 with Airyscan 2 Microscope" ;
NIFRID:synonym "ZEISS LSM 980 with Airyscan 2" ;
definition: "Upright laser scanning confocal microscope with Airyscan 2 technology. Airyscan module is new detector concept featuring 32 channel GaAsP-PMT area detector. Airyscan detector brings simultaneous improvements in spatial resolution and signal-to-noise ratio in comparison with conventional confocal microscopy." .
SCR:025049 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MendelianRandomization" ;
definition: "Software Mendelian randomization R package. Encodes several methods for performing Mendelian randomization analyses with summarized data." .
SCR:025050 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Science Gateways" ;
NIFRID:abbrev "SGX3" ;
definition: "Community of cyberinfrastructure specialists and domain scientists working together to bring science online. SGX3 Center for excellence provides opportunity to participate with SGX3 to define the future intersection of science and cyberinfrastreucture." .
SCR:025051 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID: 501100007088",
"GRID: grid.5522.0",
"ISNI: 0000 0001 2337 4740",
"Wikidata: Q189441" ;
rdfs:label "Jagiellonian University; Krakow; Poland" ;
definition: "Public research university in Kraków, Poland. Founded in 1364 by King Casimir III the Great, it is the oldest university in Poland and the 13th oldest university in continuous operation in the world. It is regarded as Poland's most prestigious academic institution." .
SCR:025052 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100014160" ;
rdfs:label "LDbase" ;
NIFRID:synonym "Learning and Development data repository" ;
definition: "NIH funded collaboration between researchers and librarians to build behavioral project oriented data repository containing decades of knowledge from educational and developmental sciences on individuals across the full range of abilities." .
SCR:025053 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tidycmprsk" ;
definition: "Software R package provides intuitive interface for working with competing risk endpoints. Used for competing risks estimation." .
SCR:025054 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Monaco" ;
definition: "Software Python library for analyzing uncertainties and sensitivities in computational models by setting up, running, and analyzing Monte Carlo simulation wrapped around that model." .
SCR:025055 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioCircos" ;
definition: "Software R package for generating circular multi-track plots." .
SCR:025056 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Numba" ;
definition: "Open source JIT compiler that translates subset of Python and NumPy code into fast machine code. Can compile large subset of numerically-focused Python, including many NumPy functions. Has support for automatic parallelization of loops, generation of GPU-accelerated code, and creation of ufuncs and C callbacks." .
SCR:025057 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "F-Leach" ;
definition: "Software tool for determination of dispersion risks due to leaching and for determination of soil quality evolution." .
SCR:025058 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CSM-Toxin" ;
definition: "Web server for predicting protein toxicity. Protein toxicity classifier, which relies on protein primary sequence. Used for predicting toxicity of biologics." .
SCR:025059 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CUTTag_tutorial" ;
definition: "Software for processing and analyzing Targets and Tagmentation data. The illustration data used in this tutorial is the profiling of histone modifications in the human lymphoma K562 cell line, but the tutorial is generally applicable to any chromatin protein, including transcription factors, RNA polymerase II, and epitope-tagged proteins." .
SCR:025061 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VirHost" ;
definition: "Software tool for predicting reservoir hosts of RNA viruses through viral genomes. Takes complete RNA viral genomes as input and predicts natural reservoir host groups from kingdom level to order level." .
SCR:025062 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "MedChemExpress" ;
definition: "Company offers research chemicals and biochemicals for scientific use. Provides customer oriented services including customized order volume ranging from milligrams to kilograms scale, structurally and synthetically diverse biologically active compounds." .
SCR:025063 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Biowest" ;
definition: "Biotechnology company in Nuaillé, France. Provides animal serum and cell culture media." .
SCR:025064 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_epMotion 5070 CB" ;
rdfs:label "Eppendorf | epMotion 5070 CB" ;
NIFRID:synonym "epMotion 5070 CB",
"epMotion® 5070 CB" ;
definition: "Automated pipetting workstation that is used for serial dilutions, reagent distribution, sample transfer from tubes to plates, and sample normalization." .
SCR:025065 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sigma | Labnet MultiGene Gradient PCR Thermal Cycler" ;
NIFRID:synonym "Labnet MultiGene™ Gradient PCR Thermal Cycler" ;
definition: "PCR thermal cycler with 96 well block (12 8 x 0.2 mL strip tubes, 96 x 0.2 mL), AC/DC input 230 V AC." .
SCR:025066 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyContact" ;
definition: "Software tool for analysis of non-covalent interactions in molecular dynamics trajectories. Implemented in Python and is universally applicable to any kind of MD trajectory supported by MDAnalysis package." .
SCR:025067 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CytoFLEX LX" ;
rdfs:label "Beckman Coulter | CytoFLEX LX Flow Cytometer" ;
NIFRID:synonym "Beckman Coulter CytoFLEX LX",
"CytoFLEX LX" ;
definition: "This model is equipped with four lasers (405, 488 561 and 638nm), and is capable of detecting FSC, SSC and 16 colors." .
SCR:025068 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Beckman Coulter | CytoFLEX SRT Cell Sorter" ;
NIFRID:synonym "Beckman Coulter CytoFLEX SRT",
"CytoFLEX SRT" ;
definition: "Offers multiple configurations with the option to easily upgrade. Instrument can be configured to use up to four lasers and up to 15-color detection to identify subtle differences between cells. Core Facility’s CytoFLEX SRT is four-laser platform (405, 488, 561 and 638nm) instrument capable of detecting FSC, SSC and 15-colors and is able to sort up to four separate populations from the same sample, and deposit them in variety of tubes and plates. Operates under CytExpert SRT Software." .
SCR:025069 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nanofcm | Flow NanoAnalyzer" ;
NIFRID:synonym "Flow NanoAnalyzer",
"NanoAnalyzer" ;
definition: "High sensitivity flow cytometry for nanoparticle analysis for life science, nanoscience and nanotechnology studies. Can be used for multiparameter characterization of natural and synthetic nanoparticles (7-1000 nm) at the single particle level.Combining light scattering and fluorescence detection, high-resolution distributions of particle size and biochemical properties can be acquired simultaneously in 1-2 minutes. UNL Flow Cytometry Core NanoAnalyzer is equipped with two lasers (488 and 640nm), and is capable of detecting SSC and two colors. Operates under NF Professional Software. System is designed to measure size and concentration of nanoparticle samples." .
SCR:025070 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | EVOS M7000 Imaging System" ;
NIFRID:synonym "EVOS™ M7000 Imaging System" ;
definition: "Fully automated, inverted, multi-channel fluorescence and transmitted light imaging system. System with acquisition tools with enhanced autofocus algorithms and automated routines for microwell plate assays, time-lapse live cell imaging, area scanning in time lapse and Z-stacks in scan mode to generate publication quality images and data." .
SCR:025071 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genotype Sparse Compression" ;
NIFRID:synonym "Genotype Sparse Compression (GSC)" ;
NIFRID:abbrev "GSC" ;
definition: "Software tool for lossless compression of VCF files, designed to efficiently store and manage VCF files in compressed format. It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities." .
SCR:025075 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2637" ;
rdfs:label "Penn State Hershey College of Medicine Atomic Force Microscopy Core Facility" ;
NIFRID:synonym "Atomic Force Microscopy Core",
"Hershey College of Medicine Atomic Force Microscopy Core Facility" ;
definition: "Provides College of Medicine research community with access to atomic force microscopy equipment and expertise." .
SCR:025076 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2656" ;
rdfs:label "Geisel School of Medicine at Dartmouth DCC Microscopy Shared Resource Core Facility" ;
NIFRID:synonym "DCC-Microscopy Shared Resource",
"Geisel School of Medicine at Dartmouth DCC-Microscopy Shared Resource" ;
definition: "Facility provides imaging instrumentation and analysis software along with training and expertise.Instrumentation and technologies available to users include Zeiss LSM800 AIRYSCAN confocal microscope integrated with Zen software; PerkinElmer / Akoya Vectra 3.0 Automated Quantitative Pathology Imaging System;Agilent/BioTek Cytation 5 with BioSpa8 live-cell microscopy system for fluorescence and phase contrast microscopy; Olympus IX-83 ZDC2 microscope equipped with PRIMO UV light-based bioengineering device for micropatterning and microfabrication; Olympus IX73 Inverted Fluorescence Microscope.Image analysis software hosted on appropriately powered workstations with cloud connectivity for high capacity storage: HALO3, Inform, Volocity, AutoDeblur, Image-J / Fiji.Transmission and scanning electron microscopy including FEI Talos F200i (200kV TEM and STEM electron microscope (TEM), equipped for micro-analysis, and cryo-EM;FEI Helios CX5 dual beam FIB-SEM system with X-ray microanalysis detectors; instruments for specimen preparation for transmission and scanning electron microscopy including ultramicrotomes Leica Ultracut UC6 and UC7, critical point dryer Samdri-970, Leica ACE 600 coater and ThermoFisher Vitrobot." .
SCR:025077 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2657" ;
rdfs:label "Geisel School of Medicine at Dartmouth DCC Irradiation, Imaging, Microscopy and Animal Cancer Models Core Facility" ;
NIFRID:synonym "DCC-Irradiation",
"Geisel School of Medicine at Dartmouth DCC Irradiation",
"Imaging",
"Microscopy and Animal Cancer Models" ;
definition: "Integrated core offers services in Irradiation, pre-clinical imaging of small and large animals, light and electron microscopy, large and small animal cancer models. Irradiation Section assists investigators in radiation treatment planning and delivery of ionizing irradiation to cells, rodents and large animals with engineered, transplanted or spontaneous tumors.Imaging Section provides technologies for non-invasive, whole-animal imaging of animals used in preclinical research studies. Microscopy Section provides access to point scanning confocal microscopy with Airyscan super resolution, conventional bright field and fluorescence light microscopy, high throughput live imaging, automated slide scanning and image analysis resources. Electron microscopy resource provides scanning transmission electron microscopy. Animal Cancer Models section supports generation and utilization of large and small animals for modeling cancer and other human diseases. Section has expertise in generating cancer models using wild type or genetically engineered animals in immunocompetent and immunocompromised backgrounds, as well as mice with humanized immune system." .
SCR:025078 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2659" ;
rdfs:label "Ohio State University Campus Microscopy and Imaging Core Facility" ;
NIFRID:synonym "Ohio State University Campus Microscopy and Imaging Facility",
"OSU-Campus Microscopy & Imaging Facility" ;
definition: "Offers services from sample preparation to image processing.Provides instrumentation for use such as electron microscopy, light microscopy, and access to other instrumentation for use in sample prep." .
SCR:025079 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2661" ;
rdfs:label "University of Colorado Boulder Intermountain Neuroimaging Consortium Core Facility" ;
NIFRID:synonym "Intermountain Neuroimaging Consortium",
"University of Colorado Boulder Intermountain Neuroimaging Consortium" ;
definition: "Magnetic resonance imaging research facility located at University of Colorado Boulder." .
SCR:025080 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2684" ;
rdfs:label "Colorado School of Mines Shared Instrumentation Facility Water Quality Analysis Core Facility" ;
NIFRID:synonym "Carbon and nitrogen analysis",
"ion chromatography" ;
definition: "Core facility houses the capability to test water using multiple instruments and techniques including : Ion Chromatography, which is an analytical technique for determining the concentration of anions in aqueous solutions such as fluoride, chloride, nitrate, phosphate and sulfate; Carbon and nitrogen analysis, which incorporates measurements of total carbon, total inorganic carbon and total organic carbon together with total nitrogen; and other parameters such as pH, alkalinity, turbidity, conductivity (and others) using instrumentation and kits." .
SCR:025081 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MIKAIA" ;
definition: "Software image analysis tool for digital pathology and spatial biology researchers." .
SCR:025082 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2666" ;
rdfs:label "Stanford University Cosmogenic Isotope Lab Core Facility" ;
NIFRID:synonym "Stanford Cosmogenic Isotope Lab" ;
NIFRID:abbrev "SCI-Lab" ;
definition: "Core for understanding Earth surface processes in bedrock, soil, water, and sediment. Interactions between cosmic rays and Earth’s upper atmosphere create unique isotopes both in the atmosphere and in materials on Earth’s surface. By assessing the ratios and/or concentrations of these isotopes, we can get a deeper insight into the exposure age, soil production rate, catchment-averaged erosion, and processes of Earth’s varied landscapes." .
SCR:025083 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2662" ;
rdfs:label "University of Florida Systems Physiology and Omics Core Facility" ;
NIFRID:synonym "Systems Physiology and Omics Core",
"University of Florida Systems Physiology and Omics Core" ;
definition: "Provides specialized resources and expertise to support scientists that want to incorporate systemic measures of mouse activity, metabolism and feeding. The systems are also embedded within light regulated environments to capture circadian, time of day, based outcomes.Supports scientists wanting to perform circadian type analyses with either pre-clinical or clinical time series data. Supports scientists wanting to incorporate -Omics measures into their studies with experience in genomics, proteomics and metabolomics assays/analyses. These services are available to support new investigators, early-stage investigators and current investigators in aging." .
SCR:025084 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PMI" ;
NIFRID:synonym "Platform for Research in Medical Imaging",
"PMI 0.4" ;
definition: "Software tool to support translation of basic research in medical image analysis into early clinical studies." .
SCR:025085 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2663" ;
rdfs:label "University of Wisconsin-Madison Carbone Cancer Center Flow Laboratory Core Facility" ;
NIFRID:synonym "UW Carbone Cancer Center Flow Lab",
"UWCCC Flow Cytometry Laboratory" ;
definition: "Facility provides technical and educational support for fluorescence based single cell analysis and isolation to further the characterization and understanding of cellular function, biomarkers, pathology, and treatment in basic, translational, and clinical research projects." .
SCR:025087 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2664" ;
rdfs:label "California Institute of Technology Flow Cytometry and Cell Sorting Core Facility" ;
NIFRID:synonym "California Institute of Technology Caltech Flow Cytometry and Cell Sorting Facility",
"Caltech Flow Cytometry and Cell Sorting Facility" ;
definition: "Facility offers cell analyzers and cell sorters as well as expertise in large range of traditional immunophenotyping and small particle, geo-physical applications." .
SCR:025088 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID: grid.453560.1; ISNI: 0000 0001 2192 7591; Crossref Funder ID: 100006271; Wikidata: Q148554;" ;
rdfs:label "Smithsonian National Museum of Natural History" ;
NIFRID:synonym "National Museum of Natural History" ;
NIFRID:abbrev "NMNH" ;
definition: "Natural history museum administered by Smithsonian Institution, located on the National Mall in Washington, D.C., United States. Houses specimens and artifacts, which are mostly animals preserved in formaldehyde. Digital records are available online. " .
SCR:025089 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NoCTURN" ;
NIFRID:synonym "Convergence Research the Non-Clinical Tomography Users Research Network" ;
definition: "FAIROS Research Coordination Network. Mirroring NSF’s “10 Big Ideas” of Convergence Research the Non-Clinical Tomography Users Research Network (NoCTURN) will leverage input from broad community of tomography educators, researchers, and industry stakeholders to propose improvements to data handling that cut across scientific disciplines. Primary goal is to develop practical recommendations that link today’s tomography data with tomorrow’s tomography discoveries." .
SCR:025090 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2667" ;
rdfs:label "Smithsonian Institution National Museum of Natural History Scientific Imaging Core Facility" ;
NIFRID:synonym "Scientific Imaging",
"Smithsonian Institution National Museum of Natural History" ;
NIFRID:abbrev "EDS",
"FESEM",
"mCTIC",
"NMNH",
"SciVis",
"SEM" ;
definition: "Scientific Imaging is comprised of Microscopy Lab, µCT Imaging Center (mCTIC), and Scientific Visualization Center (SciVis). Facility is user driven research core in support of National Museum of Natural History life sciences research. Provides preparation and examination of natural history specimens for scanning electron microscopy, stereo light microscopy, compound fluorescence microscopy, X-ray micro-computed tomography and 3D laser scanning. Produces reconstructed volumes of scanned specimens. Provides reconstruction, segmentation, analysis and animation of 3D datasets." .
SCR:025091 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "The Delft AI Cluster (DAIC)" ;
NIFRID:abbrev "DAIC" ;
definition: "High Performance Computing cluster consisting of Linux compute servers with processing power and memory for running large, long or GPU-enabled jobs." .
SCR:025092 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NSF Network for Advanced NMR" ;
NIFRID:synonym "Network for Advanced Nuclear Magnetic Resonance" ;
NIFRID:abbrev "NAN" ;
definition: "Provides distributed services from Universities of Connecticut, Georgia, and Wisconsin to democratize application of high-field NMR spectroscopy for applications in biomedicine, materials science, and chemistry. Multi-institution collaboration creating distributed research infrastructure for NMR applications including resource discovery, access to NMR spectrometers, ranging from bench top to ultra-high field, knowledgebases on best practices, and data archiving and sharing." .
SCR:025093 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ENCODE-DCC long read RNA-seq pipeline" ;
NIFRID:synonym "ENCODE-DCC/long-read-rna-pipeline" ;
definition: "Software pipeline to handle data from PacBio and Oxford Nanopore platforms. Pipeline does read alignment, corrects for mismatches, microindels and non-canonical splice junctions and then provides quantitations and QC-metrics." .
SCR:025094 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Virtual Multidisciplinary Stroke Care Clinic platform" ;
definition: "Platform containing informative videos on stroke care and rehabilitation which was created in collaboration with multidisciplinary team of healthcare professionals." .
SCR:025095 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Jess" ;
rdfs:label "Bio-Techne | ProteinSimple Jess Automated Western Blot System" ;
NIFRID:synonym "Jess Automated Western Blot System" ;
definition: "Simple Western blotting device that performs capillary based immunoassays and fully automated Western blot analysis. Automates protein separation and immunodetection of traditional Western blotting.Traditional Western blotting steps of sample separation, wash buffer incubations, and immunodetection of target proteins occur inside hands free capillary instrument." .
SCR:025096 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Roche Diagnostics" ;
definition: "Roche Diagnostics develops and produces medical tests and digital tools that provide information to help healthcare professionals find the right treatment for patients and deliver the best patient care to improve, prolong and save lives." .
SCR:025097 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Roche | Ventana Discovery Ultra" ;
NIFRID:synonym "Discovery Ultra" ;
definition: """Automated slide preparation system to run manual and fully automated experiments simultaneously with no synchronization errors. Ability to fully automate broad range of IHC and ISH assays, including FISH, gene and protein IHC/ISH, mRNA ISH and multiplex assays with any combination of IHC and ISH. Automated baking, deparaffinization, cell conditioning and staining including immunohistochemistry (IHC) and in situ hybridization (ISH)
Enhanced multiplexing and immunofluorescence, 30 slide reaction chambers allow for independent protocols for each individual slide. Ready-to-use optimized reagents.""" .
SCR:025098 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "confintr" ;
NIFRID:synonym "confintr: Confidence Intervals" ;
definition: "Software R package for calculation of standard and bootstrap confidence intervals." .
SCR:025099 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gensim" ;
definition: "Software Python library for unsupervised topic modeling, document indexing, retrieval by similarity, and other natural language processing functionalities, using modern statistical machine learning." .
SCR:025100 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tqdm" ;
definition: "Software application as fast, extensible progress bar for Python and CLI." .
SCR:025101 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nltk" ;
NIFRID:synonym "Natural Language Toolkit",
"NLTK" ;
definition: "Software suite of open source Python modules, data sets, and tutorials supporting research and development in Natural Language Processing. Platform for building Python programs to work with human language data. Provides interfaces to corpora and lexical resources such as WordNet, along with suite of text processing libraries for classification, tokenization, stemming, tagging, parsing, and semantic reasoning, wrappers for industrial strength NLP libraries, and active discussion forum." .
SCR:025102 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2682" ;
rdfs:label "University of Pittsburgh Unified Flow Cytometry Core Facility" ;
NIFRID:synonym "Unified Flow Core",
"University of Pittsburgh Unified Flow Core" ;
definition: "Core provides flow cytometry and cell sorting services. Staff offers help with instrument setup, data analysis, and consultation for experiment design. Training is available to run analytical cytometers.Houses FACSAria cell sorters, Cytek Aurora Cell Sorter, LSR Fortessas , LSR IIs, ImageStreamx Mark II and 4 full spectral cytometers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:025103 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GNPS MASST" ;
NIFRID:synonym "Global Natural Product Social Molecular Networking Platform Mass Spectrometry Search Tool",
"Mass Spectrometry Search Tool" ;
NIFRID:abbrev "MASST" ;
definition: "Web application that is embedded in GNPS, which is community service. Web enabled mass spectrometry search engine for searches of all small molecule Mass Spectrometry data. Used to search single MS/MS spectrum against public GNPS spectral libraries and all public MS/MS datasets." .
SCR:025104 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JACUSA2" ;
NIFRID:synonym "JACUSA" ;
definition: "Software tool to detect single nucleotide variants by comparing data from next-generation sequencing experiments. Variant caller to detect single nucleotide variant positions from comparing RNA-DNA and/or RNA-RNA sequencing samples. JACUSA2 is one-stop solution to detect single nucleotide variants and reverse transcriptase induced arrest events in Next-generation sequencing data." .
SCR:025105 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReDU" ;
NIFRID:synonym "Reanalysis of Data User" ;
definition: "Software framework to find and re-analyze public Mass Spectrometry data. Used to find uniformly formatted public MS/MS data in the Global Natural Product Social Molecular Networking Platform (GNPS) via formatted metadata. New or previously collected data can be added provided they adhere to the ReDU metadata standards (the implemented drag-and-drop validator is applicable to any scientific data) and data are available in GNPS/MassIVE." .
SCR:025106 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MassQL" ;
NIFRID:synonym "Mass Spec Query Language" ;
definition: "Software application for universal searching of Mass Spectrometry data. Open source MS query language for flexible and mass spectrometer manufacturer-independent mining of MS data. Implements common MS terminology to build consensus vocabulary to search for MS patterns in single mass spectrometry run. Enables set of mass spectrometry patterns to be queried directly from raw data." .
SCR:025107 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Natural Products Atlas" ;
NIFRID:synonym "The Natural Products Atlas",
"The Natural Products Atlas 2.0" ;
NIFRID:abbrev "NP Atlas" ;
definition: "Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles." .
SCR:025108 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MiMeDB" ;
NIFRID:synonym "Microbial Metabolites Database",
"The Human Microbial Metabolome Database" ;
definition: "Database containing detailed information about small molecules produced by human microbiome. Provides metabolite data including structure, names, descriptions, chemical taxonomy, chemical ontology, physico-chemical data, spectra and contains detailed information about microbes that produce these chemicals, enzymatic reactions responsible for their production, bioactivity of chemicals and anatomical location of these chemicals and microbes. Many data fields in the database are hyperlinked to other databases including FooDB, HMDB, KEGG, PubChem, MetaCyc, ChEBI, UniProt, and GenBank. Database is FAIR compliant.The data in MiMeDB are released under the Creative Commons (CC) 4.0 License." .
SCR:025109 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2668" ;
rdfs:label "Loyola University School of Medicine Flow Cytometry Core Facility" ;
NIFRID:synonym "Loyola Flow Cytometry Core",
"Loyola University Chicago Loyola Flow Cytometry Core" ;
definition: "Core Facility with conventional, full-spectrum, cell sorting and flow cytometry services. Training provided by core personnel." .
SCR:025110 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2669" ;
rdfs:label "University of Pittsburgh Single Cell Core Facility" ;
NIFRID:synonym "University of Pittsburgh Single Cell Core" ;
definition: "Core offers single cell sequencing. Provides analysis of transcriptomics, proteomics and epigenomics at single cell level. Provides comprehensive approach for cell characterization and gene expression profiling. Services include single cell gene expression, immune profiling, ATAC, and multiome analysis." .
SCR:025111 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Aperio_CS2" ;
rdfs:label "Leica | Aperio CS2 scanner" ;
NIFRID:synonym "Aperio CS2" ;
definition: "Image capture brightfield whole slide scanner for low throughput with five slide capacity and 20X and 40x magnification capabilities. 2x3 slide option available for large slides. Aperio CS2 runs on Microsoft Windows 10 operating system." .
SCR:025112 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Delft University of Technology Robotics Institute" ;
NIFRID:synonym "TU Delft Robotics Institute" ;
definition: "Unites all Delft University of Technology research in the field of robotics. Its main challenge is to get robots and humans to work together effectively in unstructured environments, and real settings. Institute takes a leading role in the creation of the next generation robots." .
SCR:025113 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2670" ;
rdfs:label "University of Pittsburgh Dietrich School Electronics Shop Core Facility" ;
definition: "Core specializes in electrical design, fabrication, and repair of research equipment and instrumentation." .
SCR:025114 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Impact One" ;
rdfs:label "Leica | Impact One Stereotaxic Impactor" ;
NIFRID:synonym "Impact One Stereotaxic Impactor",
"Leica MyNeuroLab Impact One",
"Leica MyNeuroLab Impact One Stereotaxic Impactor" ;
definition: "System used for small animal brain surgery. Allows to create neurotrauma model with unprecedented degree of reproducibility of the direction of impact and position of the injury. Controlled impact injury device. Device used for traumatic brain injury induction." .
SCR:025116 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Matrix based Flexible Project Planning" ;
NIFRID:abbrev "mfpp" ;
definition: "Software R package models, plans, and schedules flexible, such as agile, extreme, and hybrid project plans. The package contains project planning, scheduling, and risk assessment functions." .
SCR:025117 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "slow5curl" ;
definition: "Software library and tool for accessing remote BLOW5 files. Used for fetching reads from remote BLOW5 files." .
SCR:025118 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microsoft Power BI" ;
definition: "Software suite of business analytics tools to connect to all sorts of data and create visuals and reports. Interactive data visualization and reporting platform developed by Microsoft. Part of Microsoft Power Platform." .
SCR:025119 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Housekeeping and Reference Transcript Atlas" ;
NIFRID:synonym "HRT Atlas v1.0 database" ;
NIFRID:abbrev "HRT Atlas" ;
definition: "Web based database to search human and mouse housekeeping and candidate reference genes/transcripts. It also offers tissue and cell selective candidate reference transcripts and some primers for quantitative PCR normalization." .
SCR:025120 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OutLyzer" ;
definition: "Software tool for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice. Detects variations, specifically low allele frequency variation, in next generation sequencing data." .
SCR:025121 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CiteSpace" ;
definition: "Web Java application for visualizing and analyzing trends and patterns in scientific literature. Provides various functions to facilitate understanding and interpretation of network patterns and historical patterns,finding citation hotspots, decomposing network into clusters, automatic labeling clusters with terms from citing articles, geospatial patterns of collaboration, and unique areas of international collaboration. Supports structural and temporal analyses of networks derived from scientific publications, including collaboration networks, author co-citation networks, and document co-citation networks. Supports networks of hybrid node types such as terms, institutions, and countries, and hybrid link types such as co-citation, co-occurrence, and directed citing links." .
SCR:025122 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Adult Zebrafish Brain Gene Expression Database" ;
definition: "Collection of in situ hybridization data of gene expression in the brain of adult fish. Data can be viewed and downloaded." .
SCR:025123 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2675" ;
rdfs:label "University of Pittsburgh Dietrich School Mass Spectrometry Core Facility" ;
NIFRID:synonym "University of Pittsburgh Dietrich School Mass Spectrometry Facility" ;
definition: "Core provides mass spectrometry instruments including Bruker Daltonics UltrafleXtreme MALDI TOF-TOF, Shimadzu Instrument LCMS-2020,Shimadzu Instrument QP2010S GCMS,Thermo Fisher Oribtrap Exploris 240,Thermo Scientific Q-Exactive Oribtrap for determining masses of particles, and elemental composition of sample or molecule." .
SCR:025124 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2671" ;
rdfs:label "University of Pittsburgh Nanoscale Fabrication and Characterization Core Facility" ;
NIFRID:abbrev "NFCF" ;
definition: "Core supports fabrication and characterization of nanoscale materials and structures, and integration of devices at all length scales. Houses advanced equipment with core nano-level capability for fabrication and characterization, including electron-beam lithography system, dual-beam system, plasma etching, thin film deposition, TEM, multifunctional scanning probe station, modular XRD, and more." .
SCR:025125 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2674" ;
rdfs:label "University of Pittsburgh Dietrich School X-ray Crystallography Core Facility" ;
NIFRID:synonym "University of Pittsburgh Dietrich School X-ray Crystallography Facility" ;
definition: "X-Ray Diffraction Facility located in Chemistry Instrumentation Center is equipped with Bruker X8 Prospector Ultra with Copper ImuS micro-focus X-ray source and Bruker D8 Venture Dual source (Molybdenum and Copper micro-focus X-ray tubes) diffractometer with Photon III CPAD detector. Data can be collected at nitrogen-cooled temperatures as low as 90K. Core provides sample submission services for small molecule crystalography." .
SCR:025126 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2673" ;
rdfs:label "University of Pittsburgh Dietrich School NMR Core Facility" ;
NIFRID:synonym "University of Pittsburgh Dietrich School NMR Facility" ;
definition: "Facility specializes in training users in both solution phase and solid state NMR across all active nuclei and multiple NMR experients" .
SCR:025127 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2672" ;
rdfs:label "University of Pittsburgh Dietrich School Materials Characterization Laboratory Core Facility" ;
NIFRID:synonym "University of Pittsburgh Dietrich School Materials Characterization Laboratory" ;
NIFRID:abbrev "MCL" ;
definition: "Facility maintains large array of instrumentation for production and analysis of complex materials, including nanoparticles, thin films, polymers, ceramics, and molecular electronics.Oversees operations of Department Biological Instrumentation Cluster which provides access to specialized equipment used in molecular biology and biological chemistry." .
SCR:025128 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "baseline" ;
definition: "Web tool to detect under- or over-dispersion in a baseline table from baseline table." .
SCR:025129 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "BioGenex" ;
NIFRID:synonym "BioGenex Laboratories" ;
definition: "Company designs, develops and commercializes molecular pathology systems for tumor diagnosis, prognosis, precision medicine and life science research." .
SCR:025130 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Caliper Life Sciences" ;
definition: "Caliper provides products and services for life sciences research. The firm, founded in 1995, is based in Hopkinton, Massachusetts with direct sales, service and application support operations in countries around the globe." .
SCR:025131 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Lunaphore" ;
NIFRID:synonym "Lunaphore Technologies" ;
definition: "Spatial biology company, building multiplex immunofluorescence and IHC solutions for discovery and immuno-oncology research.Laboratory equipment supplier in Tolochenaz, Switzerland." .
SCR:025132 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2677" ;
rdfs:label "University of Pittsburgh School of Medicine Cell Imaging Core Facility" ;
NIFRID:synonym "Cell Imaging Core",
"University of Pittsburgh Cell Imaging Core" ;
definition: "Core for image based analysis, laser capture microdissection, and live cell fluorescence imaging. Provides range of consultation and laboratory services performed by core staff. Users training is available.Cell and Tissue imaging on confocal microscopes including Zeiss LSM 710, Leical Sp8 and Leica Stellaris." .
SCR:025133 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2678" ;
rdfs:label "University of Manitoba Genomic Centre for Cancer Research and Diagnosis Core Facility" ;
NIFRID:synonym "UMB-GCCRD",
"University of Manitoba UMB-GCCRD" ;
NIFRID:abbrev "GCCRD" ;
definition: "Advanced imaging core for multi channel fluorescence imaging,3D imaging, super resolution imaging, scanning, image analysis in cancer research. Technical services are forcused on fluorescent in situ hybridization, immunohistochemistry, and microdissection of biological material." .
SCR:025134 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2681" ;
rdfs:label "University of Pittsburgh Luminex Core Facility" ;
NIFRID:synonym "Luminex Core Laboratory",
"University of Pittsburgh Luminex Core Laboratory" ;
definition: "Facility utilizes LabMA system developed by Luminex Co., for protein analysis that permits simultaneous quantitative analysis of up to 100 different proteins, peptides, or RNA molecules in single microtiter well. Commercially available assays from Millipore, R&D Systems, Bio-Rad or Thermofisher are also used for analysis." .
SCR:025135 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2685" ;
rdfs:label "University of Florida Herbert Wertheim College of Engineering Research Service Centers Core Facility" ;
NIFRID:synonym "Herbert Wertheim College of Engineering Research Service Centers",
"University of Florida Herbert Wertheim College of Engineering Research Service Centers" ;
definition: "Core provides access to characterization and process instrumentation. Expert staff provides assistance and guidance. Services include electron microscopy and analysis (SEM, TEM, FIB, EBSD, WDS), microelectronic device fabrication (7000 sq ft cleanroom, Class 100-1000), X-ray computed tomography (CT), particle system characterization (size, zeta potential, surface area, porosity, rheology), X-ray diffraction, surface analysis (AFM, profilometry, XPS, Auger), spectroscopy (UV/Vis with integrating sphere, FTIR/NIR with micro capability and micro-Raman)." .
SCR:025137 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2690" ;
rdfs:label "Douglas Neuroinformatics Platform" ;
NIFRID:synonym "The Douglas Research Centre: Neuroinformatics Platform" ;
NIFRID:abbrev "DNP" ;
definition: "Core provides technical support and expertise to enable measurement based care and compute focused research. Service consists of computing platform, composed of redundant high-capacity storage system, along with compute cluster and workstations, tied together with unified single-sign-on user and group management. Platform has facilities for capturing form-based, interactive testing-based and arbitrary binary (imaging etc.) data. Allows clinical researchers to track the trajectories of participating patients across Douglas clinics. " .
SCR:025138 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nricens" ;
definition: "Software R package for calculating Net Reclassification Improvement for risk prediction models with time to event and binary data. NRI for risk prediction models with time to event and binary response data." .
SCR:025139 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2687" ;
rdfs:label "University of Pittsburgh Advanced Imaging Center Core Facility" ;
NIFRID:synonym "University of Pittsburgh UPitt-Advanced Imaging Center",
"UPitt-Advanced Imaging Center" ;
NIFRID:abbrev "AIC" ;
definition: "Core provides instrumentation and expertise for high-field Preclinical Magnetic Resonance Imaging and Magnetic Resonance Microscopy. Facility has instruments: Bruker 9.4 Tesla/30 cm AVANCE 3 HD scanner and Bruker 11.7 Tesla 89 mm AVANCE 3 HD micro imaging system." .
SCR:025140 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2688" ;
rdfs:label "University of Chicago Single Cell Immunophenotyping Core Facility" ;
NIFRID:synonym "Single Cell Immunophenotyping Core",
"University of Chicago Single Cell Immunophenotyping Core" ;
definition: "Core is self service facility that provides access to specialized instrumentation for phenotyping and genotyping of immune cells. Offers single cell next generation sequencing and quality control technologies. All instruments are located in the laboratories of four different CIIC investigators (KCBD 10220E and 10220C), and are available for use by the larger UChicago community." .
SCR:025141 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:water-ebi" ;
rdfs:label "Emboss Water" ;
definition: "EMBOSS Water uses Smith-Waterman algorithm to calculate the local alignment of two sequences. Pairwise sequence alignment. Used for determining protein-to-protein homology." .
SCR:025142 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pHLA3D" ;
definition: "Database of predicted three dimensional structures of Human Leukocyte Antigens molecules constructed by using homology modeling. Developed to improve epitope analysis in context of organ transplantation by providing 3D structures of HLA molecules present in current solid-phase assays for serum antibodies screening. Gives crystalographic modeling structure of HLA protein.Provides means to visualize target epitopes recognized by anti-HLA antibodies." .
SCR:025144 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HLA Eplet Registry" ;
definition: "Database of theoretical and confirmed HLA eplets recognizable by B-Cell receptors. Eplets are sorted according to their amino acid sequence positions. Used for identifying HLA epitopes." .
SCR:025145 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2692" ;
rdfs:label "University of Pittsburgh Dietrich School of Arts and Sciences Pitt Isotope Tracer Lab Core Facility" ;
NIFRID:synonym "University of Pittsburgh Dietrich School Pitt Isotope Tracer Lab" ;
NIFRID:abbrev "PIT" ;
definition: "One of several isotope labs in Department of Geology and Environmental Science formerly known as Regional Stable Isotope Lab for Earth and Environmental Science Research, has capacity for wide variety of isotopic measurements in multitude of sample media. Capabilities include: Nitrate (?15N, ?18O, D17O);Greenhouse and trace gases like carbon dioxide (?13C, ?18O), nitrous oxide (?15N, ?18O), methane (?13C); Nitrogen, carbon, and sulfur (?15N, ?13C, ?34S) in organic and other solid materials (e.g., biota, soils);Ammonium (?15N); Dry reactive nitrogen deposition (?15N-NH3, ?15-NO2, and ?15N-HNO3); and Carbonates (?13C, ?18O)." .
SCR:025146 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "10x Genomics | Chromium Connect system" ;
NIFRID:synonym "10x Genomics Chromium Connect",
"Chromium Connect" ;
definition: "System that combines proprietary 10x microfluidics technology using Chromium Automated Controller with precise, automated liquid handling that allows users to run 10x Genomics end to end library construction workflow with minimal user interaction. Integrates components customized for 10x Genomics single cell workflows, automation specific reagents and consumables, and touchscreen computer. Used to generate consistent and reproducible single cell gene expression results across experiments, users, and multiple sites." .
SCR:025147 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultima_CPX" ;
rdfs:label "MCDiagnostics | Ultima CPX Metabolic Stress Testing System" ;
definition: "Metabolic stress testing system provides breath by breath metabolic analysis during both rest and exercise for complete assessment of functional capacity and cardiorespiratory diagnostics.Testing capabilities including Exercise Capacity,Direct Fick Cardiac Output and Spirometry." .
SCR:025148 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CRISPick" ;
definition: "Web tool for prediction of sgRNAs. Helps to select optimal guide RNA for gene of interest. Support for designing guide libraries. CRISPick ranks and picks candidate CRISPRko sgRNA sequences for targets provided, while attempting to maximize on-target activity and minimizing off-target activity." .
SCR:025149 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CDD vault" ;
definition: "Hosted drug discovery informatics platform that securely manages both private and external biological and chemical data. Provides core functionality including chemical registration, structure activity relationship, chemical inventory, and electronic lab notebook capabilities." .
SCR:025150 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Dragonfly" ;
definition: "Dragonfly is a brand of Comet Technologies Canada Inc. Company develops applications to better understand image data. Providews advanced 3D visualization and analysis software for 2D, 3D, and 4D imaging studies." .
SCR:025151 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2694" ;
rdfs:label "University of Pittsburgh Genome Editing, Transgenic and Virus Core Facility" ;
NIFRID:synonym "and Virus (GETV) Core Facility",
"Genome Editing",
"MWRI Genome Editing",
"Transgenic",
"Transgenic and Virus (GETV) Core" ;
NIFRID:abbrev "GETV" ;
definition: "Core provides technical expertise, advice, and training and is comprised of three functional sections: Molecular cloning (plasmid, virus, CRISPR/Cas9); Viral vectors (lentivirus, adenovirus, adeno-associated virus); Animal services (transgenic, knockout, cryopreservation, re-derivation, and more). Services offered include Assistance for generating recombinant plasmids; Design and implementation of CRISPR/Cas9 technology for in vivo and in vitro work; Mouse and rat transgenesis,including transgenic and knockout/knockdown techniques using pronuclear injection, ES cell injection/chimera, and CRISPR/Cas9-mediated genome editing; Production of lentivirus, adenovirus, and adeno-associated virus vectors; Additional animal testing and procedures: teratoma and chimera testing to validate putative pluripotent stem cell lines, cryopreserve or re-derive of valuable transgenic lines (sperm or embryos)." .
SCR:025152 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2680" ;
rdfs:label "University of Pittsburgh Small Animal Ultrasonography Core Facility" ;
NIFRID:synonym "University of Pittsburgh UPitt - Small Animal Ultrasonography Core",
"UPitt - Small Animal Ultrasonography Core" ;
definition: "Core provides expertise and high frequency ultrasound instrumentation suitable for image acquisition and analysis applicable to your research studies. Provides Fuji/Visualsonics Vevo 3100 ultrasound imaging machine to perform ultrasounds on small animals. The scanner has high temporal and spatial resolution; current imaging probes utilize frequencies from 13-55 MHz." .
SCR:025153 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Penn State Institute for Computational and Data Sciences Center for Artificial Intelligence Foundations and Scientific Applications" ;
NIFRID:synonym "Penn State Center for Artificial Intelligence Foundations and Scientific Applications" ;
definition: "Aims to foster collaborative, interdisciplinary research across Penn State and beyond aimed at addressing the AI grand challenge of accelerating scientific progress through synergistic advances across multiple areas of AI." .
SCR:025154 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Penn State Institute for Computational and Data Sciences" ;
NIFRID:synonym "Institute for Computational and Data Sciences" ;
NIFRID:abbrev "ICDS" ;
definition: "ICDS brings researchers together to develop and apply innovative, high performance computation methods. Helps to apply big data and big simulation methods across research landscape." .
SCR:025156 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MELQUEST | Lick Analysis Formula Selection Preference Experiment System LKP2" ;
NIFRID:synonym "Rick analytical choice preference experiment system LKP2" ;
NIFRID:abbrev "LKP2" ;
definition: "Apparatus used for measuring mice licking pattern for particular solutions. Device records licking behavior by measuring number of licks per second , which is drawn as bar graph on the PC software screen ." .
SCR:025157 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Glutest Ai" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 14,2026. Device used for measuring blood glucose levels." .
SCR:025158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pulse" ;
definition: "Electrophysiology acquisition software, compatible with HEKA EPC amplifiers." .
SCR:025159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Certara D360 " ;
NIFRID:synonym "Certara D360 Scientific Informatics Discovery Platform" ;
definition: "Platform provides self service data access, integrated data visualization and analysis and collaboration tools that allow compound prioritization, development of SAR and many other scientific data workflows in chemistry and biology domains to improve effectiveness of data driven research." .
SCR:025160 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Keyence_BZ-X810" ;
rdfs:label "Keyence | BZ-X810 microscope" ;
definition: "Inverted fluorescence phase contrast microscope. Objective lenses. BZ Series infinite optical system." .
SCR:025161 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SEB3R" ;
NIFRID:synonym "Stimulus Evoked Behavioral tracking in 3D for Rodents" ;
definition: "Software tool to automate and standardize ethologically driven observation of freely moving mice. Identifies different postures of mice and associates them with emotions, offering detailed analysis of their movements frame by frame. Used for tracking mouse body language and studying emotional behaviors." .
SCR:025162 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Centers for Disease Control and Prevention NHIS Data, Questionnaires and Related Documentation" ;
NIFRID:synonym "CDC NHIS Data",
"NHIS Data",
"Questionnaires and Related Documentation" ;
definition: "Collection of National Health Interview Survey (NHIS) data, questionnaires and related documents to monitor health of the United States population through collection and analysis of data on broad range of health topics." .
SCR:025163 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2696" ;
rdfs:label "Creighton University Histology Core Facility" ;
NIFRID:synonym "Creighton University Histology Core Lab",
"CU Histology Core Lab" ;
definition: "Facility provides equipment and services for studies utilizing animal and human tissues. Services include Sample, Processing, Embedding, Sectioning, Histochemistry, Immunohistochemistry, Imaging, Microscopy. Equipment includes microtomes for paraffin sections, cryostat for frozen sections, vibratome for plastic sections, and Nikon Eclipse Ci-L microscope for brightfield and fluorescence applications." .
SCR:025164 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JaCoP" ;
NIFRID:synonym "Just Another Colocalization Plugin" ;
definition: "Software toolbox as plugin for ImageJ that supports colocalization analysis in light microscopy. Used for subcellular colocalization analysis under ImageJ that integrates current global statistic methods and novel object-based approach." .
SCR:025165 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Blyss" ;
NIFRID:synonym "Blyss SDK" ;
definition: "Software Rust FHE library specialized for private information retrieval. Includes bindings to JS and Python. Software Development Kit for private data access, built on homomorphic encryption." .
SCR:025166 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cuFHE" ;
NIFRID:synonym "CUda accelerated Fully Homomorphic Encryption" ;
definition: "Open source software library for Fully Homomorphic Encryption on CUDA enabled GPUs. CUDA accelerated Fully Homomorphic Encryption library." .
SCR:025167 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cuHE" ;
NIFRID:synonym "CUDA Homomorphic Encryption Library" ;
definition: "Software GPU-accelerated library for homomorphic encryption schemes and homomorphic algorithms defined over polynomial rings." .
SCR:025168 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cupcake" ;
definition: "Software Rust library for lattice-based additive homomorphic encryption." .
SCR:025169 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cuYASHE" ;
definition: "Software library as implementation of leveled fully homomorphic scheme YASHE on GPGPUs. Used to obtain significant performance improvements." .
SCR:025170 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FHEW" ;
NIFRID:synonym "Fastest Homomorphic Encryption in the West" ;
definition: "Open-source software library distributed under the terms of the GNU General Public License. Used to homomorphically compute simple bit operations, and refresh, bootstrap resulting output, which runs on personal computer in just about half a second." .
SCR:025171 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FINAL" ;
NIFRID:synonym "Faster FHE instantiated with NTRU and LWE" ;
definition: "Software C++ FHE library as fully homomorphic encryption scheme based on NTRU and LWE. MIT license. " .
SCR:025172 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FV-NFLlib" ;
definition: "Software library implementing Fan-Vercauteren homomorphic encryption scheme." .
SCR:025173 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HEAAN" ;
definition: "Software library that implements homomorphic encryption that supports fixed point arithmetics. This library supports approximate operations between rational numbers." .
SCR:025174 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HElib" ;
definition: "Open-source software library that implements homomorphic encryption. Supports BGV scheme with bootstrapping and Approximate Number CKKS scheme. HElib also includes optimizations for efficient homomorphic evaluation, focusing on effective use of ciphertext packing techniques and on the Gentry-Halevi-Smart optimizations." .
SCR:025175 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:cherri" ;
rdfs:label "CheRRI" ;
NIFRID:synonym "Computational Help Evaluating RNA-RNA Interactions" ;
NIFRID:abbrev "Cherri",
"cherri" ;
definition: "Software tool to detect functional RNA-RNA interaction sites, by evaluating if interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by RRI prediction algorithm by removing false positive interactions." .
SCR:025176 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bioKGQA-KGT" ;
definition: "Software contains all scripts and instructions for running Knowledge Graph-based Thought model, which is knowledge graph enhanced LLMs framework for pan-cancer question answering." .
SCR:025177 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NDP.view2" ;
NIFRID:synonym "Hamamatsu NDP.view2" ;
definition: "Image viewing software to observe digital images to the details like microscope. Supports images from all NanoZoomer series of whole slide scanners that scan glass slides at high speed." .
SCR:025178 a NLX:63400,
owl:NamedIndividual .
SCR:025179 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "krypto" ;
definition: "Software C++ implementation of multivariate quadratic FHE." .
SCR:025180 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Functional Lattice Cryptography" ;
NIFRID:abbrev "LOL" ;
definition: "Software Haskell library for ring-based lattice cryptography that supports FHE." .
SCR:025181 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lattigo" ;
definition: "Software library for lattice-based multiparty homomorphic encryption in Go. Go library for lattice-based crypto that implements various schemes." .
SCR:025182 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "libScarab " ;
definition: "Software C library implementing FHE scheme using large integers. Implementation of the Fully Homomorphic Smart-Vercauteren Cryptosystem." .
SCR:025183 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "libshe" ;
definition: "Software symmetric somewhat homomorphic encryption library based on DGHV." .
SCR:025184 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microsoft SEAL" ;
NIFRID:abbrev "SEAL" ;
definition: "Software homomorphic encryption library. C++ FHE library implementing BFV and CKKS schemes. Allows computations to be performed directly on encrypted data. This enables software engineers to build end-to-end encrypted data storage and computation services where the customer never needs to share their key with the service." .
SCR:025185 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NFLlib" ;
NIFRID:synonym "NTT-based Fast Lattice library" ;
definition: "Software NTT-based Fast Lattice library specialized on power-of-two polynomials. Open source C++ library dedicated to ideal lattice cryptography. It is specialized in polynomial rings quotiented by cyclotomic polynomial whose degree is a power of two." .
SCR:025186 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "node-seal" ;
definition: "Software homomorphic encryption library for TypeScript or JavaScript." .
SCR:025187 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NuFHE " ;
NIFRID:synonym "NuCypher Fully Homomorphic Encryption" ;
definition: "Software Python GPU-accelerated HE library, faster than cuFHE, that implements the tfhe algorithms." .
SCR:025188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenFHE" ;
NIFRID:synonym "Open-source Fully Homomorphic Encryption" ;
definition: "Open-source Fully Homomorphic Encryption library enables performing computations over encrypted data without having access to the secret key. OpenFHE is an open-source FHE library that includes efficient implementations of all common FHE schemes." .
SCR:025189 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PALISADE " ;
definition: "Open source Lattice Crypto software library. Software lattice encryption library superseded by OpenFHE." .
SCR:025190 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "petlib " ;
definition: "Software Python library that implements number of Privacy Enhancing Technologies." .
SCR:025191 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pyfhel" ;
NIFRID:synonym "Python for Homomorphic Encryption Libraries" ;
definition: "Software Python library for addition, subtraction, multiplication and scalar product over encrypted integers (BFV/BGV schemes) and approximated floating point values (CKKS scheme). This library acts as optimized Python API for C++ Homomorphic Encryption libraries. Python wrapper for SEAL, HElib, and PALISADE." .
SCR:025192 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "python-paillier" ;
definition: "Software library for Partially Homomorphic Encryption in Python. Partially HE based on Paillier scheme." .
SCR:025193 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EasyNER" ;
NIFRID:synonym "Easy Named Entity Recognition" ;
definition: "Software customzable pipeline for biomedical information extraction. Deep learning and dictionary- based biomedical Named Entity Recognition pipeline to automatically extract domain specific information from medical text and in particular research articles. Pipeline contains NER models on cell lines, chemicals, disease, gene/protein and species." .
SCR:025194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GALA" ;
NIFRID:synonym "Graph Adversarial Learning with Alignment" ;
definition: "Software tool for protein function prediction. Extracts information from both protein sequences and structures, facilitating unified learning of protein structural representations. GALA incorporates domain discriminator conditioned on both representations and predicted probabilities, which undergoes adversarial training to ensure representation invariance across diverse environments." .
SCR:025195 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SEAL-python" ;
definition: "Software Python library binding for Microsoft SEAL library." .
SCR:025196 a owl:NamedIndividual ;
rdfs:label "SparkFHE" ;
NIFRID:synonym "Spark Fully Homomorphic Encryption" ;
definition: "Software application as forked of Apache Spark with support for fully homomorphic encryption. Apache Spark with add-on for FHE computations." .
SCR:025197 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sunscreen" ;
definition: "Software application for building privacy preserving applications using Fully Homomorphic Encryption and later on zero-knowledge proofs as well. Rust compiler for BFV fully homomorphic encryption scheme." .
SCR:025198 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TenSEAL " ;
definition: "Software library for doing homomorphic encryption operations on tensors built on Microsoft SEAL, with Python API." .
SCR:025199 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tfhe" ;
NIFRID:synonym "Fast Fully Homomorphic Encryption Library over Torus" ;
definition: "Software library is original version of TFHE that implements base arithmetic and functionalities (bootstrapped and leveled). Bootstrapping in less than 0.1 seconds. Fast Fully Homomorphic Encryption Library over the Torus." .
SCR:025200 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TFHE-rs" ;
definition: "Software library as pure Rust implementation of TFHE Scheme for Boolean and Integer arithmetics over encrypted data. Rust implementation of TFHE scheme for boolean and integers FHE arithmetics." .
SCR:025201 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AWS HE toolkit" ;
NIFRID:synonym "Homomorphic Implementor Toolkit" ;
NIFRID:abbrev "HIT" ;
definition: "Software toolkit to simplify process of designing homomorphic circuits for CKKS homomorphic encryption scheme. HIT repository uses Microsoft SEAL homomorphic encryption library as backend." .
SCR:025202 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cingulata" ;
definition: "Software toolkit as compiler toolchain and RTE for running C++ programs over encrypted data by means of fully homomorphic encryption techniques." .
SCR:025203 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Concrete" ;
definition: "Software toolkit as FHE Compiler that converts Python programs into FHE equivalent. Simplifies the use of fully homomorphic encryption which enables performing computations on encrypted data directly without the need to decrypt it first. Concrete framework contains TFHE Compiler based on LLVM, making writing FHE programs easy task for developers." .
SCR:025204 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Concrete-ML" ;
definition: "Software Python-based toolkit for data scientists without prior FHE knowledge. Privacy preserving ML framework built on top of Concrete, with bindings to traditional ML frameworks." .
SCR:025205 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "E3" ;
NIFRID:synonym "Encrypt-Everything-Everywhere" ;
definition: "Software toolkit as open source homomorphic encryption framework. Provides C++ classes for supporting computation on private data. Allows programmers to incorporate privacy to their programs without expertise in cryptography. Software framework for compiling C++ programs with encrypted operands." .
SCR:025206 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EVA" ;
NIFRID:synonym "Encrypted Vector Arithmetic" ;
definition: "Software toolkit as compiler for SEAL homomorphic encryption library. Automates away parts that require cryptographic expertise. Allows to write programs that operate on encrypted data without having access to the secret key. Native library written in C++ with bindings for Python. Both Linux and Windows are supported." .
SCR:025207 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fully Homomorphic Encryption Repository" ;
NIFRID:synonym "Google FHE Repository" ;
definition: "Software toolkit to perform Fully Homomorphic Encryption operations on encrypted data set. FHE compiler for C++ that converts subset of C++ programs into FHE circuits implemented in various backend libraries." .
SCR:025208 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Marble" ;
definition: "Software toolkit as C++ framework that translates between nearly plain text style user programs and FHE computations. Marble FHE library that translates between user programs written close-to-plaintext-style and FHE computations based on underlying FHE crypto libraries." .
SCR:025209 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SHEEP" ;
NIFRID:synonym "Software Homomorphic Encryption Evaluation Platform" ;
definition: "Software toolkit as Homomorphic Encryption evaluation platform with set of native benchmarks and library agnostic language. Used to evaluate fully homomorphic encryption across libraries implementing different HE schemes within some cases incomparable security." .
SCR:025210 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "T2" ;
NIFRID:synonym "T2-FHE-Compiler-and-Benchmarks" ;
definition: "Software toolkit as extensible cross compiler and standardized benchmark suite enabling comparisons between Fully Homomorphic Encryption libraries. Cross compiler and standardized benchmarks for FHE computation that targets lattigo, HElib, PALISADE, Microsoft SEAL, and tfhe." .
SCR:025211 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HEIR " ;
NIFRID:synonym "HEIR: Homomorphic Encryption Intermediate Representation",
"Homomorphic Encryption Intermediate Representation" ;
NIFRID:abbrev "HEIR" ;
definition: "Software toolkint as compiler for homomorphic encryption. Google MLIR-based toolchain for FHE compilers." .
SCR:025212 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2732" ;
rdfs:label "University of Chicago FIB-SEM Core Facility" ;
NIFRID:synonym "Focused Ion Beam - Scanning Electron Microscope Core Facility" ;
NIFRID:abbrev "FIB-SEM" ;
definition: "Facility in the Department of the Geophysical Sciences features instruments including TESCAN LYRA3 field-emission scanning electron microscope (FESEM) with focused ion beam (FIB). It is equiped to do EDS, WDS, EBSD, etc." .
SCR:025213 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2698" ;
rdfs:label "Magee-Womens Research Institute Confocal Microscope Core Facility" ;
NIFRID:synonym "Confocal Microscope Core at Magee-Women's Research Institute",
"Magee-Womens Research Institute Confocal Microscope Core" ;
definition: "Core for imaging from single plane acquisition, to Z-stacks and 3D reconstruction, and to live imaging on slides or in tissue culture dishes. Microscopes are user operated after intensive training and demonstration of proficiency." .
SCR:025214 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2699" ;
rdfs:label "University of Pittsburgh Clinical and Translational Science Institute Biostatistics, Epidemiology and Research Design Core Facility" ;
NIFRID:synonym "and Research Design (BERD) Core",
"Biostatistics",
"CTSI Biostatistics",
"Epidemiology",
"Epidemiology and Research Design",
"University of Pittsburgh Clinical and Translational Science Institute Biostatistics",
"University of Pittsburgh CTSI Biostatistics" ;
NIFRID:abbrev "BERD" ;
definition: "Core provides consultation regarding study design, statistical analyses, power and sample size calculations and data collection for clinical and translational studies and grant applications. BERD offers consultation for collecting and managing data using the REDCap system. BERD also offers a series of workshops to provide essential elements involved in data collection, data management and creating reports for research studies." .
SCR:025215 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2702" ;
rdfs:label "University of Pittsburgh Magnetic Resonance Research Center Core Facility" ;
NIFRID:synonym "Magnetic Resonance Research Center",
"University of Pittsburgh Magnetic Resonance Research Center" ;
definition: "Core is dedicated to development and application of magnetic resonance imaging and magnetic resonance spectroscopy for medical and biological research. MRRC is whole-body imaging capable with specialty in anatomical MRI imaging of brain, spine, extremities, liver, bladder as well as functional MRI to study cognitive, sensory, and motor function in the brain." .
SCR:025216 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2701" ;
rdfs:label "University of Pittsburgh Cryo-electron Microscopy Core Facility" ;
NIFRID:synonym "Cryo-electron Microscopy Facility",
"University of Pittsburgh Cryo-electron Microscopy Facility" ;
definition: "Facility provides access to cutting edge instrumentation for high resolution structural analysis of proteins, protein complexes, viruses, macromolecular assemblies, cellular organelles, and bacterial cells., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:025217 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2704" ;
rdfs:label "University of Pittsburgh School of Medicine Cell Imaging Core Facility" ;
NIFRID:synonym "The Cell Imaging Core Laboratory at John G. Rangos Sr. Research Center" ;
definition: "Cell Imaging Core Laboratory at John G. Rangos Sr. Research Center offers cell imaging by confocal microscopy, including live cell as well as laser capture microdissection and LCM." .
SCR:025218 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2707",
"SCR_012383" ;
rdfs:label "University of Pittsburgh Small Molecule Biomarker Core Facility" ;
NIFRID:synonym "Small Molecule Biomarker Core" ;
definition: "Small Biomarker Core provides accurate and sensitive quantitative analysis in biological samples, with or without sample processing, using state-of-the-art ultra performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS). In addition to well qualified assays for common targets, experienced, knowledgeable personnel can provide assay development for novel targets" .
SCR:025219 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2706" ;
rdfs:label "University of Pittsburgh Peptide and Peptoid Synthesis Core Facility" ;
NIFRID:synonym "Peptide and Peptoid Synthesis Core" ;
definition: "Core offers services for custom synthesis and characterization of peptides, peptoids and small molecule constructs. The facility has extensive capabilities for technologically advanced custom modifications such as bioconjugations and targeted therapeutic strategies. State of the art HPLC and mass spectrometry capabilities as well as services in support of protein, siRNA, antibody and small molecule quantification and characterization are available" .
SCR:025220 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2708" ;
rdfs:label "University of Pittsburgh School of Medicine Gnotobiotic Animal Core Facility" ;
NIFRID:synonym "Gnotobiotic Animal Core Laboratory" ;
definition: "Gnotobiotic Animal Core Laboratory is a BSL2-compliant mouse facility providing isolators for studies requiring a controlled microbiotic environment. All husbandry and upkeep services are provided. Additional specialized support is also available." .
SCR:025221 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2700" ;
rdfs:label "University of Pittsburgh Drosophila Core Facility" ;
NIFRID:synonym "Drosophila Facility" ;
definition: "Drosophila Facility specializes in producing drosophila media in bulk and making it available to local investigators." .
SCR:025222 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2710" ;
rdfs:label "University of Pittsburgh Health Sciences Mass Spectrometry Core Facility" ;
NIFRID:synonym "Health Sciences Mass Spectrometry Core" ;
definition: "Health Sciences Mass Spectrometry Core provides liquid chromatography high resolution mass spectrometry (LC-HRMS) services for metabolomics, lipidomics and proteomics. Expert staff provide assistance throughout the full lifespan of all projects from experimental design and sample preparation through statistical analysis and interpretation of datasets." .
SCR:025223 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2705" ;
rdfs:label "University of Pittsburgh School of Medicine Flow Cytometry Core Facility" ;
NIFRID:synonym "Flow Cytometry Core at John G. Rangos Sr. Research Center" ;
definition: "Flow Cytometry Core at John G. Rangos Sr. Research Center is a BSL2+ compliant cytometry analysis and sorting facility located at the John G. Rangos Sr. Research Center in Lawrenceville serving investigators from across the University of Pittsburgh." .
SCR:025224 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2703" ;
rdfs:label "University of Pittsburgh School of Medicine Metabolic Core Facility" ;
NIFRID:synonym "Metabolic Core Facility at the John G. Rangos Sr. Research Center" ;
definition: "Core provides Instrument Services for analysis of 1) endogenous metabolic pathway intermediates or biomarkers from biological fluids, cell cultures, and tissues using Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS), 2) energy metabolism (cell bioenergetics) in living cells using a Seahorse Analyzer, and 3) biomarkers/metabolites to quantitate pathway intermediates using HPLC with 3 detector options (ECD, UV-VIS, FLR)." .
SCR:025225 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2712" ;
rdfs:label "University of Pittsburgh Small Animal Ultrasonography Core Facility" ;
NIFRID:synonym "Small Animal Ultrasonography Core" ;
definition: "Small Animal Ultrasonogrphy Core provides high frequency ultrasound for non-invasive, in vivo, real-time, high-resolution imaging of tissue structure and function in small animals." .
SCR:025226 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2711" ;
rdfs:label "University of Pittsburgh Health Services Research Data Center Core Facility" ;
NIFRID:synonym "Health Services Research Data Center (HSRDC)" ;
NIFRID:abbrev "HSRDC" ;
definition: "Health Sciences Research Data Center is HIPAA compliant secure computing environment where study teams can store data and do analytics from anywhere with internet access. Teams work in Windows virtual desktop with memory, storage, and computing power dedicated to each user. Knowledgeable facility staff can provide data management, help with regulatory documents like DUAs, maintain systems compliance, and custom application development." .
SCR:025227 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2715" ;
rdfs:label "University of Pittsburgh Center for Research on Healthcare Data Center Core Facility" ;
NIFRID:synonym "Univerity of Pittsburgh Center for Research on Healthcare Data Center Core Facility" ;
definition: "Provides expertise and research infrastructure across four key Cores of Biostatistics, Data Management and Information Systems, Qualitative Analysis, and Data Coordination." .
SCR:025228 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2713" ;
rdfs:label "University of Pittsburgh School of Medicine Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core Facility at the John G Rangos Sr. Research Center" ;
definition: "Bioinformatics Core Facility at the John G. Rangos Sr. Research Center provides bioinformatics as well as biostatistics services across a wide range of disease domains. The next-generation sequencing data analysis includes, but is not limited to, whole genome-, whole exome-, bulk and single cell epigenome-, bulk and single cell transcriptome, spatial transcriptome, microbiome, metabolome, proteome and lipidome data analysis. The facility specializes in T-, and B- cell repertoire data analysis, multi-omics initiatives, and multimodal analysis. Shiny dashboard and other web application development is also supported." .
SCR:025229 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2709" ;
rdfs:label "University of Pittsburgh Pitt Biospecimen Core Facility" ;
NIFRID:synonym "Pitt Biospecimen Core (PBC)" ;
definition: "Pitt Biospecimen Core provides human sample procurement in multiple UPMC hospitals across Pittsburgh. Standard operating procedures for procurement and processing are developed for each project in partnership with each study's principal investigator. A rigorous quality assurance program ensures SOP compliance. In addition to specimen banking and pathology consultation, research histology services by expert histology specialists are also available." .
SCR:025230 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2714" ;
rdfs:label "Magee-Womens Research Institute Magee Obstetric Medical and Infant Database and Biobank Core Facility" ;
NIFRID:synonym "Magee Obstetric Medical and Infant Database and Biobank" ;
NIFRID:abbrev "MOMI" ;
definition: "Core provides collection of obstetric biological materials from prenatal visits through delivery along with annotated clinical information. In addition to specimen access, MOMI staff can provide study design assistance as needed." .
SCR:025231 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2716" ;
rdfs:label "University of North Carolina at Chapel Hill Translational Genomics Lab Core Facility" ;
NIFRID:synonym "UNC LCCC Translational Genomics Lab (TGL)",
"University of North Carolina at Chapel Hill UNC LCCC Translational Genomics Lab (TGL)" ;
NIFRID:abbrev "TGL" ;
definition: "Core facility within Lineberger Comprehensive Cancer Center that performs sample processing for the molecular, pathologic, and genomic characterization of patient-derived specimens using high-end instrumentation and state-of-the-art methods. Service offerings include nucleic acid extraction, gene expression profiling, spatial genomics, next-generation sequencing library preparation, and high-throughput sequencing. Protocols leverage the reproducibility and reliability of automated instrumentation to minimize batch effects and processing errors (e.g. sample swaps). These workflows have been continuously optimized over the last decade, with a sample-to-answer historic success rate of ~90% for the >15,000 FFPE samples TGL has processed." .
SCR:025232 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NextPolish" ;
definition: "Software tool to fix base errors SNV/Indel in genome generated by noisy reads. Used to correct error bases in reference genome." .
SCR:025233 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cuteSV" ;
NIFRID:synonym "cuteSV2" ;
definition: "Software tool for long read based human genomic structural variation detection. Collects signatures of various types of SVs and employs clustering-and-refinement method to analyze signatures to implement sensitive SV detection.cuteSV2 is upgraded version of cuteSV." .
SCR:025234 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "m6anet" ;
definition: "Software Python tool for detection of m6A from direct RNA-Seq data. Leverages multiple instance learning framework to detect m6a modifications from Nanopore Direct RNA Sequencing data." .
SCR:025235 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mouse-CT26-Spatial-Transcriptomics" ;
definition: "Collection of spatial transcriptomics data of mouse CT26 sample generated by stereo-seq technology." .
SCR:025236 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StereoSiTE" ;
definition: "Software Python package for analysis and visualization of spatial transcriptomics data. Framework to spatially and quantitatively profile the cellular neighborhood organized iTME." .
SCR:025237 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2733" ;
rdfs:label "LCSB Disease Modelling and Screening Platform Core Facility" ;
NIFRID:synonym "DMSP",
"LCSB Drug Screening platform",
"Luxembourg Centre for Systems Biomedicine Disease Modelling and Screening Platform" ;
definition: "Core provides infrastructure, disease modelling and compound screening expertise, to facilitate translation of basic scientific discoveries into tangible hit drug candidates. Platform acts as interface between fundamental biomedical research and high-standard drug discovery." .
SCR:025238 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task" ;
NIFRID:abbrev "STARNET" .
SCR:025239 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IVIS_Lumina" ;
rdfs:label "Perkin Elmer | IVIS Lumina III In Vivo Imaging System" ;
NIFRID:synonym "IVIS Lumina III",
"IVIS Lumina III In Vivo Imaging System",
"PerkinElmer IVIS Lumina III" ;
definition: "Imaging system for both fluorescent and bioluminescent imaging in vivo. Lumina Series III platform offers full spectrum of wavelengths to perform almost any in vivo optical application with tunability of 20 nm. The system includes highly sensitive CCD camera, light-tight imaging chamber and complete automation and analysis capabilities. As optical imaging platform for in vivo analysis, IVIS systems include range of practical accessories developed through experience in research laboratories worldwide." .
SCR:025240 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "crypto-geofence" ;
definition: "Software Geo-fencing demo application based on Paillier scheme. Used for testing out homomorphic encryption." .
SCR:025241 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lattigo-polls" ;
definition: "Web application for scheduling meetings using lattigo. Program for Lattigo homomorphic encryption library." .
SCR:025242 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rosetta" ;
definition: "Software privacy-preserving framework based on TensorFlow. Integrates with mainstream privacy-preserving computation technologies, including cryptography, federated learning and trusted execution environment. Used to provide privacy-preserving solutions for artificial intelligence without requiring expertise in cryptography, federated learning and trusted execution environment. Rosetta reuses the APIs of TensorFlow and allows to transfer traditional TensorFlow codes into a privacy-preserving manner with minimal changes." .
SCR:025243 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tf-encrypted" ;
definition: "Software framework for Encrypted Machine Learning in TensorFlow. Bridge between TensorFlow and Microsoft SEAL library. TF Encrypted aims to make privacy-preserving machine learning readily available, without requiring expertise in cryptography, distributed systems, or high performance computing." .
SCR:025244 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CryptDB" ;
definition: "Database system that can process SQL queries over encrypted data. Protecting confidentiality with encrypted query processing." .
SCR:025245 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "encrypted-mongodb " ;
definition: "Software wrapper on MongoDB Python driver that enables to query encrypted data. Enables to store and query encrypted data on database." .
SCR:025246 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Prisma/DB" ;
definition: "Software application as cryptographic security layer for relational database systems, that currently supports Microsoft SQL Server, MySQL, MariaDB, PostgreSQL and CockroachDB. Security layer for relational database systems." .
SCR:025247 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TimeCrypt" ;
definition: "Encrypted time-series database using homomorphic encryption-based access control. End-to-end encrypted time-series data store where storage server does not see any data in the clear. The time-series streams are encrypted on the client-side, and only authorized parties can decrypt and verify queries.Used to support both scalable computation over encrypted time series data and fine-grained cryptographic access control on queries." .
SCR:025248 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lickometer Box" ;
NIFRID:synonym "Licktech" ;
definition: "Lickometer system based on open-source hardware platform with user-friendly interface software, capable of simultaneously receiving data from eight automated cages with two drinking bottles each. Device to acquire high-quality and detailed data. Adaptable to new types of sensors or other neuroscience tools capable of measuring brain activity simultaneously to the behavior." .
SCR:025249 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gridExtra" ;
definition: "Softwate R package to work with \"grid\" graphics, notably to arrange multiple grid-based plots on page, and draw tables. Miscellaneous functions for Grid graphics." .
SCR:025250 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "forestmodel" ;
definition: "Software R package that produces forest plots using 'ggplot2' from models produced by functions such as stats::lm(), stats::glm() and survival::coxph()." .
SCR:025253 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Centromics" ;
definition: "Software tool for visualing centromeres with multiple omics data. Designed for centromere sequence calling." .
SCR:025254 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2734" ;
rdfs:label "Washington University School of Medicine Knight ADRC Request Center Resources Core Facility" ;
NIFRID:synonym "ADRC Request Center Resources" ;
definition: "Provides on request resources including Data: clinical and cognitive measures as well as MRI and amyloid imaging scans; Tissue: frozen brain tissue, paraffin brain sections, antemortem CSF, DNA, fibroblast, dermal fibroblasts, plasma (fasting and non-fasting) and iPSC; Participants: eligible participants may be invited to enroll in research of other investigators after appropriate review. Researchers can use the request portal to review Center guidelines and policies; view available data and tissue; access data tables and codebooks; and submit request for resources." .
SCR:025255 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_6000_c_501" ;
rdfs:label "Roche | Cobas 6000 c501 analyzer" ;
definition: "Cobas 6000 modular analyzer with c501 analytical module for clinical chemistry testing for in vitro diagnostic use. Mid volume analyzer for clinical chemistry assays, determinations of sodium, potassium, and chloride, and for measuring HbA1c levels in whole blood. Module will perform up to 1,000 tests per hour (600 photometrics tests per hour and 400 ISE tests per hour) and holds up to 60 reagent packs on-board. Designed to use serum/plasma, urine, CSF, supernatant and whole blood sample types. Performs photometric assays as well as ion-selective electrode (ISE) determinations." .
SCR:025256 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8000_c_702" ;
rdfs:label "Roche | Cobas 8000 c 702 analyzer" ;
NIFRID:synonym "Cobas 8000 c 702",
"Roche Cobas 8000 c 702" ;
definition: "Cobas 8000 modular analyzer series is scalable module based Serum Work Area solution for range of in vitro diagnostics testing of clinical chemistry and immunochemistry designed for high throughput laboratories. Cobas 8000 modular analyzer with c 702 analytical module performs photometric assay tests for wide range of analytes and is equipped with reagent manager to allow for automatic reagent cassette decapping and loading/unloading during operation with throughput of up to 2000 tests/hour." .
SCR:025257 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_8000_e_801" ;
rdfs:label "Roche | Cobas 8000 e 801 analyzer" ;
definition: "Cobas 8000 modular analyzer with e 801 analytical unit for immunoassay tests. Cobas e 801 immunochemistry module performs range of heterogeneous immunoassay tests using ElectroChemiLuminescence technology." .
SCR:025258 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "quarTeT" ;
NIFRID:synonym "quar Telomere-To-Telomere Toolkit" ;
definition: """Web toolkit for studies of large scale T2T genomes. Collection of tools designed for T2T genome assembly and characterization, including reference guided genome assembly, ultra long sequence based gap filling, telomere identification, and de novo centromere prediction.
Includes four modules: AssemblyMapper, GapFiller, TeloExplorer, and CentroMiner.
Modules can be used alone or in combination with each other for T2T genome assembly and characterization.""" .
SCR:025259 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ImageXpress_Micro_XLS" ;
rdfs:label "University of Auckland Biomedical Imaging Research Unit Molecular Devices ImageXpress Micro XLS" ;
NIFRID:synonym "ImageXpress Micro XLS",
"Molecular Devices ImageXpress Micro XLS" ;
definition: "XLS model of ImageXpress Micro System to leverage large field-of-view optics to map macro-structures with minimal tiling. Querying of large cell populations is accelerated three fold, speeding up the characterization of highly heterogeneous samples or identification of rare sub-populations. Combined with software, the custom designed ImageXpress Micro System provides platform to translate new discoveries into scientific breakthroughs." .
SCR:025260 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Wound Healing Tool" ;
NIFRID:synonym "MRI Wound Healing Tool" ;
definition: "Software tool to analyze scratch assays. It measures the area of wound in cellular tissue on stack of images representing time-series." .
SCR:025261 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "biotools:maggot" ;
rdfs:label "Maggot" ;
NIFRID:synonym "Metadata AGGregation On data sTorage" ;
definition: "Web ecosystem for sharing metadata. Designed to annotate datasets by creating metadata file to attach to storage space. Allows users to add descriptive metadata to datasets produced within collective of research unit, platform, multi-partner project, etc. to fit to data management plan about data organization and documentation, data storage and frictionless metadata sharing." .
SCR:025262 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Reproducible Analysis" ;
NIFRID:synonym "reproanalysis" ;
NIFRID:abbrev "reproa" ;
definition: "Software pipeline system for ReproStat, written primarily in OCTAVE/MATLAB. It facilitates reproducible, inclusive, and efficient neuroimaging analyses." .
SCR:025263 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GMATCH" ;
NIFRID:synonym "SAS GMATCH macro" ;
definition: "Computerized matching of cases to controls using greedy matching algorithm with fixed number of controls per case. Controls may be matched to cases using one or more factors (X’s)." .
SCR:025264 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2720" ;
rdfs:label "University of Illinois at Urbana-Champaign Beckman Institute for Advanced Science and Technology Biomedical Imaging Core Facility" ;
NIFRID:synonym "Illinois-Biomedical Imaging Center",
"University of Illinois at Urbana-Champaign Biomedical Imaging Center" ;
NIFRID:abbrev "BIC" ;
definition: "Core supports molecular and magnetic resonance imaging. Provides facilities, equipment, and training for researchers across range of disciplines. Each BIC tool is supported by research scientists available to assist with study design, data collection, and data post-processing." .
SCR:025265 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2721" ;
rdfs:label "University of California at Davis Biological and Agricultural Engineering Shop Core Facility" ;
NIFRID:synonym "University of California at Davis Biological and Agricultural Engineering Shop" ;
NIFRID:abbrev "BAE Shop" ;
definition: "Provides support to UC research through engineering, design, fabrication, and repair of custom equipment. We can take your ideas, napkin sketches, drawings, and models and turn them into real parts, machines, tools, and systems. Services: prototyping, welding, fabrication, machining, electrical, repairs, misc. technical labor." .
SCR:025266 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2723" ;
rdfs:label "University of Illinois at Urbana-Champaign Beckman Institute for Advanced Science and Technology Microscopy Suite Core Facility" ;
NIFRID:synonym "Beckman Institute for Advanced Science and Technology Microscopy Suite",
"Microscopy Suite",
"University of Illinois at Urbana-Champaign Beckman Institute for Advanced Science and Technology Microscopy Suite" ;
definition: "Core imaging facility operating out of the University of Illinois. Offers many imaging modalities, including confocal, micro- and nano-CT, electron microscopy, scanned probe microscopy, Raman, and fluorescence. Assists users in preparing and collecting data on various projects." .
SCR:025267 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2725" ;
rdfs:label "University of Luxembourg LCSB Rodent Platform Core Facility" ;
NIFRID:synonym "LCSB Rodent Platform",
"LCSB Rodent Platform Core Facility" ;
definition: "Assist researchers in development and analysis of various in vivo neurodegenerative and cancer models including humanized and germ-free animals. Facility has capacity to house different transgenic and germ-free mouse strains in more than 2500 IVC cages within SOPF breeding barrier." .
SCR:025270 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Custom-fitting-of-implants" ;
NIFRID:synonym "custom-fitting cranial implants" ;
definition: "Tutorial to custom-design and -fit implants to continuous and discontinuous skull surfaces. Universal Guide for Skull Extraction and Custom-Fitting of Implants to Continuous and Discontinuous Skulls." .
SCR:025272 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2727" ;
rdfs:label "University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center Cytometry and Microscopy to Omics Core Facility" ;
NIFRID:synonym "Cytometry and Microscopy to Omics Facility",
"Roy J. Carver Biotechnology Center",
"UIUC" ;
NIFRID:abbrev "CMtO" ;
definition: "Facility, couples cytometry with microscopy, genomics and proteomics using instrumentation, expertise and services. Utilizes advanced super resolution microscopy techniques to gain understanding of cell sorting, analysis and enable cutting-edge spatial and single cell and multi-omics services." .
SCR:025273 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2728" ;
rdfs:label "University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center Metabolomics Core Facility" ;
NIFRID:synonym "Metabolomics Facility",
"Roy J. Carver Biotechnology Center",
"UIUC" ;
definition: "Core identifies and quantifies small molecules from variety of origins such as biological tissue, blood, serum, plasma, cell, cell medium, urine, feces, among others. Provides support for untargeted and targeted metabolite profiling, detecting such compounds as sugars and sugar phosphates, alcohols, amine and polyamines, amino acids, fatty acids, complex lipids, nucleotides, organic acids, phenolics, bile acids, steroids/hormones, neurotransmitters and neuromodulators, phthalates, and many more emerging metabolites. Helps execute projects, including protocol development, sample preparation, instrument method development, instrument data acquisition, and data processing.Multiple complementary analytical methods are utilized with mass spectrometry. Our laboratory has mass spectrometers, including liquid chromatograph-mass spectrometers such as Agilent 6560 ion mobility Q-TOF and Agilent 6546 Q-TOF systems, in addition to our Thermo Fisher Q Exactive hybrid quadrupole-orbitrap, Thermo Fisher Altis triple quadrupole, Sciex 6500+ triple quadrupole, and Sciex 5500 hybrid triple quadrupole-ion trap (QTRAP), as well as gas chromatograph-mass spectrometers including Agilent 5977A, Agilent 5975C, and Agilent 5973." .
SCR:025274 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2736" ;
rdfs:label "University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center Functional Genomics Core Facility" ;
NIFRID:synonym "UIUC-Roy J. Carver Biotechnology Center Functional Genomics" ;
definition: "Facility offers amplicon sequencing libraries, 16S sequencing, PacBio Revio long read 16S sequencing, custom long read amplicon libraries Standard Biotools (formerly Fluidigm) multiprimer amplicons, high throughput Gene Expression and SNP genotyping using Standard Biotools microfluidic system, Illumina beadchip arrays for genotyping and methylation analysis." .
SCR:025275 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2726" ;
rdfs:label "University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center DNA Services Laboratory Core Facility" ;
NIFRID:synonym "DNA Services Laboratory",
"Roy J. Carver Biotechnology Center",
"UIUC" ;
definition: "Provides service and instrumentation to support basic, environmental, agricultural, and translational medical research." .
SCR:025276 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2729" ;
rdfs:label "University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center Proteomics Core Facility" ;
NIFRID:synonym "Proteomics Facility",
"Roy J. Carver Biotechnology Center",
"UIUC" ;
definition: "Core provides expertise in characterizing proteins from diverse systems. Provides proteomics services including customized sample preparation, protein identification, detection of post-translational modifications, isotopic label based and label-free quantitation, and intact protein characterization. Equipped with high resolution mass spectrometers with nanoflow liquid chromatography systems or chip-based robots. Core uses software systems such as Mascot, Proteome Discoverer, Byonic, and MaxQuant for analysis of raw mass spectrometry data. Provides assistance in protein quantitation and deeper downstream bioinformatics analysis including gene ontology, visualization of protein networks, and pathway analysis. Consultations are always welcome." .
SCR:025277 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2731" ;
rdfs:label "University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center High Performance Computing in Biology Core Facility" ;
NIFRID:synonym "High Performance Computing in Biology",
"Roy J. Carver Biotechnology Center",
"UIUC" ;
NIFRID:abbrev "HPCBio" ;
definition: "Core for genomics research in Carl R. Woese Institute for Genomic Biology. Coordinates with IGB and National Center for Supercomputing Applications to provide technical expertise in high-performance computational biology." .
SCR:025279 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JATSdecoder" ;
definition: "Software metadata and text extraction and text manipulation tool set for statistical programming language R. Facilitates text mining projects on scientific articles in 'NISO-JATS' format by enabling individual selection of metadata and text parts." .
SCR:025280 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EPI2ME" ;
definition: "Software cloud based data analysis platform developed by Metrichor Ltd for Oxford Nanopore Technologies. Suite of data analysis workflows for wide range of applications." .
SCR:025281 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FlexStation_3" ;
rdfs:label "Molecular Devices | FlexStation 3 Multi-Mode Microplate Reader" ;
NIFRID:synonym "FlexStation 3 Benchtop Multi-Mode Microplate Reader",
"Molecular Devices FlexStation 3 Benchtop Multi-Mode Microplate Reader" ;
definition: """Monochromator based microplate reader combines performance of Molecular Devices SpectraMax M5e MultiMode Microplate Reader with integrated 8-channel or 16-channel
pipettor into one compact benchtop reader. System provides multi-detection platform capable of increasing liquid handling throughput and flexibility for biochemical-based and cellbased assays.""" .
SCR:025282 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Scientific NanoDrop 1000 Software" ;
definition: "Operating software for Thermo Scientific NanoDrop 1000 Spectrophotometer. Free NanoDrop operating software to update your instrument." .
SCR:025283 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clust" ;
definition: "Software package for automatic extraction of optimal co-expressed gene clusters from gene expression data. Automatic and optimised consensus clustering of one or more heterogeneous datasets." .
SCR:025284 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LIFEx" ;
definition: "Software for calculation of radiomic features for medical images. Enables calculation of conventional, histogram based, textural, and shape features from PET, SPECT, MR, CT, and US images, or from any combination of imaging modalities. Dedicated to researchers, radiologists, nuclear medicine physicians and oncologists to give access to 306 histogram, textural and shape indices in addition to conventional indices and where users can change calculation options." .
SCR:025285 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LSRFortessa_X-20" ;
rdfs:label "BD Biosciences | LSRFortessa X-20 Cell Analyzer" ;
definition: "Cell analyzer system can be configured with up to 5 lasers to detect up to 20 parameters simultaneously. BD FACSDiva Software controls the setup, acquisition and analysis of flow cytometry data from the BD LSRFortessa Workstation." .
SCR:025286 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "floreada.io" ;
NIFRID:synonym "Floreada.io" ;
definition: "Web application for flow cytometry analysis. Used to analyze FCS files for free in web-based app. Supports most FCS file types including FCS2.0, FCS3.0, and FCS3.1. Provides collection of flow cytometry tools which can also be used for analysis." .
SCR:025287 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AID_ISPOT_ELISPOT_FLUOROSPOT" ;
rdfs:label "AID Diagnostica | iSpot EliSpot FluoroSpot Plate Reader" ;
definition: "Plate reader for analyzing Enzymatic and fluorescent based EliSpot assays. Besides functionality of AID Classic, AID iSpot allows to analyze 1-, 2- or 3-color FluoroSpot assays. Provides one-click switch between enzymatic and fluorescent mode, without the need of hardware changes. The “FluoroAID” image overlay technology permits exact detection of cells secreting multiple cytokines. Count results and all other parameters can be exported in various formats." .
SCR:025288 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PubCompare" ;
definition: "Software tool that compares snippets of methods sections from PubMed Central, open access subset to other snippets of methods sections." .
SCR:025289 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ready Set Potato" ;
definition: "Software tool that helps users write experimental protocols." .
SCR:025290 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NucleoCounter_NC-250" ;
rdfs:label "ChemoMetec | NC-250 Automated Cell Analyzer" ;
NIFRID:synonym "ChemoMetec NucleoCounter NC-250",
"NucleoCounter NC-250",
"NucleoCounter NC-250 Automated Cell Analyzer" ;
definition: "Automated cell analyzer, which can characterize cell properties using fluorescence imaging. Offers optimized protocols to meet needs of all mammalian cell types grown under different conditions. Cell count can be performed even on cells growing on microcarriers and in sphere cultures. Performs high-speed cell count and viability determination and offers unique 5-minute Cell Cycle Assay and 1-minute Apoptosis Assay for up to eight samples at the time. The intuitive software has unlimited licenses and produces on-screen data analysis and automated PDF reports., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:025291 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "labelme" ;
NIFRID:synonym "labelme 5.2.1" ;
definition: "Software graphical image annotation tool written in Python. Image polygonal annotation with Python (polygon, rectangle, circle, line, point and image-level flag annotation)." .
SCR:025292 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FORRT Replication Database" ;
NIFRID:synonym "Framework for Open and Reproducible Research Training Replication Database" ;
definition: "Database is crowdsourced effort to include unpublished and published replication results to estimate and track replicability along various fields and provide researchers with way to assess replicability of crucial studies in quick and transparent way." .
SCR:025293 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gNOMO2" ;
definition: "Software as comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes. Enables integration of taxonomic and functional analyses in microbiome multi-omics data." .
SCR:025294 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Get Free Copy" ;
definition: "Web application to search for academic articles and research papers from various sources such as arXiv, medRxiv, bioRxiv, PMC, and Google PDF search. Provides user friendly interface to discover articles and access them for free. Provides direct links to original sources, allowing users to access full articles." .
SCR:025295 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ParaVision 360" ;
definition: """Software for preclinical imaging integrated with Bruker MRI spectrometers. Used with Bruker MRI, PET/MR, and PET/CT instruments. Enables easy and high throughput
imaging. All images, protocols, and subjects are in one location with inherent co-registration, image fusion, data processing, and analysis.""" .
SCR:025296 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IBEX Knowledge Base" ;
NIFRID:synonym "Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base" ;
definition: "Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase." .
SCR:025297 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Beckman Coulter | Avanti J-30I High-Speed Centrifuge" ;
NIFRID:synonym "Avanti J-30I High-Speed Centrifuge" ;
definition: "Refrigerated centrifuge that generates centrifugal forces required for wide variety of applications. Together with Beckman Coulter rotors are designed for use in this centrifuge. Centrifuge is microprocessor controlled, providing interactive operation." .
SCR:025298 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ZP10001_ZOOM" ;
rdfs:label "Thermo Fisher: Invitrogen | ZP10001 ZOOM Dual Power Supply" ;
NIFRID:synonym "ZOOM Dual Power Supply" ;
definition: "Two-in-one programmable power supple capable of handling high voltage/low current and high current/low voltage applications concurrently and independently. The high voltage/low current section is ideal for sample fractionation, IPG strips, IEF, and DNA sequencing applications while the low voltage/high current section is for SDS-PAGE, native PAGE, second-dimension SDS-PAGE, DNA/RNA electrophoresis, and blotting applications." .
SCR:025299 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FusionGDB2" ;
NIFRID:synonym "FusionGDB 2.0" ;
definition: "Functional annotation database of human fusion genes.FusionGDB 2.0 has updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with human genomic features across cellular role's categories, transcribed chimeric sequence and following open reading frame analysis with coding potential based on deep learning approach with Ribo-seq read features, and rigorous investigation of protein feature retention of individual fusion partner genes in protein level." .
SCR:025300 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggvenn" ;
definition: "Software R package to draw venn diagram by ggplot2." .
SCR:025301 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2765" ;
rdfs:label "DKFZ Small Animal Imaging Core Facility" ;
definition: "Supports users in application of numerous radiological methods such as ultrasound, optical imaging, µPET, µCT, µSPECT and MRT measurements to collect and quantify morphological and functional data in vivo." .
SCR:025302 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker | BioSpec 3T" ;
definition: "Bruker BioSpec preclinical MRI equipment at translational field of 3 Tesla, extends the range of multi-purpose, preclinical MRI and MRS systems in compact, easy to site footprint." .
SCR:025303 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stoelting | Motorized Mouse Stereotaxic Instrument" ;
definition: "Compact stereotaxic instrument designed for use with knock-out and transgenic mice. Instrument includes 100 micron, 3-axes left-hand manipulator arm, mouse snout clamp and tooth bar, dual-sided ear bars, and corner clamp probe holder. Stoelting’s Motorized Stereotaxic Manipulator Arms are designed for fast, accurate positioning during stereotaxic surgery. Motorized manipulator arms employ touchscreen display for easy-to-control movement of each axis. Manual movement is available anytime. Optional Drill feature available." .
SCR:025304 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "py_diAID" ;
NIFRID:synonym "python_data-independentAutomated Isolation Design" ;
definition: "Software Python package for DIA with automated isolation design. Used for Data-Independent Acquisition providing Automated Isolation Design. Optimally generates dia-PASEF and synchro-PASEF methods and places them optimally within the m/z – ion mobility (IM) plane." .
SCR:025305 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "goatools" ;
NIFRID:synonym "GOATOOLS" ;
definition: "Software Python library for Gene Ontology analysis. Performs gene ontology enrichment analyses to determine over- and under-represented terms." .
SCR:025306 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Netgraph" ;
definition: "Software Python library that aims to complement existing network analysis libraries such as networkx, igraph, and graph-tool with publication-quality visualisations within the Python ecosystem. Publication-quality Network Visualisations in Python." .
SCR:025307 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_493" ;
rdfs:label "Massachusetts General Hospital MGH CCIB DNA Core Facility" ;
NIFRID:synonym "Massachusetts General Hospital MGH CCIB DNA Core",
"MGH CCIB DNA Core" ;
definition: "Research core laboratory within Center for Computational and Integrative Biology at Massachusetts General Hospital in Boston. Provides access to instrumentation, methodologies and expertise Services include Sanger DNA sequencing,Next Generation Sequencing, Long read Sequencing, genotyping, laboratory automation, molecular biology." .
SCR:025308 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_903" ;
rdfs:label "University of California at Santa Barbara Biological Nanostructures Laboratory Core Facility" ;
NIFRID:synonym "Biological NanoStructures Laboratory",
"University of California at Santa Barbara Biological Nanostructures Laboratory" ;
definition: "Multi-purpose core research facility with sub-cores. Genetics, Analytical, Autoclave and Cell Culture Cores. Genetics Core provides Next Generation Sequencing, DNA/RNA and protein quantitation, nucleic acid QC, Real-Time PCR, and Droplet Digital PCR. Analytical Core houses analytical instruments such as UV-Vis, nanoparticle analyzers and plate readers. Some basic molecular biology equipment are also available. Cell Culture Core for researchers who need access to BSL1/BSL2 cell culture facility. Also includes autoclaves or labware sterilization and biohazardous waste disposal." .
SCR:025309 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_862" ;
rdfs:label "University of Illinois at Chicago Research Informatics Core Facility" ;
NIFRID:synonym "Research Informatics Core",
"University of Illinois at Chicago Research Informatics Core" ;
NIFRID:abbrev "RIC" ;
definition: "Research Informatics Core at University of Illinois-Chicago provides bioinformatics services including genomics, transcriptomics, epigenomics, metagenomics, metabolomics, and proteomics analysis, as well as applications in statistical analysis, systems biology, and machine learning." .
SCR:025310 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2745" ;
rdfs:label "Texas A and M University Health Institute of Bioscience and Technology Flow Cytometry and Cell Sorting Core Facility" ;
NIFRID:synonym "IBT Flow Cytometry and Cell Sorting Core Facility",
"Texas A and M University Health Institute of Bioscience and Technology Flow Cytometry and Cell Sorting Facility" ;
NIFRID:abbrev "FCCSF" ;
definition: "IBT Flow Cytometry and Cell Sorting Facility provides flow cytometry and cell sorting services, along with scientific expertise. Provides academic and commercial users with access to High Throughput Flow Cytometry automated platform in Texas Medical Center." .
SCR:025311 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhysiCell Studio" ;
definition: "Software graphical tool to allow easy editing of (XML) model, create initial positions of cells, run simulation, and visualize results. To contribute, fork and make PRs to the development branch. Used to create, execute, and visualize multicellular model using PhysiCell." .
SCR:025312 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyGenomeTracks" ;
definition: "Standalone program and library to plot beautiful genome browser tracks. Software Python plotting tool that combines multiple tracks. Enables reproducible and standardized generation of highly customizable and publication ready images." .
SCR:025313 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NHash Identifier" ;
NIFRID:synonym "Randomized N-gram Hashing Identifier" ;
definition: "Algorithm for generating unique study identifiers in distributed and validatable fashion, in multicenter research. Light-weight, block chain style resource identifier generation for tracking resource linkage, provenance, utilization, and visualization. NHash has unique set of properties: (1) it is a pseudonym serving the purpose of linking research data about study participant for research purposes; (2) it can be generated automatically in completely distributed fashion with virtually no risk for identifier collision; (3) it incorporates set of cryptographic hash functions based on N-grams, with combination of additional encryption techniques such as shift cipher; (d) it is validatable (error tolerant) in the sense that inadvertent edit errors will mostly result in invalid identifiers." .
SCR:025314 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2746" ;
rdfs:label "University of Chicago DNA Sequencing Core Facility" ;
NIFRID:synonym "UChicago Sanger Sequencing Core",
"University of Chicago DNA Sequencing Core",
"University of Chicago UChicago Sanger Sequencing Core" ;
definition: "Core provides Sanger sequencing and fragment analysis via capillary electrophoresis. Expected turnaround time is within 2 business days of order receipt." .
SCR:025315 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TooManyCellsInteractive" ;
NIFRID:abbrev "TMCI" ;
definition: "Web browser-based JavaScript application for visualizing hierarchical cellular populations as interactive radial tree. Allows users to explore, filter, and manipulate hierarchical data structures through intuitive interface while also enabling batch export of high-quality custom graphics." .
SCR:025316 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GBMatch_CNN - GBMPredictor" ;
definition: "Software tool for predicting TS and risk from glioblastoma whole slide images. Used to predict risk scores and transcriptional subtypes from whole slide images of glioblastomas." .
SCR:025317 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HiCDCPlus" ;
NIFRID:synonym "Hi-C Direct Caller Plus",
"HiC-DC+",
"HiCDCPlus (HiC-DC+)" ;
definition: "Software package for Hi-C/HiChIP interaction calling and differential analysis using efficient implementation of HiC-DC statistical framework. Enables principled statistical analysis of Hi-C and HiChIP data sets. Enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP" .
SCR:025318 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "longshot" ;
definition: """Software variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). Enables accurate variant calling in diploid genomes from single-molecule long read sequencing.
Takes as input aligned BAM/CRAM file and outputs phased VCF file with variants and haplotype information.""" .
SCR:025319 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WhatsHap" ;
definition: "Software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. Used for long reads, but works also well with short reads." .
SCR:025320 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genrich" ;
definition: "Software tool as peak-caller for genomic enrichment assays. Analyzes alignment files generated following assay and produces file detailing peaks of significant enrichment." .
SCR:025321 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Rad QuantaSoft Analysis Pro" ;
NIFRID:synonym "QuantaSoft AP" ;
definition: "Software analysis tool that enables data analysis of multiplex experiments and advanced applications and assay strategies for Droplet Digital PCR (ddPCR). For use with data files generated on QX100 or QX200 Droplet Reader using QuantSoft Standard Edition Software versions 1.4 or later." .
SCR:025322 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scGraph2Vec" ;
definition: "Software tool for gene embedding augmented by Graph Neural Network and single-cell omics data. Performs prediction and module detection simultaneously, and enhances high-dimensional information of gene embedding. Helps identify gene modules in specific tissue contexts, providing new ideas for studying gene regulatory functions in tissues and helps elucidate influence of regulatory genes on biological processes in specific tissue environment and infer more disease-related genes to explain disease risk." .
SCR:025323 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent QuikChange Primer Design" ;
NIFRID:synonym "QuikChange Primer Design" ;
definition: "Web application for mutagenic primer design for QuikChange mutagenesis experiments. Used to calculate/design appropriate primer sequences with optimal melting temperature." .
SCR:025324 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Developmental Mouse Brain atlas" ;
NIFRID:abbrev "DeMBA" ;
definition: "Continuous 3D reference atlas for postnatal mouse brain." .
SCR:025325 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "yEd" ;
NIFRID:synonym "yWorks yEd Graph Editor" ;
definition: "Software desktop application as general purpose diagramming program with multi-document interface. Cross-platform Java application to generate high-quality diagrams. Runs on Windows, Linux, Mac OS, and other platforms that support Java Virtual Machine." .
SCR:025326 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCI Colorectal Cancer Risk Assessment Tool" ;
NIFRID:synonym "Colorectal Cancer Risk Assessment Tool",
"Colorectal Cancer Risk Assessment Tool: Online Calculator",
"NCI Colorectal Cancer Risk Assessment Tool: Online Calculator" ;
NIFRID:abbrev "CCRAT" ;
definition: "web application as calculator designed for doctors and other health care providers to use with their patients. Estimates the risk of colorectal over the next five years and the lifetime risk for men and women who are Between the ages of 45 and 85, White,Black/African American, Asian American/Pacific Islander,Hispanic/Latino." .
SCR:025327 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "too-many-cells-python" ;
definition: "Software Python implementation of clustering tool named TooManyCells. Software package for spectral clustering." .
SCR:025328 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TooManyCells" ;
definition: "Software suite of tools, algorithms, and visualizations focusing on relationships between cell clades. This includes new ways of clustering, plotting, choosing differential expression comparisons. Identifies and visualizes relationships of single-cell clades." .
SCR:025329 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2770" ;
rdfs:label "University of Alberta Biological Sciences Advanced Microscopy Core Facility" ;
NIFRID:synonym "Advanced Microscopy Facility (AMF)",
"BioSci Advanced Microscopy Facility",
"University of Alberta BioSci Advanced Microscopy Facility" ;
NIFRID:abbrev "AMF" ;
definition: "Core services include paraffin embedding and histology, epifluorescence microscopy and confocal LSM, SEM and TEM sample prep and imaging." .
SCR:025330 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FARESHARE" ;
NIFRID:synonym "Fluid Acquisition Recording in Socially Housed Animal Research" ;
definition: "Open source device for fluid tracking in socially housed rats. Device uses RFID and custom hardware to individually measure and record each rat's fluid consumption and licking microstructure." .
SCR:025331 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Optima_XE-90" ;
rdfs:label "Beckman Coulter | Optima XE-90 ultracentrifuge" ;
NIFRID:synonym "Optima XE-90",
"Optima XE-90 ultracentrifuge" ;
definition: """Optima XE generates centrifugal forces for separation of particles. Classified S, it can be
used with all currently manufactured Beckman Coulter preparative rotors. Uses diffusion pump in series with mechanical vacuum pump to reduce chamber pressure to very low level. Uses solid state thermoelectric refrigeration and heating system without coolant
or water. Cooling is provided by forced air from the fans.""" .
SCR:025339 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cameraCalibrationCMOS" ;
definition: "Software for performing pixelwise calibration of sCMOS cameras. MATLAB code and instructions for routine camera calibration." .
SCR:025340 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RoSE-O-POLCAM" ;
definition: "Software for processing single-molecule and diffraction limited polarisation camera image data using dipole PSF fitting. MATLAB scripts and utilities for analysis of simulated and experimental POLCAM single-molecule orientation-localisation microscopy (SMOLM) data using RoSE-O, providing accurate and precise measurements of location and orientation of single molecules." .
SCR:025341 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "napari-polcam" ;
definition: "Software napari plugin to process and render polarisation camera data. Used for polarisation camera image processing." .
SCR:025342 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "POLCAM-Live" ;
definition: "Software for live processing of polarisation camera images." .
SCR:025343 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "POLCAM-SR" ;
definition: "Software for processing single-molecule and diffraction limited polarisation camera images." .
SCR:025345 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HaploStats" ;
NIFRID:synonym "National Marrow Donor Program HaploStats",
"NMDP HaploStats" ;
definition: "Web tool for determining HLA locus and allele disequilibria by population ethnicity." .
SCR:025346 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Deepdefense" ;
definition: "Software tool for discovery of novel immune systems in prokaryotes. Automatic annotation and classification of immune systems in prokaryotes using Deep Learning." .
SCR:025347 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ROCplot" ;
NIFRID:synonym "ROCplot.org" ;
definition: "Web analysis tool for validating predictive biomarkers of chemotherapy/hormonal therapy/anti-HER2 therapy using transcriptomic data of breast cancer patients. Designed to validate and rank new predictive biomarker candidates in real time. Platform provides resource for researchers to mine database and to validate and rank future biomarker candidates." .
SCR:025348 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCMCtreeR" ;
definition: "Software R package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree. Helps users choose parameters to reflect age information for prior age distributions, visualise time priors, and produce output files ready to be used in MCMCtree. Used to prepare MCMCtree analyses and visualize posterior ages on trees." .
SCR:025349 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Winnowmap" ;
NIFRID:synonym "Winnowmap2" ;
definition: "Software tool as long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap2 computes each read mapping through collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats." .
SCR:025350 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NECAT" ;
definition: "Software error correction and de-novo assembly tool for Nanopore long noisy reads. Nanopore data assembler." .
SCR:025351 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "drug perturbation Gene Set Enrichment Analysis" ;
NIFRID:abbrev "dpGSEA" ;
definition: "Software tool to detect phenotypically relevant drug targets through unique transcriptomic enrichment that emphasizes biological directionality of drug-derived gene sets. Exploratory tool to screen for possible drug targeting molecules." .
SCR:025352 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Applied Biosystems | SeqStudio Genetic Analyzer" ;
definition: "SeqStudio Genetic Analyzer is fluorescent dye labeled genetic analysis system using capillary electrophoresis technology. Enables both sequencing and fragment analysis applications without the need to switch polymer type or capillary array length. Allows to perform both sequencing and fragment analysis in single run." .
SCR:025353 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PTATO" ;
NIFRID:synonym "Primary Template-directed Amplification analysis TOol kit",
"PTA analysis TOol kit" ;
definition: "Software tool for single cell WGS analysis. Used to accurately detect single base substitutions, insertions-deletions (indels), and structural variants in PTA-based WGS data." .
SCR:025354 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2774" ;
rdfs:label "Newcastle University Bioimaging Unit Core Facility" ;
NIFRID:synonym "Newcastle University NU Bioimaging Unit",
"NU Bioimaging Unit" ;
definition: "Light microscopy core facility at Newcastle University based in the Faculty of Medical Sciences, providing services, access, training and support for light microscopy." .
SCR:025355 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2778" ;
rdfs:label "University of Pittsburgh Hillman Cancer Center Biostatistics Core Facility" ;
NIFRID:synonym "Biostatistics Facility (BF)",
"UPMC Hillman Cancer Center Biostatistics Facility (BF)" ;
definition: "Provides statistical and computational methods for design, execution, analysis, and reporting of cancer-related research studies and trials including biomarker analysis and grant development." .
SCR:025356 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2779" ;
rdfs:label "University of Pittsburgh Hillman Cancer Center Cancer Bioinformatic Services Core Facility" ;
NIFRID:synonym "Cancer Bioinformatic Services (CBS)",
"UPMC Hillman Cancer Center Cancer Bioinformatic Services (CBS)" ;
definition: "Provides bioinformatics support for translational genomics using sequencing, arrays, single cell, and other technologies." .
SCR:025357 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2781" ;
rdfs:label "University of Pittsburgh Hillman Cancer Center Cancer Genomics Core Facility" ;
NIFRID:synonym "Cancer Genome Facility (CGF)",
"UPMC Hillman Cancer Center Cancer Genome Facility (CGF)" ;
definition: "Supports genomics and transcriptomics platforms including nucleic acid extraction, sample QC, next-generation library preparation and sequencing. Specializes in paraffin-embedded tissue samples." .
SCR:025358 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2782" ;
rdfs:label "University of Pittsburgh Hillman Cancer Center Cancer Pharmacokinetics Pharmacodynamics Core Facility" ;
NIFRID:synonym "Cancer Pharmacokinetics Pharmacodynamics Facility (CPPF)",
"UPMC Hillman Cancer Center Cancer Pharmacokinetics Pharmacodynamics Facility (CPPF)" ;
definition: "Provides bioanalytical, pharmacokinetic and pharmacology research services that support preclinical and clinical research programs focused on oncology. Resources include HPLC-UV/fluorescence, ICP-MS, LC-MS/MS, LSC, ELISA, and in vivo rodent procedures, as well as advanced PK software suites and expertise for preclinical and clinical projects." .
SCR:025359 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2776" ;
rdfs:label "University of Louisville Micro/Nano Technology Center Core Facility" ;
NIFRID:synonym "Micro/Nano Technology Center" ;
definition: "Expertise resides in micro and nanotechnology, sensors, transducers, microelectromechanical systems (MEMS), advanced materials, biomedical devices, space and governmental applications.Offers SEM and TEM imaging services for biological samples." .
SCR:025360 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2784" ;
rdfs:label "University of Pittsburgh Hillman Cancer Center In Vivo Imaging Core Facility" ;
NIFRID:synonym "In Vivo Imaging Facility (pre clinical and clinical) (IVIF)",
"UPMC Hillman Cancer Center In Vivo Imaging Facility (pre clinical and clinical) (IVIF)" ;
NIFRID:abbrev "IVIF" ;
definition: "Provides novel quantitative imaging techniques that trace biomarkers of molecular events associated with effective cancer therapy." .
SCR:025361 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2780" ;
rdfs:label "University of Pittsburgh Hillman Cancer Center Cytometry Core Facility" ;
NIFRID:synonym "Cytometry Facility (CF)",
"UPMC Hillman Cancer Center Cytometry Facility (CF)" ;
definition: "Supports analytical cytometry and cell sorting. Offers NanoString Digital Spatial Analyzer and nCounter service and support." .
SCR:025362 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2783" ;
rdfs:label "University of Pittsburgh Hillman Cancer Center Immunologic Monitoring and Cellular Products Laboratory Core Facility" ;
NIFRID:synonym "Immune Monitoring and Cellular Production Laboratory (IMCPL)",
"UPMC Hillman Cancer Center Immune Monitoring and Cellular Production Laboratory (IMCPL)" ;
definition: "Core operates 12 clean rooms and focuses on IND manufacturing under cGMP/cGTP. Operations are monitored 24/7 by expert staff. Specializes in and collaborates on preclinical research development involving process conceptualization, technology transfer and testing implementation on human cell-based drugs for clinical trials. Immunological monitoring services are available to support clinical trials. The facility is a FACT-, CLIA-, CAP-, and FDA-accredited laboratory." .
SCR:025363 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FuncAnnot" ;
definition: "Software pipeline is set to to non-model plant GO/KO function annotations using R. It can collect data from Eggnog-mapper of custom BLAST, convert data, and make OrgDB packages." .
SCR:025364 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2805" ;
rdfs:label "Mayo Clinic Arizona Flow Cytometry Core Facility" ;
definition: "Provides cytometry services featuring sorting and analyzing. For analysis, we currently have BD LSR Fortessa, BD FACSymphony A3, and Cytek Aurora. Our cell sorters include 14-parameter, 4-laser Sony MA900 and 16-parameter, 5-laser FACSAria dedicated to BSL3 cell sorting." .
SCR:025365 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OriDB" ;
NIFRID:synonym "DNA Replication Origin Database" ;
definition: "Provides catalogue of confirmed and predicted DNA replication origin sites. At present this is limited to budding yeast and fission yeast. Data have been collated as culmination of number of genome-wide studies to identify location of replication origins throughout budding yeast genome. In addition to genome-wide studies data from large number of other origin mapping and characterization studies have been included." .
SCR:025366 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PoreWalker" ;
definition: "Web tool for identification and characterization of channels in transmembrane proteins from their three-dimensional structure." .
SCR:025367 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Incucyte Cell-By-Cell Analysis Software Module" ;
definition: "Software for analysis to determine live versus dead cells – no fluorescent dyes needed." .
SCR:025368 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Markerless Mouse Tracking for Social Experiments" ;
NIFRID:abbrev "MaSoMoTr" ;
definition: "Markerless video-based tool to simultaneously track two interacting mice of the same appearance in controlled settings for quantifying behaviors such as different types of sniffing, touching, and locomotion to improve tracking accuracy under these settings without increased human effort. It incorporates conventional handcrafted tracking and deep-learning-based techniques. The tool is trained on small number of manually annotated images from basic experimental setup and outputs body masks and coordinates of the snout and tail-base for each mouse." .
SCR:025369 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NanoDrop_Lite" ;
rdfs:label "Thermo Fisher | NanoDrop Lite Spectrophotometer" ;
NIFRID:synonym "NanoDrop Lite Spectrophotometer" ;
definition: "Compact, personal UV-Vis microvolume spectrophotometer that complements the full-featured NanoDrop 2000/2000c and NanoDrop 8000 instruments." .
SCR:025370 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Countess_II" ;
rdfs:label "Thermo Fisher: Invitrogen | Countess II Automated Cell Counter" ;
NIFRID:synonym "Countess II Automated Cell Counter" ;
definition: "Fully automated cell counter and assay platform that uses optics and image analysis algorithms to analyze trypan blue-stained cells in suspension. Benchtop device that measures cell concentration and viability." .
SCR:025372 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xRead" ;
definition: "Software application as coverage-guided approach for scalable construction of read overlapping graph. Used to handle numbers of datasets from large genomes, especially with limited computational resources." .
SCR:025373 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2789" ;
rdfs:label "Harvard University Chan School of Public Health Bioinformatics Core Facility" ;
NIFRID:synonym "Harvard University HSPH Harvard Chan Bioinformatics Core",
"HSPH Harvard Chan Bioinformatics Core" ;
NIFRID:abbrev "HSPH" ;
definition: "Provides single point of contact for Harvard researchers interested in bioinformatics support, applying genomic approaches together with established and developing methodologies from epidemiology, environmental health, biostatistics and bioinformatics to improve human health.Services include analysis all types of next-generation sequencing data from RNA-seq and single cell RNA-seq to variant sequencing (exome or whole genome), to ChIP-seq or bisulfite sequencing. Offers bioinformatics training program for Harvard researchers interested in learning basic data skills and analysis of high-throughput sequencing data." .
SCR:025374 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2797" ;
rdfs:label "University of British Columbia MRI Research Core Facility" ;
NIFRID:synonym "UBC MRI Research",
"University of British Columbia UBC MRI Research" ;
definition: "Facility consist of Philips 3.0 Tesla MRI scanner for studies on humans, Bruker small bore 9.4 Tesla MRI scanner, and computing facility for image archival and analysis. Scanners are entirely dedicated to research, and MR scanning is carried out on cost recovery basis. The scanners were selected to cater to a very broad range of in vivo applications and the Imaging Centre staff is trained to support any research projects that the scanners can accommodate." .
SCR:025375 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2798" ;
rdfs:label "Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Proteomics Core Facility" ;
NIFRID:synonym "Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Proteomics",
"Network Biology Collaborative Centre Proteomics" ;
definition: "Provides mass-spectrometry based identification and quantification of proteins. Facility specializes in functional proteomics with focus on protein proximity and protein interaction mapping. Services include access to reagents, plasmids, sample preparation, mass spectrometry, and data analysis.Applications include: proximity-dependent biotinylation mapping to identify neighboring proteins in cells ,protein-protein interaction mapping,post-translational modification identification (with a focus on phosphorylation),differential protein abundance,chemical proteomics (identifying on- and off-target binding to small molecules or biologics)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:025376 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Counter Plugin for ImageJ" ;
NIFRID:synonym "Cell Counter" ;
definition: "Software plugin will open new cell counter GUI in ImageJ to facilitate manual cell counting." .
SCR:025377 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CyTekBio | Guava easyCyte HT System" ;
NIFRID:synonym "Cytek Guava easyCyte HT System",
"Cytek® Guava® easyCyte™ HT System" ;
definition: "Compact benchtop flow cytometer based on capillary system with HTS high throughput screening. Uses microcapillary laser based technology to detect mammalian and microbial cells, particles, and beads. System can resolve the fluorescence from up to 12 fluorophores simultaneously." .
SCR:025378 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FAE" ;
NIFRID:synonym "FeAture Explorer",
"FeAture Explorer (FAE)" ;
definition: """Open-source software Python package for developing and comparing radiomics models.
Used to build radiomics models and evaluate them using independent testing dataset. It also provides easy model comparison and result visualization.""" .
SCR:025380 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhageGE" ;
NIFRID:synonym "Phage Genome Exploration" ;
definition: "Interactive webserver for exploratory analysis and visualisation of bacteriophage genomes." .
SCR:025381 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HERBs" ;
NIFRID:synonym "Head-fixed Environment for Rodent BehaviorS" ;
definition: "Open source hardware and software solution for flexible implementation of complex behaviors in head-fixed mice. Low cost and requires little to no programming experience. Allows neural activity to be seen during testing, which will show relations between neuronal activity and behavior during tasks such as alternative forced choice, GoNoGo, and sensory stimulus presentation." .
SCR:025382 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LAMBADA" ;
NIFRID:synonym "Lightsheet Aligned Mouse Brain Annotated Developmental Atlas" ;
definition: "Reference atlas of the developing post-natal mouse brain. Provides data and annotations on distribution of cells and gene expression in mouse brain." .
SCR:025383 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2806" ;
rdfs:label "Dartmouth Genomic Data Sciences Core Facility" ;
NIFRID:synonym "Dartmouth Genomic Data Sciences Core",
"Geisel School of Medicine at Dartmouth Genomic Data Sciences Core",
"Genomic Data Sciences Core" ;
NIFRID:abbrev "GDSC" ;
definition: "Core offers statistical analysis of genomics data. Provides suite of standardized analysis pipelines for common data types like RNA-seq, ATAC-seq, and genome assembly. For more complex datasets, such as single-cell genomics, provides tailored analysis solutions. Core team assists with all project stages, from experimental design to publication support and data management. GDSC hosts several multi-day bioinformatics workshops designed to introduce fundamental concepts for analysis of genomics data." .
SCR:025384 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2807" ;
rdfs:label "Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Flow Cytometry Core Facility" ;
NIFRID:synonym "Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Flow Cytometry",
"Network Biology Collaborative Centre Flow Cytometry" ;
definition: "Core provides flow cytometry analyzers and cell sorters, with specialty in image-based flow cytometry and cell sorting.Services include unassisted and full-service cell sorting, training on theory and on instruments, consultation on experiment design, protocol development, data analysis, manuscript preparation and grant submission. Applications include image-based analysis powered by machine learning on the Amnis ImageStream; image-based cell sorting using the BD BACS Discover S8; cell sorting for a variety of applications including multi-color sort for bulk culture, indexed cell sort into 96-well plates, cell cycle phase sort and primary tissue sorting for RNA or DNA analysis." .
SCR:025385 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2808" ;
rdfs:label "Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Next-Generation Sequencing Core Facility" ;
NIFRID:synonym "Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Next-Generation Sequencing",
"Network Biology Collaborative Centre Next-Generation Sequencing" ;
definition: "Core provides both short and long read sequencing capabilities for analysis of gene function and expression.Facility specializes in functional genomics and single cell biology. Services include consultation, sample preparation (especially for spatial and single cell applications), quality control, sequencing analysis, bioinformatics support, and assistance with grant and publication writing related to the services. Applications include:gene function analysis - pooled CRISPR screening, multiplexed barcode screens; whole genome sequencing - both short- and long-read sequencing; bulk gene expression profiling; single cell biology (single cells and single nuclei); spatial profiling; pathogen detection and profiling." .
SCR:025386 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID: grid.250674.2; ISNI: 0000 0004 0626 6184;" ;
rdfs:label "Lunenfeld-Tanenbaum Research Institute" ;
definition: "Medical research institute in Toronto, Ontario and part of the Sinai Health System. It was originally established in 1985 as the Samuel Lunenfeld Research Institute, the research arm of Mount Sinai Hospital, by an endowment from the Lunenfeld and Kunin families." .
SCR:025387 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CISNET Publication Support and Modeling Resources " ;
definition: "Portal provides access to technical modeling information, raw data, and publication extensions stemming from the work of the CISNET consortium to improve understanding of cancer control interventions in prevention." .
SCR:025388 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MOVARSim" ;
NIFRID:synonym "Modelling Of cancer-specific Variants And sequencing Reads Simulation" ;
definition: """Software simulator that leverages data-driven information to set both variants and reads
characteristics, producing realistic tumoral samples. Computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation.""" .
SCR:025389 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2811" ;
rdfs:label "Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Advanced Imaging Core Facility" ;
NIFRID:synonym "Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Advanced Imaging",
"Network Biology Collaborative Centre Advanced Imaging" ;
definition: "Advanced imaging facility for microscopy needs where users have access to technologies in advanced microscopy.Services include consultation on experimental design, advice on appropriate systems, training and support for assisted and unassisted use, as well as help with data analysis and image generation for publications. Applications include Fluorescence and brightfield image acquisition; Whole-slide scanning; Dynamic live-cell imaging; Super-resolution imaging." .
SCR:025390 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2809" ;
rdfs:label "Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre High-Throughput Screening Core Facility" ;
NIFRID:synonym "Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre High-Throughput Screening",
"Network Biology Collaborative Centre High-Throughput Screening" ;
definition: "Provides instrumentation and expertise for the automation of laboratory processes. Facility has automated screening platforms and accessory equipment to enable flexible and scalable in vitro and in vivo assays including organoids. Services include access to chemical and genome-wide siRNA libraries, assay development and implementation, and data analysis. Applications include drug discovery and lead validation; ELISA-based assays for immune surveillance; protein biomarker discovery using OLINK proteomics technology; multiplexed barcode screening assays." .
SCR:025391 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2810" ;
rdfs:label "Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre High-Content Screening Core Facility" ;
NIFRID:synonym "Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre High-Content Screening",
"Network Biology Collaborative Centre High-Content Screening" ;
definition: "Provides optical imaging and analysis of fixed and live cells. Services include assistance with selecting imaging platform, developing customized imaging assays, training in imaging and data analysis and assistance with image/data preparation for presentations and publications. Applications include Multi-plate based imaging applications; High-resolution cell characterization and sub-cellular localization using IN cell Analyzers;3D Spheroid and Organoid imaging using a Nikon A1R BioPipeline;Live-cell analysis (confluency, growth tracking) using Incucyte - imaging within incubator." .
SCR:025392 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ III" ;
rdfs:label "SeekGene | Scitech Korea Multicenter Animal Spinal Cord Injury Studies MASCIS impactor" ;
NIFRID:synonym "Multicenter Animal Spinal Cord Injury Studies (MASCIS) impactor" ;
definition: "Impactor that allows for reproducible spinal cord and head contusions." .
SCR:025393 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VT4" ;
rdfs:label "Virginia Tech Advanced Blast Simulator large" ;
NIFRID:synonym "Advanced Blast Simulator - large" ;
definition: "A blast device that capable of accommodating large samples and it is available for cadaver, animal, materials, and physical surrogate testing. It is driven by a gas detonation system." .
SCR:025394 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pittsburgh Precision Instruments | Cortical Controlled Impactor" ;
NIFRID:synonym "Cortical Controlled Impactor" ;
definition: "Pneumatic-powered CCI device, with adjustable velocity and angle on impact used for neuroscience research." .
SCR:025395 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VT1" ;
rdfs:label "Virginia Tech Advanced Blast Simulator small" ;
NIFRID:synonym "Advanced Blast Simulator - small" ;
definition: "Blast device that is appropriate for testing specimens, such as small animals and material samples. It operates with compressed air or helium in the driver, which is seperated from the test section by a diaphragm." .
SCR:025396 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "E-Scope" ;
definition: "Miniaturized calcium imaging microscope with integrated dense electrode technology for synchronous acquisition of neural activity across distant regions of the brain. Device based off open-sourced UCLA Miniscope to synchronously measure single cell activity at or near spike-time resolution across distant brain regions in freely behaving mice. Used to perform calcium imaging, with dense electrode electrophysiological recording, allowing simultaneous recordings from two remote brain regions in freely behaving mouse." .
SCR:025397 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eppendorf | ThermoMixer C" ;
definition: "Benchtop shaker combines mixing performance with temperature control. Provides easy-to-exchange SmartBlocks for all common lab tubes, new and improved program functions, and high level of stability for every mixing frequency." .
SCR:025398 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2816" ;
rdfs:label "University of Ottawa Transmission Electron Microscopy Core Facility" ;
NIFRID:synonym "TEM Core Facility",
"Transmission Electron Microscopy (TEM) Core",
"Transmission Electron Microscopy Core",
"University of Ottawa Transmission Electron Microscopy Core" ;
NIFRID:abbrev "TEM" ;
definition: "Provides unique imaging (JEOL JEM-1400plus) and tissue processing solutions for your research, in partnership with CHEO’s Electron Microscope Laboratory. Provides training for use of the instrument, and training for sample preparation/processing." .
SCR:025399 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "V-pipe" ;
definition: "Software pipeline for analysis of next-generation sequencing data derived from intra-host and environmental viral populations. Designed for analysing NGS data of short viral genomes. Used for assessing viral genetic diversity from high-throughput data." .
SCR:025400 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "International Radiosurgery Research Foundation" ;
NIFRID:abbrev "IRRF" ;
definition: "Foundation consists of academic and clinical centers of excellence where brain stereotactic radiosurgery is performed. Aims to facilitate retrospective and prospective clinical trials and outcomes analysis that evaluate the role of SRS for wide spectrum of clinical indications. Mission is to perform research, provide education, and publish information related to stereotactic radiosurgery for the purpose of improving public health." .
SCR:025401 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model-_Number_CM_1850" ;
rdfs:label "Leica | CM 1850 UV cryostat" ;
definition: "Cryostat for histopathology applications. Intended for cutting frozen sections of standard and non-standard materials. Designed to rapidly freeze material in temperature controlled environment. Has ability to quickly disinfect the cryo chamber at any time with ultra-violet light (UVC). The UV light is intended to reduce the user to significant dangers from bacteria, spores, and viruses." .
SCR:025402 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DokuMate" ;
definition: "DokuMate helps standardize and reuse documents, simplifies and speeds-up editing, and automates many tedious tasks. A docId” is one of the “magic” Content Control tag names. A docId is an alphanumerical ID (e.g., “R01-01-C00”, “R01-11-100”, “R01-11-410”, “R01-30-100”) that uniquely identifies and sorts documents (e.g., Schedule C, Exhibit 1, Attachment 4.1, Appendix 1) within a larger set of documents, e.g., all documents belonging to (a) a specific RFP or (b) the set of contracts between a first party and a second party." .
SCR:025403 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Lyrasis" ;
definition: "Organization that works with knowledge professionals to create, support and deliver programs, services and technologies that allow for equitable access to world knowledge and cultural heritage. Hosts data-migration, content licensing, and community supported software programs for libraries, archives, museums and research organizations worldwide." .
SCR:025404 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eko konnect" ;
definition: "A cluster of the Nigerian Research and Education Network (NgREN). Network to support network connectivity and collaborations between education and research organisations as part of wider efforts for sustainable National Research and Education Network (NREN)." .
SCR:025405 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RSpace" ;
definition: "Web next-gen digital research platform for Institutional Research Data Management. Fully integrated sample management and electronic lab notebook solution. Electronic lab notebook for physical sciences. Works with IGSN." .
SCR:025406 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyBehave" ;
definition: "Open source software interface and framework for controlling behavioral experiments in neuroscience and psychology. Python-based framework for designing and controlling behavioral experiments in animals. Used to develop, perform, and control behavioral tasks." .
SCR:025407 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spectran" ;
definition: "Software R package with web based GUI for spectral analysis of light." .
SCR:025408 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LightLogR" ;
definition: "Software R package to process personal light exposure data from wearables." .
SCR:025409 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Omada" ;
definition: "Software R package to automate RNAseq clustering processes and make robust unsupervised clustering of transcriptomic data more accessible through automated machine learning based functions." .
SCR:025410 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CAT Bridge" ;
NIFRID:synonym "Compounds And Transcripts Bridge" ;
definition: "Web comprehensive multi-omics integration and analysis tool. Used to identify gene-metabolite pairs with biological association by fusing transcriptomic and metabolomic data." .
SCR:025411 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Incucyte Neurotrack Analysis Software" ;
NIFRID:synonym "Sortoris Incucyte Neurotrack" ;
definition: "Software tool to automatically process Incucyte images and to analyze neurite dynamics with or without labels in living cells in each well of 96- or 384-well plates. Analyses can be performed directly on phase contrast images obviating need for cell labels in monoculture experiments, or on fluorescent images using non-perturbing probes as may be required in reagents for co-culture systems models." .
SCR:025412 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EventIDE" .
SCR:025413 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_025417" ;
rdfs:label "CellBin" ;
definition: "Software tools for generating single-cell gene expression data. Software pipeline for high-resolution and large field-of-view spatial transcriptomic data of Stereo-seq. Provides comprehensive and systematic platform for generating high-confidence single-cell spatial gene expression profiles, which specifically includes image stitching, image registration, tissue segmentation, nuclei segmentation and molecule labeling." .
SCR:025415 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D Printed Hindlimb Stabilization Apparatus" ;
definition: "Custom SolidWorks parts used in implementing hindlimb stabilization apparatus. Open source 3D-Printed Hindlimb Stabilization apparatus for measurement of stimulation evoked ankle flexion in rat.Apparatus is made up of 3 key components: Foot Pedal, Knee-Locking component, and Acrylic Base Platform. The design is adjustable for variations in anatomy across sex and size of rodents, and is low in cost. Components are almost entirely 3D-printed, and any other supplies are published along with the build instructions." .
SCR:025418 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lcMLkin" ;
NIFRID:synonym "Maximum Likelihood Estimation of Relatedness" ;
definition: "C++ program to infer biological relatedness from low coverage 2nd generation sequencing data. It uses information from genotype likelihoods rather than observed genotypes in maximum likelihood framework in order to estimate the overall coefficient of relatedness as well as individual kinship components between two samples. Maximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data." .
SCR:025419 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VolcaNoseR" ;
definition: "Web app for creating, exploring, labeling and sharing volcano plots . The plot can be annotated to show genes/proteins based on their top ranking or based on user input." .
SCR:025420 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Qiagen | Tissue Lyser III" ;
NIFRID:synonym "TissueLyser III" ;
definition: "Lyser simultaneously disrupts multiple biological samples through high-speed shaking in tubes or 96-well plates with stainless steel, zirconium, ceramic or glass beads. Using the appropriate adapter set, up to 192 samples can be processed at the same time. Alternatively, grinding jar set can be used to process large samples. Touchscreen and rotary knob make it easier to run and customize disruption protocols. Has pre-programmed protocols and customizable protocols for maximum sample versatility. Allows to create custom program cycles to set disruption parameters.TissueLyser II accessories, including adapter sets, are compatible with the TissueLyser III." .
SCR:025421 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Marshall Scientific | J Research PTC-200 Thermal Cycler" ;
NIFRID:synonym "Bio-Rad PTC 200",
"Peltier Thermal Cycler-200 MJ Research PTC-200 Thermal Cycler",
"PTC 200 Thermo Cycler" ;
definition: "Hot Bonnet heated lid fitted into PTC 200 Thermo Cycler controls pressure and height.Various plastic wares can be accommodated by system. Enables oil-free cycling.Equipped with interchangeable sample blocks and heat pump. Single control units of this model can also be supplied with different alpha modules and alpha blocks to increase functionality." .
SCR:025422 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "STMSGAL" ;
definition: "Software framework for analyzing ST data by incorporating graph attention autoencoder and multi-scale deep subspace clustering.Used for Unveiling Patterns in Spatial Transcriptomic Data." .
SCR:025423 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "glmulti" ;
definition: "Software R package for model selection and multimodel inference. Used for automated model selection and model-averaging. Provides wrapper for glm and other functions, automatically generating all possible models with specified response and explanatory variables." .
SCR:025424 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "metaviz" ;
definition: "Software R package to create plots of meta-analytic data. Used to create forest plots, funnel plots, and their variants, such as rainforest plots, thick forest plots, additional evidence contour funnel plots, and sunset funnel plots. In addition, functionalities for visual inference with funnel plot in context of meta-analysis are provided." .
SCR:025425 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Puncta Analyzer" ;
NIFRID:synonym "Puncta Analyzer v2" ;
definition: "Software tool for detecting and quantifying punctate co-localization in multi-channel images." .
SCR:025426 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COMSOL model of Magnetic coil" ;
definition: "Software application as model of magnetic field distribution of magnetic coil visualized using COMSOL Multiphysics." .
SCR:025427 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2818" ;
rdfs:label "Yale School of Medicine Flow Cytometry Core Facility" ;
NIFRID:synonym "YSM Flow Core Facility" ;
definition: "Core provides comprehensive flow cytometry analysis and cell sorting including instrumentation, technical support, training and consultation." .
SCR:025429 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Luxembourg LCSB Aquatic Platform Core Facility" ;
definition: "Aquatic Platform consists of semi-automated installation that provides zebrafish housing, husbandry, and experimental services to support biomedical research and teaching activities. Facility can house adult zebrafish, offering robotic feeding, maintenance of constant micro-environmental parameters, and semi-automated cleaning systems that ensure excellent conditions for research quality and animal welfare." .
SCR:025431 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spiroarteriocardiorhythmograph" ;
NIFRID:synonym "blood circulation",
"functional diagnostics",
"functional diagnostics of nervous regulation of blood circulation",
"nervous regulation",
"SACR",
"Spiroateriokardioritmograf" ;
NIFRID:abbrev "SAKR-M" ;
definition: """Design of SAKR-M device includes computer, pneutronic unit, spirometric sensor, finger
cuff, ECG electrodes and power supply adapter. Used for functional diagnostics of nervous regulation of blood circulation. Integrated method of studying cardiorespiratory system to analyze heart rate variability , arterial blood pressure variability and respiratory patterns.""" .
SCR:025432 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2819" ;
rdfs:label "Peter MacCallum Cancer Centre Advanced Histology and Microscopy Core Facility" ;
NIFRID:synonym "Centre for Advanced Histology and Microscopy",
"Peter MacCallum Cancer Centre Advanced Histology and Microscopy" ;
NIFRID:abbrev "CAHM" ;
definition: "Provides tools and expertise in bio image analysis, histology, and microscopy. Facility allows for the preparation, visualization, and quantification of biological samples at the cellular and sub cellular levels. Researchers can choose to utilize our instruments independently or collaborate with our skilled staff through our fee-for-service options." .
SCR:025433 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5723" ;
rdfs:label "University of Edinburgh Genomics Core Facility" ;
NIFRID:synonym "Edinburgh Genomics Core Facility" ;
definition: "Core provides secure receipt, processing, archiving and analysis of biological samples. Offers support for clinical research from sample collection to genetic analysis, working to the principles of Good Clinical Practice for Laboratories. Facility provides access to genomic technologies and services including next-generation sequencing (Illumina), third-generation sequencing (PacBio and Oxford Nanopore), bespoke bioinformatics analysis, and genomics and bioinformatics training." .
SCR:025434 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NetMHCIIpan" ;
NIFRID:synonym "NetMHCIIpan-4.0",
"NetMHCIIpan-4.0 server" ;
definition: "Web server predicts peptide binding to any MHC II molecule of known sequence using Artificial Neural Networks." .
SCR:025435 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pVACtools" ;
definition: "Software toolkit to identify and visualize cancer neoantigens. Cancer immunotherapy tools suite consisting of following tools: pVACseq as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from VCF file; pVACbind as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from FASTA file; pVACfuse as tool for detecting neoantigens resulting from gene fusions; pVACvector as tool designed to aid specifically in construction of DNA-based cancer vaccines; pVACview as application based on R Shiny that assists users in reviewing, exploring and prioritizing neoantigens from results of pVACtools processes for personalized cancer vaccine design." .
SCR:025436 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "con/duct" ;
NIFRID:synonym "duct" ;
definition: "Software application as helper to run command, capture stdout/stderr and details about running." .
SCR:025437 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpinalJ" ;
definition: "Software tool extension to ImageJ for spinal cord. Used for efficient preparation and imaging of whole spinal cord and the absence of 3D reference atlas." .
SCR:025438 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cellarium" ;
definition: "Software platform to annotate cell types." .
SCR:025439 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRISMA-P" ;
NIFRID:synonym "Preferred Reporting Items for Systematic reviews and Meta-Analyses for Protocols",
"PRISMA for Protocols" ;
definition: "Reporting guideline published in 2015 and aiming to facilitate the development and reporting of systematic review protocols." .
SCR:025440 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CADIMA" ;
definition: "Web tool facilitating the conduct and assuring for the documentation of systematic reviews, systematic maps and further literature reviews." .
SCR:025441 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Q500" ;
rdfs:label "QSonica | Q500 sonicator" ;
NIFRID:synonym "Q500 Sonicator",
"Q500 System with Standard Probe" ;
definition: "Laboratory scale ultrasonic processor for nanoparticle dispersion, emulsification, cell lysis, homogenization, particle size reduction, and wide range of other applications." .
SCR:025442 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "KM Data Corporation" ;
NIFRID:synonym "KM Data Co.",
"Ltd." ;
definition: "Develops and supports KeyMolnet integrated platform for bioinformation, and provides analysis services using KeyMolnet. KeyMolnet provides support for disease mechanism analysis, drug discovery target discovery, expression data analysis obtained by microarrays and high-speed sequencers, and data analysis such as proteomics and metabolomics, based on molecular network information, disease information, and drug information collected by our researchers from the latest papers." .
SCR:025444 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HipHop" ;
NIFRID:synonym "Heterozygous Offspring are Precluded",
"hiphop",
"Homozygous Identical Parents" ;
definition: "Software R library for parentage assignment using Bi-Allelic Genetic Markers. Used for assignment of parentage with molecular markers. Improved paternity assignment among close relatives using simple exclusion method for bi-allelic markers." .
SCR:025445 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "APIS" ;
NIFRID:synonym "Adaptive Parentage Inference Software" ;
definition: "Software R package to assign offspring to their parents without any prior information other than offspring and parental genotypes, and user-defined, acceptable error rate among assigned offspring. Auto-adaptive parentage inference software that tolerates missing parents." .
SCR:025446 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CERVUS" ;
definition: "Software package for parentage analysis in plant and animal populations. It combines robust likelihood-based method with simple graphical interface." .
SCR:025447 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fneighbor" ;
definition: "Software wrapper command for command neighbor of the PHYLIP package. Implements Neighbor-Joining method of Saitou and Nei and UPGMA method of clustering. Constructs tree by successive clustering of lineages, setting branch lengths as the lineages join." .
SCR:025448 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VCF2Dis-1" ;
definition: "Software tool to calculate p-distance matrix based Variant Call Format." .
SCR:025449 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2817" ;
rdfs:label "University of Technology Sydney Microbial Imaging Core Facility" ;
NIFRID:synonym "University of Technology Sydney UTS-Microbial Imaging Core Facility",
"University of Technology Sydney UTS-Microbial Imaging Facility",
"UTS-Microbial Imaging Facility" ;
NIFRID:abbrev "MIF" ;
definition: "Provides services including High-resolution imaging of bacteria and parasites, and their interactions with host eukaryotic cells; High-resolution imaging of biological processes of larger eukaryotic cells, spheroids, tissues and organs including the use of micro-fluidic devices. Provides equipment for biological specimen preparation for optical and electron microscopy. Provides training and support on the use of both basic and advanced microscopes including:transmitted light, wide-field fluorescence, confocal laser-scanning, super-resolution, high-content imaging, slide-scanning microscopy and range of image analysis and 3D-image visualisation software like FIJI, Huygens, Leica AIVIA, ZEISS ZEN Intellesis and Bitplane Imaris." .
SCR:025450 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2821" ;
rdfs:label "University of Alabama at Birmingham Cryo-Electron Microscopy Core Facility" ;
NIFRID:synonym "Cryo-Electron Microscopy Facility (CEMF)",
"UAB Cryo-EM Facility",
"University of Alabama at Birmingham Cryo-Electron Microscopy Facility" ;
NIFRID:abbrev "CEMF" ;
definition: "Core supports the application of cryo-EM in making new scientific discoveries. Provides access and training in the use of cutting edge cryo-EM technology and techniques for the characterization of biological samples from the cellular to the atomic scale." .
SCR:025451 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Global Cancer Observatory" ;
NIFRID:abbrev "GCO" ;
definition: "Interactive web-based platform presenting global cancer statistics to inform cancer control and cancer research. Focuses on the visualization of cancer indicators using data from IARC’s Cancer Surveillance Branch (CSU), including GLOBOCAN;Cancer Incidence in Five Continents (CI5); International Incidence of Childhood Cancer (IICC); and several cancer survival benchmarking projects (SurvCan and SURVMARK)." .
SCR:025452 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Global Cancer Observatory Cancer Today" ;
NIFRID:synonym "World Health Organization" ;
definition: "Global resource for cancer epidemiology. Presents national estimates of incidence, mortality and rate. Enables comprehensive assessment of cancer burden worldwide in 2022, based on GLOBOCAN estimates of incidence, mortality and prevalence for year 2022 in 185 countries or territories for 36 cancer types by sex and age group. Provides data visualization tools for exploring global cancer burden in 2022." .
SCR:025453 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ColabFold" ;
definition: "Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding." .
SCR:025454 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AlphaFold" ;
NIFRID:synonym "AlphaFold2",
"AlphaFold v2" ;
definition: "Software package provides implementation of inference pipeline of AlphaFold v2. Incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into design of deep learning algorithm. Used for protein structure prediction." .
SCR:025455 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhysiMeSS" ;
NIFRID:synonym "PhysiCell Microenvironment Structure Simulation" ;
definition: "PhysiCell add-on which allows users to simulate ECM components as agents. PhysiCell addon for extracellular matrix modelling." .
SCR:025456 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Swiss Pathogen Surveillance Platform" ;
NIFRID:synonym "Swiss Pathogen Data Platform" ;
NIFRID:abbrev "SPSP" ;
definition: "Secure One-health online platform that enables near real-time sharing under controlled access of pathogen sequencing data and their associated clinical/epidemiological metadata. Data exchange platform for bacterial, viral and fungal genomics and associated metadata." .
SCR:025458 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH PRECISION Human Pain Network" ;
NIFRID:synonym "PRECISION Pain Network" ;
definition: "Project titled Program to Reveal and Evaluate Cells-to-gene Information that Specify Intricacies, Origins, and Nature of Human Pain (PRECISION) Network to develop meaningful resource for knowledge transfer, and to integrate and share Human Pain Associated Genes and Cell Datasets. Building knowledge platform to visualize, query, and interact with these data will support researchers and help accelerate dissemination of vital data to the larger scientific community. These goals align with NIH Helping to End Addiction Long-term (HEAL) Initiative, which seeks to accelerate the discovery and successful translation of non-addictive pain therapeutics. PRECISION Human Pain Network will leverage prior interdisciplinary collaboration to create workflows, tools, and infrastructure to define data and metadata types, to improve data management and sharing, and to integrate datasets and visualization tools." .
SCR:025459 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ,
;
rdfs:label "PathfindR" ;
definition: "Software R package for comprehensive identification of enriched pathways in omics data through active subnetworks. Uses protein interaction networks to find enriched pathways from transcriptomic data." .
SCR:025460 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GE | Discovery MR750 3.0T MR system" ;
NIFRID:synonym "Discovery MR750",
"fast scan times",
"GE Discovery MR750 3.0T MR system" ;
definition: "Whole body magnetic resonance imaging scanner designed to support high resolution, high signal-to-noise ratio and fast scan times. This MRI system features superconducting magnet that operates at 3. O Tesla." .
SCR:025461 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GE HealthCare" ;
definition: "Provides digital infrastructure, data analytics and decision support tools to help in diagnosis, treatment and monitoring of patients." .
SCR:025462 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TC20" ;
rdfs:label "Bio-Rad TC20 Automated Cell Counter" ;
NIFRID:synonym "TC20 Automated Cell Counter",
"TC20 Automated Cell Counter (Bio-Rad)" ;
definition: "Automated cell counter accurately counts cells in one simple step using auto-focus technology and cell-counting algorithm. Enables accurate cell counting in less than 30 seconds." .
SCR:025463 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Technopath | Biolog OmniLog PM System" ;
NIFRID:synonym "Biolog OmniLog",
"OmniLog PM system" ;
definition: "Instrument that runs Biolog's microplate metabolic arrays. Incubates and monitors 50 microplates, or 1,920 phenotypic assays simultaneously to measure physiological responses in diverse microbial cells. OmniLog PM system includes software for analysis of Biolog Phenotype MicroArray panels." .
SCR:025464 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BEADL:BEhavioral tAsk Description Language" ;
NIFRID:synonym "BEhavioral tAsk Description Language" ;
NIFRID:abbrev "BEADL" ;
definition: "Universal framework for describing behavioral tasks. Language to abstract and standardize behavioral task descriptions on two layers. Graphical layer specifies elements to describe behavioral tasks as state machine in formal flow diagram and how task controlling system interacts with subject. This graphical layer has been designed to be easy to understand while retaining all aspects of behavioral task. The second layer is corresponding, XML-based description of task. This layer forms rigid, yet extensible foundation of BEADL and hides hardware implementation related details form graphical representation.BEADL-specific extension for Neurodata Without Borders data standard defines how behavioral outcomes of task are stored in NWB including corresponding BEADL task description." .
SCR:025465 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NWB Inspector" ;
definition: "Software Python-based package designed to asses quality of Neurodata Without Borders files and based on compliance with Best Practice. Meant as companion to PyNWB validator, which checks for strict schema compliance. Attempts to apply some commonsense rules and heuristics to find data components of file that pass validation, but are probably incorrect, or suboptimal, or deviate from best practices. In other words, while PyNWB validator focuses on compliance of structure of file with the schema, the inspector focuses on compliance of actual data with best practices. Meant as data review aid. It does not catch all best practice violations, and any warnings it does produce should be checked by knowledgeable reviewer." .
SCR:025466 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroSift" ;
definition: "Browser-based tool designed for visualization of Neurodata Without Borders files, whether stored locally or hosted remotely, and enables interactive exploration of DANDI Archive." .
SCR:025467 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NWB Graphical User Interface for Data Entry" ;
NIFRID:abbrev "NWB GUIDE",
"NWB Guide" ;
definition: "Desktop app that provides no-code user interface for converting neurophysiology data to Neurodata Without Borders." .
SCR:025468 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker AMIX software" ;
definition: "Software that can handle NMR and MS data and combines both technologies for even deeper insights and more comprehensive analysis." .
SCR:025469 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2822" ;
rdfs:label "University of Virginia School of Medicine Biomolecular Magnetic Resonance Core Facility" ;
NIFRID:synonym "Biomolecular Magnetic Resonance Facility",
"UVA School of Medicine Biomolecular Magnetic Resonance Facility" ;
definition: "Facility has NMR spectrometers used to execute experiments typically used for structure elucidation and dynamics characterization of both small and large (ie. protein) molecules in solution. All spectrometers are connected to the internet. Data can be readily transferred for remote processing and the campus has a site license for Mestrenova NMR data processing and visualization software. Assistance is available for all who wish to use NMR spectroscopy. Advice on all aspects of solution NMR spectroscopy is available from the facility manager." .
SCR:025470 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2823" ;
rdfs:label "University of Virginia School of Medicine Research Histology Core Facility" ;
NIFRID:synonym "Research Histology Core",
"UVA School of Medicine Research Histology Core" ;
definition: "Core provides standard and customized research specific histology services including routine formalin fixation and paraffin embedding, and sectioning, automated Hematoxylin and Eosin staining as well as selection of manually prepared special stains and preparation of frozen section." .
SCR:025471 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2824" ;
rdfs:label "University of Virginia School of Medicine Radiochemistry Core Facility" ;
NIFRID:synonym "University of Virginia School of Medicine Radiochemistry Core",
"UVA School of Medicine Radiochemistry Core" ;
NIFRID:abbrev "UVARCF" ;
definition: "Provides access to high-quality novel and existing radiopharmaceuticals (radiolabeled small molecules, peptides, proteins, and antibodies), that can be imaged by Positron Emission Tomography (PET) method, to meet their preclinical and clinical needs. Radiochemistry core is Good Manufacturing Practices (cGMP) certified facility as required by the U.S. Pharmacopeia Chapter 823 and 21CFR part 212 and is BSL-2 certified facility to conduct research." .
SCR:025472 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2825" ;
rdfs:label "University of Virginia School of Medicine Molecular Imaging Core Facility" ;
NIFRID:synonym "Molecular Imaging Core",
"UVA School of Medicine Molecular Imaging Core" ;
definition: "Core specializes in imaging small animals and samples with variety of modalities depending on the investigator’s needs. These modalities include MRI, X-Ray CT, PET, SPECT, luminescence, and fluorescence. We work closely with the Radiochemistry Core Lab which can synthesize custom, targeted PET and SPECT imaging agents." .
SCR:025473 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2826" ;
rdfs:label "University of Virginia School of Medicine Genetically Engineered Murine Model Core Facility" ;
NIFRID:synonym "UVA School of Medicine Genetically Engineered Murine Model (GEMM) Core",
"UVA School of Medicine Genetically Engineered Murine Model Core" ;
NIFRID:abbrev "GEMM" ;
definition: "Core provides services to produce and preserve genetically engineered mouse strains for animal model research.Supports animal model research endeavors, to advance genetic and reproductive technologies for model creation and preservation, and to serve as resource for design, development and derivation of customized mouse strains." .
SCR:025474 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2827" ;
rdfs:label "University of Virginia School of Medicine Exercise Physiology Core Facility" ;
NIFRID:synonym "Exercise Physiology Core Laboratory",
"University of Virginia School of Medicine Exercise Physiology Core Laboratory",
"UVA School of Medicine Exercise Physiology Core Laboratory" ;
NIFRID:abbrev "EPCL" ;
definition: "Promotes the expansion and enhancement of clinical research that incorporates exercise physiology and body composition into research questions. Offers measures of resting and exercise oxygen consumption, lactate threshold assessment, endothelial function, regional distribution of body fat, body composition assessment, anthropometry, and the use of acute exercise and/or exercise training as an intervention." .
SCR:025475 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2828" ;
rdfs:label "University of Virginia School of Medicine Center for Human Therapeutics cGMP Core Facility" ;
NIFRID:synonym "University of Virginia School of Medicine Center for Human Therapeutics cGMP Facility",
"UVA School of Medicine Center for Human Therapeutics cGMP Facility" ;
definition: "Offers manufacturing of cellular and biologics for safety and initial efficacy testing in first–in– human, pilot, and Phase I clinical trials. Facilitates bench–to–bed translation into novel cellular therapies. Provides focused scientific, technical, and regulatory support for investigator-initiated investigational new drug applications (INDs) in cell and gene therapy. Current and completed trials include hematologic malignancies multiple myeloma, breast cancer, prostate cancer, glioblastoma, neuroblastoma, and pancreatic cancer. The potential applications of cellular therapy and biologics are not limited to cancer, a large number of disease indications such as cardiovascular, autoimmune diseases, diabetes, neurological diseases, etc." .
SCR:025476 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2829" ;
rdfs:label "University of Virginia School of Medicine Biomolecular Analysis Core Facility" ;
NIFRID:synonym "Biomolecular Analysis Facility",
"University of Virginia School of Medicine Biomolecular Analysis Facility",
"UVA School of Medicine Biomolecular Analysis Facility" ;
NIFRID:abbrev "BAF" ;
definition: "Core provides services and expertise in the areas of proteomics, metabolomics, small molecules, and molecular interactions. The staff can assist in data collection for experiments as well as provide help in experimental design and data analysis. Value added work such as grant writing and publication methods/figures is provided free of charge." .
SCR:025479 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhenoCapture" ;
definition: "Software for scientific image capture and analysis." .
SCR:025480 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pwr:Basic functions for Power Analysis" ;
NIFRID:abbrev "pwr" ;
definition: "Software R package for power calcualtions. Basic functions for power analysis." .
SCR:025481 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IsoSeq" ;
definition: "Software package to identify transcripts in PacBio single-molecule sequencing data. Scalable De Novo isoform discovery from single-molecule PacBio reads." .
SCR:025482 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Skera" ;
definition: "Software Pacbio analysis tool. Deconcat PacBio reads." .
SCR:025483 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Starcode" ;
definition: "Software for DNA sequence clustering. General purpose DNA sequence clustering tool with strong focus on error correction." .
SCR:025484 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "C3Poa" ;
NIFRID:synonym "Concatemeric Consensus Caller with Partial Order alignments." ;
definition: "Software to detect DNA splint sequence raw reads. Computational pipeline for calling consensi on R2C2 nanopore data." .
SCR:025485 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DotDotGoose" ;
definition: "Software tool to assist with manually counting objects in images. Used for many conservation applications." .
SCR:025486 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tRNA Analysis of eXpression" ;
NIFRID:synonym "tRNA Analysis of eXpression (tRAX)" ;
NIFRID:abbrev "tRAX" ;
definition: "Software package built for in-depth analyses of tRNA-derived small RNAs (tDRs), mature tRNAs, and inference of RNA modifications from high-throughput small RNA sequencing data. Used for integrating analysis of tRNAs, tRNA-derived small RNAs, and tRNA modifications." .
SCR:025487 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "The Great Genoytper" ;
definition: "Software workflow begins by preprocessing short-read samples of raw data to create counting colored De Bruijn graph. Graph based method for population genotyping of small and structural variants. Population genotyping workflow." .
SCR:025488 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "American College of Surgeons National Cancer Database" ;
NIFRID:abbrev "NCDB" ;
definition: "Clinical oncology database sourced from hospital registry data collected in Commission on Cancer-accredited facilities. These data are used to analyze and track patients with malignant neoplastic diseases, their treatments, and outcomes." .
SCR:025489 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Seattle Children's Research Institute Microscopy and Histopathology Collaborative Laboratory Core Facility" ;
NIFRID:synonym "Seattle Children's Research Institute Microscopy and Histopathology Collaborative Laboratory" ;
definition: "Provides technology and service capabilities in super resolution microscopy, image analysis, immunohistochemistry, and histopathology services. Provides consultations and technical support on histopathology services and experimental design." .
SCR:025490 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Seattle Children's Research Institute Genomics and Spatial Biology Collaborative Laboratory Core Facility" ;
NIFRID:synonym "Genomics and Spatial Biology Collaborative Laboratory (CoLab)",
"Seattle Children's Research Institute Genomics and Spatial Biology Collaborative Laboratory" ;
definition: "Provides technology and service capabilities in long and short read sequencing, spatial transcriptomics, and single cell assays." .
SCR:025491 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2777" ;
rdfs:label "University of Colorado Anschutz Medical Campus Genetically Engineered Murine Models Core Facility" ;
NIFRID:synonym "Genetically Engineered Murine Models (GEMM) Core",
"University of Colorado Anschutz Medical Campus Genetically Engineered Murine Models (GEMM) Core" ;
NIFRID:abbrev "GEMM" ;
definition: "Core provides full-service mouse genetic engineering support to researchers.Helps to select model for your research program, design and build any requisite constructs and reagents, and produce live mice. The most popular requests are for CRISPR-based gene edited mice and transgenic mice. Services include creation of engineered alleles for knockouts, conditional knockouts, SNP knockins, tag and marker insertions, deletions of up to 300kb, duplications, and transgenic alleles. These novel mouse models have been made on a wide spectrum of genetic background strains, including but not limited to C57BL/6J, C57BL/6N, NOD, BALB/cJ, FVB/Crl, NSGS, various 129 substrains, collaborative cross strains, and on mice that are already genetically modified. Breeding and genotyping program supports breeding to establish germline transmission and can also create cohorts for investigators. Provides strain cryopreservation, rederivation and rescue services, as well as cryostorage." .
SCR:025492 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2820" ;
rdfs:label "University of Miami The Miami Project Imaging Core Facility" ;
NIFRID:synonym "The Miami Project Imaging Core Facility" ;
definition: "Imaging Core provides equipment and services available to all UM researchers. Offers training and assistance in range of light microscope techniques including spinning disk confocal, super resolution imaging, lightsheet imaging of cleared organ and stereology systems. Offers image analysis software (Imaris neuroscience package) including 3D image rendering, surface creation, spot detection and filament tracing." .
SCR:025493 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pre-rob" ;
definition: "Neural networks for RoB assessment in preclinical publications. BERT-model based automated tool that assesses bias of preclinical research studies." .
SCR:025494 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cytek SpectroFlo" ;
NIFRID:synonym "SpectroFlo" ;
definition: "Flow Cytometry acquisition software." .
SCR:025495 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cNMF" ;
NIFRID:synonym "consensus Non-negative Matrix Factorization" ;
definition: "Source code and example data for running consensus Non-negative Matrix Factorization on single-cell RNA-Seq data." .
SCR:025496 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaboSERV" ;
definition: "Browser based platform for selecting, exchanging, and visualizing metabolomics data with controlled data access. Used to facilitate collaborative metabolomics research and to enable researchers to make their experimental data findable, accessible, interoperable, and re-usable as defined by the FAIR principles." .
SCR:025497 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WASP" ;
definition: "Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery." .
SCR:025498 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sinto" ;
definition: "Software tools for single-cell data processing." .
SCR:025500 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Philips | Alice 6 LDx Diagnostic sleep system" ;
NIFRID:synonym "Alice 6 LDx",
"Alice 6 LDx Diagnostic sleep system" ;
definition: "Diagnostic sleep system developed by Phillips Respironics. Base station can be paired with LDxS head box for 19 EEG inputs or LDxN for 32 EEG inputs." .
SCR:025502 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReachOut" ;
definition: "Open source hardware-software platform for analyzing reaching movement kinematics in mice. Used for studying fine motor skills in mice performing reach-to-grasp task. Behavioral platform uses readily available and 3D-printed components and was designed to be affordable and universally reproducible. Provides schematics, 3D models, code, and assembly instructions." .
SCR:025503 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2865" ;
rdfs:label "Versiti Blood Research Institute Shared Resources Core Facility" ;
NIFRID:synonym "VBRI Shared Resources",
"Versiti Blood Research Institute Shared Resources" ;
definition: """Core forms network of laboratories dedicated to advancing biomedical research by providing access to specialized services, advanced equipment, and expert staff.
Services include Bioinformatics, Biorepository, Flow Cytometry, Grant Application Support, Histology, Hybridoma, Microscopy, Molecular and Single Cell Biology, Protein Shared Instrumentation,Thrombosis and Hemostasis, Viral Vector.""" .
SCR:025504 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID: grid.280427.b; ISNI: 0000 0004 0434 015X; Wikidata: Q30253349;" ;
rdfs:label "Versiti Blood Research Institute" ;
NIFRID:synonym "Versiti Blood Center of Wisconsin" ;
definition: "Versiti Blood Research Institute is national leader in innovative blood health solutions. Provides blood and blood products to hospitals and collects blood annually. Investigators study blood disorders like hemophilia, blood cancers like leukemia, and other blood diseases." .
SCR:025505 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scp package" ;
NIFRID:synonym "Single Cell Proteomics" ;
NIFRID:abbrev "scp" ;
definition: "Software R package to process and analyse mass spectrometry-based single cell proteomics data." .
SCR:025506 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Roche | Ventana BenchMark ULTRA IHC/ISH System" ;
definition: "Automated, standardized IHC and ISH staining system. Immunohistochemistry and in situ hybridization slide staining system with individual slide drawers." .
SCR:025507 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2864" ;
rdfs:label "Auburn University Flow Cytometry and High-Speed Cell Sorting Laboratory Core Facility" ;
NIFRID:synonym "Auburn University Flow Cytometry and High-Speed Cell Sorting Laboratory" ;
definition: "Flow Cytometry Laboratory at Auburn University College of Veterinary Medicine provides operator-managed and assisted support for flow cytometry analyses and high-speed cell sorting." .
SCR:025508 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vectra Polaris | Automated Quantitative Pathology Imaging System" ;
NIFRID:synonym "Akoya PhenoImager HT" ;
definition: "Advanced, high-throughput digital scanning platform used in cancer immunology and pathology research. It allows scientists to visualize, analyze, quantify, and phenotype immune cells in intact tissue samples. Uses patented multispectral imaging to identify and measure up to nine overlapping biomarkers on a single tissue section or tissue microarray." .
SCR:025509 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sleepware G3" ;
definition: "Software platform and database to manage studies from our in-lab PSG, Alice 6, and portable sleep testing devices, Alice NightOne and Alice PDx." .
SCR:025510 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sierra" ;
definition: "Software R package to detect differential transcript usage from data generated by commonly used polyA-captured scRNA-seq technology." .
SCR:025511 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "olsrr" ;
definition: "Software tools for developing Ordinary Least Squares regression models." .
SCR:025512 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "glmmTMB " ;
NIFRID:synonym "generalized linear mixed models using Template Model Builder" ;
definition: "Software R package for fitting generalized linear mixed models and extensions, built on Template Model Builder." .
SCR:025513 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MatrixEQTL" ;
NIFRID:synonym "Matrix Expression Quantitative Trait Loci" ;
definition: "Software tool for ultra fast eQTL analysis via large matrix operations." .
SCR:025514 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "intervaltree" ;
definition: "Software mutable, self-balancing interval tree for Python 2 and 3. Queries may be by point, by range overlap, or by range containment." .
SCR:025515 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cellsnp-lite" ;
definition: "Software C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs." .
SCR:025516 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "aod: Analysis of Overdispersed Data" ;
NIFRID:synonym "Analysis of Overdispersed Data" ;
NIFRID:abbrev "aod" ;
definition: "Software R package to analyse overdispersed counts or proportions." .
SCR:025517 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "glmpca" ;
NIFRID:synonym "generalized version of principal components analysis" ;
definition: "Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data." .
SCR:025518 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scGBM" ;
definition: "Software application for model-based dimensionality reduction of scRNA-seq data. Quantifies uncertainty in each cell's latent position and leverages these uncertainties to assess confidence associated with given cell clustering. On real and simulated single-cell data produces low-dimensional embeddings that better capture relevant biological information while removing unwanted variation. Used for model-based dimensionality reduction for single-cell RNA-seq with generalized bilinear models." .
SCR:025519 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GPU-assisted Distance Estimation Software" ;
NIFRID:synonym "GPU-Assisted Distance Estimation Software" ;
NIFRID:abbrev "GADES" ;
definition: "Software package to compute distance matrices in sparse or dense mode with GPU or CPU." .
SCR:025520 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lima" ;
definition: "Software tool to identify barcode and primer sequences in PacBio single-molecule sequencing data. It powers the Demultiplex Barcodes GUI-based analysis application," .
SCR:025521 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2830" ;
rdfs:label "University of Colorado School of Medicine Electron Microscopy Core Facility" ;
NIFRID:synonym "Electron Microscopy Core Facility",
"University of Colorado Anschutz Medical Campus Electron Microscopy Core Facility" ;
definition: "Service facility which provides instrumentation and image analysis on recharge basis. Offers full specimen preparation and imaging services. Specimen preparation for electron microscopy studies including negative staining, plastic embedding, ultramicrotome and immunogold." .
SCR:025522 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Seattle Children's Research Institute Flow Cytometry Core Facility" ;
definition: "Flow Cytometry Core at Seattle Children's Research Institute, offers cell analyzer and sorter capabilities to researchers across the institute." .
SCR:025523 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2853" ;
rdfs:label "Indiana University School of Medicine Biochemical Genetics Laboratory Core Facility" ;
NIFRID:synonym "Indiana University School of Medicine Biochemical Genetics Laboratory",
"IU Biochemical Genetics Laboratory" ;
NIFRID:abbrev "IUBGL" ;
definition: "Clinical testing lab that performs targeted metabolomics analyses designed to diagnose and manage patients with inherited metabolic disease.Services include Quantitative Acylcarnitine panel,Quantitative Amino acid panel,Quantitative Methylmalonic acid,Quantitative Free and Total Carnitine Analysis,Semi-Quantitative Urine Organic Acid Profile,Blood Spot Analyte Quantification,Custom Development of Quantitative Metabolite Assays." .
SCR:025524 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2854" ;
rdfs:label "Indiana University School of Medicine Behavioral Phenotyping Core Facility" ;
NIFRID:synonym "Indiana University School of Medicine Behavioral Phenotyping Core" ;
definition: "Facility where IUSM and external investigators can request studies within broad spectrum of rodent behavioral paradigms. Housed on the fourth and fifth floors of Stark Neurosciences Research Institute in the Neurosciences Research Building, the core, available to all IU School of Medicine investigators. Core validates all assays; allows for testing of pharmacological or other manipulations to study disease models; incorporates necropsy endpoints to behavioral assays as needed; provides guidance on interpretation and analysis of data." .
SCR:025525 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2849" ;
rdfs:label "Indiana University School of Medicine Biospecimen Management Core Facility" ;
NIFRID:synonym "Indiana University School of Medicine Biospecimen Management Core" ;
definition: "Core consists of the Specimen Storage Facility (SSF) and the Clinical and Translational Support Laboratory (CTSL), which together offer cost efficient sample processing and storage services with focus on consistent quality and sample integrity." .
SCR:025526 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2852" ;
rdfs:label "Indiana University School of Medicine Bioinformatics Core Facility" ;
NIFRID:synonym "Indiana University School of Medicine Bioinformatics Core" ;
definition: "Bioinformatics Core provides advanced computation and informatics approaches to analyze large and complex biological datasets. Core offers services including Next Generation Sequence Data Analysis; Microarray Data Analysis; Proteomics Data Analysis;Multi-omics Data Integration;Statistical Genetics;Pharmacokinetics/Pharmacodynamics Data Analysis; Drug Absorption, Disposition, Metabolism, Elimination and Transportation Prediction, and Drug Exposure Prediction;Public Domain Database Access and Custom Data Annotation." .
SCR:025527 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2851" ;
rdfs:label "Purdue University Biological Evaluation Core Facility" ;
NIFRID:synonym "Biological Evaluation Shared Resource" ;
definition: "Core performs highly customizable efficacy testing of novel drug or therapies for antitumor activity. We also acquire blood or tissues for pharmacokinetic or pharmacodynamic analyses." .
SCR:025528 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2848" ;
rdfs:label "Indiana University School of Medicine Biostatistics and Health Data Science Core Facility" ;
NIFRID:synonym "Indiana University School of Medicine Biostatistics and Health Data Science Core" ;
definition: "Core collaborates with investigators in the planning, statistical design, data management, and analysis of health related clinical, laboratory and epidemiological research projects. Grant development assistance is provided without charge." .
SCR:025529 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2850" ;
rdfs:label "Indiana University School of Medicine Biospecimen Collection and Banking Core Facility" ;
NIFRID:synonym "Biospecimen Collection and Banking Core (BC2)",
"Indiana University School of Medicine Biospecimen Collection and Banking Core" ;
definition: "Core offers services related to biospecimen and data collection in support of cancer research. Provides collection of well-annotated samples from patients with malignancy and normal controls to support studies exploring the biologic basis of cancer, move basic findings to clinic, and probe the biology underlying clinical and population phenomena." .
SCR:025530 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2846" ;
rdfs:label "Indiana University Bloomington Biostatistics Consulting Center Core Facility" ;
NIFRID:synonym "Biostatistics Consulting Center" ;
definition: "Provides study design and data analysis for health-related research, including grant or protocol development, sample size and power calculations, data management, data analysis, and scientific writing. Support can range from hourly support on a short-term project to including a biostatistician on a long-term grant collaboration." .
SCR:025531 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2844" ;
rdfs:label "Indiana University School of Medicine Cell and Gene Therapy Manufacturing Core Facility" ;
NIFRID:synonym "Cell and Gene Therapy Manufacturing",
"Indiana University School of Medicine Cell and Gene Therapy Manufacturing" ;
definition: "Core collaborates with investigators through all phases of cell and gene therapy manufacturing, from pre-clinical design through treatment of patients. Facility comprises the Cell Immunotherapy and Transduction Facility (CIT), the Vector Production Facility (VPF), and the Bioprocess Development and Cell Manufacturing Lab (BDL)." .
SCR:025532 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2845" ;
rdfs:label "Purdue University Birck Nanotechnology Center Core Facility" ;
NIFRID:synonym "Birck Nanotechnology Center" ;
definition: "Nanofabrication cleanroom, bio-pharma clean room, nanometrology laboratories, nanomanufacturing laboratories, microelectronics and microfuidics fabrication and testing laboratories, 3D cell culture and tissue chip laboratories." .
SCR:025533 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2840" ;
rdfs:label "Indiana University School of Medicine Medical Genomics Core Facility" ;
NIFRID:synonym "Indiana University School of Medicine Center for Medical Genomics" ;
definition: "Provides high-throughput genomics services including: genomic DNA sequencing, transcriptome RNA sequencing, miRNA sequencing, methylome or targeted methylation sequencing, protein DNA/RNA interaction (ChIP-seq, ATAC-seq and CLIP-seq), 10x single cell or single nuclei sequencing, and SNP genotyping." .
SCR:025535 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2843" ;
rdfs:label "Indiana University School of Medicine Cellular Response Technologies Core Facility" ;
NIFRID:synonym "Indiana University School of Medicine Cellular Response Technologies Core" ;
definition: "Conduct validated and highly reproducible in vitro and in vivo angiogenesis, endothelial, hematopoietic and multi-parametric flow cytometry assays and their role in normal and patient-related hematologic and cardiovascular disorders. The ABC also manages an IncuCyte Zoom and Seahorse XFp." .
SCR:025536 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Purdue University Center for Research Computing Core Facility" ;
NIFRID:synonym "Center for Research Computing" ;
definition: "CRC houses two complementary resources: the High-Performance Computing section, providing over 35,000 cores of computational power with the associated support infrastructure for both hardware and installed software, and the Cyberinfrastructure section, empowering Faculty and industry partners to develop research software and environments that support advanced data and information processing services including acquisition, storage, management, integration, mining" .
SCR:025537 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2838" ;
rdfs:label "Purdue University Chemical Genomics Core Facility" ;
NIFRID:synonym "Chemical Genomics Facility",
"Purdue University Chemical Genomics Facility" ;
NIFRID:abbrev "CGF" ;
definition: "Provides access to large chemical and CRISPR libraries and state-of-the-art instrumentation in high-throughput screening (HTS) and high content screening (HCS) campaigns to facilitate the identification of chemical or genomic tools to study biological pathways and the discovery of lead agents for the development of novel therapeutics and diagnostic approaches. The facility also provides assistance in assay development" .
SCR:025538 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2839" ;
rdfs:label "Indiana University School of Medicine Proteome Analysis Core Facility" ;
NIFRID:synonym "IUSM Center for Proteome Analysis" ;
definition: "Provides numerous types of mass-spectrometry based proteomics services, including global proteome quantitation, affinity purification-mass spectrometry, targeted mass spectrometry analysis for precise quantitation, post-translational modification analysis, and a variety of consulting services." .
SCR:025539 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2836" ;
rdfs:label "Indiana University School of Medicine Clinical Pharmacology Analytical Core Facility" ;
NIFRID:synonym "Clinical Pharmacology Analytical Core" ;
NIFRID:abbrev "CPAC" ;
definition: "Core provides drug and metabolite concentrations from a variety of biological matrices such as (but not limited to): plasma, urine, CSF, and tissue using HPLC-MS/MS. Additional services include protein binding of drugs, formulation studies, drug stability, drug metabolism, and metabolite screening." .
SCR:025540 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2837" ;
rdfs:label "Indiana University Bloomington CISAB Mechanisms of Behavior Laboratory Core Facility" ;
NIFRID:synonym "CISAB Mechanisms of Behavior Laboratory",
"Mechanisms of Behavior Core" ;
definition: "Mechanisms of Behavior Core offers the equipment, reagents, bench space, and expertise to answer questions related to the roles of genetics and hormones in relation to animal behavior." .
SCR:025541 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2842" ;
rdfs:label "Purdue University Center for Comparative Translational Research Core Facility" ;
NIFRID:synonym "Purdue University Comparative Translational Research" ;
definition: "Core facilities pre-clinical studies of orthopedic devices intended for animal and human use, clinical studies of treatment and prevention of respiratory diseases in horses and animal clinical trials evaluating the treatment of bladder cancer in Scottish Terriers, an animal model of human bladder cancer." .
SCR:025542 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenBiomApps" ;
definition: "Software R package as collection of functions to compute the Clopper-Pearson Confidence Interval and the required sample size. Density, distribution function, quantile function and random generation for the Generalized Binomial Distribution.Enhanced model for burn-in studies, where failures are tackled by countermeasures." .
SCR:025543 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "km.ci" ;
definition: "Software R package to compute various confidence intervals for the Kaplan-Meier estimator, namely: Peto's CI, Rothman CI, CI's based on Greenwood's variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by Nair and Hall and Wellner." .
SCR:025544 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D Developmental Mouse Brain Common Coordinate Framework" ;
NIFRID:synonym "DevCCF" ;
definition: "Open access multimodal 3D atlases of developing mouse brain that can be used to integrate mouse brain imaging data for visualization, education, cell census mapping, and more. Atlas ages include E11.5, E13.5, E15.5, E18.5, P4, P14, and P56. Web platform can be utilized to visualize and explore the atlas in 3D. Downloadable atlas can be used to align multimodal mouse brain data. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system. Anatomical labels are manually drawn in 3D based on the prosomeric model. For additional references, the P56 template includes templates and annotations from the aligned Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) and aligned Molecular Atlas of the Adult Mouse Brain." .
SCR:025545 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2835" ;
rdfs:label "Purdue University Cryo-Electron Microscopy Core Facility" ;
NIFRID:synonym "Cryo-Electron Microscopy",
"Purdue Cryo-EM Facility" ;
definition: "Facility provides access to instrumentation enabling users to collect data for high-resolution single particle reconstructions and tomographic studies of cells and larger complexes." .
SCR:025546 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2834" ;
rdfs:label "Indiana University School of Medicine Electrophysiology Core Facility" ;
NIFRID:synonym "Electrophysiology Core",
"Indiana University School of Medicine Electrophysiology Core" ;
definition: "Electrophysiology Core performs rodent brain slice electrophysiological recordings to measure brain cell function." .
SCR:025547 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2833" ;
rdfs:label "Purdue University Flow Cytometry and Cell Sorting Core Facility" ;
NIFRID:synonym "Flow Cytometry and Cell Separation Facility",
"Flow Cytometry and Cell Sorting Facility",
"Purdue University Flow Cytometry and Cell Sorting Facility" ;
definition: "Core Facility provides instrumentation, data analysis software, training and technical expertise for flow cytometry analysis and cell sorting. Our capabilities also include the characterization of genome and transcriptomes using the Fluidigm C1 and 10X Genomics systems, in partnership with the Purdue Genomics Core Facility." .
SCR:025548 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BOND_RX" ;
rdfs:label "Leica | BOND RX Stainer" ;
NIFRID:synonym "BOND RX Stainer" ;
definition: "Fully automated research stainer that automates staining step which ensures that microscope slides are produced with consistent, reproducible, and efficient way. Utilizes biological assay called immunohistochemistry.BOND RX model expands on the capabilities of IHC by including other assays." .
SCR:025549 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pbmm2" ;
definition: "Software application as minimap2 frontend for PacBio native data formats. SMRT C++ wrapper for minimap2's C API." .
SCR:025550 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2870" ;
rdfs:label "Peter MacCallum Cancer Centre Research Flow Core Facility" ;
NIFRID:synonym "Peter MacCallum Cancer Center Research Flow Core",
"Peter MacCallum Cancer Center Research Flow Core (RFC)" ;
definition: "Internationally recognised shared resource laboratory which provides researchers with access to equipment, education and expertise that enables isolation, separation and analysis of cell populations." .
SCR:025551 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2871" ;
rdfs:label "University of Nebraska-Lincoln Methodology and Evaluation Research Core Facility" ;
NIFRID:synonym "Methodology and Evaluation Research Core Facility" ;
NIFRID:abbrev "MERC" ;
definition: "Provides range of evaluation and data services to support client needs.Through consulting, evaluation, methodology, and training, we work to fill gaps and improve and empower data driven decision making.At the proposal stage of grants, we can design evaluation plans to meet your project needs, with the associated narrative text, budget, and letter of collaboration, as needed. We can also fill gaps post-award, or provide support with internal funding. We can assist with logic models, Broader Impacts, methodologies, needs assessments, survey design and implementation, support with Institutional Review Board applications, and trainings in our areas of expertise." .
SCR:025552 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2872" ;
rdfs:label "Notre Dame Freimann Life Science Center Core Facility" ;
NIFRID:synonym "Freimann Life Sciences Center (FLSC)" ;
NIFRID:abbrev "FLSC" ;
definition: "Home to virtually all laboratory animals. Services include Procurement, Animal care, Breeding, Training,Limited procedures for research." .
SCR:025553 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2873" ;
rdfs:label "Indiana University School of Medicine Genome Editing Center Core Facility" ;
NIFRID:synonym "Indiana University School of Medicine Genome Editing Center" ;
definition: "Provides access to genome editing technologies by assisting with generation of genetically modified mouse models and cell lines." .
SCR:025554 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2876" ;
rdfs:label "Indiana University School of Medicine HANDS In Autism Interdisciplinary Training and Resource Center Core Facility" ;
NIFRID:synonym "HANDS In Autism Interdisciplinary Training & Resource Center",
"Helping Answer Needs by Developing Specialists in Autism Interdisciplinary Training & Resource Center",
"Indiana University School of Medicine HANDS In Autism Interdisciplinary Training and Resource Center" ;
NIFRID:abbrev "HANDS Core" ;
definition: "Provides evidence-based services, training, coaching and consultation across range of local community and state stakeholder networks e.g., families, medical providers, school personnel, community organizations. This involvement and integration in addressing the behavioral, educational, and vocational needs of consumers across a range of ages i.e., early childhood through adulthood, functioning and disability types has assisted in: providing consultative expertise related to assessment and intervention with autism spectrum disorder and related developmental e.g., developmental and/or intellectual disabilities or neurodevelopmental disorders; reaching extensive audience for recruitment efforts; facilitating efforts related to community-based mixed methods, clinical trials and other research endeavors e.g., survey development and dissemination, behavioral assessment and intervention related to individuals with ASD/DD/ID across lifespan." .
SCR:025555 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2874" ;
rdfs:label "Notre Dame Genomics and Bioinformatics Core Facility" ;
NIFRID:synonym "Genomics and Bioinformatics Core Facility (GBCF)" ;
NIFRID:abbrev "GBCF" ;
definition: "Offers comprehensive services and support for genomics experiments and bioinformatics analysis. This includes next generation Illumina sequencing, a variety of standard and specialty DNA and RNA library construction methods, consultation, and analysis support." .
SCR:025556 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2877" ;
rdfs:label "Indiana University School of Medicine Histology and Histomorphometry Core Facility" ;
NIFRID:synonym "Indiana University School of Medicine Histology and Histomorphometry Core" ;
definition: "Provides histological and histomorphometric services for basic science (non-clinical) research. Mineralized (plastic embedded), soft tissue (paraffin embedded), and cryopreserved specimens can be processed by the facility. Histology Core is core facility of the Indiana Center for Musculoskeletal Health and part of the Bone and Body Composition Core of the Indiana Clinical Translational Sciences Institute (CTSI). Histology Core provides histological services for basic science (non-clinical) research. Both mineralized (plastic embedded) and soft tissue (paraffin embedded) specimens can be prepared by the facility." .
SCR:025557 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2875" ;
rdfs:label "Purdue University Bindley Genomics Core Facility" ;
NIFRID:synonym "Bindley Core for Genomics (BCG)",
"Purdue University Bindley Genomics Core" ;
NIFRID:abbrev "BCG" ;
definition: "Core provides both next generation Illumina NovaSeq and MiSeq and Sanger sequencing with additional method to provide entire plasmid sequences via service called WideSeq." .
SCR:025558 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2879" ;
rdfs:label "Indiana University School of Medicine Human Vascular Imaging Core Facility" ;
NIFRID:synonym "Human Vascular Imaging Core (HVIC)",
"Indiana University School of Medicine Human Vascular Imaging Core" ;
NIFRID:abbrev "HVIC" ;
definition: "Core provides following services: Brachial artery flow-mediated dilation; Brachial artery nitroglycerin-mediated dilation; Carotid artery intima media thickness." .
SCR:025559 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2878" ;
rdfs:label "Purdue University Histology Research Laboratory Core Facility" ;
NIFRID:synonym "Histology Research Laboratory (HRL)",
"Purdue University Histology Research Laboratory" ;
NIFRID:abbrev "HRL" ;
definition: "Full service histology laboratory that provides general histology, immunohistochemistry, frozen sectioning, decalcified and undecalcified bone histology, and slide digitization services. Board certified veterinary pathologists are also available for consultation." .
SCR:025560 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2880" ;
rdfs:label "Indiana University School of Medicine South Bend Imaging and Flow Cytometry Core Facility" ;
NIFRID:synonym "IU South Bend Imaging and Flow Cytometry Core Facility",
"IUSM South Bend Imaging and Flow Cytometry Core Facility" ;
definition: "Provides standard confocal or multiphoton resources for imaging live or fixed samples and a 5 color flow cytometric analyzer are available. Data analysis software for each resource is also available on site." .
SCR:025561 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "American Association for Cancer Research" ;
NIFRID:abbrev "AACR" ;
definition: "Cancer research organization dedicated to accelerating the conquest of cancer. The mission is to prevent and cure cancer through research, education, communication, collaboration, science policy and advocacy, and funding for cancer research. Through its programs and services, the AACR fosters research in cancer and related biomedical science, accelerates dissemination of new research findings, promotes science education and training, and advances the understanding of cancer etiology, prevention, diagnosis, and treatment throughout the world." .
SCR:025562 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mlr3verse" ;
definition: "Software R package intended to simplify both installation and loading of packages from mlr3 ecosystem. Meta-package for installing/updating mlr3* packages." .
SCR:025563 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ezBIDS" ;
NIFRID:synonym "ez Brain Imaging Data Structure" ;
definition: "Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms." .
SCR:025564 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2881" ;
rdfs:label "Indiana University Bloomington Imaging Research Core Facility" ;
NIFRID:synonym "Imaging Research Facility (IRF)" ;
NIFRID:abbrev "IRF" ;
definition: "Neuroimaging facility that enables cutting-edge neuroscience research and training using non-invasive imaging methodologies, including both MRI and EEG." .
SCR:025565 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2886" ;
rdfs:label "Indiana University School of Medicine Infectious Diseases Laboratory Core Facility" ;
NIFRID:synonym "Indiana University Infectious Diseases Laboratory",
"Indiana University School of Medicine Infectious Diseases Laboratory" ;
definition: "Performs clinical research studies including evaluation of new molecular technologies for diagnosis of wide array of sexually transmitted and newly emerging pathogens, developing novel assays to meet the needs of individual research collaborators, and tailoring services to successfully meet study objectives. The laboratory has the capability to identify and type human papillomavirus." .
SCR:025566 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2882" ;
rdfs:label "Indiana University School of Medicine Immunohistochemistry Research Lab Core Facility" ;
NIFRID:synonym "Immunohistochemistry Research Core",
"Immunohistochemistry Research Lab (IHC Research Lab)" ;
definition: "Immunohistochemistry Research Lab specializes in assisting researchers with histologic and immunohistochemical labeling of cells or tissue sections as well as collaborations with surgical pathologists." .
SCR:025567 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2884" ;
rdfs:label "Indiana University School of Medicine In-Vivo Imaging Core Facility" ;
NIFRID:synonym "In-Vivo Imaging Core",
"Indiana University School of Medicine In-Vivo Imaging Core" ;
definition: "Core provides imaging services for clinical trials, observational, and preclinical studies. Provides radiochemistry support for molecular imaging. Currently, the Imaging Core is equipped with state-of-the-art imaging systems, including 3T MRI scanners, PET-CT scanners, Bruker 9.4 T preclinical PET-MRI scanner, a Siemens Eclipse Medical Cyclotron, and Radiochemistry Facilities." .
SCR:025568 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2885" ;
rdfs:label "Indiana University School of Medicine Center for Biological Microscopy Core Facility" ;
NIFRID:synonym "Indiana Center for Biological Microscopy" ;
NIFRID:abbrev "ICBM" ;
definition: "Provides researchers with access to laser-scanning confocal, 2-photon and epi-fluorescence microscopes. Personnel train individual researchers to use all imaging systems and provide expert help in design, conduct and analysis of imaging studies. As necessary, center personnel can also be hired to conduct microscopy studies for laboratories lacking necessary expertise." .
SCR:025569 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2883" ;
rdfs:label "Indiana University School of Medicine In Vivo Therapeutics Core Facility" ;
NIFRID:synonym "In Vivo Therapeutics Core (IVT)",
"IUSCCC In Vivo Therapeutics Core" ;
NIFRID:abbrev "IVTC" ;
definition: "Core supports research and development of safe and more efficacious drug treatment. Provides cost-effective and comprehensive services including, but not limited to, on-site breeding facilities as well as in vivo pharmacology models to facilitate development and testing of novel pharmacological and cellular therapies." .
SCR:025570 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "One-rat Turnstile" ;
NIFRID:synonym "One-rat Turnstile (ORT)" ;
NIFRID:abbrev "ORT" ;
definition: "Open-source apparatus to enable continuous individual monitoring, training, and testing of rats without removing them from their social environment. This system utilizes RFID technology to track individual animals, minimizing human intervention and providing precise behavioral data." .
SCR:025571 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mlr3extralearners" ;
definition: "Software R package used for machine learning. Extra learners for use in mlr3." .
SCR:025572 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Anaconda" ;
NIFRID:synonym "Anaconda3" ;
definition: "Software assists with any operations you may need to manage your organization’s users and resources.Helps to create environment for many different versions of Python and package versions. Used to install, remove, and upgrade packages in project environments." .
SCR:025573 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2887" ;
rdfs:label "University of California Irvine Center for Neural Circuit Mapping Viral Core Facility" ;
NIFRID:synonym "Center for Neural Circuit Mapping Viral Core",
"University of California Irvine Center for Neural Circuit Mapping Viral Core" ;
definition: "Viral production facility aims at development and production of viral vectors for in-vivo and in-vitro experimentation purposes. Equipment coupled with our expertise allows use to ensure high quality products. Provides all related sequence data, vector maps, plasmids and ready-to-use viruses once your orders are completed." .
SCR:025574 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2867" ;
rdfs:label "Emory University Pediatric Biomarkers Core Facility" ;
NIFRID:synonym "Emory Pediatric Biomarkers Core",
"Emory University Emory Pediatric Biomarkers Core" ;
definition: "Biomarkers Core offers high quality analysis of biological samples to support pediatric research. Provides equipment and technical expertise to assay samples using methods that combine the features of gas-liquid chromatography and mass spectrometry." .
SCR:025575 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Accord" ;
NIFRID:synonym "Accord Healthcare" ;
definition: "Global pharmaceutical company that develops, manufactures and distributes essential medicines for hospitals and retail pharmacies." .
SCR:025576 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Niguarda Hospital Milan Department of Hematology, Oncology and Molecular Medicine Core Facility" ;
NIFRID:synonym "Niguarda Hospital Milan Department of Hematology",
"Oncology and Molecular Medicine" ;
definition: "Core performs histopathological, cytopathological, intraoperative diagnostic and autopsy activities. Offers service of laboratory diagnostic tests. Facility also deals with evaluation of cytoaspiration sampling of mediastinal lymph nodes, using videobronchoscopic technique in collaboration with Thoracic Surgery." .
SCR:025577 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ISOLDE" ;
definition: "Software environment to ease task of building macromolecular models into low to medium resolution experimental maps. Physically realistic environment for model building into low-resolution electron-density maps. Can generate maps directly from crystallographic F/sigF data in MTZ format and automatically re-calculate them when model changes, and/or generate \"static\" maps from pre-calculated F/phi data." .
SCR:025578 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dam Removal Information Portal" ;
NIFRID:abbrev "DRIP" ;
definition: "Portal contains information about the geographic locations of dam removals and any associated scientific studies evaluating outcomes to physical, biological, and water quality parameters. Results can be downloaded based on customized search criteria specified by the user." .
SCR:025579 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CannSeek Database of Cannabis sativa SNPs" ;
definition: "Database of Cannabis sativa Single Nucleotide Polymorphisms discovered from NGS sequences and BioSamples available in NCBI. Sequence reads were called against cs10, Purple kush, and Finola reference assemblies using GATK and Parabricks pipelines." .
SCR:025580 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PharmKGB" ;
NIFRID:synonym "Pharmacogenomics Knowledgebase" ;
definition: "NIH-funded resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relationships." .
SCR:025581 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggbiplot" ;
definition: "Software R package to provide ggplot2 implementation of biplot, simultaneous plot of scores for observations and vectors for variables for principal component-like analyses." .
SCR:025582 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2888" ;
rdfs:label "Peter MacCallum Cancer Centre Victorian Centre for Functional Genomics Core Facility" ;
NIFRID:synonym "Peter MacCallum Cancer Centre Victorian Centre for Functional Genomics",
"Victorian Centre for Functional Genomics" ;
definition: "Core to perform novel discovery-based high throughput compound, CRISPR and RNAi screens at any scale in both 2D and 3D formats, using liquid handling instruments, automated high content imaging microscopes, live imaging systems and large reagent libraries." .
SCR:025583 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_108" ;
rdfs:label "BioComp Instruments | Gradient Master" ;
NIFRID:synonym "BioComp Instruments Gradient Forming",
"Gradient Forming" ;
definition: "Generates linear gradients using process called tilted tube rotation. Process involves layering two end point solutions directly in centrifuge tube, capping it and placing it in magnetic tube holder that adheres to rotary steel plate on instrument. Gradient Master takes over and tilts tube to the proper angle, rotates it for designated time and returns it to its original vertical position, ready to use." .
SCR:025584 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioComp Instruments | Piston Gradient Fractionator" ;
NIFRID:synonym "BioComp Piston Gradient Fractionator" ;
definition: "Piston fractionation leaves gradient undisturbed while piston descends from the top, displacing layers through centre of its patented trumpet shaped tip, keeping flow smooth and precise. Used to fractionate based on distance rather than drop or time." .
SCR:025585 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Optima_XPN_100_IVD" ;
rdfs:label "Beckman Coulter ultracentrifuge Optima XPN-100 IVD" ;
NIFRID:synonym "ultrcentrifuge Optima XPN-100 IVD" ;
definition: "Optima XPN generates centrifugal forces for separation of particles.Centrifuge is intended to separate human samples, including blood, urine, and other bodily fluids to prepare samples for downstream in vitro diagnostic procedures, which may include molecular diagnostic, chemistry, immunoassay, and coagulation tests. This centrifuge should be operated by laboratory professionals only.Floor model preparative ultracentrifuge offers temperature from 0 to 40℃, meets environmental protection requirements, adopts microcomputer controlled variable reluctance drive system, vacuum friction reduction system." .
SCR:025586 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Biacore_X100" ;
rdfs:label "Cytiva | Biacore X100" ;
NIFRID:synonym "Biacore X100" ;
definition: """Automated system for comprehensive, label-free analysis and characterization
of biomolecular interactions in real-time. Can be used for applications, including structure function studies, pathway analysis, biomarker discovery and validation, drug target identification and validation, and assay development.""" .
SCR:025587 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2890" ;
rdfs:label "Indiana University School of Medicine Center for Electron Microscopy Core Facility" ;
NIFRID:synonym "IU School of Medicine Center for Electron Microscopy (iCEM)" ;
NIFRID:abbrev "iCEM" ;
definition: "Offers cryo-electron microscopy, transmission electron microscopy, and scanning electron microscopy. Provides technical services to help design and then implement experiments needing each type of microscopy." .
SCR:025588 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2891" ;
rdfs:label "University of Notre Dame Keck Center for Transgene Research Core Facility" ;
NIFRID:synonym "University of Notre Dame Keck Center for Transgene Research",
"W. M. Keck Center for Transgene Research" ;
definition: "Core develops and uses gene-targeting technology to investigate pathophysiological roles of genes of blood coagulation, anticoagulation, and fibrinolytic pathways in hemostasis, with associated relevance to embryonic development, cancer, infection, and inflammation." .
SCR:025589 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2892" ;
rdfs:label "Indiana University Bloomington Laboratory Animal Resources Core Facility" ;
NIFRID:synonym "Indiana University Bloomington Laboratory Animal Resources",
"Laboratory Animal Resources (LAR)" ;
NIFRID:abbrev "LAR" ;
definition: "LAR provides housing, food, water, bedding, enrichment and medical care for animals housed in LAR animal facilities to be used for research." .
SCR:025590 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2893" ;
rdfs:label "Indiana University School of Medicine Laboratory Animal Resource Center Core Facility" ;
NIFRID:synonym "Indiana University School of Medicine Laboratory Animal Resource Center (LARC)" ;
NIFRID:abbrev "LARC" ;
definition: "Core provides basic husbandry, training, supplies, and specialized service support for medical research at IU School of Medicine." .
SCR:025591 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2894" ;
rdfs:label "Indiana University Bloomington Laboratory for Biological Mass Spectrometry Core Facility" ;
NIFRID:synonym "Indiana University Bloomington Laboratory for Biological Mass Spectrometry (LBMS)",
"Laboratory for Biological Mass Spectrometry (LBMS)" ;
NIFRID:abbrev "LBMS" ;
definition: "Core uses mass spectrometry to characterize proteins as well as other biologically-derived molecules. Specializes in characterization of protein post-translational modifications, including glycosylation, phosphorylation, acetylation and persulfidation.Provides identification of protein-interactions including determination of protein-protein crosslinks and quantitative comparisons of complex samples." .
SCR:025592 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dynamo" ;
definition: "Software environment for subtomogram averaging of cryo-EM data. Development tool for subtomogram averaging of cryo-EM data in high-performance computing environments." .
SCR:025593 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PCAtools" ;
NIFRID:synonym "Principal Component Analysis tools" ;
definition: "Software R package to analyse large volumes of data. Extracts structure of data without the need to build any model to represent it. Provides functions for data exploration via PCA, and allows the user to generate publication ready figures." .
SCR:025594 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cloud-SPAN " ;
NIFRID:synonym "Cloud SPecialised ANalyses" ;
definition: "Cloud-based high performance computing for specialised analyses on environmental omics." .
SCR:025595 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2895" ;
rdfs:label "Purdue University Life Science Microscopy Core Facility" ;
NIFRID:synonym "Life Science Microscopy Facility (LSMF)",
"Purdue University Life Science Microscopy Facility" ;
NIFRID:abbrev "LSMF" ;
definition: "Electron microscopy core with both service and individual use options." .
SCR:025596 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2899" ;
rdfs:label "Notre Dame University Mass Spectrometry and Proteomics Core Facility" ;
NIFRID:synonym "Notre Dame University Mass Spectrometry and Proteomics Facility" ;
definition: "Core provides analysis of large and small molecules using several ionization methods, low or high resolution, hyphenated techniques, proteomics, and metabolomics." .
SCR:025597 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2896" ;
rdfs:label "Indiana University Bloomington Light Microscopy Imaging Center Core Facility" ;
NIFRID:synonym "Indiana University Bloomington Light Microscopy Imaging Center",
"Light Microscopy Imaging Center (LMIC)" ;
NIFRID:abbrev "LMIC" ;
definition: "Provides access and training for confocal and super-resolution light microscopy systems with support for experimental design and data visualization." .
SCR:025598 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2897" ;
rdfs:label "Indiana University Bloomington Macromolecular Crystallography Integrated with Crystallization Automation Core Facility" ;
NIFRID:synonym "Macromolecular Crystallography Facility Integrated with the Crystallization Automation Facility (MCF/CAF)" ;
NIFRID:abbrev "MCF/CAF" ;
definition: "Macromolecular X-ray Crystallography Facility provides all resources for Crystal Screening and Optimization, Data Collection and Structure Determination of macromolecules." .
SCR:025599 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2898" ;
rdfs:label "Notre Dame University Magnetic Resonance Research Center Core Facility" ;
NIFRID:synonym "Notre Dame University Magnetic Resonance Research Center" ;
definition: "Core supports research in chemistry, biochemistry, molecular biology, engineering and related fields. The MRRC operates six solution-state NMR spectrometers (400 to 800 MHz), a solid-state 300 MHz NMR instrument, and an X-band EPR spectrometer. Most instruments are equipped with sample changers for increased sample throughput." .
SCR:025600 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cfDNA UniFlow" ;
definition: "Workflow for preprocessing cfDNA samples. Unified, standardized, and ready-to-use workflow for processing whole genome sequencing cfDNA samples from liquid biopsies. Includes steps for pre-processing raw cfDNA samples, quality control and reporting. Additionally, several optional utility functions like GC bias correction and estimation of copy number state are included. Provides specialized methods for extracting coverage derived signals and visualizations comparing cases and controls." .
SCR:025601 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "stMMR" ;
definition: "Software tool for spatial domain identification from spatially resolved transcriptomics with multi-modal feature representation." .
SCR:025602 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ATP Bio" ;
NIFRID:synonym "Advanced Technologies for the Preservation of Biological Systems" ;
definition: """Aims to stop biological time and extend ability to bank and transport cells, aquatic embryos, tissue, skin, whole organs, microphysiological systems and whole organisms. Builds advanced biopreservation technologies to eliminate or mitigate ice formation,
cryoprotective agent toxicity, and slow and/or non-uniform rewarming.""" .
SCR:025603 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Micromix" ;
definition: "Web infrastructure for visualizing and remixing microbial ‘omics data. Software visualization platform to view next-generation sequencing data, such as RNA-seq counts." .
SCR:025604 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Differential Gene Set Enrichment Analysis" ;
NIFRID:synonym "Differential Gene Set Enrichment Analysis (DGSEA)" ;
NIFRID:abbrev "DGSEA" ;
definition: "Software tool to determine whether two priori sets of genes show statistically significant differences between two biological states. Statistical approach to quantify relative enrichment of two gene sets." .
SCR:025605 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DEqMS" ;
definition: "Software R package to perform statistical analysis of differential protein expression for quantitative proteomics data." .
SCR:025606 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2900" ;
rdfs:label "Australian Drosophila Transgenic Core Facility" ;
NIFRID:synonym "Australian Drosophila Transgenic Facility" ;
NIFRID:abbrev "ADTF" ;
definition: "Core offers specialised microinjection services for generating transgenic strains of fruit fly Drosophila melanogaster." .
SCR:025607 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automated Systematic Search Deduplicator" ;
NIFRID:synonym "Automated Systematic Search Deduplicator:ASySD" ;
NIFRID:abbrev "ASySD" ;
definition: "Open source, interoperable software tool to remove duplicate citations in biomedical systematic reviews." .
SCR:025608 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RiboSnake" ;
definition: "Software 16S rRNA analysis workflow with QIIME2 and Snakemake." .
SCR:025609 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2902" ;
rdfs:label "University of Nebraska Lincoln Single Cell Genomics Core Facility" ;
NIFRID:synonym "Single Cell Genomics Core",
"University of Nebraska Lincoln Single Cell Genomics" ;
NIFRID:abbrev "SCGC" ;
definition: "Facility provides access to Chromium iX platform from 10X Genomics. This allows user to barcode single cells or nuclei and process them for single cell RNA-seq, single nucleus ATAC-seq or single nucleus Multiome ATC + Gene Expression protocols." .
SCR:025610 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MDAnalysis" ;
definition: "Software object oriented Python library to analyze trajectories from molecular dynamics simulations in many popular formats." .
SCR:025611 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Peter MacCallum Cancer Institute" ;
NIFRID:synonym "Peter MacCallum Cancer Centre" ;
NIFRID:abbrev "Peter Mac" ;
definition: "Australian oncology research institute, cancer treatment and professional oncologist training centre located in Melbourne, Victoria." .
SCR:025612 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BIDIFAC+" ;
NIFRID:synonym "BIDIFAC",
"bidifac",
"Bidimensional matrix factorization" ;
definition: "Multiomic data integration software. R code to perform factorization and dimension reduction of bidimensionally linked data matrices. Used to decompose variation into series of low-rank components that may be shared across any number of row sets e.g., omics platforms or column sets e.g., cancer types." .
SCR:025613 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "2s-LCA" ;
NIFRID:synonym "two-stage Linked Component Analysis" ;
definition: "Software for multi-omic data integration. Used to jointly decompose multiple biologically related experimental data sets with biological and technological relationships that can be structured into the decomposition." .
SCR:025614 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GRNBoost2" ;
NIFRID:synonym "Gene Regulatory Network Boost",
"GRNBoost" ;
definition: "Algorithm for regulatory network inference using gradient boosting, based on GENIE3 architecture. Used for inference of gene regulatory networks." .
SCR:025615 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sentieon DNAseq" ;
definition: "Software pipeline for DNAseq analysis. Used to calculate required modification of quality scores assigned to individual read bases of sequence read data." .
SCR:025616 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReAdW" ;
definition: "Proteomics software used to convert ThermoFinningan RAW mass spectrometry files to mzXML format." .
SCR:025617 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "POTFUL" ;
NIFRID:synonym "Plant cO-expression Transcription Factor regULators" ;
definition: "Software Python pipeline for integrating co-expression and transcription factor target protein networks to infer gene regulation." .
SCR:025618 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MatchIt" ;
definition: "Software R package to select matched samples of original treated and control groups with similar covariate distributions. Can be used to match exactly on covariates, to match on propensity scores, or perform variety of other matching procedures. Nonparametric preprocessing for parametric causal inference." .
SCR:025619 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IOBR" ;
NIFRID:synonym "Immuno-Oncology Biological Research" ;
definition: "Software R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology. Used for comprehensively interpreting multi-omics data." .
SCR:025620 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SomaticSignatures" ;
definition: "Software R package for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments." .
SCR:025621 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KataegisPortal" ;
definition: "Software R package to detect and visualize Kataegis events from single nucleotide variants." .
SCR:025622 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2903" ;
rdfs:label "Peter MacCallum Cancer Centre Genotyping Core Facility" ;
definition: "Provides mouse genotyping service, from extraction of genomic DNA from tissue to reporting of genotypes. Offers Mycoplasma testing of any cell line and authentication of human cell lines." .
SCR:025623 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2904" ;
rdfs:label "Northwestern University Reactor Engineering and Catalyst Testing Core Facility" ;
NIFRID:synonym "Northwestern University Reactor Engineering and Catalyst Testing (REACT) Core Facility",
"Reactor Engineering and Catalyst Testing Core Facility" ;
NIFRID:abbrev "REACT" ;
definition: "Core is dedicated to aiding students and investigators in advancement of understanding chemical properties of solid interfaces used for environmental and energy processes. Facility provides range of instrumentation and services for students and industrial researchers interested in catalysis." .
SCR:025624 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2905" ;
rdfs:label "Penn State College of Medicine Pulmonary Immunology and Physiology Core Facility" ;
NIFRID:synonym "Penn State College of Medicine Pulmonary Immunology and Physiology Core",
"Pulmonary Immunology and Physiology Core" ;
definition: "Core provides development and testing of small animal models to be used for pre-clinical pulmonary research. BSL2 facility that allows the assessment of pulmonary function related to airway hyper-responsiveness, ventilation-induced lung injury, postnatal lung development, airway remodeling, chronic inflammation, allergy, environmental exposures and infection. Services offered include oxygen profiling, infection and treatment; ability to deliver, measure and test pre-clinical potential of therapeutic interventions via aerosol; and housing of small animals." .
SCR:025626 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hTFtarget" ;
definition: "Comprehensive database for regulations of Human Transcription Factors and their targets. Provides tools for visualization, interpretation, and analysis of pathway knowledge." .
SCR:025627 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SCIEX_Triple_Quad_6500+" ;
rdfs:label "SCIEX Triple Quad 6500+ LC-MS system" ;
NIFRID:synonym "SCIEX Triple Quad 6500+",
"SCIEX Triple Quad 6500+ LC-MS",
"Triple Quad 6500+ system" ;
definition: "System features multi-component IonDrive technology including IonDrive High Energy Detector+ to enable to see low mass to high mass compounds, in positive or negative polarity in single injection." .
SCR:025628 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Foundation Medicine" ;
NIFRID:abbrev "FMI" ;
definition: """American company based in Cambridge, Massachusetts, which develops, manufactures, and sells genomic profiling assays based on next-generation sequencing technology for solid tumors, hematologic malignancies, and sarcomas. Specializes in precision medicine.
FMI routinely analyzes cancer specimens using advanced sequencing technology of FoundationOne to profile tumor genomics.""" .
SCR:025629 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sysmex Inostics" ;
NIFRID:synonym "Sysmex Inostics Inc." ;
definition: "Biotechnology company in Baltimore, Maryland, specializing in liquid biopsy. Offers comprehensive NGS testing services for clinical trials, enhancing oncology drug development and patient outcomes." .
SCR:025630 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miloR" ;
definition: "Software R package implementation of Milo for testing for differential abundance in k-nearest neighbor graphs. Milo can identify perturbations that are obscured by discretizing cells into clusters. Used for differential abundance analysis on KNN graph from single-cell datasets." .
SCR:025631 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tTFtarget" ;
NIFRID:synonym "tRFtarget 1.0",
"tRFtarget 2.0" ;
definition: "Transcription factor target database. Platform consolidating both computationally predicted and experimentally validated binding sites between transfer RNA-derived fragments and target genes or transcripts across multiple organisms." .
SCR:025632 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mixed effects association testing for single cells" ;
NIFRID:synonym "Mixed-effects Association testing for Single Cells",
"Mixed-effects modeling of Associations of Single Cells" ;
NIFRID:abbrev "MASC" ;
definition: "Software tool for testing whether specified covariate influences membership of single cells in any of multiple cellular subsets while accounting for technical confounds and biological variation." .
SCR:025634 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2906" ;
rdfs:label "Weill Cornell Medicine Genomics Resources Core Facility" ;
NIFRID:synonym "Genomics Resources Core Facility" ;
NIFRID:abbrev "GRCF" ;
definition: "Core offers services from experimental design and sample preparation to instrumentation, data analysis, interpretation, and validation. Provides sequencing technologies and team of well trained staff." .
SCR:025635 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Azure Biosystems | Sapphire FL Biomolecular Imager" ;
NIFRID:synonym "Sapphire FL" ;
definition: "Sapphire FL is second generation Sapphire and ultimate biomolecular imager for FLEXIBILITY. With customizable and user-changeable laser and filter modules. Offers customizable and user changeable optical modules, 5–1000 μm resolution scans, Z-plane range from -1.0 to +6 mm, 5 anesthesia ports for imaging living animals, chemiluminescence detection through Chemiluminescence Module." .
SCR:025636 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "signed ks test" ;
definition: "Software tool as modified R ks.test to obtain sign and force exact p-value." .
SCR:025637 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "correctipy" ;
definition: "Software Python package for computing corrected test statistics for comparing machine learning models on correlated samples. Software package version of correctR." .
SCR:025638 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SVNTest" ;
definition: "Test project for NITRC development." .
SCR:025639 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford Bruker timsTOF Ultra nanoLC/MS" ;
NIFRID:synonym "Bruker tims Trapped Ion Mobility-Time-of-Flight Ultra",
"Bruker timsTOF Ultra",
"Bruker timsTOF Ultra nanoLC/MS" ;
definition: "Bruker timsTOF Ultra boasts increased sensitivity and resolution whilst allowing for exceptionally low sample input and resolution whilst allowing for exceptionally low sample input." .
SCR:025640 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroVar" ;
definition: "Software genetic expression and variation data visualization tool for neurological diseases biomarkers." .
SCR:025641 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pathogens Portal Norway" ;
definition: "Portal provides information about available datasets, resources, tools, and services related to pandemic preparedness in Norway. Portal gives researchers, clinicians and policymakers access to collection of biomolecular data about pathogens." .
SCR:025642 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "vEMstitch" ;
definition: "Software algorithm for fully automatic image stitching of volume electron microscopy.Used to stitch input biological tiles while correcting local distortion." .
SCR:025643 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genetic Tools Atlas" ;
NIFRID:synonym "Allen Genetic Tools Atlas" ;
NIFRID:abbrev "GTA" ;
definition: "Searchable catalog of enhancer-adeno-associated viruses (AAVs) that have been developed and tested at the Allen Institute for Brain Science. We present a suite of enhancer AAVs that can provide access to specific cell types when delivered to the whole brain. Multiple epigenomic and transcriptomic datasets were interrogated to reveal candidate enhancers that are selectively accessible in particular cell populations. Enhancer AAVs were constructed and screened for desirable expression and a sizeable subset of enhancer AAVs were subjected to further characterization by single cell transcriptomics and/or brain-wide expression imaging in mouse. In the GTA, we present a large toolkit for selective gene expression in cell types of interest. Genetic Tools Atlas is part of the growing Brain Knowledge Platform." .
SCR:025644 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Single-sample Mutation-based Pathway Analysis" ;
NIFRID:synonym "Single-sample Mutation-based Pathway Analysis (ssMutPA)" ;
NIFRID:abbrev "ssMutPA" ;
definition: "Software R tool designed for single-sample mutation-based pathway analysis by integrating somatic mutation data with protein-protein interaction (PPI) networks." .
SCR:025645 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Rad | Bio-Plex MAGPIX Multiplex Reader" ;
NIFRID:synonym "BioPlex MAGPIX Multiplex Reader" ;
definition: "Compact reader for analysis of up to 50 analytes in single sample.Designed to read assays developed on magnetic xMap (MagPlex) beads and comes with Bio-Plex Manager analysis software. Bio-Plex MAGPIX Multiplex Reader is now discontinued. Bio-Rad will continue to provide premium Luminex instrumentation: the Bio-Plex® 200 System and Bio-Plex® 3D Suspension Array System and service, support, accessories, and software for customers with the Bio-Plex MAGPIX Multiplex Reader." .
SCR:025646 a owl:NamedIndividual ;
rdfs:label "Stoelting | Touch Test Sensory Probes" ;
definition: "Semmes-Weinstein Von Frey Aesthesiometer for touch assessment. The Semmes-Weinstein monofilaments provide an approximate logarithmic scale of actual force, and a linear scale of perceived intensity. They have a long history of effective use in clinical settings, and can be used to diagnose pathologies of hyper- or hypo-aesthesia. Subsets within the set of 20 probes distinguish pathologies on different parts of the body (foot, hand, lip, cheek,etc.)." .
SCR:025647 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ugo Basile | Hot/Cold Plate" ;
NIFRID:synonym "Ugo Basile Hot/Cold Plate - Screening of Thermal Hyperalgesia/Allodynia" ;
definition: """Instrument screens thermal hyperalgesia and allodynia,conditions often observed in patients with neuropathic pain or inflammation. Also used for testing analgesic and
anti-inflammatory drugs. Plate test includes all the latest technologies necessary to run constant temperature, linear ramping temperature (toward hot or toward cold) and complex temperature ramps thanks to the included X-Pad software.New model includes keypad (cabled or optional Bluetooth) to score pain endpoints or stereotyped behaviors. Temperature range goes from -5° to 65°C and animal holders of different heights are available.""" .
SCR:025648 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellMiner" ;
NIFRID:synonym "Cell Miner" ;
definition: "Database and query tool designed for cancer research community to facilitate integration and study of molecular and pharmacological data for the NCI-60 cancerous cell lines. The NCI-60, panel of 60 diverse human cancer cell lines used by the Developmental Therapeutics Program of the U.S. National Cancer Institute to screen over 100,000 chemical compounds and natural products since 1990." .
SCR:025649 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellMinerCDB" ;
NIFRID:synonym "Cell Miner CDB",
"CellMiner Cross-Database",
"CellMinerCDB 1.2" ;
definition: "Web application integrating cancer cell line pharmacogenomics. Enables exploration and analysis of cancer cell line pharmacogenomic data across different sources. Focuses on cancer patient-derived human cell line molecular and pharmacological data. CellMinerCDB (v1.2) includes several improvements." .
SCR:025650 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GraphRBF" ;
NIFRID:synonym "Graph RBF" ;
definition: "Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning." .
SCR:025651 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ExpressAnalystR" ;
definition: "Software R package of ExpressAnalyst for gene expression analysis. Underlying R package synchronized with ExpressAnalyst web server." .
SCR:025652 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GraphRBF" ;
definition: "Software tool as protein-protein/nucleic acid interaction site prediction model built by enhanced graph neural networks and prioritized radial basis function neural networks. Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning." .
SCR:025653 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Diasorin xPonent" ;
NIFRID:synonym "xPONENT" ;
definition: "Software package for control of MAGPIX, Luminex 200, and FLEXMAP 3D. Software’s graphical user interface follows typical assay workflow but can be customized to meet the needs of specific laboratory. Navigation wizards and automated routine operations such as startup, shutdown, calibration, and performance verification further enhance system usability and result in increased walk-away time. Allows to acquire samples, perform analysis, and run system maintenance routines and remote web monitoring. Basic package includes the ability to calculate allelic ratios to analyze and/or normalize genotyping data." .
SCR:025654 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012224" ;
rdfs:label "MorphoSource" ;
definition: "Publicly accessible 3D data repository where subject experts, educators, and general public can find, view, interact with, and download 3D and 2D media representing physical objects important to the world’s natural history, cultural heritage, and scientific collections. Media data are contributed by a community that includes museums, institutions, researchers, scholars, and other subject experts who use MorphoSource to archive data, share findings, and increase scholarly impact. Contributed media represent both biological objects such as fossils and representatives of living species, as well as artifacts and objects created by humans that are critical to our shared cultural heritage." .
SCR:025655 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Onekey AI-Platform" ;
NIFRID:synonym "OnekeyAI" ;
definition: "Software integrated research platform for multimodal medical data analysis and prediction employing AI techniques. Offers comprehensive functionalities to support various stages of medical research, including data preprocessing, feature extraction, model training, and prediction." .
SCR:025656 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MAP Database Guide for Membrane Protein Solubilization" ;
NIFRID:synonym "Membrane Active Polymers Database Guide for Membrane Protein Solubilization" ;
definition: "Open access web app that allows users to search for optimal condition for extraction of membrane proteins into membrane active polymers which allows for retention of native membrane environment around target protein." .
SCR:025657 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PaleoClim database" ;
NIFRID:synonym "Paleoclim" ;
definition: "Database of downscaled paleoclimate outputs at 2.5 minute resolution (~5 km at equator) that includes surface temperature and precipitation estimates from snapshot-style climate model simulations using HadCM3, a version of the UK Met Office Hadley Centre General Circulation Model. Database contains climatic data for three key time periods spanning from 3.3 to 0.787 million years ago: the Marine Isotope Stage 19 (MIS19) in the Pleistocene (~787 ka), the mid-Pliocene Warm Period (~3.264–3.025 Ma), and MIS M2 in the Late Pliocene (~3.3 Ma). Set of historical climate layers (climate grids) with spatial resolution of about 2.5 min. These data can be used for mapping and spatial modelling in Geographic Information Systems (GIS) or other computer programs." .
SCR:025658 a owl:NamedIndividual ;
rdfs:label "Chinese National Earth System Science Data Center" ;
definition: "A raster layer of global vegetation types, in Chinese. Please note the website is not functional from the US." .
SCR:025659 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chinese Geospatial Data Cloud" ;
definition: "Web app for global DEM data with spatial resolution of about 30m. This data can be used for mapping and spatial modelling in GIS or other computer programs." .
SCR:025660 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chinese CASEarth Data Sharing and Service Portal" ;
definition: """Portal built for the release and sharing of data resources of "Big Earth Data Science Engineering Program (CASEarth)" launched by the Chinese Academy of Sciences. A global raster data of land cover and land use. This data can be used for mapping and spatial modeling in Geographic Information Systems (GIS) or other computer programs.
This website is not accessible from the USA.""" .
SCR:025661 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2907" ;
rdfs:label "University of Idaho UI COBRE Nutrition Analytics Core Facility" ;
NIFRID:synonym "University of Idaho COBRE Nutrition Analytics Core Facility" ;
NIFRID:abbrev "NACL" ;
definition: "Core facility that provides expertise and instruments/equipment to promote research in nutrition and/or women’s health by leveraging resources from new and existing institutional programs and fostering collaborations across disciplines. Consists of hub laboratory suite with wet bench laboratory, body composition assessment and resting metabolic rate laboratories, computer laboratory, metabolic kitchen, and network of partnering laboratories distributed across the UI and the state of Idaho." .
SCR:025662 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "In-Vitro-Sholl" ;
NIFRID:synonym "In vitro astrocyte sholl analysis in R" ;
definition: "Software R analysis code for analyzing fluorescence microscopy images to determine complexity of cultured astrocytes. Sholl profile analysis based on mixed-effect models." .
SCR:025663 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2909" ;
rdfs:label "Rockefeller University Comparative Bioscience Center Core Facility" ;
NIFRID:abbrev "CBC" ;
definition: "Core provides comprehensive program of animal care in support of the university's in vivo research. Offers maintaining variety of common and unique laboratory animals in addition to providing veterinary, diagnostic and research technical services. Fully accredited by Association for Assessment and Accreditation of Laboratory Animal Care International. Comprehensive animal care and use program." .
SCR:025664 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2908" ;
rdfs:label "National Cancer Institute Genomics and Pharmacology Core Facility" ;
NIFRID:synonym "Genomics and Pharmacology Facility" ;
definition: "Provides pharmacogenomics resource for study of cancer. Multiple tools are available, currently including the CellMiner family with CellMiner, CellMinerCDB (cross data-base), CellMinerCDB: Small Cell Lung Cancer (SCLC), CellMinerCDB: National Center for Advancing Translational Sciences (NCATS) andCellMinerCDB: Sarcoma. These sites include multiple cancerous cell lines sets and data types. In addition there is CIMMiner for cluster image maps and MIMminer, with several scholarly molecular interaction maps." .
SCR:025665 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " Repertoire Builder" ;
definition: "Web app for high-throughput structural modeling for B-cell and T-cell receptors. Used for generating atomic-resolution, three-dimensional models of B cell receptors or T cell receptors from their amino acid sequences." .
SCR:025666 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AbAdapt" ;
definition: "Web application for antibody-specific epitope prediction. Used for predicting antibody-antigen complex structures from sequence." .
SCR:025667 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ImmuneScape" ;
definition: "Web structural modeling tool for TCR-pMHC complexes from amino acid sequences. TCR-pMHC modeling from amino acid sequences." .
SCR:025668 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DOI:10.5281/zenodo.10667839" ;
rdfs:label "Visual Physiology Opsin Database" ;
NIFRID:synonym "The Visual Physiology Opsin Database" ;
NIFRID:abbrev "VPOD" ;
definition: "Database of opsin genotype-phenotype data and machine-learning models trained to predict opsin phenotypes. Database of all heterologously expressed opsin genes with λmax phenotypes." .
SCR:025669 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ownCloud" ;
NIFRID:synonym "Kiteworks Company ownCloud" ;
definition: "Open-source software project for content collaboration and sharing and syncing of files in distributed and federated enterprise scenarios. Used for file synchronization and sharing of data. Platform that allows users to securely store, access, and manage files from anywhere, on any device. Designed for privacy and control, it offers customizable storage solutions, collaboration tools, and integrations, making it ideal for businesses and individuals seeking secure, self-hosted alternative to traditional cloud services." .
SCR:025670 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Autodesk Fusion" ;
NIFRID:synonym "Fusion" ;
definition: "Commercial software tool for technical drawing.Comprehensive 3D CAD, CAM, and CAE tool that integrates industrial and mechanical design, simulation, collaboration, and machining into single, cloud-based platform." .
SCR:025671 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2910" ;
rdfs:label "Duran i Reynals Hospital Flow Cytometry Core Facility" ;
NIFRID:synonym "Hospital Flow Cytometry Platform",
"Hospital Flow Cytometry Platform from IDIBELL" ;
definition: "Facility provides equipment for flow cytometry analysis and high-speed cell sorting. Unit personnel support users for experimental design, data analysis and acquisition." .
SCR:025672 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TD_Drive" ;
NIFRID:synonym "TD Drive",
"The TD Drive" ;
definition: "Parametric, open-source implant for multi-area electrophysiological recordings in behaving and sleeping rats. 3D-printable implant for rats, capable of symmetric, bilateral wire electrode recordings, currently in up to six distributed brain areas simultaneously." .
SCR:025673 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | 3DHistech PANNORAMIC SCAN II" ;
NIFRID:synonym "PANNORAMIC SCAN II" ;
definition: "Medium capacity digital slide scanner by 3DHISTECH with 150-slide capacity and brightfield and fluorescence scanning." .
SCR:025674 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CABS-Flex" ;
NIFRID:synonym "CABS-Flex 2.0" ;
definition: "Web server for fast simulation of protein structure fluctuations. Protein modeling software and simulation engine that allows for modeling of large-scale conformational transitions of protein systems. CABS-flex web server version 2.0 new features include extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and new, enhanced web server interface." .
SCR:025675 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mCSM-PPI2" ;
definition: "Web server that implements integrated computational approach for predicting effects of missense mutations in protein-protein affinity. Used to study effects of single point mutations on protein-protein interactions." .
SCR:025676 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2911" ;
rdfs:label "New York University School of Medicine Langone Health Multi-Omics Study Design and Data Integration Core Facility" ;
NIFRID:synonym "NYU Langone’s Multi-Omics Study Design and Data Integration Resource" ;
NIFRID:abbrev "MOSDIR" ;
definition: "Core facility that specializes in multi-omics data analysis, particularly within the realm of downstream statistical modeling and analysis." .
SCR:025677 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Waters | ACQUITY UPLC H-Class System with 2D LC" ;
NIFRID:synonym "ACQUITY UPLC Systems with 2D LC Technology" ;
definition: "Used in field of analytical chemistry in liquid chromatography systems for sorting through complex mixtures of substances with samples containing many closely related compounds. System provides Enhanced Separation Power because two-dimensional approach enables higher resolution separation, particularly useful for complex samples with compounds that elute closely together; Increased Sensitivity by minimizing interference from co-eluting compounds, 2D LC improves detection and quantification limits for target analytes; Comprehensive Analysis for both targeted analysis of specific compounds and exhaustive profiling of complex mixtures are possible through combination of heart-cutting and comprehensive sampling techniques; Improved Peak Capacity with better peak resolution and more accurate identification." .
SCR:025678 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "R package:stats-package" ;
definition: "Software R package contains functions for statistical calculations and random number generation." .
SCR:025679 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "R package: maxstat" ;
definition: "Software R package to perform test of independence of response and one or more covariables using maximally selected rank statistics." .
SCR:025681 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Molecular Devices CellReporterXpress Automated Image Acquisition and Analysis Software" ;
NIFRID:synonym "CellReporterXpress Automated Image Acquisition and Analysis Software" ;
definition: "Automated image acquisition and analysis software that works with the ImageXpress Pico system. Performs quantitative analysis of images acquired from automated microscopy. Enables distributed analysis of images from slides or microplates." .
SCR:025682 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Roche | cobas�� e 601" ;
NIFRID:synonym "cobas e 601" ;
definition: "Automated electrochemiluminescence detector for immunoassay analysis. Designed for quantitative and qualitative in vitro assay determinations for broad range of applications including anemia; bone, cardiac and tumor markers; critical care; fertility/hormones; maternal care; and infectious diseases." .
SCR:025683 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "USC-SIPI Image Database" ;
definition: "Collection of digitized images.Maintained primarily to support research in image processing, image analysis, and machine vision." .
SCR:025684 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CVG - UGR Image Database" ;
definition: "Image database where images are in PBM or PGM format and compressed with GNU Zip and GNU TAR." .
SCR:025685 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "InterPlanetary File System" ;
NIFRID:abbrev "IPFS" ;
definition: "Open system to manage data without central server. Peer-to-peer content delivery network built around the content addressing: store, retrieve, and locate data based on fingerprint of its actual content rather than its name or location." .
SCR:025686 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Encyclopedia of RNA Interactomes" ;
NIFRID:synonym "ENCORI",
"starBase" ;
definition: "Openly licensed platform to work with RNA-RNA and protein-RNA interactions with software and pipelines to deeply mining thousands of high-throughput sequencing data of RNA-RNA interactome, CLIP-seq and degradome sequencing." .
SCR:025687 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ratan-lab (SUMO)" ;
NIFRID:abbrev "SUMO" ;
definition: "Software for multiomic nonnegative matrix factorization." .
SCR:025688 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReSpect for Phytochemicals" ;
NIFRID:synonym "RIKEN tandem mass spectral database" ;
definition: "Collection of literature and in-house MSn spectra data for research on plant metabolomics." .
SCR:025689 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2901" ;
rdfs:label "Beth Israel Deaconess Medical Center Genomics Proteomics Core Facility" ;
NIFRID:synonym "BIDMC Genomics Proteomics Core",
"BIDMC Genomics Proteomics Core (Proteomics)" ;
definition: "Core provides high throughput transcriptional profiling, genotyping, protein quantitation, protein profiling and identification, real-time PCR and robotics. Genomics core offers Affymetrix gene chip technologies, both cartridge based and 96 well high throughput, analysis of genomic information with as little as 50ng of RNA, RNA extracted from paraffin based samples, or partially degraded RNA. Proteomics services include design, performance and analysis of proteomic studies." .
SCR:025690 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GLIPH2" ;
NIFRID:synonym "GLIPH",
"GLIPH version 2",
"GROUPING OF LYMPHOCYTE INTERACTIONS BY PARATOPE HOTSPOTS" ;
definition: "Web tool to explore cluster TCRs that are predicted to bind the same MHC-restricted peptide antigen. When multiple donors have contributed to the clusters, and HLA genotypes for those donors are available, GLIPH additionally can provide predictions of which HLA-allele is presenting the antigen." .
SCR:025691 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scRepertoire" ;
definition: "Software R toolkit for analyzing single-cell immune repertoire profiling. Used for single-cell immune receptor analysis." .
SCR:025692 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2913" ;
rdfs:label "University of Virginia School of Medicine Research and Clinical Trials Analytics Core Facility" ;
definition: "Core provides multi-disciplinary team of specialists in human subject research data who support School of Medicine’s research community across the globe. Can create and supply datasets, reports, extracts, data marts and databases. Provides secure web applications for building and maintaining databases and surveys including 21 CFR part 11 compliance and research data biorepository database management." .
SCR:025693 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stereotaxic Topographic Atlas of the Mouse Brain" ;
NIFRID:synonym "The Stereotaxic Topographic Atlas of the Mouse Brain (STAM)" ;
NIFRID:abbrev "STAM" ;
definition: "3D topographical atlas that depict anatomical structures of whole mouse brain, achieving precise single-cell resolution localization. Visualization platform, which includes services for exploring two-dimensional canonical anatomical sections, three-dimensional topography, and arbitrary-angle slices of brain atlas. Platform integrates different functionalities such as neuroanatomical knowledge base, virtual surgery, and automatic registration of user-uploaded slices." .
SCR:025694 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pluto Bio" ;
NIFRID:synonym "PlutoBio" ;
definition: "Collaborative life sciences platform built for life science organizations to manage multiple programs, track key results and biomarkers, and share biological data securely. Used to store, search, analyze, and visualize complex biological data including large, raw data files and run bioinformatics pipelines." .
SCR:025695 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2917" ;
rdfs:label "Peter MacCallum Cancer Centre Molecular Genomics Core Facility" ;
NIFRID:synonym "Molecular Genomics Core",
"Molecular Genomics Core facility" ;
NIFRID:abbrev "MGC" ;
definition: "Core works with researchers, clinicians and other research technology platforms to establish the best possible approach for any genomics experiment. Offers expertise on variety of off-the-shelf sequencing products and implementation or customisation of new protocols to meet demands of cancer research." .
SCR:025696 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioRad QuantaSoft Analysis Software" ;
NIFRID:synonym "QuantaSoft Analysis software" ;
definition: "Software analysis tool that enables data analysis of multiplex experiments and advanced applications and assay strategies for Droplet Digital PC." .
SCR:025697 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | CytoVision system" ;
definition: "Image analysis and management system that provides cytogenetics laboratories with integrated, scalable platform for brightfield and fluorescence samples. Combines expertise in image analysis, robotics and microscopy to offer complete cytogenetics solution. Used for FISH imaging system and digital analysis." .
SCR:025698 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2813" ;
rdfs:label "University of Pittsburgh Organoid Research Core Facility" ;
NIFRID:synonym "University of Pittsburgh UPitt- Organoid Research Core",
"UPitt- Organoid Research Core" ;
NIFRID:abbrev "ORC" ;
definition: "Core has large collection of unique patient-derived organoids (PDOs). Staff provides high-quality training in organoid development and culture, consultation services to assist with experimental design, execution, and data analysis." .
SCR:025699 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2914" ;
rdfs:label "Peter MacCallum Cancer Centre Research Laboratory Support Services Core Facility" ;
NIFRID:synonym "Peter MacCallum Cancer Center Research Laboratory Support Services" ;
definition: "Core provides media and buffer preparation, labware sterilising services, consumable provision, general wet laboratory support services." .
SCR:025700 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Behavioral Observation Research Interactive Software" ;
NIFRID:abbrev "BORIS" ;
definition: "Multiplatform standalone program that allows user-specific coding environment to be set for computer-based review of previously recorded videos or live observations. Allows project-based ethogram to be defined that can then be shared with collaborators, or can be imported or modified. Event logging software for video/audio coding and live observations. BORIS is a free and open-source software available for GNU/Linux, Windows and MacOS." .
SCR:025701 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Nubmer_Elyra_7" ;
rdfs:label "Zeiss | Elyra 7 microscope" ;
NIFRID:synonym "Elyra 7",
"ZEISS Elyra 7" ;
definition: "Super resolution microscope with Lattice SIM² to double the conventional SIM resolution and to discriminate sub-organelle structures, even those no more than 60 nm apart. Enables to combine super-resolution and high-dynamic imaging without the need for special sample preparation or expert knowledge of complex microscopy techniques. Enables resolving structures down to 60 nm, observing live cell dynamics at up to 255 fps, accelerating image acquisition in all three dimensions, getting the sharpest sectioning in wide-field microscopy, utilizing imaging techniques on one platform." .
SCR:025702 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Amersham_Typhoon_5" ;
rdfs:label "Cytiva | Amersham Typhoon 5" ;
NIFRID:synonym "Amersham Typhoon 5 Biomolecular Imager" ;
definition: "Laser scanner with exceptional data quality through extremely sensitive detection, high image resolution, and very broad linear dynamic range. Amersham Typhoon 5 model offers five-laser configuration option with advanced photomultiplier tubes. Has the same capabilities as Amersham Typhoon RGB model, with the addition of near-infrared (NIR) functionality." .
SCR:025703 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "demuxSNP" ;
definition: "Software R package for demultiplexing single-cell RNA sequencing data." .
SCR:025704 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Optima_Max-XP" ;
rdfs:label "Beckman Coulter | Optima Max-XP Tabletop Ultracentrifuge" ;
NIFRID:synonym "Optima Max-XP",
"Optima Max-XP Tabletop Ultracentrifuge" ;
definition: "Benchtop ultracentrifuge with separations for volumes as low as 175 ul, touch screen navigation, speeds up to 150,000 RPM, and RCF capability of up to 1019000 x g." .
SCR:025706 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ECTI_Atopic_Dermatitis" ;
NIFRID:synonym "Effective Corneocyte Topographical Index_Atopic_Dermatitis" ;
definition: "Software repository presents objective, quantifiable method for assessing severity of atopic dermatitis." .
SCR:025709 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_025680" ;
rdfs:label "LI-COR | ODYSSEY M Imaging System" ;
NIFRID:synonym "LI-COR ODYSSEY M",
"ODYSSEY M" ;
definition: """Imager has multiple detection modes with up to 19 fluorescent and luminescent channel combinations to power wide range of assays including 3-Color Quantitative Western Blots,
3-Color In-Cell Western Assays, Cell Analysis Studies, ELISA, Tissue Section Imaging, Viral Titration Assays. Imager includes sCMOS image sensor and 5-micron resolution.""" .
SCR:025710 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GlioVis " ;
definition: "Web application for data visualization and analysis to explore brain tumors expression datasets. Contains public glioma RNA seq data and analysis. Data portal for visualization and analysis of brain tumor expression datasets." .
SCR:025711 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Omicshare " ;
definition: "Web bioinformatics platform that integrates interactive bioinformatics tools, original omics books, bioinformatics forums, and video tutorials. Used for RNA seq analysis, heat map illustration, etc." .
SCR:025712 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Orbitrap_ID-X_Tribrid" ;
rdfs:label "Thermo Fisher | Orbitrap ID-X Tribrid Mass Spectrometer" ;
NIFRID:synonym "Orbitrap ID-X Tribrid",
"Orbitrap ID-X Tribrid Mass Spectrometer" ;
definition: "Mass spectrometer combines mass analyzer technology dedicated to small molecule analysis with data acquisition strategy of Thermo Scientific AcquireX smart MSn, to collect more meaningful data. Captures more low-abundance analytes." .
SCR:025713 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Vanquish_Horizon_UHPLC" ;
rdfs:label "Thermo Fisher | Vanquish Horizon UHPLC System" ;
NIFRID:synonym "Vanquish Horizon UHPLC system" ;
definition: "System for applications requiring high-quality Ultra High Performance Liquid Chromatography. Uses high pressure to separate and identify components of mixture. Provides accurate separation, retention times, peak area, detector sensitivity and reduced baseline noise for high flow rates." .
SCR:025714 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VICTOR_X" ;
rdfs:label "Perkin Elmer | VICTOR X Multilabel Plate Reader" ;
definition: """Bench top reader covering all of main non-radioactive reading technologies.VICTOR X models provide standard features such as temperature control, shaking, scanning, adjustable measuring height, bottom fluorescence reading, dual label/ratio reading and kinetics. System enhancements includes Expanded temperature control (up to +50 °C) for b etter control of assay conditions; New excitation filter wheel and expanded absorbance
wavelength (up to 1000 nm) enable versatile use of filters and broader spectrum analysis for greater assay flexibility; Improved chassis design to facilitate maintenance; Improved dispenser unit for enhanced functionality in kinetics assays.""" .
SCR:025715 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FACSAria_Fusion" ;
rdfs:label "BD Biosciences | FACSAria Fusion Cell Sorter" ;
NIFRID:synonym "BD FACSAria Fusion" ;
definition: "Cell sorter has UV, Violet, Blue, Yellow/Green and Red lasers and can detect up to 18 colors. Can sort up to 4 populations simultaneously. Samples can be sorted into 12 x 75 mm FACS tubes or 1.5 ml Eppendorf tubes. Uses BD FACSDiva software to control setup, acquisition, and analysis of flow cytometry data from operator workstation." .
SCR:025716 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Nikon_Eclipse_Ts2" ;
rdfs:label "Nikon | Eclipse Ts2 inverted microscope" ;
NIFRID:synonym "Eclipse Ts2",
"Nikon Eclipse Ts2" ;
definition: "Inverted microscope with LED light and built-in Diascopic/Epi-fluorescence illumination with cameras." .
SCR:025717 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.10919.30; ISNI 0000 0001 2259 5234; Crossref Funder ID 100007465; Wikidata Q279724" ;
rdfs:label "UiT The Arctic University of Norway" ;
NIFRID:synonym "Arctic University of Norway" ;
definition: "State University in Norway and the northernmost university. Located in the city of Tromsø, Norway.The main focus of the university is on auroral light research, space science, fishery science, biotechnology, linguistics, multicultural societies, Saami culture, telemedicine, epidemiology and spectrum of Arctic research projects. The close vicinity of the Norwegian Polar Institute, the Norwegian Institute of Marine Research and the Polar Environmental Centre gives Tromsø added weight and importance as international centre for Arctic research." .
SCR:025718 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "DevATLAS" ;
rdfs:label "DevATLAS" ;
NIFRID:synonym "Developmental Activation Timing-based Longitudinal Acquisition System" ;
definition: "Whole brain developmental map of neuronal circuit maturation. Generated by whole brain spatiotemporal mapping of circuit maturation during early postnatal development. Standard reference for normative developmental trajectory of neuronal circuit maturation, as well as high throughput platform to pinpoint when and where circuit maturation is disrupted in mouse models of neurodevelopmental disorders, such as fragile X syndrome." .
SCR:025719 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HumanIslets" ;
definition: "Data visualization portal for HumanIslets project. Integrated platform for human islet data access and analysis. Includes data on human islet donors, allows users to access linked datasets describing molecular profiles, islet function and donor phenotypes, and to perform various statistical and functional analyses at donor, islet and single-cell levels. Provides set of resources and tools to support metabolism and diabetes research community." .
SCR:025720 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harmonized DRG and TG Reference Atlas" ;
definition: "Harmonized cell atlases using sc/snRNA-seq data obtained from dorsal root ganglia and trigeminal ganglio mammalian datasets." .
SCR:025721 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cancerRxTissue" ;
definition: "Web application for drug sensitivity predictions for Cancer Genome Atlas RNA-seq data and Drug Sensitivity Predictions for GTEx RNA-seq data. Used to predict drug sensitivity for both normal and tumor tissues. You can query, visualize, and download predicted IC50 values of drugs using ID, name, target or pathway." .
SCR:025722 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VAEN " ;
definition: "Software application as deep generative neural network based approach to impute drug response. Includes imputed half maximal inhibitory concentration (IC50) value of anticancer drugs." .
SCR:025723 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Flask-RESTful" ;
definition: "Software framework for creating REST APIs. Python Flask-RESTful API frameworks." .
SCR:025724 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AngularJS " ;
definition: "Software structural framework for dynamic web service.Discontinued free and open-source JavaScript-based web framework for developing single-page applications." .
SCR:025725 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ElemeFE element-angular" ;
definition: "Open-source angularjs theme. Element for Angular." .
SCR:025727 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PAL:Proactive Automatized Lifestyle intervention" ;
definition: "Behavior change intervention software. Participants enter their data as part of online survey, and software generates individualized feedback letters." .
SCR:025728 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2918" ;
rdfs:label "Penn State Hershey College of Medicine Institutional Biorepository Core Facility" ;
NIFRID:synonym "Penn State Hershey College of Medicine Institutional Biorepository" ;
definition: "Biorepository collection is comprised of blood samples, tissues and other biological materials donated by patients, coupled with information about their health, environment, lifestyle, medical care and responses to medical treatment. Biorepository is accredited by College of American Pathologists." .
SCR:025729 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaCycle" ;
definition: "Software R package for detecting rhythmic signals from large scale time-series data. Used to evaluate periodicity in large scale data." .
SCR:025730 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fast DP" ;
definition: "Software single data reduction pipeline to provide merging statistics and merged intensities in correct pointgroup as quickly as possible after data collection is complete, to test assumptions made in planning experiment, to characterize quality of data in terms of downstream requirements and to detect radiation damage. Fast Data Processsing with XDS." .
SCR:025731 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LumiCycle_96" ;
rdfs:label "ActiMetricts | LumiCycle 96 system" ;
NIFRID:synonym "ActiMetricts LumiCycle 96",
"LumiCycle 96" ;
definition: "96-Channel luminometer for circadian biology. Performs high throughput luminometry on self-luminous tissues. System is equipped with 8 photomultiplier tubes, each selected for low dark counts and high sensitivity in green portion of spectrum at which luciferase emits light. Turntable and moving PMT mounting alternately brings each sample under its detector. In addition to its high-precision photon counting hardware, LumiCycle has software for collection and analysis of circadian rhythms in luminometry data." .
SCR:025732 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Infinite_M1000" ;
rdfs:label "Tecan | Infinite M1000" ;
NIFRID:synonym "Infinite M1000",
"Infinite M1000 microplate reader" ;
definition: "Multifunctional monochromator based microplate reader. Offers luminescence scanning to complement its existing 3D and ultra fast absorbance and fluorescence scanning capabilities. Allows for very low volume absorbance measurements. Provides double orbital shaking for more efficient reagent mixing, Optimal Read function for reliable cell-based measurements, and injector module for precisely controlled pipetting for triggering fast kinetic reactions and bulk dispensing." .
SCR:025733 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2919" ;
rdfs:label "University of Miami Miller School of Medicine Analytical Imaging Core Facility" ;
NIFRID:synonym "Analytical Imaging Core Facility (AICF)" ;
NIFRID:abbrev "AICF" ;
definition: "Core provides access to analytical and imaging techniques for cellular and tissue imaging as well as molecular analysis of pathology specimens. Training is provided for investigators, fellows, and technical staff in proper use of techniques and instruments." .
SCR:025734 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Metapathways" ;
NIFRID:synonym "MetaPathways v3.5" ;
definition: "Software modular pipeline for constructing pathway/genome databases from environmental sequence information. Used for predicting metabolic functions of given DNA sequences. Produces structured data products as pathway-genome databases with human-readable and machine-interpretable representations. MetaPathways v3.5 is updated algorithm for sequence feature prediction, annotation, metabolic inference, and coverage metrics including genome resolved metagenomes." .
SCR:025736 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mission Bio | Tapestri Platform" ;
NIFRID:synonym "Tapestri Platform" ;
definition: "Tapestri single-cell DNA sequencing platform provides both genotype and phenotype data from the same cell. Platform consists of instrument, DNA cartridge, which represents microfluidics device, and reagents. Cartridge is equipped with reservoirs that are used to load reagents required for automated cell processing. Pressure supplied by instrument drives reagents from reservoirs through microfluidic device and out to PCR collection tubes that are mounted below cartridge. Cartridge and tubes can be loaded and unloaded from instrument and disposed of after completion of workflow. User interacts with instrument via touch screen interface, which can be used to select programs, monitor status of running programs, and more." .
SCR:025737 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Applied Biosystems | QuantStudio Absolute Q Digital PCR System" ;
definition: "PCR System is plate based digital PCR platform powered by proprietary microfluidic array plate technology that enables all necessary steps for dPCR including compartmentalizing, thermal cycling and data acquisition to be conducted on single instrument. Uses nucleic acid quantification technique that allows absolute quantification without the need for standard curves. Bulk reaction mix is distributed or digitized into thousands of small independent reactions so that each micro-chamber contains either one or zero copies of the target. Statistical methods are then used to calculate the original concentrations based on the number of positive and negative micro-chambers." .
SCR:025738 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QuantStudio Absolute Q Digital PCR System Software" ;
NIFRID:synonym "AppliedBiosystem QuantStudio Absolute Q Digital PCR System Software" ;
definition: "System software used for analyzing dPCR data. If you have purchased QuantStudio Absolute Q Digital PCR system, you may download the system software. Software is available in Thermo Fisher Connect folder." .
SCR:025739 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Max Planck Institute of Biochemistry Imaging Facility" ;
NIFRID:synonym "Imaging Facility" ;
NIFRID:abbrev "MPIB-IF" ;
definition: "Facility for light microscopy and flow cytometry. Users are instructed by staff in operation of hardware and software and, if necessary, are supported in acquisition, processing and quantitative evaluation of images." .
SCR:025740 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Max Planck Institute of Biochemistry Crystallization Core Facility" ;
NIFRID:synonym "Cristallization Facility",
"Max Planck Institute of Biochemistry Cristallization Facility" ;
NIFRID:abbrev "MPIB-CCF" ;
definition: "Facility for protein crystallisation and X-Ray crystallography. Provides structural biology infrastructure and performs crystallization experiments." .
SCR:025741 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5776" ;
rdfs:label "Max Planck Institute of Biochemistry Protein Production and Structural Validation Core Facility" ;
NIFRID:synonym "Max Planck Institute of Biochemistry Protein Production and Structural Validation Facility",
"Max Planck Institute of Biochemistry Protein Production Facility",
"Protein Production and Structural Validation Facility",
"Protein Production Facility" ;
NIFRID:abbrev "MPIB-PPCF" ;
definition: "Facility for protein production. Provides services for protein expression and purification, assists with projects in designing strategies for high level expression of soluble proteins, provides vectors and strains. Offers clonning the gene of interest into expression vectors, rapid screening for optimal combinations of vectors, strains and expression conditions and producing protein of interest in E. coli, Pichia pastoris, mammalian and insect cells. Produces biomass at 1L to 10L scale using multiple bioreactor system for high cell density fermentation of bacteria and yeast cells and reusable bioreactor for cell culture. Proteins are then purified using standard techniques and chromatography systems. Quality control is routinely assessing protein identity, purity, stability and folding using set of different biochemical and biophysical methods." .
SCR:025742 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Max Planck Institute of Biochemistry Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core Facility" ;
NIFRID:abbrev "MPIB-BIO" ;
definition: "Facility for bioinformatics. Offers to assist wet-lab researchers in our institute for their bioinformatics data analysis." .
SCR:025743 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Max Planck Institute of Biochemistry Biochemistry Core Facility" ;
NIFRID:synonym "Biochemistry Core Facility" ;
NIFRID:abbrev "MPIB-BCB" ;
definition: "Facility for bioorganic chemistry and biophysics. Offers services for studying protein structure and folding, protein-protein or protein-ligand interactions and protein complex formation, synthesis, purification and characterization of organic compounds, automated solid phase synthesis of peptides." .
SCR:025744 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Max Planck Institute of Biochemistry Cryo-EM Core Facility" ;
NIFRID:synonym "Cryo-EM Facility",
"Max Planck Institute of Biochemistry Cryo-EM Facility" ;
NIFRID:abbrev "MPIB_CEMF" ;
definition: "Facility for cryo-electron microscopy. Provides microscope access, training as well as scientific and technical support for MPIB-internal users wishing to perform cryo-EM experiments, from sample preparation to data processing." .
SCR:025745 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Max Planck Institute of Biochemistry Mass Spectrometry Core Facility" ;
NIFRID:synonym "Mass Spectrometry Facility",
"Max Planck Institute of Biochemistry Mass Spectrometry Facility" ;
NIFRID:abbrev "MPIB-MS" ;
definition: "Mass spectrometry core facility. Facility uses chromatography systems, mass spectrometers and workflows for in-depth analysis of biomolecules." .
SCR:025746 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Max Planck Institute of Biochemistry NGS Core Facility" ;
NIFRID:synonym "NGS Core Facility" ;
NIFRID:abbrev "MPIB-NGS" ;
definition: "Facility for high-throughput sequencing. Provides Next-Generation Sequencing services, supports library preparation and quality control for various applications including RNA-Seq: rRNA depletion-total RNA, mRNAseq; DNA-Seq: ChIP-Seq, Cut andTag seq, Hi-Cseq, Micro-Cseq, WGS; Single Cell: scRNAseq, scATACseq, snRNAseq, seRNAseq." .
SCR:025747 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2927" ;
rdfs:label "Augusta University Georgia Cancer Center Flow and Mass Cytometry Core Facility" ;
NIFRID:synonym "Georgia Cancer Center Flow and Mass Cytometry Core" ;
definition: "Core provides access to flow and mass cytometers, support equipment, and associated software and services. Our instrumentation affords the ability to perform almost every published flow and mass cytometry protocol." .
SCR:025748 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SubtiWiki" ;
definition: "Comprehensive database about Gram-positive model bacterium Bacillus subtilis. Provides curated information about its genes and proteins, as well as intricate protein–protein interactions, regulatory elements, expression data and metabolic pathways." .
SCR:025749 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Delft High Performance Computing Centre Core Facility" ;
NIFRID:synonym "Delft High Performance Computing Centre",
"Delft High Performance Computing Centre (DHPC)",
"Delft University of Technology High Performance Computing Centre" ;
NIFRID:abbrev "DHPC" ;
definition: "Provides computational services including hardware, software and expertise for complex analysis and modelling ." .
SCR:025750 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TSTA" ;
NIFRID:synonym "Thread and SIMD-based Trapezoidal pairwise/multiple sequence Alignment" ;
definition: "Software tool as sequence alignment algorithm that combines SIMD instruction sets and thread acceleration. Pairwise and multiple sequence alignment accelerated by simd and threads" .
SCR:025751 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hidex | AMG Automatic Gamma Counter" ;
NIFRID:synonym "Hidex AMG gamma counter" ;
definition: "Gamma counter with optional internal balance specifically designed for nuclear medicine applications. Dedicated to Nuclear Medicine and PET applications. Used to measure gamma radiation emitted by radionuclide in samples." .
SCR:025753 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Replidec" ;
NIFRID:synonym "replidec" ;
definition: "Software that predicts three phage replication cycles, including virulent, temperate, and chronic cycles in viral sequences. Replication cycle decipher for Phages." .
SCR:025754 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "North Star Imaging US Labs" ;
definition: "Industrial x-ray facilities with microfocus and high energy 2D and CT systems. Provides instruments for biological CT scanning as service." .
SCR:025755 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scupa" ;
NIFRID:synonym "Single-Cell Unified Polarization Assessment" ;
definition: "Software R package for immune cell polarization assessment of scRNA-seq data. Single-cell unified polarization assessment of immune cells using single-cell foundation model. Used for comprehensive immune cell polarization analysis." .
SCR:025756 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CoCoPyE" ;
definition: "Software tool for quality assessment of microbial genomes. Used to predict completeness and contamination of bacterial and archaeal genomes. Provides taxonomic classification of the input. Feature-based learning and prediction of genome quality indices." .
SCR:025757 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MAXIV | CoSAXS beamline" ;
NIFRID:synonym "CoSAXS",
"CoSmall Angle X-ray Scattering",
"MAX IV CoSAXS beamline" ;
definition: "Multipurpose Small Angle X-ray Scattering instrument offers high brilliance, monochromatic and tuneable X-rays, with performance in low beam divergence, high X-ray flux, and variable beam size in both directions in full range of sample-detector distances provided by beamline up to 16 m. Several techniques are available through modular operation: time-resolved SAXS, SAXS/WAXS, protein solution SAXS, microfocusing SAXS, anomalous X-ray scattering and XPCS." .
SCR:025758 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Oxford |Nanopore Technologies | Prometheus" ;
NIFRID:synonym "NanoTemper Prometheus",
"Prometheus NT.4" ;
definition: "Instrument that uses nanoDSF to analyze protein folding and stability. Provides precise stability data across multiple parameters to characterize thermal unfolding, particle sizing, and aggregation of proteins. Used in variety of applications, including protein engineering, membrane protein research, formulation development, and quality control." .
SCR:025759 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Applied Photophysics | Chirascan V100 Circular Dichroism spectrometer" ;
NIFRID:synonym "Chirascan V100",
"Chirascan V100 Circular Dichroism spectrometer" ;
definition: "Chirascan V100 circular dichroism spectrometer for circular dichroism analysis, generating data that contribute to biomolecular characteristics, mechanisms, and interactions. Used for studying chiral molecules." .
SCR:025760 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Malvern Panalytical | Zetasizer Nano" ;
NIFRID:synonym "Malverne Zetasizer Nano" ;
definition: "Light scattering system. Instrument measures size of particles contained within sample. Used to measure particle size of dispersed systems from sub-nanometer to several micrometers in diameter." .
SCR:025763 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Revivity | VICTOR Nivo Multimode Microplate Reader" ;
NIFRID:synonym "VICTOR Nivo Multimode Microplate Reader" ;
definition: "Microplate reader for biochemical and cell-based assays, it measures at any wavelength, with top and bottom reading of all standard technologies. Used to measure Absorbance, Luminescence, Alpha, Fluorescence Intensity, TR Fluorescence." .
SCR:025764 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Izon | qEV Automatic Fraction Collector" ;
NIFRID:synonym "Automatic Fraction Collector",
"Automatic Fraction Collector (AFC)",
"qEV Automatic Fraction Collector" ;
definition: "Fraction collector with automate extracellular vesicle isolation using combination of qEV size-exclusion columns to increase uniformity of collected volumes, decrease experimental run-time, and eliminate many inaccuracies that are inherent in manual collection of Packed Cell Volume." .
SCR:025765 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Michigan Rogel Cancer Center Immune Monitoring Core Facility" ;
NIFRID:synonym "University of Michigan Rogel Cancer Center Immune Monitoring Core",
"University of Michigan Rogel Cancer Center Immune Monitoring Shared Resource" ;
definition: """Provides immunologic and biological support for ongoing research projects and clinical trials. Services include measuring multiple cytokines in single assay, determining cytokine concentrations in various biological specimens and monitoring immune cell activation through investigative analytic procedures. Offers sample processing expertise for blood and tissue
samples, including both plasma or serum and peripheral bloodmononuclear cells.""" .
SCR:025766 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2928" ;
rdfs:label "University of Michigan Rogel Cancer Center Experimental Irradiation Core Facility" ;
NIFRID:synonym "University of Michigan Rogel Cancer Center Experimental Irradiation Shared Resource" ;
definition: "Core provides irradiation services for investigators, including those whose primary interests are not in radiation biology, but who need this tool in support of other efforts, such immunosuppression of animals prior to stem cell transplantation through total body irradiation. Facility is equipped to perform moderate dose rate gamma irradiation (0.1-4 Gy/min) of cell cultures, tissue specimens or animals as well as low dose rate irradiation (0.05-0.3 Gy/hr) of cell cultures." .
SCR:025767 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BeStSel" ;
NIFRID:synonym "Beta Structure Selection" ;
definition: "Web server for accurate protein secondary structure prediction and fold recognition from circular dichroism spectra." .
SCR:025768 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PDBMD2CD" ;
definition: "This resource is no longer in service. Documented on September 19,2024. Web application to provide predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures." .
SCR:025769 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioXTAS RAW" ;
NIFRID:synonym "BioXTAS RAW 2" ;
definition: "Software tool as GUI based Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data.Small-angle scattering data reduction and analysis. Available on Windows, macOS (and OS X), and Linux." .
SCR:025770 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " R2 Genomics Analysis and Visualization Platform" ;
definition: "Platform for genomic analysis. Open access online genomics datascience and discovery platform designed to assist the bio-medical researchers with limited to no Bioinformatics skills to perform data mining tasks in the omics field." .
SCR:025772 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Leica_CM_1860_UV" ;
rdfs:label "Leica | CM1860 cryostat" ;
NIFRID:synonym "Leica CM1860 UV cryostat" ;
definition: "Leica CM1860 UV cryostat for high-quality cryosections with compact design, and user-friendly interface for optimal results." .
SCR:025773 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Vitrobot_Mark_IV" ;
rdfs:label "Thermo Fisher | Vitrobot Mark IV system" ;
NIFRID:synonym "Thermo Scientific Vitrobot Mark IV System",
"Vitrobot Mark IV" ;
definition: "Vitrification Robot is fully PC-controlled device for rapid cooling of aqueous samples. System offers semi-automated vitrification to provide fast, easy, and reproducible sample preparation for cryo-EM. Performs cryo-fixation process at constant physical and mechanical conditions like temperature, relative humidity, blotting conditions, and freezing velocity." .
SCR:025774 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRICISION X-Ray | SmART+ irradiator" ;
NIFRID:synonym "Small Animal Radiation Therapy system" ;
definition: "System for image-guided radiation with software and advanced set of imaging modalities, including Cone-Beam CT, µCT and Bioluminescence (BLI). Focal irradiation system that mimics clinical radiotherapy and imaging." .
SCR:025775 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biotage | Syro II Peptide Synthesizer" ;
NIFRID:synonym "Biotage Syro II Peptide Synthesizer",
"Syro II" ;
definition: "Fully automated multi-channel peptide synthesizer equipped with a two arm pipetting robot for faster washing and dispensing of reagents. Parallel synthesizer for solid phase peptide synthesis. Standard system is configured with two reactor blocks with other reactor block options available including heating block kits and Tip reactor blocks." .
SCR:025777 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "brainplotlib" ;
definition: "Software Python package that plots data on cortical surface." .
SCR:025778 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Invicro Vivoquant" ;
NIFRID:synonym "Vivoquant" ;
definition: "Software multi-modality post-processing suite for SPECT, CT, PET, MR, Optical and and Autoradiography imaging data." .
SCR:025779 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRQy" ;
definition: "Software quality assurance and checking tool for quantitative assessment of magnetic resonance imaging and computed tomography data. Used for quality control of MR imaging data." .
SCR:025780 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HistoQC" ;
definition: "Software quality control tool for digital pathology slides. Used to identify and delineate slide artefacts and discover cohort-level outliers." .
SCR:025781 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2929" ;
rdfs:label "University of California at San Francisco Advanced Microscopy Core Facility" ;
NIFRID:synonym "UCSF EM core",
"W.M Keck Foundation Advanced Microscopy Laboratory" ;
definition: "Core includes instrumentation for structural biology with focus on cryo-electron microscopy. Used for imaging ranging from atomic resolution to whole cells, with emphasis on linking structural and dynamics information with biological functions." .
SCR:025782 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TraceDrawer" ;
definition: "Software for evaluating, comparing and presenting real-time interaction data. Used for quantification of kinetics and affinity through curve fitting, with large number of binding models to choose from. Can extract experimental information from measurement, requiring minimal user input." .
SCR:025783 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Feature Specific Quantile Normalization " ;
NIFRID:abbrev "FSQN" ;
definition: "Software R package to perform feature specific quantile normalization. Designed to quantile normalize each feature in data set according to its corresponding feature in target distribution. This eliminates distribution based differences resulting from the use of different gene expression profiling platforms." .
SCR:025784 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2930" ;
rdfs:label "University of Maine Microscopy and Image Analysis Core Facility" ;
NIFRID:synonym "Microscopy and Image Analysis Core at University of Maine",
"University of Maine Microscopy and Image Analysis Core" ;
NIFRID:abbrev "MIAC" ;
definition: "Core offers imaging for diverse applications, including multi-color experiments, live sample imaging, protein colocalization, large sample tiling, and Z-stack 3D/4D imaging, as well as weak label detection. Provides expert guidance in microscopy and image analysis, training and support to advance research across various model organisms." .
SCR:025785 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "10,000 Brains Project" ;
definition: "Funding organization for neurodegenerative disorders and use of AI in it. 501(c)(3) philanthropic initiative that seeks to accelerate the use of artificial intelligence (AI) in the fight against neurodegenerative diseases." .
SCR:025786 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID: grid.21106.34; ISNI: 0000 0001 2182 0794; Crossref Funder ID 100011130; Wikidata: Q1307345" ;
rdfs:label "University of Maine; Orono; United States" ;
definition: "Public land-grant research university in Orono, Maine. It was established in 1865 as the land-grant college of Maine and is the flagship university of the University of Maine System." .
SCR:025787 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SIMS" ;
NIFRID:synonym "interpretable machine learning for single cell",
"scalable" ;
definition: "Software label transfer tool for single-cell RNA sequencing analysis. Scalable, Interpretable Modeling for Single-cell RNA-seq data classification." .
SCR:025788 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Michigan School of Medicine Advanced Genomics Core Facility" ;
NIFRID:synonym "Advanced Genomics Core",
"University of Michigan Advanced Genomics Core Research Facility",
"University of Michigan School of Medicine Advanced Genomics Core Research Facility" ;
definition: "Provides next generation services. Provides centralized expertise in advanced methods that enables all researchers to effectively exploit them for making scientific discoveries." .
SCR:025789 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Michigan Institutional Animal Care and Use Committee Core Facility" ;
NIFRID:synonym "University of Michigan Committee for Use and Care of Animals" ;
NIFRID:abbrev "IACUC" ;
definition: "Core ensures that animal welfare standards are maintained along with conduct of accurate, valid scientific research through supervision, coordination, training, guidance, and review of every project proposed to include use of vertebrate animals or cephalopods at University of Michigan." .
SCR:025790 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Michigan Unit for Laboratory Animal Medicine Core Facility" ;
NIFRID:synonym "Unit for Laboratory Animal Medicine",
"University of Michigan Unit for Laboratory Animal Medicine" ;
NIFRID:abbrev "ULAM" ;
definition: "Core partners with University of Michigan research community to achieve animal welfare standards in pursuit of impactful science. Provides training laboratory animal veterinarians and veterinary care to all animals used at the University of Michigan." .
SCR:025792 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReplidecPlus" ;
NIFRID:synonym "replidec+" ;
definition: "Software tool to predict phage replication cycle." .
SCR:025793 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Novo Nordisk | Metabolomics Platform Bruker timsTOF Pro 2 mass spectrometer coupled with Agilent 1290 Bio UPLC- Timon" ;
NIFRID:synonym "Bruker timsTOF Pro 2 mass spectrometer coupled with Agilent 1290 Bio UPLC- Timon" ;
definition: "University of Copenhagen Novo Nordisk Foundation Center for Basic Metabolic Research Metabolomics Platform Core Facility is equipped with a high resolution mass spectrometer with two distinct separation technologies - a second generation dual Trapped Ion Mobility Spectrometry (TIMS) analyzer which provides collision cross section values and Parallel Accumulation Serial Fragmentation (PASEF) which allows downstream selection of precursor ions for fragmentation. The mass spectrometer is coupled with Agilent 1290 Bio UPLC, with binary solvent pump, multi-sampler and thermostatted column oven." .
SCR:025794 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cancereffectsizeR" ;
definition: "Software R package to estimate mutation rates and quantify somatic selection in cancer." .
SCR:025795 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2931" ;
rdfs:label "University of Copenhagen Novo Nordisk Foundation Center for Basic Metabolic Research Metabolomics Platform Core Facility" ;
NIFRID:synonym "Metabolomics Platform",
"Metabolomics Platform Core Facility",
"Novo Nordisk Foundation Center for Basic Metabolic Research Metabolomics Platform" ;
definition: "Provides standardized mass spectrometry-based services for detection of metabolites in various biological samples. Offers development of novel techniques, access to advanced analytical instrumentation, guidance with experimental design, support with post-acquisition data analyses and assistance with publications and planning future studies." .
SCR:025796 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2920" ;
rdfs:label "University of Cincinnati Center for Advanced Structural Biology Core Facility" ;
NIFRID:synonym "Center for Advanced Structural Biology",
"University of Cincinnati Center for Advanced Structural Biology" ;
definition: "Integrates technology in single-particle cryogenic electron microscopy. Thermo Scientific Talos L120C Transmission Electron Microscope is available for visualizing nanoparticles, negatively stained proteins or conventional biological samples. It can be operated at 80kV or 120kV. Thermo Scientific Glacios 200 kV cryogenic TEM is equipped with both Ceta-16M camera and TFS Falcon 4 direct electron detector, in addition to Selectris Energy Filter. This system is able to generate images for atomic resolution structures for single particle analysis projects. Glacios also includes software for micro-Electron Diffraction data set collection. Available services include Training and access to the Mark IV Vitrobot plunge freezer,Training and access to the Talos L120C TEM system, Training and access to the Glacios 200 kV cryogenic TEM system, Assisted TEM analysis by CASB personnel." .
SCR:025797 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2921" ;
rdfs:label "University of Cincinnati Advanced Cell Analysis Service Center Core Facility" ;
NIFRID:synonym "Advanced Cell Analysis Service Center",
"University of Cincinnati Advanced Cell Analysis Service Center" ;
definition: "Offers access to microscopes and flow cytometry equipment for researchers. Available services include Upright and inverted widefield microscopy, Confocal Microscopy (Zeiss LSM 710), Super-Resolution Microscopy (Nikon SIMe), Live Cell Microscopy (Incucylte), Flow Cytometry (BD LSR Fortessa), Cell Sorting (BD Aria III)." .
SCR:025798 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hi-GDT" ;
definition: "Software Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants." .
SCR:025799 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Benchmark_D1000" ;
rdfs:label "Benchmark Scientific | D1000 homogenizer" ;
NIFRID:synonym "D1000 Handheld Homogenizer" ;
definition: "Rotor stator handheld homogenizer works by drawing sample, in liquid, into generator probe with variable speed rotor, and then forcing it out through slots in stator to mechanically shearing sample. Most samples are completely homogenized in 30 seconds or less. 130W motor drives rotor at speeds from 8,500 to 30,000 rpm. Speed is adjustable in six steps to meet sample processing needs. A separate on/off switch allows homogenizer to be left at appropriate setting. Generator probes are available in four sizes. 5mm and 7mm diameter have 50mm length for use with samples in microbtubes. 10mm x 115mm is ideal for use with 15 and 50ml tubes and 14mm x 130 mm, for 50ml tubes and vessels up to 250ml. The unit is supplied with one each of the 5mm and 7mm generator probes. All generator probes are made of stainless steel and can be sterilized by autoclaving." .
SCR:025800 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2937" ;
rdfs:label "Stanford University MicroCT Core Facility" ;
NIFRID:synonym "MicroCT Facility",
"Stanford University MicroCT" ;
NIFRID:abbrev "MCT" ;
definition: "Core provides nondestructive, high-resolution images of internal structure of variety of natural and engineered materials using X-ray micro-computed tomography. microCT can resolve structures on micrometer scale." .
SCR:025801 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2938" ;
rdfs:label "Stanford University Mineralogy and Petrology Lab Core Facility" ;
NIFRID:synonym "Mineralogy and Petrology Lab",
"Stanford University Mineralogy and Petrology Lab" ;
NIFRID:abbrev "M and P" ;
definition: "Core offers qualitative and quantitative characterization of Earth materials by providing optical microscopes for high-resolution imaging of loose materials and thin sections, computational resources for image processing, and bench space for light processing of samples before or after use of the Sample Preparation Lab." .
SCR:025802 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pySCENIC" ;
NIFRID:synonym "Python Single-Cell rEgulatory Network Inference and Clustering" ;
definition: "Software tool as Python implementation of the SCENIC pipeline which enables to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data." .
SCR:025803 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GSEApy" ;
NIFRID:synonym "Gene Set Enrichment Analysis python" ;
definition: "Software Python package for performing gene set enrichment analysis. Used for characterizing gene expression changes by analysis of large single-cell datasets." .
SCR:025804 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "infercnvpy" ;
definition: "Software application to infer copy number variation from single-cell transcriptomics data. Scalable Python library to infer CNV events from single cell transcriptomics data." .
SCR:025805 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SINSAGE | MiniChemi Imaging and Analysis System" ;
NIFRID:synonym "MiniChemi",
"MiniChemi Imaging and Analysis System" ;
definition: "MiniChemi compact and advanced imaging system designed for chemiluminescent and fluorescent imaging with super-cooled CCD sensor and big prime lens. Weak chemiluminescent or fluorescent signals can be detected. Western Blot imager." .
SCR:025806 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker OPUS" ;
NIFRID:synonym "OPUS",
"OPUS 8.2" ;
definition: "Software developed by Bruker for analysis and processing of spectroscopic data. Used for measurement, processing and evaluation of IR, NIR and Raman spectra." .
SCR:025807 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Quasar" ;
definition: "Software analysis toolboxes extending Orange suite. Used to build flexible spectral data processing workflows and explore various analysis ideas interactively." .
SCR:025808 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SEER*Stat" ;
definition: "Statistical software for analysis of SEER and other cancer-related databases.Used to view individual cancer records and to produce statistics for studying impact of cancer on population." .
SCR:025809 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCI SEER Cancer Stage Variable Documentation" ;
NIFRID:synonym "Cancer Stage Variable Documentation",
"NCI Cancer Stage Variable Documentation" ;
definition: "Portal provides links to documentation for several stage variables that are available in the SEER data for analysis." .
SCR:025810 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCI Division of Cancer Control and Population Sciences SEER-Medicare Comorbidity SAS Macros" ;
NIFRID:synonym "SEER-Medicare Comorbidity SAS Macros" ;
definition: "Portal provides SAS Macros to calculate comorbidity weights. Used to assist SEER-Medicare investigators with their analyses. NCI recommends use of the 2021 macro. The 2014 and 2000 versions are provided for those needing to reproduce prior results. These macros offer the option of including Medicare hospital (MedPAR) claims only, or also considering physician (NCH) and outpatient claims. The Rule-Out option is recommended in the latter situation. Note that diagnoses using ICD-10 codes, starting in October 2015, are not included in the 2000 and 2014 macros. NCI does not accept responsibility for the completeness or accuracy of the codes and weights used in the macros. Investigators may modify the macros if they wish to include different diagnosis codes or condition weights." .
SCR:025811 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCI Division of Cancer Control and Population Sciences SEER-Medicare Linked Data Resource" ;
NIFRID:synonym "SEER-Medicare Linked Data Resource" ;
definition: "Portal to reflect the linkage of two large population based sources of data that provide detailed information about Medicare beneficiaries with cancer." .
SCR:025812 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Alex's Lemonade Stand Foundation for Childhood Cancer Childhood Cancer Repository" ;
NIFRID:synonym "Childhood Cancer Repository" ;
definition: "Repository stores tissue samples and uses them to create cell lines. The cell lines and xenografts can be used as model to understand cancers and to test new treatments. Researchers all over the world can request cell lines and models to use in their research." .
SCR:025813 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Integrated DNA Technologies" ;
NIFRID:synonym "Integrated DNA Technologies (IDT)" ;
NIFRID:abbrev "IDT" ;
definition: "Company offers range of products and services for next generation sequencing, CRISPR genome editing, qPCR, gene expression, and other molecular biology applications." .
SCR:025814 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Immudex" ;
NIFRID:synonym "Immudex Precision Immune Monitoring" ;
definition: "Danish Reagents and Diagnostics company with headquarters in Copenhagen, Denmark that offers Dextramer products for detecting and characterizing antigen-specific T and B cells, non-conventional T cells, and antigen-presenting cells." .
SCR:025815 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Pure Protein LLC" ;
definition: "Biotechnology company focused on development and commercialization of proprietary technologies related to the human leukocyte antigen system, exclusively licensed from the University of Oklahoma. Pure Protein, in conjunction with its affiliates and subsidiaries, aims to bring novel therapies and diagnostic tools to patients across wide range of application areas spanning from therapeutic development in fields of oncology, autoimmunity, and infectious disease, to antibody mediated rejection in transplantation." .
SCR:025816 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Mimotopes" ;
definition: "Peptide company, which provides custom peptide synthesis, catalogue peptides, PepSet peptide libraries, reagents, antibodies, and array of other immunology services for research market, offering range of options for customisation and modification." .
SCR:025817 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "TWIST Bioscience" ;
definition: "Public biotechnology company based in South San Francisco that manufactures synthetic DNA and DNA products, makes gene synthesis, oligo pools, exome, NGS target enrichment, variant libraries and other synthetic DNA tools. Researchers can access quality tools for more accurate NGS, highly customizable Gene Synthesis at scales that fit any workflow, more accurate genomic screens that require fewer resources, and libraries with optimized discovery power as every variant is directly synthesized." .
SCR:025818 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MicroBeta2 LumiJET" ;
rdfs:label "Perkin Elmer | MicroBeta2 LumiJET Microplate Counter" ;
NIFRID:synonym "MicroBeta2 LumiJET Microplate Counter" ;
definition: "Microplate counter that measure radioactivity, as well as luminescence, available in 1-, 2-, 6-, and 12-detector configurations with 16-shelf loading capacity. Robotic loading option allows efficient integration into robotics systems. MicroBeta2 LumiJET model is available with choice of single or dual injectors per detector, and is also available with 1-, 2-, 6-, and 12-detector configurations. Both 96- and 384-well plates can be used. The injector configuration of the MicroBeta2 LumiJET enables flash luminescence studies." .
SCR:025819 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "ZellNet Consulting" ;
NIFRID:synonym "New York",
"NY",
"ZellNet" ;
definition: "Company specializes in immune monitoring services within biotechnology sector. Offers expert Elispot services, flow cytometry experiment design, and statistical analysis for immune response testing." .
SCR:025824 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EuCanImage FHIR ETL Implementation" ;
definition: """Software application as ETL implementation for EuCanImage, encouraging semantic interoperability of clinical data obtained in studies by transforming it into machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create dictionaries following FHIR compliant structure. Code Language is written in Python 3.11.
Outputs are JSON files compliant with FHIR 4.3 schemas.This script is specifically created for the Extract, Transform and Load implementation for EuCanImage, and will follow the structures obtained from the REDCap databases within the study.""" .
SCR:025825 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Chinese National Genomics Data Center" ;
NIFRID:synonym "National Genomics Data Center" ;
NIFRID:abbrev "NGDC" ;
definition: "Provides open access to suite of resources, with the aim to translate big data into big discoveries. Offers range of resources for biological big data deposition, integration, and translation." .
SCR:025826 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100012342" ;
rdfs:label "Chinese Genome Sequence Archive" ;
NIFRID:synonym "Genome Sequence Archive",
"Genome Sequence Archive Family" ;
NIFRID:abbrev "GSE" ;
definition: "Public archive of raw sequence data in National Genomics Data Center as part of the China National Center for Bioinformation. GSA accepts worldwide data submissions, performs data curation and quality control for all submitted data. Provides data storage and sharing services." .
SCR:025827 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Decoder-seq" ;
definition: "Software application as dendrimeric DNA coordinate barcoding design for spatial RNA sequencing, which offers both high sensitivity and high resolution in mRNA detection." .
SCR:025828 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Akoya Biosciences | Vectra 3 Automated Quantitative Pathology Imaging System" ;
NIFRID:synonym "Vectra 3 Automated Quantitative Pathology Imaging System" ;
definition: "Vectra 3 automated quantitative pathology imaging system, together with the inForm software, provides multispectral and automated multi-slide imaging of up to 6 slides to detect and measure weakly expressed and overlapping biomarkers in H and E, IHC or IF intact FFPE tissue sections or TMAs within familiar digital pathology workflow." .
SCR:025829 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IPUMS USA" ;
NIFRID:synonym "Integrated Public Use Microdata USA" ;
definition: "Website and database providing access to integrated, high-precision samples of American population drawn from sixteen federal censuses, from the American Community Surveys of 2000-present, and from the Puerto Rican Community Surveys of 2005-present. Preserves and harmonizes U.S. census microdata and provides easy access to this data with enhanced documentation." .
SCR:025830 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100011993",
"WONDER" ;
rdfs:label "CDC WONDER" ;
NIFRID:synonym "Centers for Disease Control and Prevention WONDER",
"Wide-ranging ONline Data for Epidemiologic Research",
"WONDER" ;
definition: "Databases utilize rich ad-hoc query system for the analysis of public health data. Reports and other query systems are also available." .
SCR:025831 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Quanteon_4_lasers" ;
rdfs:label "Agilent | NovoCyte Quanteon Flow Cytometer Systems 4 Lasers" ;
NIFRID:synonym "NovoCyte Quanteon Flow Cytometer Systems 4 Lasers",
"Quanteon 4 laser flow cytometer" ;
definition: "Quanteon 4 laser flow cytometer that can be configured with up to 25 independent photomultipliers." .
SCR:025832 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Tempus" ;
definition: "Biotechnology company that specializes in collection and analysis of molecular and clinical data to advance precision medicine." .
SCR:025833 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hacksig" ;
definition: "Software R package to compute gene expression signature scores." .
SCR:025834 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2924" ;
rdfs:label "Emory University Pediatric Biostatistics Core Facility" ;
NIFRID:synonym "Emory University and Children's Healthcare of Atlanta Pediatric Biostatistics Core",
"Emory University EU-Pediatric Biostatistics Core",
"EU-Pediatric Biostatistics Core" ;
definition: "Offers statistical expertise and services. Provides assistance and collaboration in study design, grant applications, protocol development, data analysis, publication preparation, and statistical education." .
SCR:025835 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2926" ;
rdfs:label "Emory University Animal Physiology Core Facility" ;
NIFRID:synonym "Emory Pediatric Animal Physiology Core",
"Emory University and Children's Healthcare of Atlanta Animal Physiology Core",
"EU Animal Physiology Core" ;
definition: "Centralized core specializing in survival surgery, technical procedures, and ultrasound imaging for rats and mice and assistance for surgical procedures in other species." .
SCR:025836 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2932" ;
rdfs:label "University of Washington Mouse CRISPR Core Facility" ;
NIFRID:synonym "University of Washington UW Mouse CRISPR Core",
"UW Mouse CRISPR Core" ;
NIFRID:abbrev "UWMCC" ;
definition: "Service facility offering generation of novel transgenic mouse models using CRISPR/Cas9 gene editing technology. Standard service includes consultation, design, testing, prep, mouse embryo microinjection, and genotyping." .
SCR:025837 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2939" ;
rdfs:label "Harvard Medical School Single Cell Core Facility" ;
NIFRID:synonym "Harvard Medical School Single Cell Core",
"Single Cell Core" ;
NIFRID:abbrev "SCC" ;
definition: "Core specializes in single cell and spatial transcriptomics, and multiomics. Provides custom services, education, training and expertise in multiple high-throughput single cell technologies." .
SCR:025838 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MadicLab | PSA094 Desktop Small Animal PET" ;
NIFRID:synonym "Desktop Small Animal PET" ;
definition: "MadicLab Box series uses PSA series microscopic PET technology for small animals. Compact, benchtop body design. Provides advanced technical support for whole-body imaging and in vivo characterization of preclinical small animal models." .
SCR:025839 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Perkin Elmer | Quantum GX2 micro-CT imaging system" ;
NIFRID:synonym "Quantum GX2 micro-CT imaging system" ;
definition: "Offers increased imaging fields of view to accommodate larger samples in vivo and enables high-resolution imaging of ex vivo samples. Manual x-ray filter assembly provides opportunities to optimize imaging protocols and coupled with the high-resolution, high-speed integrated platform." .
SCR:025840 a owl:NamedIndividual ;
rdfs:label "EnrichDO" ;
definition: "Software R package as global weighted model for disease ontology enrichment analysis. Used for annotating and enrichment analysis with disease ontology." .
SCR:025841 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2934" ;
rdfs:label "Harvard Medical School Harvard Cryo-Electron Microscopy Center for Structural Biology Core Facility" ;
NIFRID:synonym "Harvard Cryo-Electron Microscopy Center for Structural Biology",
"Harvard Medical School Harvard Cryo-Electron Microscopy Center for Structural Biology" ;
definition: "Joint effort by Harvard Medical School, Dana-Farber Cancer Institute, Boston Childrens Hospital, and Massachusetts General Hospital to provide cryo-EM instrumentation and expertise for Harvard structural biology community. Facility offers consultation and training by staff in specimen preparation, microscope operation, image acquisition, and data analysis." .
SCR:025842 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2935" ;
rdfs:label "Harvard Medical School Mouse Behavior Core Facility" ;
NIFRID:synonym "Harvard Medical School HMS Mouse Behavior Core",
"HMS Mouse Behavior Core" ;
NIFRID:abbrev "MBC" ;
definition: "Core offers mouse behavioral equipment and assays to test motor, cognitive, and affective behaviors. Trained users have access to behavioral testing rooms and procedure room. MBC staff offers consultation, training, and guidance in execution and interpretation of assays." .
SCR:025843 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fairgraph" ;
definition: "Software Python library for working with metadata in EBRAINS Knowledge Graph. High-level Python API for EBRAINS Knowledge Graph." .
SCR:025844 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2940" ;
rdfs:label "Harvard Medical School Nascent Transcriptomics Core Facility" ;
NIFRID:synonym "Harvard Medical School Nascent Transcriptomics Core",
"Nascent Transcriptomics Core" ;
definition: "Core specializes in analysis of nascent transcriptome using PRO-seq and TT-seq NGS methods. Provides services allowing users to submit prepared cells and receive analyzed data. Offers free consultations to help with experimental design, answer questions, and discuss data analysis." .
SCR:025845 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NucBalancer" ;
definition: "Software tool to assist in optimizing nucleotide pooling strategies for high-throughput genomic analyses. Used to evaluate nucleotide distribution uniformity across positions and allows users to set customizable red flag thresholds, ensuring optimal results while accommodating variability." .
SCR:025846 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Perth Scientific | Hirschmann Neubauer Haemocytometer Counting Chamber" ;
NIFRID:synonym "Haemocytometer Counting Chamber",
"Neubauer Haemocytometer Counting Chamber" ;
definition: "Cell counting chamber. Used to count cells or other particles in suspensions under microscope." .
SCR:025847 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "10x Genomics Xenium Explorer" ;
NIFRID:synonym "Xenium Explorer" ;
definition: "Desktop application for Windows and MacOS that allows to interactively visualize data generated by the Xenium Analyzer instrument." .
SCR:025848 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "10x Genomics Space Ranger" ;
NIFRID:synonym "Space Ranger" ;
definition: "Software analysis pipeline that process 10x Genomics Visium data with brightfield or fluorescence microscope images, allowing users to map whole transcriptome in variety of tissues." .
SCR:025849 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MethylSig" ;
definition: "Software R package as whole genome DNA methylation analysis pipeline. Used for testing differentially methylated cytosines or regions in whole-genome bisulfite sequencing or reduced representation bisulfite sequencing experiments. Several options exist for either site-specific or sliding window tests, and variance estimation." .
SCR:025850 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MethylDackel" ;
definition: "Software tool to process coordinate sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires indexed fasta file containing reference genome as well." .
SCR:025851 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BWA-METH" ;
NIFRID:synonym "bwa-meth" ;
definition: "Software tool for fast and accurate alignment of BS-Seq reads using bwa-mem and 3-letter genome." .
SCR:025852 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2944" ;
rdfs:label "University of California at Berkeley Vincent J. Coates Proteomics/Mass Spectrometry Laboratory Core Facility" ;
NIFRID:synonym "UCB Proteomics/Mass Spectrometry Laboratory" ;
definition: "Core provides multidimensional LC-MS/MS analysis including Protein ID, Proteomics Profiling, Targeted Proteomics and Post Translational Modification analysis. Quantitative proteomic services are provided using label free quantitative proteomic (LFQ) profiling, Tandem mass tagging (TMT) or SILAC approaches. Provides support for macromolecular complexes using Nano ESI." .
SCR:025853 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "STAR-Fusion" ;
definition: "Software tool to leverage chimeric and discordant read alignments identified by STAR aligner to predict fusions. Component of Trinity Cancer Transcriptome Analysis Toolkit. Used to identify candidate fusion transcripts supported by Illumina reads. Maps junction reads and spanning reads to reference annotation set." .
SCR:025854 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Arriba" ;
definition: "Software tool for gene fusion detection from RNA-Seq data. Fusion detection algorithm specifically designed to meet demanding requirements of HTS-assisted precision oncology. Capable of detecting aberrant transcripts that are not called by most fusion detection methods but may be clinically relevant. This includes tumor suppressor genes that are occasionally inactivated by rearrangements within the gene or by translocations to introns or intergenic regions." .
SCR:025855 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Step_One_Plus" ;
rdfs:label "Thermo Fisher: Applied Biosystems | Step One Plus Real-Time PCR System" ;
definition: "Real-time PCR system that enables precise quantitative real-time PCR results. High-quality qPCR results, 4-color, 96-well PCR instrument." .
SCR:025856 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Orion Star A211 Benchtop pH Meter" ;
NIFRID:synonym "Orion Star A211 Benchtop pH Meter" ;
definition: "Benchtop pH Meter to record accurate and reliable pH, mV, ORP and temperature measurements." .
SCR:025857 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "czid.org" ;
definition: "Collaborative open project of Chan Zuckerberg Initiative and Chan Zuckerberg Biohub. The no-code, cloud-based bioinformatics tool for researchers. Used to analyzing genomic data for free. Hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data." .
SCR:025859 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2941" ;
rdfs:label "Harvard Medical School Beth Israel Deaconess Medical Center Bioinformatics Core Facility" ;
NIFRID:synonym "Beth Israel Deaconess Medical Center BIDMC Bioinformatics Core",
"BIDMC Bioinformatics Core",
"Harvard Medical School Beth Israel Deaconess Medical Center Bioinformatics Core",
"Harvard Medical School BIDMC Bioinformatics Core" ;
definition: "BIDMC Bioinformatics Core is Unit of the Precision RNA Medicine Core and provides support for management, integration and contextual analysis of biological high-throughput data, training on tools, databases and best practice." .
SCR:025860 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2942" ;
rdfs:label "University of Freiburg Cryo-Electron Microscopy Core Facility" ;
NIFRID:synonym "Cryo-Electron Microscopy Facility (CEF) Freiburg",
"CryoEM Facility",
"University of Freiburg Cryo-Electron Microscopy Facility (CEF) Freiburg",
"University of Freiburg CryoEM Facility" ;
definition: "Core offers services related to cryo electron microscopy. Services include grid preparation, screening and data collection, as well as user training." .
SCR:025861 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Cancer Institute Division of Cancer Control and Population Sciences Social Determinants of Health by US Census Tract" ;
NIFRID:synonym "Social Determinants of Health by US Census Tract" ;
definition: "Portal provides access to data set including, for each U.S. census tract (defined using 2010 census tract boundaries), certain social determinants of health data elements, including race/ethnicity, education, poverty, urban/rural, socioeconomic status, and racial residential segregation indices defined using 2008-2012 American Community Survey data and 2010 definitions of rural urban commuting areas." .
SCR:025862 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2945" ;
rdfs:label "Johns Hopkins University School of Medicine Mass Spectrometry and Proteomics Core Facility" ;
NIFRID:synonym "Johns Hopkins University School of Medicine Mass Spectrometry and Proteomics Facility" ;
definition: "Core assists investigators to identify and quantify proteins and their modifications that are differentially expressed in cells, tissues or body fluids, to track interactions with binding partners during changes in signal transduction, and to identify proteolytic cleavage sites and map post-translational modifications by providing following proteomic services: Consultation, Sample preparation,Protein Identification,Protein Modifications, Protein Quantification, Targeted Quantification, High Resolution Mass Analysis,Training and Self-Service Equipment. Core offers workshops to use the Core’s MALDI-TOF mass spectrometer, Typhoon gel imaging scanner and 2D gel electrophoresis equipment and proteomic software." .
SCR:025863 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Prostruc" ;
NIFRID:synonym "ProStruc" ;
definition: "Web tool for protein structure prediction, leveraging sequence alignment, template-based modeling, deep learning, and validation techniques. With input of either amino acid sequence or FASTA file, ProStruc generates protein structures. ProStruc automates process of blast searches, template selection, structural modeling, and validation, including RMSD, TM-score, and QMEAN." .
SCR:025864 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CopywriteR" ;
definition: "Software R package for DNA copy number detection from off-target sequence data. Used to extract DNA copy number information from targeted sequencing by utiizing off-target reads." .
SCR:025865 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SpectraMax_Paradigm" ;
rdfs:label "Molecular Devices | SpectraMax Paradigm Multi-Mode Microplate Reader" ;
NIFRID:synonym "SpectraMax Paradigm Multi-Mode Microplate Reader" ;
definition: "Microplate Reader measures absorbance, fluorescence, time-resolved fluorescence including HTRF, fluorescence polarization, AlphaScreen, AlphaLISA, and luminescence assays for up to 1536-well plates. Detection cartridge modularity allows for easy addition of new read modes within minutes without requiring service visit, while providing flexibility for future applications." .
SCR:025866 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_297" ;
rdfs:label "Boston Children's Hospital Molecular Genetics Core Facility" ;
NIFRID:synonym "BCH Molecular Genetics Core Facility",
"Molecular Genetics Core Facility" ;
definition: "Provides genomic technology services and expertise. Services offered include Nanopore PromethION sequencing, Electronic optical mapping on Nabsys, Optical Genome mapping on Bionano Saphyr, NGS (Illumina-based), Sanger Sequencing, Single cell analysis/RNAseq, Transcriptomic spatial profiling, Gene expression analysis , Droplet Digital PCR & qPCR, Microsatellite/fragment analysis, SNP genotyping , Chromosomal microarray analysis, Sample prep and QC, Project consultation, Bioinformatics support." .
SCR:025867 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Maxwell | RSC Instrument" ;
NIFRID:synonym "Maxwell Rapid Sample Concentrator Instrument",
"Rapid Sample Concentrator" ;
definition: "Instrument provides automated DNA or RNA purification. Sample lysis and binding to paramagnetic particles is primary separation principle. Up to 16 samples can be prepared in single run. Instrument is controlled through graphical user interface running on Tablet PC and has ability to record and report sample tracking and method run data. Reports can be printed and exported to storage location or USB drive." .
SCR:025868 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PythonVideoAnnotator" ;
definition: "Software graphical application written in Python, to analyze videos and create notes for events in the video. Used to identify animals’ behaviors based on information extracted from video." .
SCR:025869 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_STB-10" ;
rdfs:label "Strex | Manual Cell Stretching System STB-10" ;
NIFRID:synonym "Manual Cell Stretching System STB-10" ;
definition: "System for evaluative purposes applies cell stretching and compression force and is operated manually. Has two versions available: 4 cm2 or 10 cm2 stretch chambers. Can mechanically stimulate monolayer and cultured cells and tissue to increase cell growth and shape." .
SCR:025870 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "uAI Research Portal" ;
NIFRID:synonym "United Imaging Intelligence uAI Research Portal" ;
definition: "AI-powered integrated research platform for one-stop analysis of medical images. Provides advanced functionality such as automatic segmentation, registration, and classification for variety of application domains. Has major merits including Advanced built-in algorithms applicable to multiple imaging modalities (i.e., CT, MR, PET, DR), diseases (i.e., tumor, neurodegenerative disease, pneumonia), and applications (i.e., diagnosis, treatment planning, follow-up); Iterative deep learning-based training strategy for fast delineation of ROIs of large-scale datasets, thereby saving clinicians' time and obtaining novel and more robust models; Modular architecture with customization and extensibility, where plugins can be designed for specific purposes." .
SCR:025871 a owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ABL800_FLEX" ;
rdfs:label "RADIOMETER | ABL800 FLEX blood gas analyser" ;
NIFRID:synonym "ABL800 FLEX blood gas analyser",
"Radiometer ABL800 FLEX",
"Radiometer ABL800 FLEX blood gas analyser" ;
definition: "Radiometer blood-gas analyser is intended for in vitro testing of samples of whole blood for the parameters pH, pO2, pCO2, potassium, sodium, calcium, chloride, glucose, lactate, total bilirubin, and co-oximetry parameters (total hemoglobin, oxygen saturation, and the hemoglobin fractions FO 2 Hb, FCOHb, FMetHb, FHHb, FHbF)." .
SCR:025872 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ABL90_FLEX_PLUS" ;
rdfs:label "RADIOMETER | ABL90 FLEX PLUS blood gas analyser" ;
NIFRID:synonym "ABL90 FLEX PLUS",
"ABL90 FLEX PLUS blood gas analyzer",
"Radiometer ABL90 FLEX PLUS blood gas analyzer" ;
definition: "Cassette-based ABL90 FLEX analyzer can deliver 17 parameters from sample as small as 65 μL. ABL90 measures blood gas, electrolytes, metabolites and co-oximetry. The ABL90 analyzer can measure sample from syringe, capillary tube or test tube. Portable, automated analyzer that measures pH, blood gases, electrolytes, glucose, lactate, bilirubin, creatinine." .
SCR:025881 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2957" ;
rdfs:label "Africa Microscopy Initiative Imaging Centre Core Facility" ;
NIFRID:synonym "Africa Microscopy Initiative Imaging Centre",
"AMI Imaging Center" ;
definition: "AMI Imaging Center houses advanced, commercial light microscopes. These instruments are tailored for use in the life sciences and provide high spatial and temporal resolution to study variety of biology." .
SCR:025882 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Blobtoolkit" ;
NIFRID:synonym "BlobToolKit" ;
definition: "Software suite based on BlobTools to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. Used for genome assembly QC and contaminant cobiont detection and filtering. Can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. Can be used during assembly to filter non-target DNA. BlobToolKit is comprised of four distinct components: BlobTools2 (command line tools to create and filter datasets), Specification (a formal specification and validator for the JSON-based data format), Viewer (interactive dataset visualization), and INSDC-pipeline (a Snakemake pipeline to run the BlobToolKit workflow on publicly available datasets)." .
SCR:025883 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dorado" ;
definition: "Software tool as Oxford Nanopore basecaller. Used to determine nucleotide sequence." .
SCR:025884 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SMARTER Database" ;
NIFRID:synonym "SMAll RuminanTs breeding for Efficiency and Resilience Database",
"SMARTER-database" ;
definition: "SMARTER-database aims to collect data produced by SMAll RuminanTs breeding for Efficiency and Resilience project and to merge them with already available genotype data. Used to explore genomic diversity in small ruminants." .
SCR:025885 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AlphaFold Server" ;
NIFRID:synonym "AlphaFold 3" ;
definition: "Web-service that can generate highly accurate biomolecular structure predictions containing proteins, DNA, RNA, ligands, ions, and also model chemical modifications for proteins and nucleic acids in one platform. Powered by AlphaFold 3 model." .
SCR:025886 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FungiLT" ;
definition: "Software classifier tool based on deep learning methods for classification and annotation of large-scale fungal ITS sequences. Used for fungal species classification." .
SCR:025888 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AdaptiveSplit" ;
NIFRID:synonym "Adaptivesplit" ;
definition: "Software Python package for external validation of machine learning models with adaptive sample splitting." .
SCR:025889 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2969" ;
rdfs:label "Rockefeller University High Performance Computing Core Facility" ;
definition: "Provide Rockefeller University researchers and collaborators with infrastructure necessary for computationally intensive workloads, as well as training and support for using these resources." .
SCR:025890 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NovoCyte_3000" ;
rdfs:label "Agilent | NovoCyte 3000 Flow Cytometer" ;
NIFRID:synonym "Novocyte",
"Novocyte 3000 Flow Cytometer" ;
definition: "Agilent NovoCyte 3000 Flow Cytometer with 3 lasers (488, 405, 640 nm) and up 13 colors. 6 colors from violet laser; 5 colors from blue laser; 2 colors from red laser. NovoExpress software used for acquisition." .
SCR:025891 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2958" ;
rdfs:label "Colorado State University Microscopes for Open Access Imaging Core Facility" ;
NIFRID:synonym "Colorado State University Microscopes for Open Access Imaging",
"Colorado State University Microscopes for Open Access Imaging (MOAI)",
"Microscopes for Open Access Imaging",
"Microscopes for Open Access Imaging (MOAI)" ;
NIFRID:abbrev "MOAI" ;
definition: "Light and fluorescence microscopy core facility with Zeiss, Nikon, 3I, Leica and Olympus Microscopes. Distributed light microscopy core facility consisting of inverted and upright confocal microscopes (laser scanning and spinning disk) some with superresolution, atomic force microscopy, total internal fluorescence reflection (TIRF), high throughput multicolor imaging of fixed tissue sections or cells on slides, and live cell imaging in most modalities." .
SCR:025892 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2950" ;
rdfs:label "Brandeis University Light Microscopy Core Facility" ;
NIFRID:synonym "Brandeis Light Microscopy Core Facility",
"Brandeis University Brandeis Light Microscopy Core Facility" ;
NIFRID:abbrev "LMCF" ;
definition: "Facility houses 13 high-end light microscopes including point scanning and spinning disk confocals, Airyscan, 3D-STED super resolution, widefield and TIRF systems. Core offers training, consultation and access to powerful analysis computers with licensed softwares." .
SCR:025893 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_513" ;
rdfs:label "University of Kansas Medical Center Mass Spectrometry and Proteomics Core Facility" ;
NIFRID:synonym "Mass Spectrmetry/Proteomics Core Laboratory",
"University of Kansas Medical Center Mass Spectrmetry/Proteomics Core Laboratory" ;
definition: "Mass spectrometry based proteomics." .
SCR:025894 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_280" ;
rdfs:label "Oklahoma Medical Research Foundation OMRF Clinical Genomics Center Core Facility" ;
NIFRID:synonym "Oklahoma Medical Research Foundation OMRF Clinical Genomics Center",
"OMRF Clinical Genomics Center" ;
definition: "Offers high-throughput sequencing and genotyping services utilizing cutting edge Illumina and Xoford Nanopore systems. Sequencing facility in Oklahoma. Equipped with an Illumina NovaSeq 6000, Illumina NextSeq 2000, Illumina MiSeq, Illumina iSeq, Oxford Nanopore PromethION 2, and Oxford Nanopore MinION,Illumina iScan and Autoloader for extremely-high throughput genotyping projects. Core can perform all aspects of NGS, ranging from whole genome sequencing to single-cell transcriptomics." .
SCR:025895 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_492" ;
rdfs:label "University of Cincinnati Proteomics Laboratory Core Facility" ;
NIFRID:synonym "University of Cincinnati Proteomics Laboratory",
"University of Cincinnati Proteomics Laboratory (UCPL)" ;
NIFRID:abbrev "UCPL" ;
definition: "Core is equipped with protein separation and mass spectrometry equipment as well as trained personnel to perform comparative analyses of complex protein mixtures and to identify differentially-expressed proteins. Offers guidance and consultation." .
SCR:025896 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WorkFlowHub" ;
definition: """Registry for describing, sharing and publishing scientific computational workflows.
Aims to facilitate discovery and re-use of workflows in accessible and interoperable way. This is achieved through extensive use of open standards and tools, including CWL, RO-Crate, Bioschemas and GA4GH's TRS API, in accordance with FAIR principles.WorkflowHub supports workflows of any type in its native repository.""" .
SCR:025899 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BGI | DNBSeq PE150 BGISEQ-500 sequencing system" ;
definition: "System composed of DNBseq PE150 sequencing platform for RNA sequencing transcriptome with BGISEQ-500 desktop sequencer which uses DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics sequencing technologies to generate short reads at large scale. DNBseq PE150 sequencing platform uses DNA nanoballs that are loaded onto flow cells and then read using fluorescent probes. The platform then uses lasers to excite the probes and take millions of images to identify bases." .
SCR:025900 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Biograph_mMR_3_Tesla" ;
rdfs:label "Siemens | Biograph mMR 3.0 Tesla scanner" ;
NIFRID:synonym "Biograph mMR",
"Siemens Biograph mMR 3.0 Tesla PET/MR Scanner" ;
definition: "Siemens Biograph mMR represents major technological breakthrough in imaging field by combining positron emission tomography (PET) and magnetic resonance imaging (MRI) in one scanner. This system allows simultaneous acquisition of MR and PET images in human subjects." .
SCR:025901 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2955" ;
rdfs:label "Peter MacCallum Cancer Centre Bioinformatics Core Facility" ;
NIFRID:synonym "Peter MacCallum Cancer Center Bioinformatics Core Facility" ;
definition: "Provides services for data analysis, pipeline management, and artificial intelligence research and operations. Data types analysed by the core include whole-genome and whole-exome sequencing, targeted re-sequencing, radiological images, RNA-sequencing, single-cell RNA sequencing, ChIP-sequencing, NanoString and various types of microarray data. Core also develops and maintains software infrastructure required for bioinformatics processing, including pipelines and cloud provision systems." .
SCR:025902 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "2023 U.S. Census Quick Facts about Alabama, Maryland, Missouri and Connecticut" ;
definition: "Data about Alabama, Maryland, Missouri and Connecticut people and economy." .
SCR:025903 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MultiNicheNet" ;
definition: "Software tool for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data." .
SCR:025904 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SRplot" ;
definition: """Web server that integrated data visualization and graphing functions together. Can be run easily with all Web browsers, with user-friendly graphical interface, users can paste your data directly into input box according to defined file format. Resulting graphs can be downloaded in bitmap (PNG or TIFF) or vector (PDF or SVG) format in publication quality.
Used for data visualization and graphing.""" .
SCR:025927 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BD Biosciences FCAP Array software" ;
NIFRID:synonym "FCAP Array v3",
"Flow Cytometric Analysis Program Array V3 software" ;
definition: "Software can use data files exported in FCS 2.0 or 3.0 formats, providing analysis capability for major BD instrument platforms that use BD FACSuite, BD FACSDiva, BD FACSArray, BD Accuri C6, or BD CellQuest Pro software." .
SCR:025936 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HD6" ;
rdfs:label "Uvitech | Uvidoc HD6 gel imager" ;
NIFRID:synonym "Uvidoc HD6" ;
definition: "Unique stand-alone platform and voice-controlled DNA/protein gel workstation for gel imaging." .
SCR:025961 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VR device based mental stress test program" ;
definition: "Software is developed based on Android Unity 3D platform, utilizing Java language. Used to simulate mental stress tasks using VR device (from Huaxing Virtual Reality Co., Ltd.). During test, subjects rest calmly under starry sky in resting state. Mental stress test consists of three tasks, each lasting about 3 minutes: modified Stroop task, public speaking, and mental arithmetic tests. Download link also includes companion Android mobile monitoring app for viewing participant's VR screen." .
SCR:025962 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2967" ;
rdfs:label "UTHealth Houston Center for Advanced Microscopy Core Facility" ;
NIFRID:synonym "Center for Advanced Microscopy at UTHealth at Houston",
"McGovern Medical School Center for Advanced Microscopy" ;
definition: "Microscopy facility serving Texas Medical Center. Facilitates utilization of advanced light microscopy techniques and quantitative image analysis to advance research programs of McGovern Medical School, UTHealth, and the greater Texas Medical Center. Fluorescence microscopy and image analysis core." .
SCR:025963 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneDOC" ;
definition: "Software tool for multiple species sequence alignment. Used for editing and annotating multiple sequence alignments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:025964 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "expanded Human Oral Microbiome Database" ;
NIFRID:abbrev "eHOMD" ;
definition: "Provides comprehensive curated information on bacteria in human mouth and aerodigestive tract, including pharynx, nasal passages, sinuses and esophagus. eHOMD taxonomy provides provisional naming scheme for currently unnamed taxa, based on 16S rRNA sequence phylogeny, so that strain, clone and probe data from any laboratory can be directly linked to a stably named reference scheme." .
SCR:025965 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggpicrust2" ;
definition: "Software R package for analyzing and interpreting results of PICRUSt2 functional prediction. Offers range of features, including pathway name/description annotations, advanced differential abundance methods, and visualization of differential abundance results. Used for PICRUSt2 predicted functional profile analysis and visualization." .
SCR:025966 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LinDA" ;
NIFRID:synonym "Linear models for differential abundance analysis of microbiome compositional data",
"Linear models for differential abundance analysis of microbiome compositional data (LinDA)" ;
definition: "Software linear models for differential abundance analysis of microbiome compositional data. Used to tackle compositional effects in differential abundance analysis. It fits linear regression models on centered log2-ratio transformed data, identifies bias term due to transformation and compositional effect, and corrects bias using mode of regression coefficients. It could fit mixed-effect models." .
SCR:025967 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Apache" ;
NIFRID:synonym "Apache HTTP Server Project" ;
definition: "Apache HTTP Server Project is collaborative software development effort aimed at creating freely-available source code implementation of HTTP (Web) server. Project is jointly managed by group of volunteers located around the world, using the Internet and the Web to communicate, plan, and develop the server and its related documentation." .
SCR:025968 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "stats" ;
definition: "Software package contains functions for statistical calculations and random number generation." .
SCR:025969 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Selenium WebDriver" ;
NIFRID:synonym "WebDriver" ;
definition: "Software remote control interface that enables introspection and control of user agents. Provides platform- and language-neutral wire protocol as way for out-of-process programs to remotely instruct behavior of web browsers." .
SCR:025970 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sfsmisc" ;
definition: "Software R package as collection of useful utility functions from Seminar for Statistics (SfS) at ETH Zurich." .
SCR:025971 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Supervisor" ;
definition: "Web client/server system that allows its users to control number of processes on UNIX-like operating systems." .
SCR:025972 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MySQL-server" ;
NIFRID:synonym "My Structured Query Language Server" ;
definition: "Open source Relational Database Management System that enables users to store, manage, and retrieve structured data efficiently." .
SCR:025973 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Laravel" ;
definition: "PHP web application framework for building modern, full-stack web applications. Provides features such as thorough dependency injection, expressive database abstraction layer, queues and scheduled jobs, unit and integration testing." .
SCR:025974 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PHP" ;
NIFRID:synonym "Hypertext Preprocessor" ;
definition: "Popular general-purpose scripting language that is especially suited to web development." .
SCR:025975 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ArCH" ;
NIFRID:synonym "ArCH: Artifact Filtering Clonal Hematopoiesis Variant Calling Pipeline",
"Artifact Filtering Clonal Hematopoiesis Variant Calling Pipeline" ;
definition: "Software somatic variant calling pipeline designed to detect low variant allele fraction clonal hematopoiesjsonsis variants." .
SCR:025976 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "InSituType" ;
definition: "Software R package for performing cell typing in SMI and other single cell data." .
SCR:025977 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "STdeconvolve" ;
definition: "Software R package as unsupervised, reference-free approach to infer latent cell-type proportions and transcriptional profiles within multi-cellular spatially-resolved pixels from spatial transcriptomics datasets." .
SCR:025978 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpaGCN" ;
definition: "Software graph convolutional network to integrate gene expression and histology to identify spatial domains and spatially variable genes. SpaGCN integrates information from gene." .
SCR:025979 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "spatialGE" ;
NIFRID:synonym "R package",
"spatialGE in R" ;
definition: "Software R package for spatial analysis of spatial transcriptomics data. Used for visualization and analysis of spatially-resolved gene expression." .
SCR:025980 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Moffitt spatialGE" ;
NIFRID:synonym "Moffitt Cancer Center spatialGE",
"spatialGE" ;
definition: "Web application, a user friendly, point-and-click implementation of spatialGE R package. Contains collection of methods for visualization and spatial statistics analysis of tissue microenvironment and heterogeneity using spatial transcriptomics experiments. Used for user-friendly analysis of spatial transcriptomics data." .
SCR:025981 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rwnull / insitu_probe_generator" ;
definition: "Code generated for use in Python to create DNA probes for use in hybridisation chain reaction, which allows for spatial resolution of mRNA expression with fluorescently tagged hairpins that bind to DNA probes. Used to generate HCR-style Probe Pairs for mRNA visualization." .
SCR:025982 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Elabscience" ;
definition: "Company provides reagents for detecting membrane and intracellular proteins (Flow cytometry antibodies), secreted proteins (ELISA kits), cell glycolipid metabolic intermediates and inorganic salts (Metabolism Assays), and comprehensive assessments of cellular function and health (Cell Apoptosis Assay, Cell cycle Assay, Cell Proliferation /Cytotoxicity/Viability)." .
SCR:025983 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PlasGO" ;
definition: "Software Python library (Linux or Ubuntu only) for predicting cluster level Gene Ontology terms of plasmid encoded proteins." .
SCR:025984 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BbrowserX" ;
NIFRID:synonym "BioTuring BbrowserX" ;
definition: "Analytics platform for large-scale single-cell datasets, equipped with AI-assisted features, and designed for scientists without coding experience." .
SCR:025985 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellKb" ;
NIFRID:synonym "CellKb Immune" ;
definition: "Manually curated cell type markers for fast and accurate cell type annotation in scRNA-seq datasets. Used for cell identification based on marker genes. Provides extensive search capabilities, more data and regular updates compared to other cell type marker databases, in addition to Manual curation of all data and annotations; Multiple marker gene sets for every cell type with information about publication, disease, tissue and experimental conditions, and reliability scores; Marker gene sets from single-cell and bulk RNA-seq experiments; Canonical markers for cell types;Consensus signatures for every cell type in different tissues and disease conditions;Cell type specific protein-protein interaction networks." .
SCR:025986 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2968" ;
rdfs:label "Johns Hopkins Reference Histology Core Facility" ;
NIFRID:synonym "Johns Hopkins Reference Histology" ;
definition: "Provides histology services for Autopsy, Cytology, Renal Pathology and Medical Archives Office within Department of Pathology. In conjunction with Pathology Send Out and Archives divisions, provides histology for clinical trial requests, scientific study or interest involving pathology materials. Services include: Complete routine paraffin histology services, including processing and sectioning; Special stains, including but not limited to carbohydrates, connective tissue, fats, lipids, microorganisms, nuclear elements, pigments, silver techniques; Immunopathology slide preparation techniques;DNA slide preparations; Frozen tissue sections; Oversized tissue processing and sectioning ;Histopathology teaching sets; Customized procedures.Services are provided for both human and animal tissue samples." .
SCR:025987 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2959" ;
rdfs:label "Syracuse University BioInspired Materials Research Core Facility" ;
NIFRID:synonym "BioInspired Materials Research Core",
"Syracuse University BioInspired Materials Research Core" ;
definition: "Provides services involved in fundamental studies of biochemical and physical processes controlling cell functions to development of new technologies for biomedical applications." .
SCR:025988 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Holeboard" ;
definition: "Open-source holeboard for studying rodent behavior. Used in neuroscience for assessing exploration, anxiety, and spatial memory in rodents. The project provides a cost-effective solution, offering detailed instructions on sensor integration, circuit assembly, and Arduino programming for conducting experiments. Design files and other details are available on GitHub." .
SCR:025989 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SAXSpoint_5.0" ;
rdfs:label "Anton Paar | SAXSpoint 5.0" ;
NIFRID:synonym "Anton Paar SAXSpoint 5.0",
"SAXSpoint 5.0",
"Small-Angle X-ray Scattering point 5.0" ;
definition: "Laboratory based X-ray beamline instrument. It performs Small-Angle X-ray Scattering (SAXS) and Wide-Angle X-ray Scattering (WAXS) to analyze the nanostructure of materials without requiring synchrotron facilities. SAXS system resolves nanostructures up to 620 nm. Offers flexible analysis of almost any material under ambient and non-ambient conditions. Number of additional optional features equip SAXSpoint 5.0 for future applications up to the micrometer range (USAXS)." .
SCR:025990 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellBender" ;
definition: "Software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing data. Deep generative model for noise removal in droplet-based single-cell RNA sequencing." .
SCR:025991 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2960" ;
rdfs:label "Douglas Mental Health University Institute Douglas Brain Bank Core Facility" ;
NIFRID:synonym "Douglas Brain Bank",
"Douglas Mental Health University Institute Douglas Brain Bank" ;
definition: "Based at the Douglas Research Centre, the Douglas Brain Bank (DBB) houses a large collection of brains from people with diverse psychiatric disorders, including schizophrenia, major depression, bipolar disorder and substance use disorders, as well as brains from individuals with various neurological and developmental disorders such as amyotrophic lateral sclerosis (ALS), Alzheimers disease and autism spectrum disorder (ASD). In addition, the DBCBB manages a large relational database containing demographic, clinical and developmental histories from donors." .
SCR:025992 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Alfa Cytology" ;
definition: "Biotechnology company focused on pioneering cancer basic research services. Provides early discovery and development of preclinical studies. Offers services range from genetic analysis, tumor biology research, and biomarker validation, to comprehensive cancer model customization services." .
SCR:025993 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2544" ;
rdfs:label "Versiti Blood Research Institute Bioinformatics Core Facility" ;
NIFRID:synonym "Bioinformatics Core" ;
definition: "Core offers bioinformatics consultation, training, and data analysis to help investigators analyze and understand large-scale biological datasets required from different platforms, including next generation sequencing, array-based technologies and mass spectrometry. Provides development and operation of standard and advanced data processing pipelines, covering tasks such as bulk next-generation sequencing analysis (e.g., RNA-Seq, DNA-Seq, methyl-Seq, and ChIP-Seq), single-cell analysis, transcriptome and genome annotation, variant detection and interpretation and metagenomics. Our team members have extensive experience in bioinformatics, biostatistics, genomics, genetics, transcriptomics and translational informatics in human, animal and microbial systems. Our expertise includes big data analysis, statistical analysis, machine learning, neuro network, software development and high-performance computing. Our approach prioritizes scientific collaboration, going beyond mere service provision to leverage our skills and knowledge for the success of your projects. Offers support for grant applications, including key personnel involvement, support letters, and analytical method write-ups." .
SCR:025998 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ingenia_3.0T" ;
rdfs:label "Philips | Ingenia 3.0T MRI Scanner" ;
NIFRID:synonym "Ingenia 3.0T MRI Scanner" ;
definition: "First digital broadband MR system. MRI scanner samples the Magnetic Resonance signal directly in the coil on the patient, and sends it to the reconstructor via fiber-optic cable. Enables imaging with fewer coils and reduce patient set up time." .
SCR:025999 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cirrus_5000" ;
rdfs:label "Zeiss | Cirrus 5000 Optical Coherence Tomography scanner" ;
NIFRID:synonym "Zeiss Cirrus 5000 Optical Coherence Tomography (OCT)" ;
definition: "ZEISS CIRRUS 5000 non-invasive OCT angiography (OCTA) technology, you can confidently visualize retinal microvasculature and monitor change over time." .
SCR:026000 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ZEISS_HFA3" ;
rdfs:label "Zeiss | Humphrey Field Analyzer" ;
definition: "Analyzer allows detection and assessment of changes in glaucoma progression using mixed SITA tests taken on any HFA instrument." .
SCR:026001 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Diaphot_300" ;
rdfs:label "Nikon | Diaphot 300 Inverted Microscope" ;
definition: "Inverted microscope designed for advanced microscopy applications. Allows for observing samples from below, making it ideal for examining living cells and tissue cultures.Includes fluorescence, phase contrast, and differential interference contrast imaging. Can be upgraded to use modern digital camera systems through the side port or one of the two eyepiece tubes." .
SCR:026005 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "R plus" ;
definition: "Software provides direct mapping refence between expanded molecular alphabet and N-nary digits in the absence of high-performance transcoding algorithm at present. Transcoding scheme for DNA data storage based on expanded molecular alphabet." .
SCR:026008 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Swedish Reference Genome Portal" ;
definition: "Portal showcases, aggregates, and facilitates the visualisation of non-human eukaryotic genome assemblies and genome annotations for species studied by Swedish research community, aiming to foster collaboration, highlight researchers’ work, and promote open science and FAIR data sharing." .
SCR:026009 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PKSolver" ;
definition: "Software program for pharmacokinetic and pharmacodynamic data analysis in Microsoft Excel." .
SCR:026010 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HitPredict" ;
definition: "Database of quality assessed protein-protein interactions in nine species." .
SCR:026011 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Q55" ;
rdfs:label "Qsonica | Q55 Sonicator" ;
definition: "Compact ultrasonic processor. This model is effective for standard cell disruption and many other small volume applications. Probes are available in three different sizes." .
SCR:026012 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Covaris | CP02 Automated Dry Pulverizer" ;
NIFRID:synonym "Covaris cryoPREP Dry Pulverizers" ;
definition: "Covaris cryoPREP Dry Pulverizer enables dry, non-contact cryopulverization of tissue samples in a closed system without the risk of carryover or cross-contamination. The cryoPREP system provides a simple and robust tissue processing method for low and high mass inputs. The specially engineered tissueTUBE is used to process samples and extract biomolecules from a diverse set of tissue samples ranging in mass from 15 mg up to 2 g. Both manual and automated versions of the cryoPREP Dry Pulverizers are available to suit your needs." .
SCR:026013 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CT-Expo" ;
definition: "MS Excel application for assessing the radiation doses delivered to patients undergoing CT examinations, based on computational methods that were used to analyze the data collected in the German survey on CT practice in 1999. The program enables the calculation of all dose quantities of practical value, such as axial dose free-in-air, weighted CTDI, dose-length product, effective dose and uterine dose. In contrast to existing programs for CT dose assessment, CT-Expo offers a number of unique features, such as gender-specific dose calculation for all age groups (adults, children, newborns), applicability to all existing scanner models including correction of scanner-specific influences, and the possibility of comparison with the results from the German CT survey on CT practice. Three different application modules offer free and standardized dose calculations as well as a comprehensive benchmarking section including guidance on dose optimization. The program is available as shareware in both German and English version." .
SCR:026015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phynteny" ;
definition: "Software synteny-based tool for annotation of bacteriophage genes. Used to predict function of phage hypothetical proteins using LSTM model trained with Phage Synteny." .
SCR:026016 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phold" ;
definition: "Software tool for phage genome annotation using protein structures. Sensitive annotation tool for bacteriophage genomes and metagenomes using protein structural homology." .
SCR:026017 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pharokka" ;
definition: "Software fast scalable bacteriophage genome annotation tool. Used to annotate bacteriophage genomes easily, rapidly and consistently with standards compliant outputs." .
SCR:026018 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Siemens | SOMATOM Definition AS" ;
NIFRID:synonym "SOMATOM Definition AS" ;
definition: "Single-source multislice CT scanner featuring adaptive scanning technology that adapts to patient and clinical conditions to reduce radiation dose. Medical imaging device that uses X-rays to create 3D pictures of the inside of the body." .
SCR:026019 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyradiomics" ;
definition: "Software Python package for extraction of Radiomics features from 2D and 3D images and binary masks." .
SCR:026020 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2965" ;
rdfs:label "Louisiana State University Health Sciences Center Shreveport Feist Weiller Cancer Center Biorepository Core Facility" ;
NIFRID:synonym "Feist Weiller Cancer Center Biorepository",
"FWCC Biorepository",
"Louisiana State University Health Sciences Center Shreveport Feist Weiller Cancer Center Biorepository" ;
definition: "Provides IRB-approved research projects or clinical trials with human tissue samples or hematological samples. Supports translational research by functioning as primary fresh-frozen tissue acquisition and processing facility for human solid tissue and hematopoietic specimens.FWCC Biorepository works in collaboration with medical and surgical teams at Ochsner LSU Health Shreveport, the Department of Pathology to procure remnant tissue for research purposes, and investigators in need of biospecimens for their research. Provides customized services and equipment to assist investigators in the procurement, analyses, and clinicopathologic correlation of human tissue specimens." .
SCR:026021 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pracma" ;
NIFRID:synonym "pracma: Practical Numerical Math Functions",
"Practical Numerical Math Functions" ;
definition: "Software R package provides functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting." .
SCR:026022 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mendeley Desktop" ;
definition: "Software literature management and referencing tool. Used for managing citations and stored articles." .
SCR:026023 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AtomicJ" ;
definition: "Software application for analysis of force microscopy recordings, including images and force curves. Allows for fast and reliable processing of single force curves and force maps, providing estimation of mechanical properties of sample." .
SCR:026024 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "McPAS-TCR" ;
definition: "Manually curated database of T cell receptor sequences associated with various pathologic conditions including pathogen infections, cancer and autoimmunity and their respective antigens in humans and in mice. Links TCR sequences to their target antigen and/or to the organ with which they are associated and subsequent pathologies. Database can be searched by source organism, disease, tissue, T cell type, antigen sequence, MHC class, etc." .
SCR:026025 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "M Dialysis | 70 Brain Microdialysis Catheter" ;
NIFRID:synonym "70 Brain Microdialysis Catheter",
"70 Microdialysis Catheter" ;
definition: "Sterile single use 70 Microdialysis Catheter is flexible catheter designed for implantation in brain tissue. Intended to enable microdialysis of the extracellular fluid of brain tissue." .
SCR:026026 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Intercellular Junction Organization Quantification" ;
NIFRID:abbrev "IJOQ" ;
definition: "Software Python tool for fully automated analysis of cell-cell junction integrity. Used for fluorescence microscopy analysis." .
SCR:026027 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Junction Analyzer Program" ;
NIFRID:abbrev "JAnaP" ;
definition: "Software Python tool for semi-automated analysis of cell-cell junction phenotype. Used to semi-automate quantification of junctional protein presentation." .
SCR:026028 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SAFARI" ;
NIFRID:synonym "Sensitive Alignments from a RYmer Index" ;
definition: "C++ software program for alignment of ancient DNA to a pangenome reference graph. Used to recover more alignments from ancient DNA samples, which suffer from characteristic substitution patterns due to chemical damage." .
SCR:026029 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SEQUIN:Synaptic Evaluation and QUantification by Imaging Nanostructure" ;
NIFRID:synonym "Synaptic Evaluation and QUantification by Imaging Nanostructure" ;
NIFRID:abbrev "SEQUIN" ;
definition: "Analysis software for identification of synaptic loci from 3D image datasets." .
SCR:026030 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hispanic Community Health Study/Study of Latinos" ;
definition: "Multi-center epidemiologic study in Hispanic/Latino populations to assess role of acculturation in prevalence and development of disease, and to identify factors playing protective or harmful role in health of Hispanics/Latinos." .
SCR:026031 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Visual Studio Code" ;
definition: "Software tool as streamlined code editor with support for development operations like debugging, task running, and version control. Aims to provide just the tools developer needs for quick code-build-debug cycle." .
SCR:026032 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NovoBreak" ;
definition: "Software tool to discover somatic and germline structural variation breakpoints in whole genome sequencing data. Can report accurate breakpoints of Deletions, Duplications, Inversions and Translocations. Designed for Illumina paired-end data. Local assembly for breakpoint detection in cancer genomes." .
SCR:026033 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Infinicyt Software" ;
NIFRID:synonym "Cytognos Infinicyt Software",
"Infinicyt",
"Infinicyt 2.0.6" ;
definition: "Software tool for multiparametric analysis of complex flow cytometry data. Compatible with FCS standard files .Offers features to enhance data integration, interpretation, and visualization. Users can create personalized analysis templates for different types of analyses, with no limit on the number of profiles or diagrams." .
SCR:026034 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_THUNDER" ;
rdfs:label "Leica | THUNDER Imager Tissue microscope" ;
NIFRID:synonym "Leica THUNDER Imager Tissue",
"THUNDER Imager Tissue" ;
definition: "Microscope allows real-time fluorescence imaging of 3D tissue sections typically used in neuroscience and histology research. Acquire rich, detailed images of thick tissues, free from the haze of out-of-focus blur." .
SCR:026035 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Van Andel Institute Brain Bank" ;
definition: "Brain bank that houses donated brains from people with neurodegenerative diseases and neurologically normal age-matched controls. VAI Brain Bank drives insight and discovery by providing scientists the samples needed to investigate the intricate underpinnings of Parkinson’s, dementias, and other neurodegenerative diseases." .
SCR:026036 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ iScan_Coreo" ;
rdfs:label "Roche | Ventana iScan Coreo Slide Scanner" ;
definition: """Slide scanner provides automation for small-to medium-volume labs looking to make the
transition to digital pathology. Scanner offers walk-away scanning of up to 160 slides, and produces high-quality images and offers advanced slide handling.""" .
SCR:026037 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2966" ;
rdfs:label "Douglas Institute Molecular and Cellular Microscopy Platform Core Facility" ;
NIFRID:synonym "Douglas Institute Molecular and Cellular Microscopy Platform",
"Molecular and Cellular Microscopy Platform" ;
definition: "Provides access to various microscopes and services, support and training for fluorescence microscopy experiments and image analysis. Facility offers imaging tasks from basic neuron reconstruction to high-speed, deep-tissue optogenetic experiments in brain slices or live animals." .
SCR:026038 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "q2-predict-dysbiosis" ;
NIFRID:abbrev "Q2PD" ;
definition: "Function-based gut microbiome health index." .
SCR:026039 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EVOS_FL_Auto" ;
rdfs:label "Thermo Fisher | EVOS FL Auto Imaging System" ;
NIFRID:synonym "EVOS FL Auto" ;
definition: "High-performance, fully-automated, inverted, multi-channel fluorescence and transmitted light imaging system controlled by the integrated EVOS FL Auto software." .
SCR:026040 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Metasoft" ;
definition: "Software tool for genome-wide association study analysis, designed to perform range of basic and advanced meta-analytic methods." .
SCR:026041 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "coloc" ;
NIFRID:synonym "coloc v5.2.3" ;
definition: "Software package to perform genetic colocalisation analysis of two potentially related phenotypes, to ask whether they share common genetic causal variant(s) in a given region.Colocalisation Tests of Two Genetic Traits." .
SCR:026042 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SMR" ;
NIFRID:synonym "SMR v1.3.1",
"Summary-data-based Mendelian Randomization" ;
definition: "Software tool to test for pleiotropic association between expression level of gene and complex trait of interest using summary-level data from GWAS and expression quantitative trait loci eQTL studies. Used to prioritize genes underlying GWAS hits for follow up functional studies." .
SCR:026043 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Abmart" ;
NIFRID:synonym "Abmart Shanghai Co.",
"Ltd." ;
definition: "Company specializing in antibody customization and antibody-related services. Develops functional antibodies and antibodies for detection of pharmaceutical targets and monoclonal antibodies with development time from six months to weeks." .
SCR:026044 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker MetaboScape" ;
NIFRID:synonym "MetaboScape" ;
definition: "Software to process non-targeted analyses from Bruker's ESI and MALDI imaging instruments. Supports workflows ranging from basic ID to advanced statistics." .
SCR:026045 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2984" ;
rdfs:label "Columbia University Zuckerman Institute Molecular Tools - Virology, Antibodies and Genetic Access Core Facility" ;
NIFRID:synonym "Antibodies and Genetic Access",
"Antibodies and Genetic Access Core Facility",
"Zuckerman Institute Molecular Tools Virology" ;
definition: "Core provides investigators access to state-of-the-art vector technology for preclinical studies and other basic research applications." .
SCR:026046 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "USC Patient Engagement Studio " ;
NIFRID:synonym "University of South Carolina Engagement Studio" ;
definition: "Platform brings together patients and caregivers, community groups, health system innovators and clinicians, and academic researchers to produce meaningful research and innovation that advances health and research outcomes." .
SCR:026047 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Taiwan Birth Reporting System Database" ;
NIFRID:synonym "TBRS database" ;
definition: "Provides comprehensive national registry that systematically records all live births in Taiwan. It captures essential data on maternal and infant health, including maternal demographics, prenatal care, gestational age, birth weight, delivery method, and congenital anomalies. Established to facilitate public health monitoring and research, the TBRS enables studies on birth trends and outcomes, such as preterm birth and low birth weight, and provides a valuable resource for investigating the impacts of maternal health, environmental factors, and healthcare access on neonatal outcomes.TBRS database is instrumental in informing maternal and child health policies in Taiwan." .
SCR:026048 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Taiwan National Health Insurance Database" ;
NIFRID:synonym "TNHI database" ;
definition: "Provides comprehensive dataset based on National Health Insurance program, which has covered over 99% of Taiwan's population since its launch in 1995. Database includes anonymized data on outpatient and inpatient visits, prescriptions, surgeries, diagnostics, and other medical information, ensuring individual privacy protection. NHI database is extensively utilized in fields such as public health, epidemiology, drug safety, and chronic disease monitoring, providing critical insights for research on major health conditions like cancer and cardiovascular diseases. Researchers use the NHIRD for long-term follow-up studies, treatment outcome analyses, and identifying disease risk factors, making it a valuable resource for healthcare policy and medical decision-making." .
SCR:026049 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Cubebio" ;
definition: """Biomedical company specializing in cancer diagnosis. Research oriented company with competitive networking and marketing skills by forming mutually beneficial partnerships.
Aims to lead the popularization of cancer screening by changing the paradigm of cancer diagnostics that allows cancer screening anywhere, anytime.""" .
SCR:026050 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vanderbilt Cryopreserved Mouse Repository" ;
definition: "Contains unique collection of genetically-modified mice that available for rederivation. All lines have been either generated or modified by Vanderbilt investigators, and are not available in any other repository." .
SCR:026051 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Janvier Labs" ;
definition: "Independent family-owned business established in 1960 by Roger Janvier. Company has become international company that is among the world leaders in the production of laboratory rodents and associated services." .
SCR:026052 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Korea Mouse Phenotyping Center" ;
definition: "Center to develop genetically engineered mice, analyze mouse phenotypes, and establish nationwide infrastructure for mouse research. South Korean government designated KMPC as principal organization for preclinical trials using mice and hamsters." .
SCR:026053 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "CLEA Japan, Inc." ;
definition: "Company to mass-produce Specific Pathogen Free mice and rats, and has been supplying them to many bioscience related companies and research institutes. Total system supplier of experimental animals, their diets and equipment, to support bioscience research and development with vision of health, welfare, and environment for human." .
SCR:026054 a "Organisation",
owl:NamedIndividual ;
rdfs:label "genOway" ;
definition: "Offers preclinical models and solutions to bio-pharmaceutical and academic researchers. Experienced in designing genetically modified models, featuring genetically modified mice, rats, and cell lines, and understanding of biological physiology to provide unmatched preclinical solutions." .
SCR:026055 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Inotiv" ;
definition: "Company supplies critical research models, including rodents, rabbits, and nonhuman primates." .
SCR:026056 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Cyagen Biosciences" ;
definition: "Global provider of genetically modified rodent models and innovative cell and gene therapy solutions for research and development, including: disease model development, AAV discovery, drug efficacy studies, and more." .
SCR:026057 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5360" ;
rdfs:label "University of Northampton Advanced Imaging Core Facility " ;
NIFRID:synonym "Northampton Advanced Imaging Facility (NAIF)",
"University of Northampton Advanced Imaging Facility (NAIF)" ;
definition: "Core provides services for advanced imaging and flow cytometry. Equipment, training and services are available for both internal users and external users from other academic institutions and industry." .
SCR:026058 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Basement Membrane Extract (BME)-free Database" ;
definition: "Database with products that can serve as alternative for basement membrane extracts (BMEs) for in vitro applications. BME-free database is publicly available and is part of 3Rs Research Tools Programme, which is managed and hosted by 3Rs Centre Utrecht." .
SCR:026059 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_RM2235" ;
rdfs:label "Leica | RM2235 Rotary Microtome" ;
NIFRID:synonym "RM2235 Rotary Microtome" ;
definition: "Manual high-performance microtome with mechanical precision specimen feed, designed above all for the manual sectioning of biological specimens embedded in paraffin.Can also be used for cutting harder materials. This product has been discontinued and replaced by HistoCore BIOCUT." .
SCR:026060 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XT-1800i" ;
rdfs:label "Sysmex | XT-1800i Automated Hematology Analyzer" ;
definition: "Automated benchtop hematology analyzer for high quality blood cell analysis. Provides testing for up to 80 samples per hour, enabling rapid turnaround time." .
SCR:026061 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Prelude_SPLC" ;
rdfs:label "Thermo Fisher | Prelude SPLC Sample Preparation and Liquid Chromatography System" ;
NIFRID:synonym "Prelude SPLC Sample Preparation and Liquid Chromatography System" ;
definition: "System to automate most aspects of sample preparation prior to liquid chromatography analysis, particularly for use with mass spectrometry, by integrating sample introduction, cleanup, and chromatographic separation on single platform, significantly reducing manual steps and improving sample throughput." .
SCR:026062 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChromoPainter" ;
definition: "Software tool to discover haplotypes in sequenced data. Colors each individual as hybrid of all other sequences. The \"coancestry matrix\" exposes ancestral associations among individuals. ChromoPainter algorithm uses Hidden Markov Model and outputs range of features, such as expected number of recombination events and sample haplotypes." .
SCR:026063 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clair3" ;
definition: "Software tool as germline small variant caller for long-reads. Symphonizing pileup and full-alignment for high-performance long-read variant calling." .
SCR:026064 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "American Community Survey (2022) - Asian Ethnicities Table" ;
definition: "American Community Survey is annual demographics survey program conducted by the U.S. Census Bureau. American Community Survey releases new data every year through variety of data tables. This table (B02018) specificially provides data on estimated number of individuals who identified as Asian, including ethnicities." .
SCR:026065 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "All of Us Research Program Social Determinants of Health Survey" ;
NIFRID:synonym "Social Determinants of Health Survey" ;
definition: "National research resource within All of Us Research Program which asks about social determinants of health, including a participant’s neighborhood, social life, stress, and feelings about everyday life." .
SCR:026066 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "All of Us Research Program Basics Survey" ;
NIFRID:synonym "Basics Survey" ;
definition: "National research resource within All of Us Research Program which is the core survey and asks basic demographic questions, including questions about a participant’s work and home." .
SCR:026067 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "All of Us Research Program Lifestyle Survey" ;
NIFRID:synonym "Lifestyle Survey" ;
definition: "National research resource within All of Us Research Program which asks about participant’s use of tobacco, alcohol, and recreational drugs." .
SCR:026068 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Life_888" ;
rdfs:label "Andor | iXon Life 888 EMCCD" ;
NIFRID:synonym "iXon Life 888 EMCCD" ;
definition: "iXon Life Electron Multiplying CCD platform for fluorescence microscopy applications and is engineered to deliver single photon sensitivity." .
SCR:026069 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microfluidic trapping chip for culture and assay of cell clusters and objects" ;
definition: "Microfluidic cartridge for automatically hydrodynamically loading objects (e.g., cell clusters) into traps in parallel trapping channels with one object per trap. This improves loading of cell clusters compared to well-based systems." .
SCR:026070 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Device and system for producing mature adipocytes" ;
definition: "Device and system for 3-dimensional adipocyte expansion to produce mature adipocytes and synthetic adipose tissue with cellular properties of mature adult organisms, including cell size and cytoarchitecture, in vitro drug screening and/or toxicity assays, disease modeling, and therapeutic applications." .
SCR:026071 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cartridge-based system for long term culture of cell clusters" ;
definition: "Microfluidic systems including housing configured to receive cartridge, housing including channels for loading one or more biological cells within wells of the cartridge. Three-dimensional scaffolds, devices, and systems comprising such scaffolds that mimic the in vivo structure, physical properties, and protein composition of extracellular matrix surrounding pancreatic islet cells and adipocytes, with use for, e.g., in vitro drug screening and/or toxicity assays, disease modeling, and therapeutic applications. The cartridge including a plurality of wells for receiving one or more biological cells. The microfluidic systems include a structure with channels for introducing a medium into the housing and through channels the cartridge." .
SCR:026072 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CRISPR-Cas9 conjugation platform for engineering designer beta cells" ;
definition: "This technology relies on newly described chemical modifications that allow site-specific and multiple-site conjugation of a wide assortment of molecules on both the termini and internal sites of Cas9, creating a platform for endowing Cas9 with diverse functions. Using this platform, Cas9 can be modified to more precisely incorporate exogenously supplied single-stranded oligonucleotide donor (ssODN) at the DNA break site. We demonstrate that the multiple-site conjugation of ssODN to Cas9 significantly increases the efficiency of precision genome editing, and such a platform is compatible with ssODNs of diverse lengths." .
SCR:026073 a NLX:63400,
owl:NamedIndividual ;
definition: "Software package to facilitate microbiome exploration and ensuring nice plotting." .
SCR:026074 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TEMP2" ;
definition: "Software tool for detecting transposon insertions using short-read whole-genome sequencing data. Used to detect germline transposon insertions, estimate number of uninherited/somatic transposon insertions by removing artificial insertion introduced by chimeric reads." .
SCR:026075 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "All of Us Research Program Data and Statistics Dissemination Policy " ;
definition: "Guidelines for accessing and sharing data collected by the All of Us Research Program. It aims to ensure responsible data use while promoting transparency and collaboration in research to advance precision medicine." .
SCR:026076 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2974" ;
rdfs:label "Dartmouth Geisel School of Medicine Biological Mass Spectrometry and Proteomics Shared Resource Core Facility" ;
NIFRID:synonym "Biological Mass Spectrometry and Proteomics",
"Geisel School of Medicine at Dartmouth Biological Mass Spectrometry and Proteomics" ;
definition: "Core offers quantitative and qualitative proteomics services using LC-MS/MS technologies. Servies include sample preparation from harvested cell pellets, elutions post-enrichment or purification, or gel bands through data acquisition, quantification, and statistical analysis." .
SCR:026077 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "M6Allele" ;
definition: "Software toolkit for detection of allele-specific RNA N6-methyladenosine modifications." .
SCR:026080 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCKAN Explorer" ;
definition: "Web application as JavaScript-based intuitive search interface to explore the SPARC Connectivity Knowledgebase of the Autonomic Nervous System." .
SCR:026082 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RAWGraphs" ;
definition: "Web-based open-source data visualization software made in JavaScript. Aims at providing missing link between spreadsheet applications (e.g. Microsoft Excel, Apple Numbers, OpenRefine) and vector graphics editors (e.g. Adobe Illustrator, Inkscape, Figma)." .
SCR:026086 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GraphViz" ;
NIFRID:synonym "Graph Visualization Tools" ;
definition: "Software package of open-source graph visualization tools. Provides also libraries for software applications to use the tools. Provides a way of representing structural information as diagrams of abstract graphs and networks." .
SCR:026087 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Blazegraph" ;
NIFRID:synonym "Blazegraph DB" ;
definition: "Graph database supporting Blueprints and RDF/SPARQL APIs. Supports up to 50 Billion edges on single machine. It is in production use for Fortune 500 customers such as EMC, Autodesk, and many others. It supports key Precision Medicine applications and has wide-spread usage for life science applications. Used to support Cyber analytics in commercial and government applications." .
SCR:026088 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCKAN" ;
NIFRID:synonym "SPARC Connectivity Knowledgebase of the Autonomic Nervous System",
"SPARC Connectivity Knowledgebase of the Autonomic Nervous System (SCKAN)" ;
definition: "Semantic store of detailed, formal knowledge about ANS connectivity between the central nervous system and end organs. As key component of NIH SPARC program, SCKAN enables integration, discovery, and querying of ANS connectivity across multiple scales." .
SCR:026090 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ESTIMATE" ;
definition: "Software application provides researchers with scores for tumor purity, level of stromal cells present, and infiltration level of immune cells in tumor tissues based on expression data." .
SCR:026091 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kardia" ;
definition: "Software Matlab based toolbox for heart rate analysis." .
SCR:026092 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rhinotypeR" ;
definition: "Software R package to automate comparison of sequence data against prototype strains, streamlining genotype assignment process." .
SCR:026093 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WAPIAW3" ;
definition: "Source and cluster submission code for transdiagnostic patient-control classification in 17 ICD-10 diagnostic groups in the UK BioBank dataset." .
SCR:026094 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Shenzhen Huixin Biomedical Technology | EXODUS" ;
NIFRID:synonym "Automatic exosome isolation system",
"exosome isolation system" ;
definition: "Automatic, label-free exosome isolation system. Used to isolate high-quality, intact exosomes with excellent yield and purity from variety of bio-fluids and sample volumes." .
SCR:026096 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Nano100" ;
rdfs:label "ALLSHENG | Nano100 Micro-specrophotometer" ;
NIFRID:synonym "Nano100 Micro-specrophotometer",
"Nano-100 micro-spectrophotometer" ;
definition: "Nano-100 microspectrophotometer to measure concentration of nucleic acid, protein and cell solution. 0.5 to 2μl of sample volume is required for each measurement. No cuvette is required. At the end of measurement, sample could be either wiped off directly or recovered with pipettor." .
SCR:026098 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "CloudSeq Biotech Inc" ;
NIFRID:synonym "Shanghai Cloud Sequence Biotechnology Co Ltd" ;
definition: "Company is leader in the field of epigenetic modification and transcriptomics in China. Provides innovative enterprise to carry out RNA modification, transcriptome and eccDNA research in China, providing various RNA modifications, various RNA molecules (mRNA and non-coding RNA), various sequencing technologies (IP, single base) and eccDNA systematic solutions." .
SCR:026100 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Heracell_150i" ;
rdfs:label "Thermo Fisher | Heracell 150i CO2 Incubator" ;
definition: "Thermo Scientific Heracell 150i CO2 Incubator provides in-vitro environment for cultivating cell and tissue cultures. Allows simulation of special physiological conditions for these cultures due to exact control of temperature, CO2 and humidity." .
SCR:026101 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cam-Su Genomic Resource Center" ;
NIFRID:synonym "CAM-SU Genomic Resource Center of Soochow University" ;
definition: "CAM-SU Genomic Resource Center of Soochow University is National Center for International Research, shared UK-Chinese mutant ES Cell Repository for Asian-Pacific research community, and platform for mouse model production and phenotyping and mammalian genome function deciphering. Constructs human-specific gene mutations in human embryonic stem cells via CRISPR system for disease modeling, functional annotation, drug discovery, and more. CAM-SU Genomic Research Center also conducts research in stem cells and organoids to accelerate bioresource development." .
SCR:026102 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bees" ;
definition: "Software R code for analysis of social evolution in bees. Social complexity trait database and code. R scripts for analysis of bees evolution." .
SCR:026103 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ClairS" ;
definition: "Software tool as somatic variant caller designed for paired samples and primarily ONT long-read. Method for long-read somatic small variant calling." .
SCR:026104 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "phenoptr" ;
definition: "Software R package for working with inForm data. Contains functions that make it easier to read and analyze data tables and images created by Akoya Biosciences' inForm software." .
SCR:026105 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cell-Dyn_Emerald" ;
rdfs:label "Abbott | Cell-Dyn Emerald analyzer" ;
NIFRID:synonym "Cell-Dyn Emerald analyzer" ;
definition: "System is 3-part compact automated hematology analyzer designed for in vitro diagnostic to use in low volume clinical laboratories. Provides measurable results for comprehensive panel of hematological parameters, electronic impedance, absorption spectrophotometry, electronic valves, cyanide-free lyse reagent, LCD color touch screen and USB ports." .
SCR:026106 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ E-BOX_CX5_TS" ;
rdfs:label "Vilber | E-BOX CX5 TS gel imager" ;
NIFRID:synonym "E-BOX CX5 TS imager" ;
definition: "Stand alone gel imager for gel documentation. Provides high-resolution images of DNA, RNA or protein gels. Images can either be printed out directly or saved in internal storage. Transfer of data to PC is possible." .
SCR:026107 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoGVP" ;
NIFRID:synonym "Automated Germline Variant Pathogenicity" ;
definition: "Software tool integrates ClinVar variant annotation with modified InterVar classification approach, based on American College of Medical Genetics-Association for Molecular Pathology guidelines, to output germline variant classification. Since AutoGVP input only requires VCF file, it can facilitate large-scale, clinically focused classification of germline sequence variants." .
SCR:026108 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoPVS" ;
NIFRID:synonym "Automatic PVS1 interpretation",
"AutoPVS1" ;
definition: "Software automatic classification tool for PVS1 interpretation of null variants." .
SCR:026109 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Integrated Proteome Resources" ;
NIFRID:abbrev "iProX" ;
definition: "Integrated proteome resources center in China to accelerate data sharing in proteomics. Composed of data submission system and proteome database. Submission system is established under the guidance of data-sharing policy made by ProteomeXchange consortium. Registered users can submit their proteomic datasets to iProX in public or private modes. Once associated manuscript has been published, dataset becomes automatically public." .
SCR:026110 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mustache" ;
NIFRID:synonym "Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation" ;
definition: "Software tool for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps in high resolutions (10kbp all the way to 500bp and even more). Used to detect chromatin loops caused by interaction of DNA segments with variable size." .
SCR:026111 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "distiller-nf" ;
definition: "Software modular Hi-C mapping pipeline for reproducible data analysis. Nextflow-based modular Hi-C mapping pipeline." .
SCR:026112 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UpSetR" ;
definition: "Software R package for visualization of intersecting sets and their properties." .
SCR:026113 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRROC" ;
NIFRID:synonym "Precision-Recall and Receiver Operating Characteristic" ;
definition: "Software package for computing and visualizing precision-recall and receiver operating characteristic curves in R for weighted and unweighted data." .
SCR:026114 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GGally" ;
definition: "Software R package that extends ggplot2 by adding several functions to reduce complexity of combining geoms with transformed data. Some of these functions include pairwise plot matrix, scatterplot plot matrix, parallel coordinates plot, survival plot, and several functions to plot networks." .
SCR:026115 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dendroextras" ;
definition: "Software R package providing additional functions to cut, label and colour dendrogram clusters." .
SCR:026116 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dendextend" ;
definition: "Software package extending R core dendrogram functions." .
SCR:026117 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "data.table" ;
definition: "Software R data.table package extends data.frame. Provides high-performance version of base R's data.frame with syntax and feature enhancements for ease of use, convenience and programming speed." .
SCR:026118 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cooltools" ;
definition: "Software suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Provides suite of computational tools with paired python API and command line access, which facilitates workflows either on high-performance computing clusters or via custom analysis notebooks. As part of the Open2C ecosystem, cooltools also provides detailed introductions to key concepts in Hi-C-data analysis with interactive notebook documentation." .
SCR:026119 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepMEI" ;
definition: "Software tool to detect mobile element insertion in human short read sequencing data." .
SCR:026120 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HVSeeker" ;
definition: "Software tool for distinguishing between bacterial and phage sequences. Consists of two separate models: one analyzing DNA sequences and the other focusing on proteins." .
SCR:026121 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "statista" ;
definition: "Platform for data and statistics. Website provides data-driven services, collection of statistics, reports, and insights on over 80,000 topics." .
SCR:026122 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PeptideMiner" ;
definition: "Software pipeline that uses profile hidden Markov models of neuropeptide families to search query datasets for neuropeptide homologues." .
SCR:026123 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VirtualDub" ;
definition: "Open-source software for video capture and video processing for Microsoft Windows. Designed to process linear video streams, including filtering and recompression. It uses AVI container format to store captured video. Video capture/processing utility for 32-bit and 64-bit Windows platforms. Used for processing AVI files, although it can read (not write) MPEG-1 and also handle sets of BMP images." .
SCR:026124 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Western Blot Quantification Toolkit in MATLAB" ;
definition: "Software package to quantify intensity of bands on western blot." .
SCR:026125 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MATLAB Programs for Flow Cytometry" ;
definition: "Software package contains suite of functions that enables analysis of flow cytometry data." .
SCR:026126 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2976" ;
rdfs:label "McGill University Goodman Cancer Institute Histology Innovation Platform Core Facility" ;
NIFRID:synonym "Goodman Cancer Institute-Histology Innovation Platform",
"McGill University Goodman Cancer Institute-Histology Innovation Platform" ;
definition: "Core provides expertise, cutting edge technology, and efficient workflows in histological processing, analysis and interpretation." .
SCR:026127 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SynergyFinder web application" ;
definition: "Stand-alone web-application for interactive analysis and visualization of multi-drug (2 or more drugs) multi-dose combination response data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025." .
SCR:026128 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Alfa Cytology" ;
definition: "Biotechnology company specialized in innovative solutions for cancer research. Provides Cancer Modeling Services to accelerate cancer therapeutics discovery and development. Contract research organization that specializes in early discovery and preclinical studies and provides cancer diagnostic biomarker development services." .
SCR:026130 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microm | HM440E sliding microtome" ;
NIFRID:synonym "Microm HM 440 E Microtome" ;
definition: "Ergonomically designed sliding microtome with electronic control systems and high-precision mechanics to achieve optimal section quality and reproducibility of even the most difficult-to-cut specimens. It can accommodate specimen sizes up to 80 x 60 mm, and can cut sections ranging from 1 to 100 microns. Employs automatic fine/trim-feed system to protect knife and specimen by enabling specimen retraction during return travel. Enables continuous upward and downward travel of specimen through motorized coarse feed system. This system employs three different speed settings and multi-purpose button control, allowing fast adjustment of specimen and knife edge distance." .
SCR:026131 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biodepot Launcher" ;
definition: "Software desktop application that facilitates installation, management and deployment of containerized bioinformatics workflows. Provides interactive interface to launch containerized analytical workflows that can be used to process biomedical data." .
SCR:026132 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SAMHSA 2023 NSDUH Annual National Report on Drug Use and Health" ;
NIFRID:synonym "2023 NSDUH Annual National Report on Drug Use and Health" ;
definition: "Substance Abuse and Mental Health Services portal provides information about 2023 National Survey on Drug Use and Health. This report highlights 2023 estimates of substance use, mental health, and treatment in the United States. These national indicators are measured among people aged 12 or older in the civilian, noninstitutionalized population. Estimates are presented by age group and by race/ethnicity for selected measures. Along with the full report, which includes both figures and text descriptions, set of slides is available which includes just the figures from the report." .
SCR:026134 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CB-dock2" ;
definition: "Web server for protein-ligand blind docking, integrating cavity detection, docking and homologous template fitting. Given the three-dimensional structure of protein and ligand, can predict their binding sites and affinity for computer-aided drug discovery." .
SCR:026135 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spatial DB" ;
definition: "Database for spatially resolved transcriptomes. Provides curated spatially resolved transcriptomic data from published papers, aiming to provide comprehensive and accurate resource of spatial gene expression profiles in tissues. Allows users to browse spatial gene expression profile and compare spatial gene expression profile of any two datasets generated by same or different techniques side by side." .
SCR:026136 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DropletUtils" ;
definition: "Software R package provides number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix." .
SCR:026137 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | Bravo Automated Liquid Handling Platform" ;
NIFRID:synonym "Agilent Bravo Automated Liquid Handling Platform" ;
definition: """Robotic liquid handling system that automates sample preparation for screening applications such as compound management, cell-based assays, and genomic assays.
Compact liquid handler can be placed on small bench and fits in flow hood. With more than 60 accessories ranging from thermal cycler to shaker, the system can be tailored to automate most sample preparation protocols. VWorks control software allows users to create and run flexible liquid handling protocols.""" .
SCR:026138 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2985" ;
rdfs:label "Paris Brain Institute Data Analysis Core Facility" ;
NIFRID:synonym "APHP",
"CNRS",
"Data Analysis Core Facility",
"France; DAC;",
"Hôpital de la Pitié Salpêtrière",
"Inserm",
"Institut du Cerveau - Paris Brain Institute - ICM",
"Paris",
"Paris Brain Institute",
"Sorbonne Université",
"Sorbonne Université Paris Brain Institute Data Analysis Core Facility; Data Analysis Core Facility Paris Brain Institute; Data Analysis Core" ;
NIFRID:abbrev "DAC" ;
definition: "Core provides structural support and expertise in processing, integrating, analyzing and managing neuroscience data." .
SCR:026139 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "ChemPartner" ;
definition: "Life sciences contract research organization. Provides integrated life science services for drug discovery with expertise in chemistry, biology and pharmacology, DMPK, and exploratory toxicology as well as biologics discovery." .
SCR:026140 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Portable-CELLxGENE" ;
definition: "Software executable version of CELLxGENE and CELLxGENE-gateway to allow single-cell transcriptomic data to be annotated using without using the command line or installing extra software." .
SCR:026143 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SeuratExtend" ;
definition: "Software R package that streamlines single-cell RNA-seq analysis by integrating essential tools and databases with the Seurat framework. Provides comprehensive functionality for functional enrichment, trajectory inference, gene regulatory network reconstruction, and enhanced visualization." .
SCR:026144 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Tissue-Tek_VIP_6_AI" ;
rdfs:label "Sakura | Tissue-Tek VIP 6 AI Vacuum Infiltration Processor" ;
NIFRID:synonym "Tissue-Tek VIP 6 AI Vacuum Infiltration Processor" ;
definition: "Tissue processor with automated onboard preparation of mixed solutions, automatic in-process reagent exchange, and Tissue-Tek iSupport remote monitoring." .
SCR:026145 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Ultimate 3000 RSLCNano UPLC system" ;
NIFRID:synonym "Thermo Scientific UltiMate 3000 RSLCnano",
"Ultimate 3000 RSLCNano UPLC system" ;
definition: "System provides ProFlow technology for nano-flow applications and is designed to provide high resolution, speed, and sensitivity for low-flow LC or LCMS applications, such as proteomics and metabolomics. It has wide flow-pressure footprint that supports nano, capillary, and micro applications." .
SCR:026146 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HM_355S" ;
rdfs:label "Thermo Fisher | Epredia HM 355S Automatic Microtome" ;
NIFRID:synonym "HM 355S Automatic Microtome",
"Rotary Microtome HM 355S" ;
definition: "Heavy duty, motorized microtome that can section large specimens with high quality. It's designed to be ergonomic and comfortable to use. Used for precise sectioning of hard and paraffin specimens in research, clinical, and industrial labs." .
SCR:026147 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Shimadzu" ;
definition: "Leading-edge science and technologies in analytical and measuring instruments including chromatographs and mass spectrometry. Manufactures precision instruments, measuring instruments and medical equipment." .
SCR:026148 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LUMC Mutalyzer 3" ;
NIFRID:synonym "Mutalyzer 3" ;
definition: "Software suite is designed to be of help when working with Human Genome Variation Society sequence variant nomenclature descriptions." .
SCR:026149 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Illustrator for Biological Sequences " ;
NIFRID:abbrev "IBS" ;
definition: "Software package called illustrator of biological sequences. Can be used for representing organization of either protein or nucleotide sequences. Multiple options are provided, and biological sequences can be manipulated, recolored or rescaled in user-defined mode. Final representational artwork can be directly exported into publication-quality figure. Used as illustrator for presentation and visualization of biological sequences. Standalone package was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available" .
SCR:026150 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "ScienCell Research Laboratories" ;
definition: "Biotechnology company to research and develop cell products for experimental use. Provides normal human and animal cells, cell culture media and reagents, gene analysis tools, cell-derived molecular biology products, cell-based assay kits, and stem cell products for research community. Focused on studying and developing cell therapeutic strategies to significantly improve quality of life for patients with degenerative diseases." .
SCR:026151 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Galaxy Ecology tools" ;
definition: "Software Galaxy tools dedicated to ecology data management and analysis, available through Galaxy Tool Shed." .
SCR:026152 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AlphaEaseFC" ;
NIFRID:synonym "AlphaEaseFC 4.0" ;
definition: "Software used for quantitative Western blot imaging and analysis. Designed to look at multiple proteins simultaneously on single assay. This software is sensitive enough to distinguish co-migrating proteins, such as phosphorylated and unphosphorylated." .
SCR:026153 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker NanoScope Analysis" ;
NIFRID:synonym "NanoScope Analysis" ;
definition: "Software application used with Bruker's atomic force microscopes and scanning probe microscopes. Software package for analyzing SPM data including images, ramp data, HSDC data, collected using Bruker SPMs." .
SCR:026154 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GEPIA2" ;
rdfs:label "Gene Expression Profiling Interactive Analysis 2" ;
definition: "Enhanced web server for large-scale expression profiling and interactive analysis. GEPIA2 is updated and enhanced version of GEPIA, offering more functionalities, higher resolution data analysis, and additional features like ability to analyze specific cancer subtypes, quantify gene signatures based on single-cell sequencing studies, and allow users to upload their own RNA-seq data for comparison with the TCGA and GTEx datasets; essentially providing more comprehensive and advanced platform for gene expression analysis compared to the original GEPIA version." .
SCR:026155 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CancerSEA" ;
NIFRID:synonym "Cancer Single-cell State Atlas" ;
definition: "Database that aims to comprehensively explore distinct functional states of cancer cells at the single-cell level. Provides functional state-associated PCG/lncRNA repertoires across all cancers, in specific cancers, and in individual cancer single-cell datasets. Provides interface for comprehensively searching, browsing, visualizing and downloading functional state activity profiles of cancer single cells and corresponding PCGs/lncRNAs expression profiles." .
SCR:026156 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpatialData" ;
definition: "Software framework for processing spatial omics data. Data framework that comprises FAIR storage format and collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets." .
SCR:026157 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Squidpy" ;
NIFRID:synonym "Spatial Single Cell Analysis in Python" ;
definition: "Software tool for analysis and visualization of spatial molecular data. Scalable framework for spatial omics analysis. Builds on top of scanpy and anndata, from which it inherits modularity and scalability. Provides analysis tools that leverages spatial coordinates of data, as well as tissue images." .
SCR:026158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "10x Genomics Xenium Onboard Analysis" ;
NIFRID:synonym "Xenium Onboard Analysis" ;
definition: "Software pipeline that simultaneously collects and processes Xenium In Situ Gene Expression data. Used for analyzing and visualizing in situ gene expression data produced by the Xenium Analyzer." .
SCR:026159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Keras" ;
definition: "Deep learning framework, with support for JAX, TensorFlow, and PyTorch. Used to build and train models for computer vision, natural language processing, audio processing, timeseries forecasting, recommender systems. Offers consistent and simple APIs, minimizes number of user actions required for common use cases, and provides clear and actionable error messages. Keras also gives the highest priority to crafting documentation and developer guides." .
SCR:026160 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ENVI" ;
definition: "Deep learnining based variational inference method to integrate scRNA-seq with spatial transcriptomics data. ENVI learns to reconstruct spatial onto for dissociated scRNA-seq data and impute unimagd genes onto spatial data." .
SCR:026161 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sherlock Computing Cluster" ;
definition: "Shared high-performance computing cluster. All research teams on Sherlock have access to a base set of managed computing resources, GPU-based servers, and a multi-petabyte, high-performance parallel file system for short-term storage. Stanford Faculty can supplement these shared nodes by purchasing additional servers. By investing in the cluster, PI groups not only receive exclusive access to the nodes they purchase, but also get access to all the other owner compute nodes when they're not in use, thus giving them access to the whole breadth of Sherlock resources." .
SCR:026162 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TRUST4" ;
definition: "Software tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from fluid and solid tissues, including tumors. Performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 and reports consensus contigs of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to identify the corresponding gene and CDR3 details. TRUST4 supports both single-end and paired-end bulk or single-cell sequencing data with any read length." .
SCR:026163 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Destiny" ;
definition: "Software R package for single cell and other data analysis using diffusion maps. Package for diffusion maps, with additional features for large-scale and single cell data." .
SCR:026165 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VarSome " ;
definition: "Web service to search for variants, CNVs, genes, transcripts, publications, diseases. Annotation tool and search engine for human genomic variants, and platform enabling sharing of knowledge on specific variants. Enables users to look up variants in their genomic context, collects data from multiple databases in central location and most importantly, aims to enable community to freely and easily share knowledge on human variation." .
SCR:026167 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPATA2" ;
definition: "Software package provides framework of functions and shiny-applications to work with spatial expression data. Used for spatial transcriptomics analysis." .
SCR:026168 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Luxembourg Centre for Systems Biomedicine" ;
NIFRID:abbrev "LCSB" ;
definition: "Research institute in Esch-sur-Alzette, Luxembourg to study brain and its diseases. Collaboration between biologists, medical and computer scientists, physicists, engineers as well as mathematicians offers new insights into complex biological mechanisms and disease processes, with the aim of developing new tools for diagnostics, prevention, and therapy. LCSB has established strategic partnerships with scientific partners worldwide and with all major biomedical research units in Luxembourg. Carries out collaborative projects with hospitals and research-oriented companies, accelerating translation of fundamental research results into clinical applications." .
SCR:026169 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2981" ;
rdfs:label "University of Texas Medical Branch at Galveston Next Generation Sequencing Core Facility" ;
NIFRID:synonym "The University of Texas Medical Branch at Galveston UTMB NGS core",
"UTMB NGS core" ;
definition: "Core offers Next Generation Sequencing services using Element Biosciences AVITI short read sequencer, PacBio Revio and Oxford Nanopore Promethion/GridIon long read sequencers along with 10X Genomics X, 10X Genomics Visium CytAssist, and 10X Xenium Analyzer single cell/spatial technologies." .
SCR:026170 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2982" ;
rdfs:label "National Cancer Institute Advanced Microscopy Applications Unit Core Facility" ;
NIFRID:synonym "Advanced Microscopy Applications Unit (ADMiRA)",
"Instituto Nacional de Cancerolog�a Advanced Microscopy Applications Unit (ADMiRA)",
"RAI",
"UNAM" ;
NIFRID:abbrev "ADMiRA" ;
definition: "Core answers research questions in any scientific, medical or industrial discipline through capture, processing, image analysis, training and sample preparation services for microscopy. Provides technical and scientific support in advanced microscopy and image processing and analysis." .
SCR:026171 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TransHLA" ;
definition: "Software tool to discern whether peptide will be recognized by HLA as epitope. Capable of directly identifying peptides as epitopes without the need for inputting HLA alleles. Hybrid transformer model for peptide-HLA epitope detection." .
SCR:026172 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MiniAmp" ;
rdfs:label "Thermo Fisher: Applied Biosystems | MiniAmp Thermal Cycler" ;
NIFRID:synonym "MiniAmp Thermal Cycler" ;
definition: """Thermal Cycler is benchtop PCR machine which features 5-inch color touchscreen for easy control and is also accessible through Thermo Fisher Connect , giving you the freedom to design and securely upload your methods from any mobile device or desktop computer. Designed for amplification of nucleic acids using Polymerase Chain Reaction process. User interface includes touchscreen with graphical display that shows time, status, and temperature for each run. Touchscreen keypad allows to enter information into fields on
display screen.""" .
SCR:026173 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mammal Diversity Database" ;
definition: "Updatable online database of mammal taxonomic and biodiversity information hosted by American Society of Mammalogists. Provides information on species-level and higher taxonomic changes, thereby promoting more rigorous study of mammalian biodiversity worldwide. The initial objective has been to aggregate, curate, and compile, new citations on species descriptions and taxonomic revisions into regular releases that are downloadable in comma-delimited format. Downstream goals include expanded hosting of ecological, trait, and taxonomic data." .
SCR:026174 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MorphPod" ;
definition: "Deep learning phenotyping of Arabidopsis fruit morphology. Deep learning model weights and inference code to detect Arabidopsis thaliana siliques in scans of stem material. Phenotyping code to extract length, diameter area and volume metrics of siliques from model outputs." .
SCR:026175 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gimp_image_annotator" ;
definition: "Software lightweight GIMP plug-in to alllow for computer vision-assisted image annotation using GIMP selection toolbox." .
SCR:026176 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2992" ;
rdfs:label "University of South Carolina X-Ray Photoelectron Spectroscopy Core Facility" ;
NIFRID:abbrev "XPS" ;
definition: "Facility provides quantitative compositional information from top atomic layers of sample surface for the elements lithium to uranium. Core can also obtain information regarding chemical states of any elements present. This facility houses Kratos AXIS Supera+ Spectrometer Unit." .
SCR:026177 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2991" ;
rdfs:label "University of South Carolina Mouse Experimentation and Germ-Free Core Facility" ;
NIFRID:synonym "MEGF Core facility",
"Mouse Experimentation and Germ-Free Core Facility (MEF/GFC)",
"Mouse Experimentation and Gnotobiotic Core",
"University of South Carolina Mouse Experimentation and Germ-Free Facility" ;
NIFRID:abbrev "MEGF" ;
definition: "Provides support to experiments that use mouse models to elucidate mechanisms of normal physiology and disease processes, and to develop and test novel agents and therapies to treat diseases. Provides centralized facililty for breeding, genotyping, maintaining colonies, conducting animal experiments, collecting tissues, analyzing experimental results, and training personnel in proper procedures for conducting animal experiments. Core also hosts germ-free mouse facility that works with PI's to produce, distribute, and conduct experiments in germ-free and gnotobiotic mouse models. MEF/GCF offers expertise with genetic, induced, or orthotopic models of disease and coordinates with other USC Cores with respect tissue processing and preparation for various types of analyses." .
SCR:026178 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2990" ;
rdfs:label "University of South Carolina Functional Genomics Core Facility" ;
NIFRID:synonym "University of South Carolina Functional Genomics Core" ;
NIFRID:abbrev "FGC" ;
definition: """Core offers resources and solutions for conducting genomics, transcriptomics, epigenomics and functional genomics projects. We work with researchers to determine project goals and design custom solutions. We assist at all stages of the project, from support in grant development to generation of publication-quality data. Services include Consultations,
Bioinformatics, Nucleic Acids purification, quantification and QC DNA Sequencing (SANGER and NGS), Library Constructions for NGS applications,Microarray Hybridization, Real Time PCR, Custom epigenomics applications, Lentiviral vectors and lentiviruses construction and production, CRIPR-CAS9sgRNAs and RNAi/shRNAs knockdown of individual genes and functional screening of sgRNA and shRNA libraries for target identification.""" .
SCR:026179 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2989" ;
rdfs:label "University of South Carolina Electron Microscopy Core Facility" ;
NIFRID:synonym "University of South Carolina Electron Microscopy Center" ;
NIFRID:abbrev "EMC" ;
definition: "Electron Microscopy Center at USC is core facility providing all levels of technical support and consultation in area of light microscopy, electron microscopy, and elemental analysis. Provides microscopy and specimen preparation services for biological and materials science research. Offers training and access to all microscopes and ancillary equipmen." .
SCR:026180 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CODARFE" ;
NIFRID:synonym "COmpositinal Data Analysis with Recursive Feature Elimination" ;
definition: "Software tool for selecting predictors such as bacteria for any continuous environmental variable such as pH, illness measurements, diseases index, etc. Sparse compositional microbiome-predictors selection and prediction of continuous environmental factors. Used for unlocking prediction of continuous environmental variables based on microbiome." .
SCR:026181 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "de novo tools" ;
definition: "Software suite of scripts to detect and analyse de novo variants from multi-sample vcf." .
SCR:026182 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SaLSa" ;
definition: "Software MATLAB package for analyzing and categorizing behaviors using pose estimation data. Integrates semi-automatic labeling with machine learning, specifically Long Short-Term Memory neural networks, to classify behavioral \"syllables” (distinct, repeatable behaviors). Combinatory approach of semi-automatic labeling and long short-term memory to classify behavioral syllables." .
SCR:026183 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2993" ;
rdfs:label "University of Louisville School of Medicine Molecular Modeling Core Facility" ;
definition: "Core offers services including molecular modeling of proteins and nucleic acids, virtual drug screening, computational biophysics." .
SCR:026184 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GALA" ;
NIFRID:synonym "GAp-free Long-read Assembler" ;
definition: "Softawer framework for de novo chromosome-by-chromosome assembly with long reads. Long-reads gap-free chromosome-scale assembler." .
SCR:026185 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "optmatch" ;
definition: "Software package for optimal matching in R. Distance based bipartite matching using minimum cost flow, oriented to matching of treatment and control groups in observational studies. Routines are provided to generate distances from generalised linear models (propensity score matching), formulas giving variables on which to limit matched distances, stratified or exact matching directives, or calipers, alone or in combination." .
SCR:026186 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BraiAn" ;
definition: "Software Python library for navigation, visualisation, and analysis of whole-brain quantification data. Integrated suite for multi-marker automated segmentation, whole-brain statistical analysis, and data visualisation. Used for quantitative multi-marker image analysis of whole-brain registered datasets." .
SCR:026187 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microscopy_lif_Adjust_MATLAB" ;
definition: "Software tool for batched microscopy image contrast adjustment and pseudocoloring in Matlab." .
SCR:026188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microscopy_lif_Channel_Quant_MATLAB" ;
definition: "Software tool for quantification of positive channel area in Matlab." .
SCR:026189 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UK Biobank Pharma Proteomics Project" ;
NIFRID:synonym "Pharma Proteomics Project" ;
NIFRID:abbrev "UKB-PPP" ;
definition: "Pharma Proteomics Project is precompetitive biopharmaceutical consortium characterizing plasma proteomic profiles of UK Biobank participants. Collaboration between UK Biobank and biopharmaceutical companies characterising plasma proteomic profiles of UKB participants. Project generates the largest open-access plasma proteomics dataset to date, offering insights into trans protein quantitative trait loci across multiple biological domains, and highlighting genetic influences on ligand–receptor interactions and pathway perturbations across diverse collection of cytokines and complement networks." .
SCR:026190 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2994" ;
rdfs:label "Stanford Ecosystems Shared Laboratory Core Facility" ;
definition: "Ecosystems Laboratory provides bench space, laboratory supplies, chemicals, sample preparation equipment, and sample storage space to enhance and facilitate research within Stanford University community." .
SCR:026191 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spatial Cognition Platform" ;
definition: "Behavioral platform designed to distinguish between different navigational elements. Flexible and user-friendly software and hardware allows for modifications to the researcher’s specific needs, allowing for capabilities of testing in nonspatial tasks as well. Can be used in conjunction with in vivo electrophysiology, as well as video tracking methods." .
SCR:026192 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2987" ;
rdfs:label "Yale Keck Mass Spectrometry and Proteomics Resource Core Facility" ;
NIFRID:synonym "Yale University YU-Keck MS & Proteomics Resource",
"YU-Keck MS & Proteomics Resource" ;
definition: "Core provides proteomics and small molecule mass spectrometry services to separate, characterize, profile, and quantify analytes from complex biological samples." .
SCR:026193 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ZetaStitcher" ;
definition: "Software tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes." .
SCR:026194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "spatial_tri-omics" ;
definition: "Software repository to share the raw data processing and visualization codes used in the spatial tri-omics project." .
SCR:026195 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2998" ;
rdfs:label "University of Liverpool Egg Facility (LIV-SRF)" ;
NIFRID:synonym "Egg Facility",
"LIV-SRF Egg Facility",
"University of Liverpool Egg Core Facility",
"University of Liverpool Egg Facility" ;
definition: "Through the use of fertilised hen's eggs, the Egg Facility offers researchers methods for scientific research that can reduce or replace the use of mammalian models. It provides expertise in chorioallantoic membrane assays, specialising in cancer xenograft models, including patient-derived xenografts, to translate in vitro cancer studies and test therapeutic approaches." .
SCR:026196 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XenofilteR" ;
definition: "Software tool for computational deconvolution of mouse and human reads in tumor xenograft sequence data." .
SCR:026197 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GPTZero" ;
definition: "Artificial Intelligence detection software developed to identify artificially generated text, such as those produced by large language models." .
SCR:026198 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Amerigo Scientific" ;
definition: "Distribution company focused on providing products and services to biomedical and life science research communities. Offers high-quality adsorbent resins, catalyst resins, chelating resins, and other ion exchange resins." .
SCR:026199 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "North American Association of Central Cancer Registries" ;
NIFRID:synonym "North American Association of Central Cancer Registries (NAACCR)" ;
NIFRID:abbrev "NAACCR" ;
definition: "Professional organization that develops and promotes uniform data standards for cancer registration. Provides education and training, certifies population-based registries, aggregates and publishes data from central cancer registries and promotes the use of cancer surveillance data and systems for cancer control and epidemiologic research, public health programs, and patient care to reduce the burden of cancer in North America. Data Standards and Data Dictionary is intended for hospital and central cancer registries, programmers, and analysts. It provides detailed specifications and codes for each data item in the NAACCR data exchange record layout." .
SCR:026200 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pollux" ;
definition: "Software platform independent error correction tool for single and mixed genomes. Used for correcting errors across platforms." .
SCR:026201 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Columbia University Zuckerman Institute Molecular Tools Core Facility" ;
NIFRID:synonym "Antibodies and Genetic Access Tools",
"The Zuckerman Institute Molecular Tools Core",
"Zuckerman Institute: Molecular Tools - Virology" ;
definition: "Full service viral vector production core that provides investigators access to vector technology for preclinical studies and other basic research applications. Staff will provide expert consultation services for advanced study design, safe use of viral vector technologies and viral construction services for multiple viral vector types." .
SCR:026202 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DSigDB" ;
NIFRID:synonym "Drug Signatures Database",
"drug SIGnatures DataBase" ;
definition: "Online database provides collection of gene sets based on quantitative inhibition and/or drug-induced gene expression changes data of drugs and compounds. Allows users to search, view and download drugs/compounds and gene sets." .
SCR:026203 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Olympus_BX63" ;
rdfs:label "Olympus | BX63 Automated Fluorescence Microscope" ;
definition: """Fully motorized system allows automation of complex multidimensional experiments.
Uses motorized nosepiece to focus onto sample, enabling stage to be fixed for added stability.""" .
SCR:026204 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Bruker_Skyscan_1278" ;
rdfs:label "Bruker | Skyscan 1278 Micro-CT Scanner" ;
NIFRID:synonym "SkyScan 1278 Micro-CT system" ;
definition: "Scanner for in-vivo, low radiation imaging. Offers new micro-CT spatial beam shaper, which reduces absorbed radiation dose by up to five times while maintaining high quality image output. High throughput, high speed, microCT for scanning small laboratory animals including mice and rats. Has highly sensitive flat-panel detector that is able to deliver images of mouse heart and lung activities without using contrast agent, reducing animal stress and cost of study. Full-body animal scan can take 8 seconds or less, thus reducing overall run times and increasing the speed of data collection. Results can be directly sent to mobile devices for volume rendering and manipulations using software supplied." .
SCR:026205 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ Orbitrap_Astral" ;
rdfs:label "Thermo Fisher | Orbitrap Astral Mass Spectrometer" ;
NIFRID:synonym "Orbitrap Astral Mass Spectrometer" ;
definition: "Mass spectrometer combines faster throughput, deeper coverage, and higher sensitivity while delivering accurate and precise quantitation over high dynamic range. Suited for accurate and precise quantitation at unprecedented depth of coverage and higher throughput from single cells to bulk samples." .
SCR:026206 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Flatiron Health" ;
definition: "Commercial company, operating within healthcare technology sector, specifically focused on oncology. Develops oncology cloud platform, integrating clinical data and providing insights to cancer care providers and life science companies. Provides real-world evidence solutions, enabling collection, analysis, and interpretation of data from oncology patients." .
SCR:026207 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Electrotek " ;
definition: "Company produces anaerobic workstations. Offers range of units to suit all sizes of laboratories and will consider manufacture of special cabinets to customers' own specification. Anaerobic workstations can also be used for microaerophylic and other types of work by using different gas supplies." .
SCR:026210 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoMnT" ;
definition: "Software Python package for correcting sequencing errors within Short Tandem Repeat regions from Oxford Nanopore (ONT) sequencing data and genotyping monoallelic STR regions." .
SCR:026213 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Wes" ;
rdfs:label "Bio-Techne | ProteinSimple Wes Automated Western Blot System" ;
definition: "Protein characterization system that automated the Western blotting process from protein separation, immunoprobing, detection, and analysis of data.Gel-free, blot-free, and hands-free. It used glass rods and tubes to form a column that separated proteins by molecular weight. The Wes system was discontinued on July 30, 2021, but ProteinSimple will continue to support the platform through July 30, 2026. Users can upgrade to Jess or Abby to get the functionality of Wes with additional features." .
SCR:026214 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2999" ;
rdfs:label "Baylor College of Medicine Metabolomics Core Facility" ;
NIFRID:synonym "Metabolomics Core at Baylor College of Medicine",
"The Metabolomics Core at Baylor College of Medicine" ;
definition: "Core provides Untargeted Metabolomics, Untargeted Lipidomics, Targeted Metabolomics, Metabolomics Flux and analysis services." .
SCR:026215 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scVital" ;
definition: "Software tool to embed scRNA-seq data into species-agnostic latent space to overcome batch effect and identify cell states shared between species. Deep learning algorithm for cross-species integration of scRNA-seq data." .
SCR:026216 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MINTbase" ;
NIFRID:synonym "Mitochondrial and Nuclear tRNA fragment database" ;
definition: "Web-based framework that serves the dual-purpose of being content repository for tRFs and tool for interactive exploration of these newly discovered molecules. Framework for interactive exploration of mitochondrial and nuclear tRNA fragments. Can report comparative information on how tRF is distributed across all anticodon/amino acid combinations, provides alignments between tRNA and multiple tRFs with which user can interact, provides details on published studies that reported tRF as expressed." .
SCR:026217 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AACR GENIE cBioPortal" ;
definition: "International data-sharing consortium focused on generating an evidence base for precision cancer medicine by integrating clinical-grade cancer genomic data with clinical outcome data of cancer patients treated at multiple institutions worldwide." .
SCR:026218 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OncoTree" ;
definition: "Community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research. Cancer classification system for precision oncology." .
SCR:026219 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3000" ;
rdfs:label "University of California San Francisco Clinical Cancer Genomics Laboratory Core Facility" ;
NIFRID:synonym "UCSF Clinical Cancer Genomics Laboratory (CCGL)",
"University of California San Francisco Clinical Cancer Genomics Laboratory (CCGL)" ;
NIFRID:abbrev "CCGL" ;
definition: "Core performs standard-of-care and advanced molecular testing for patients with cancer, and to provides special expertise in solid tumors. Services include targeted gene sequencing, microsatellite instability testing, fluorescence in situ hybridization (FISH), and next-generation sequencing (NGS). CCGL is staffed with board-certified surgical pathologists and board-certified molecular pathologists who can properly evaluate the quality of samples submitted for testing as well as make correlations between the pathologic diagnosis of a tumor and the molecular findings in the tumor." .
SCR:026220 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "InfectiousPathogenDetector2" ;
NIFRID:synonym "Infectious Pathogen Detector (IPD) 2.0" ;
NIFRID:abbrev "IPD2",
"IPD 2.0" ;
definition: "IPD2 is updated version of InfectiousPathogenDetector, in-silico GUI-based automated pathogen analysis pipeline for seamless analysis of data from heterogenous NGS platforms. IPD performs integrated variants analysis, along with systematic quantification of pathogen genomes. IPD additionally has an in-built SARS-CoV-2 analysis module, for assignment of viral clades of the samples analyzed and an automated report generation." .
SCR:026221 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "spatialSNV" ;
definition: "Software tool for calling and analyzing SNVs from spatial transcriptomics data." .
SCR:026222 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HCP Suite" ;
definition: "Software collection consisting of Python-based framework for connectome-based analysis using Ray to parallelize CPM and set of scripts to perform common operations and analyses on the Human Connectome Project's neuroimaging data with focus on task-based fMRI." .
SCR:026223 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpaSNE" ;
definition: "Software extension of t-distributed stochastic neighbor embedding, the spatially resolved t-SNE (SpaSNE) designed to preserve both global gene expression and spatial structure for spatially resolved profiling data. Gives comprehensive low-dimensional visualization that could best reflect the molecular similarities of cells and the spatial interactions between cells." .
SCR:026224 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ClassyFire" ;
definition: "Web-based application for automated structural classification of chemical entities. Automated chemical classification with a comprehensive, computable taxonomy. Provides hierarchical chemical classification of chemical entities as well as structure-based textual description, based on chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds." .
SCR:026225 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIST Chemistry WebBook" ;
NIFRID:synonym "National Institute of Standards and Technology Chemistry WebBook" ;
definition: "Database that provides access to organic compounds data compiled and distributed by NIST under the Standard Reference Data Program." .
SCR:026226 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WinSCP" ;
definition: "Free file manager, SSH File Transfer Protocol, File Transfer Protocol, WebDAV, Amazon S3, and secure copy protocol client for Microsoft Windows." .
SCR:026227 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenChrom" ;
NIFRID:synonym "Lablicate GmbH OpenChrom" ;
definition: "Open source software for chromatography, spectrometry and spectroscopy. Data from different systems can be imported and analyzed. Runs under Windows, macOS and Linux. Supports to handle GC/MS, GC/FID, HPLC-UV/VIS, FTIR, PCR and NMR data." .
SCR:026228 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CAL*Explorer" ;
definition: "Interactive website for cancer statistics using California Cancer Registry data. Provides detailed statistics for cancer site by gender, race/ethnicity, age, county/region, and for select number of cancer sites, by histology." .
SCR:026229 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2995" ;
rdfs:label "Montana State University Research Cyberinfrastructure Core Facility" ;
NIFRID:synonym "Montana State University - Research Cyberinfrastructure" ;
NIFRID:abbrev "RCI" ;
definition: "Core provides centralized support, systems, and services for IT specific to research. Systems and services include areas of high-performance computing, virtual machine hosting, large scale storage, and high-performance networking and data transfer.Provides MSU researchers with consulting on technology budgets and implementation for grants and support for IT components of major research instrumentation, software, and specialized or unique research technology needs." .
SCR:026230 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent Seahorse XF Cell Mito Stress Test Report Generator" ;
definition: """Microsoft Excel Macro that automatically calculates and reports assay parameters of the Seahorse XF Cell Mito Stress Test as absolute Oxygen Consumption Rate in pmol
O2/min and supports assay result data from all Agilent Seahorse XF Analyzers.""" .
SCR:026231 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ghostipy" ;
definition: "Software signal processing and spectral analysis toolbox designed for local field potential recordings." .
SCR:026232 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pRNASeqTools" ;
definition: "Software integrated pipeline for plant NGS analysis." .
SCR:026235 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Wuxi AppTec" ;
definition: "Pharmaceutical, biopharmaceutical, and medical device company founded in December 2000 in Shanghai. Contract research organization." .
SCR:026236 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "XenoSTART" ;
definition: "Oncology translational research organization focused on development and utilization of Patient-Derived Xenograft models. Preclinical contract research organization specializing in patient-derived xenografts." .
SCR:026237 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Texas MD Anderson Cancer Genomics Library Core Facility" ;
NIFRID:synonym "Cancer Genomics Library",
"MD Anderson Cancer Genomics Library",
"University of Texas MD Anderson Cancer Genomics Library" ;
definition: "Facility for sequencing samples for the MD Anderson Cancer Center." .
SCR:026238 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TNBCtype" ;
definition: "Website for predicting the subtype of triple negative breast cancer sample based on its gene expression profile." .
SCR:026239 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BETSY" ;
NIFRID:synonym "Bioinformatics ExperT SYstem" ;
definition: "Software system for performing bioinformatics analyses. System includes knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. Backwards-chaining rule-based expert system comprised of data model that can capture richness of biological data, and inference engine that reasons on knowledge base to produce workflows. Knowledge base is populated with rules to analyze microarray and next generation sequencing data." .
SCR:026240 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Protected Planet" ;
definition: "Provides data on protected areas and other effective area-based conservation measures, updated monthly with submissions from governments, non-governmental organizations, landowners and communities.Through Protected Planet website, users can explore World Database on Protected Areas (WDPA), World Database on OECMs, Global Database on Protected Area Management Effectiveness (GD-PAME), and associated information." .
SCR:026241 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Global Environment Facility" ;
definition: "Provides information about family of funds for the environment. With GEF support,countries address the root causes of challenges as they strive for international environmental goals. Fund data from the Global Environment Facility." .
SCR:026242 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "World Health Organization Global Health Expenditure Database" ;
definition: "Global Health Expenditure Database provides comparable data on health expenditure for 194 countries and territories since 2000 with open access to the public. WHO works collaboratively with Member States to update the database (Explore the Data) annually, using available information such as health accounts data, government expenditure records and official statistics." .
SCR:026243 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "BirdLife International" ;
definition: "Registered charity and company limited by guarantee with mission to conserve birds, their habitats and global biodiversity, working with people toward sustainability in the use of natural resources. Registered in England. Provides bird species range map." .
SCR:026244 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Survival Analysis" ;
definition: "Software R package also called event history analysis in social science, or reliability analysis in engineering, deals with time until occurrence of event of interest. However, this failure time may not be observed within the relevant time period, producing so-called censored observations. Used for analysis of time to event data." .
SCR:026245 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "aactr" ;
definition: "Software R client for the Aggregate Content of ClinicalTrials.gov (AACT) database API." .
SCR:026246 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openMINDS core metadata model" ;
NIFRID:synonym "openMINDS_core" ;
NIFRID:abbrev "openMINDS core" ;
definition: "Software repository hosts one of metadata models of openMINDS metadata framework. It defines modular metadata schemas for describing general origin, location and content of neuroscience research products." .
SCR:026247 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openMINDS controlledTerms metadata model" ;
NIFRID:abbrev "openMINDS controlledTerms",
"openMINDS_controlledTerms" ;
definition: "Software repository is part of open Metadata Initiative for Neuroscience Data Structures (openMINDS). It contains the schema-templates as well as corresponding terminologies (as JSON-LDs) for all terms that are defined and maintained centrally in this repository. Where applicable, the defined terms are connected to a matching ontological term. Schemas of openMINDS_core as well as openMINDS_SANDS reference to these controlled terms." .
SCR:026248 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openMINDS chemicals metadata model" ;
NIFRID:abbrev "openMINDS chemicals",
"openMINDS_chemicals" ;
definition: "Software repository hosts one of the metadata models of the openMINDS metadata framework. It defines modular metadata schemas for describing chemical substances and mixtures." .
SCR:026249 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openMINDS computation metadata model" ;
NIFRID:abbrev "openMINDS computation",
"openMINDS_computation" ;
definition: "Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS core, by providing schema-templates for adding metadata for simulation, data analysis and visualization." .
SCR:026250 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openMINDS ephys metadata model" ;
NIFRID:abbrev "openMINDS ephys",
"openMINDS_ephys" ;
definition: "Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS, by providing metadata schemas for in-depth descriptions of electrophysiology experiments." .
SCR:026251 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openMINDS publications metadata model" ;
NIFRID:abbrev "openMINDS publications",
"openMINDS_publications" ;
definition: "Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS, by providing metadata schemas for representing publications in neuroscience, including interactive publications such as Live Papers. It includes schemas for articles, books, preprints, blog posts, live papers, etc., linked to other openMINDS entities such as Datasets. The schemas closely follow those in Schema.org but extend them for improved interoperability with openMINDS." .
SCR:026252 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openMINDS specimenPrep metadata model" ;
NIFRID:abbrev "openMINDS specimenPrep",
"openMINDS_specimenPrep" ;
definition: "Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS, by providing metadata schemas for in-depth descriptions of specimen preparations (surgery, tissue slicing, etc.)." .
SCR:026253 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openMINDS stimulation metadata model" ;
NIFRID:abbrev "openMINDS stimulation",
"openMINDS_stimulation" ;
definition: "Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS, by providing metadata schemas for in-depth descriptions of stimuli and stimulation protocols in neuroscience." .
SCR:026255 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5943" ;
rdfs:label "Field Museum of Natural History XCT Laboratory Core Facility" ;
NIFRID:synonym "Field Museum of Natural History XCT Laboratory" ;
NIFRID:abbrev "XCT Lab" ;
definition: "Facility for computed tomography (3D) imaging of objects in the Field Museum and part of the Museum’s Core Lab Group. Includes two North Star Imaging (NSI) XCT scanners. The larger of the two scanners is an X5000 with a dual tube setup: one 450kV mini-focus tube, and one 225kV micro-focus tube. This scanner can house samples up to 500lbs and 1.2m in longest dimension, and has excellent penetrating power for imaging dense samples like fossils and meteorites. The smaller scanner is an X25 with a 150kV Hamamatsu tube, which is excellent for imaging smaller and/or less dense samples in extremely high resolution, such as small animal skeletons. In addition to the scanners, the lab is equipped with two high-powered computers for post-scan data processing. Available software includes NSI’s suite of inspection and reconstruction software, VG Studio, ORS Dragonfly, 3DSlicer, Meshlab, and Blender." .
SCR:026256 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Paris Brain Institute Research and Development Unit Core Facility" ;
NIFRID:synonym "RnD Unit",
"RnD Unit prototyping platform" ;
definition: "Core provides development services for innovative hardware and software scientific equipment." .
SCR:026258 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Qualimap 2" ;
definition: "Software platform-independent application written in Java and R that provides both Graphical User Inteface and command-line interface to facilitate quality control of alignment sequencing data and its derivatives like feature counts. Used for advanced multi-sample quality control for high-throughput sequencing data." .
SCR:026259 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fluxfix" ;
definition: "Web isotopologue analysis tool for metabolomics experiment. Used to compute tracer analysis. Transforms raw mass spec AUC values into the percent representation of each isotopologue measured." .
SCR:026260 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Skipper" ;
definition: "Software workflow that converts unprocessed reads into annotated binding sites using improved statistical framework. Used for analysis of CLIP-seq data and to process CLIP data from fastq files." .
SCR:026261 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3001" ;
rdfs:label "University of Texas MD Anderson Advanced Technology Genomics Core Facility" ;
NIFRID:synonym "Advanced Technology Genomics Core",
"Advanced Technology Genomics Core (ATGC)",
"MD Anderson Advanced Technology Genomics Core",
"MD Anderson Advanced Technology Genomics Core Facility" ;
definition: """Genomics core facility with goal to use instrumentation and innovative technical expertise in order to provide investigators with genomic data from comprehensive range of genomic services in timely manner. Services include Next-Generation Sequencing, Sanger Sequencing
Single Cell Sequencing, Microarray Services, Fluorescent Fragment Length Analysis, nanoString nCounter Analysis, Bionano Optical Genome Mapping, Spatial Transcriptomics,
Nanopore Sequencing.""" .
SCR:026262 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3002" ;
rdfs:label "University of Texas MD Anderson Cytogenetics and Cell Authentication Core Facility" ;
NIFRID:synonym "MD Anderson Cytogenetics and Cell Authentication Core",
"MD Anderson Cytogenetics and Cell Authentication Core Facility" ;
definition: "Facility offers conventional as well as molecular cytogenetic services including karyotyping, analysis of genomic instability, fluorescence in situ hybridization, telomere analysis, Spectral Karyotyping, species identification, inter-species and intra-species cell line contamination, STR fingerprinting service for cell line authentication, mycoplasma contamination testing and distribution of cell lines." .
SCR:026263 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MuSE" ;
NIFRID:synonym "Mutation calling using a Markov Substitution model for Evolution" ;
definition: "Software tool for detecting somatic point mutations in high throughput DNA sequencing data of tumors. Used for modeling evolution of allelic composition of tumor and normal tissue at each reference base. Adopts sample-specific error model to depict inter-tumor heterogeneity, which greatly improves overall accuracy." .
SCR:026264 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FACETS" ;
definition: "Software tool for estimating genome copy numbers from high throughput DNA sequencing data. Allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Used to implement Fraction and Copy number Estimate from Tumor/normal Sequencing." .
SCR:026265 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MuSiCal" ;
NIFRID:synonym "Mutational Signature Calculator" ;
definition: "Software Python toolkit for mutational signature analysis. Used to estimate mutational signatures from somatic mutations in genome." .
SCR:026266 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Xenome" ;
definition: "Software tool to distinguish host and graft reads from next generation sequencing assays of xenograft samples. Performs classification of xenograft-derived sequence read data." .
SCR:026267 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Broad Institute GDAC Firehose" ;
definition: "Born of the desire to systematize analyses from The Cancer Genome Atlas pilot and scale their execution to the dozens of remaining diseases to be studied, GDAC Firehose now sits atop terabytes of analysis-ready TCGA data and reliably executes thousands of pipelines per month." .
SCR:026268 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TomoVision sliceOmatic" ;
definition: "Medical image analysis software to measure, segment and analyze multi-slice scanner data." .
SCR:026269 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "epiAneufinder" ;
definition: "Software R package used for calling Copy Number Variations from single-cell ATAC data." .
SCR:026270 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3017" ;
rdfs:label "University of Nebraska Medical Center Bioassay Core Facility" ;
NIFRID:synonym "University of Nebraska Medical Center Bioassay Core" ;
definition: "Core provides equipment, personnel, and protocols for routine and advanced cellular and molecular assays for research." .
SCR:026271 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2996" ;
rdfs:label "University of Texas at Austin Shared Instrumentation Facility" ;
NIFRID:synonym "Shared Instrumentation Facility",
"The University of Texas at Austin Shared Instrumentation Facility" ;
definition: "Facility provides access to and operational support for easy-to-operate equipment for sample preparation and analysis, including gel imagers, plate readers, and qPCRs. They provide training on instrument operation and grant access for independent use after completed training." .
SCR:026272 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2997" ;
rdfs:label "Brandeis University Louise Mashal Gabbay Cellular Visualization Center Electron Microscopy Core Facility" ;
NIFRID:synonym "Brandeis Electron Microscopy Facility- The Louise Mashal Gabbay Cellular Visualization Center",
"Brandeis EM facility",
"Brandeis University Brandeis Electron Microscopy Facility",
"Brandeis University Louise Mashal Gabbay Cellular Visualization Center Electron Microscopy Facility" ;
definition: "Facility offers preparation and visualization ranging from standard 2D EM methods to high resolution 3D cryo-EM. Instruments, training and assisted use are available for Brandeis faculty, staff, and lab members, as well as members of the broader scientific community, including other academic institutions and for-profit organizations." .
SCR:026273 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MERSCOPE_Ultra" ;
rdfs:label "Vizgen | MERSCOPE Ultra" ;
definition: """System automates sample imaging, imaging analysis, and cell segmentation, delivering high-resolution, high-throughput imaging without compromising sensitivity. Powered by MERFISH technology, MERSCOPE Ultra includes high-performance analysis computer, along with the necessary reagents and software to accurately quantify and localize RNA and protein in
tissue samples. High-resolution in situ spatial genomics platform that offers tissue-wide view of up to 1000 custom genes at single-cell resolution.""" .
SCR:026274 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Vizgen" ;
definition: "Biotechnology company in Cambridge, Massachusetts, developing the next generation of genomic profiling tools that enable researchers to gain new insight into the biological systems that underlie human health and disease with spatial context. The company's MERSCOPE platform enables massively multiplexed, genome-scale nucleic acid imaging with high accuracy and unrivaled detection efficiency at subcellular resolution." .
SCR:026275 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_X-Rad320" ;
rdfs:label "PRICISION X-Ray | X-Rad320 irradiator" ;
NIFRID:synonym "X-Rad320 irradiator" ;
definition: "Self-contained X-ray system for delivering precise radiation dosage to specimens in biological or small animal research laboratory. The shielded cabinet includes Adjustable Specimen Shelf, Sample Viewing Window and Beam Hardening Filter Holder.TouchRAD Control Panel is multi-user, password protected touch screen interface with transportable database that can track individual system usage.Passwords, programmed exposure settings, and database management are controlled by super-user.X-ray tube is used specifically for radiation therapy having highly homogenous beam. Options available include: Dose Measurement & Control, Motorized Specimen Shelf,Turntable, Fixed Beam Collimators, Adjustable Collimator, and Specimen Holding Fixtures." .
SCR:026277 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3018" ;
rdfs:label "University of Louisville Biophysical Core Facility" ;
definition: "Biophysical Core Facility supports structural biology studies focused on characterization of biophysical properties of biomolecules and their interactions with binding partners or novel drug candidates. Offers range of biophysical techniques for initial screening of hit/lead compound binding as well as rigorous characterization of the thermodynamic and hydrodynamic properties of various biological macromolecules (most commonly proteins and nucleic acids), macromolecular association reactions, and ligand-macromolecule interactions. Biophysical techniques include differential scanning fluorimetry, microscale thermophoresis, isothermal titration calorimetry, differential scanning calorimetry, circular dichroism spectroscopy, fluorescence spectroscopy, absorbance spectroscopy and analytical ultracentrifugation." .
SCR:026278 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpliceAI Lookup" ;
definition: "Website to identify the effects of certain gene mutations on splice behaviour." .
SCR:026279 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Promega | Quantus Fluorometer" ;
NIFRID:synonym "Quantus Fluorometer" ;
definition: "Compact, dual-channel fluorometer designed to provide highly sensitive fluorescent detection when quantifying nucleic acids. Fluorometer is optimized with preprogrammed settings for Promega QuantiFluor Dye Systems (QuantiFluor dsDNA, RNA and ssDNA Systems) to quantitate nucleic acids and offers flexibility to create customized methods and quantitation settings for other fluorescent dyes." .
SCR:026280 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RWRtoolkit" ;
definition: "Software set of command-line and R tools for performing Random-walk with performing Random-walk on multiplex networks in any species." .
SCR:026281 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Amino_acid_composition_and_hydrophobicity_analysis" ;
definition: "Software package to analyze amino acid content and hydrophobicity profile of given set of protein sequences in fasta file. Used for analysis of amino acid composition and hydrophobicity of test sequences from fasta files." .
SCR:026282 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "watvina" ;
definition: "Software tool as implicit or explicit water model based docking with Autodock vina engine, supporting pharmacophore /position constrained docking.Facilitates drug design with support for explicit or implicit waters, pharmacophore or position-constrained docking, and external torsion parameters (akin to amber/gaff/charmm force fields). Water Model supported protein-ligand docking with Autodock Vina engine." .
SCR:026283 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenFold" ;
NIFRID:synonym "OpenFold 2.0" ;
definition: "Software tool as trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2" .
SCR:026284 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HapHiC" ;
definition: "Software fast, reference-independent, allele-aware scaffolding tool based on Hi-C data. Allele-aware scaffolding tool that uses Hi-C data to scaffold haplotype-phased genome assemblies into chromosome-scale pseudomolecules." .
SCR:026285 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ednet" ;
definition: "Software application provides dataset of all student-system interactions collected over 2 years by Santa, multi-platform AI tutoring service with more than 780K users in Korea available through Android, iOS and web." .
SCR:026286 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "deconstructSigs" ;
definition: """Software tool to determine contribution of known mutational processes to tumor sample.
Delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution.""" .
SCR:026287 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bertin Technologies | Precellys Minilys Personal Tissue Homogenizer" ;
definition: "Small sample tissue homogenizer for 0.5mL or 2mL tubes at 3.000, 4.000 or 5.000 rpm." .
SCR:026288 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "I-DSD Registry" ;
definition: """International registry for wide range of conditions that may be associated with difference or
disorder of sex or pubertal development. Registry platform and network that aims to improve clinical practice, research and understanding of wide range of rare conditions affecting sex development and maturation through sharing of knowledge and experience.""" .
SCR:026289 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3005" ;
rdfs:label "University of Pennsylvania School of Medicine Advanced Core for Microscope Engineering Core Facility" ;
NIFRID:synonym "Advanced Core for Microscope Engineering (ACME)",
"University of Pennsylvania Advanced Core for Microscope Engineering (ACME)",
"University of Pennsylvania School of Medicine Advanced Core for Microscope Engineering (ACME)" ;
NIFRID:abbrev "ACME" ;
definition: "Core provides custom built ad hoc optical microscopy solutions, advanced image analysis, and consultation services to researchers across the Penn campus and beyond." .
SCR:026293 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cancer Therapeutics Response Portal (CTRP)" ;
definition: "Cancer Therapeutics Response Portal (CTRP) links genetic, lineage, and other cellular features of cancer cell lines to small-molecule sensitivity with the goal of accelerating discovery of patient-matched cancer therapeutics. CTRP can be mined to develop insights into small-molecule mechanisms of action and novel therapeutic hypotheses, and to support future discovery of drugs matched to patients based on predictive biomarkers." .
SCR:026294 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Western Australia Genomics WA Core Facility" ;
NIFRID:synonym "Genomics WA",
"University of Western Australia Genomics WA" ;
definition: "Core provides consultation, expert advice and streamlined library preparation, next generation sequencing and data analysis services." .
SCR:026295 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DRESDEN-concept Genome Center" ;
NIFRID:synonym "TUD Dresden University of Technology DRESDEN-concept Genome Center",
"TUD Dresden University of Technology DRESDEN-concept Genome Center Core Facility" ;
NIFRID:abbrev "DcGC" ;
definition: "Technology platform offering infrastructure and expertise in omics technologies, sequencing and data analysis. Organized in Technology Units: Short-Read, Long-Read, Single-Cell, Spatial Omics, Bioinformatics, and OpenLab." .
SCR:026296 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenSmart" ;
NIFRID:synonym "GenScript GenSmart" ;
definition: "Free online tool for performing codon optimization to improve gene expression. GenScript’s patented algorithms are integrated into the tool to optimize the computing capability of high-performance sequence generation. Used to optimize design of wild type or recombinant gene sequences towards higher expression in prokaryotic and mammalian expression systems." .
SCR:026297 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NovoCyte_Penteon" ;
rdfs:label "Agilent | NovoCyte Penteon Flow Cytometer" ;
NIFRID:synonym "NovoCyte Penteon Flow Cytometer",
"NovoCyte Penteon Flow Cytometer Systems 5 Lasers" ;
definition: "Provides flexibility to choose from up to 30 fluorescence channels utilizing up to 5 lasers with up to 30 independent detectors." .
SCR:026298 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IncuCyte_SX5" ;
rdfs:label "Thermo Fisher: Sartorius | IncuCyte SX5 Live Cell Analysis System" ;
NIFRID:synonym "IncuCyte SX5 Live Cell Analysis System" ;
definition: "Live-cell imaging and analysis system. It leverages up to five total fluorescence channels (up to three simultaneously) including long wavelength, low phototoxicity NIR channel that makes it ideal for long-term time-lapse experiments. Offers high-resolution imaging, real-time kinetic monitoring and automated analysis capabilities." .
SCR:026299 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Flexmap_3D" ;
rdfs:label "RnD Systems | Luminex Flexmap 3D" ;
NIFRID:synonym "Luminex FLEXMAP 3D Instrument System" ;
definition: "Flow-based reader, is multiplexing platform from Luminex with fast read time, compatibility with both 96- and 384-well plates, and ease of integration with front-end automation systems for high-throughput applications. Can analyze up to 500 analytes in single sample and is compatible with all R &D System Luminex assays and Quantist Analysis Software." .
SCR:026300 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sony_MAB900" ;
rdfs:label "Sony biotechnology | MA900 Multi-Application Cell Sorter" ;
NIFRID:synonym "MA900 Multi-Application Cell Sorter",
"MA900 system" ;
definition: "MA900 system include patented micro fluidic chip-based design, comprehensive fluidic controls, and advanced automation that simplifies operation to make sorting less subjective and improve reliability. Provides up to 14 parameters from 4 lasers with possibility to choose from 4 excitation lasers—488 nm, 405 nm, 561 nm, and 638 nm—on two beam spots. Free-form PMTs enable detection of fluorescence signals from each beam spot, allowing detection of up to 12 fluorescence parameters and two scatter parameters." .
SCR:026301 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_z-Movi" ;
rdfs:label "Lumicks | Z-Movi Cell Avidity Analyzer" ;
NIFRID:synonym "Z-Movi Cell Avidity Analyzer" ;
definition: "Compact analyzer that fits inside the flow hood for sterile and safe sample handling. Used to measure the avidity between immune cells and their targets, enabling to identify the most potent immunotherapeutic effector cells." .
SCR:026303 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AMI_HTX" ;
rdfs:label "Spectral Instruments | Imaging Ami HTX system" ;
NIFRID:synonym "Ami HTX",
"Ami HTX Imaging System",
"Spectral Instruments Imaging Ami HTX" ;
definition: "General purpose imaging system capable of fluorescence, luminescence, and photographic imaging. Includes x-ray imaging capability." .
SCR:026304 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Synthego" ;
definition: "Biotech company dedicated to advancing the frontiers of CRISPR cell and gene therapies through CRISPR technology and expertise. Provides genome engineering solutions and access to CRISPR solutions.CRISPRevolution is a line of products from Synthego and features synthetic guide RNA products designed to accelerate CRISPR/Cas9 and Cpf1 genome engineering research." .
SCR:026305 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DREAM implant" ;
NIFRID:synonym "Adaptable",
"and Modular implant",
"Dynamic",
"Economical",
"Recoverable" ;
definition: "Design for chronic electrophysiology implant. Light-weight, can be used in head-fixed or freely moving mice, and is capable of probe recovery for multiple reuses of probes. Includes 3D print designs and step by step instructions for surgery, experimental sessions, and explantation. System includes micro drive, 3D printable Faraday cage, and miniaturized head-fixation system." .
SCR:026307 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Penn State Critical Illness and Sepsis Research Center Core Facility" ;
NIFRID:synonym "Penn State Critical Illness and Sepsis Research Center" ;
definition: "Offers centralized access to critical care clinicians and researchers from diverse disciplines, fostering multidisciplinary collaboration. Supports investigators seeking intramural or extramural partnerships to advance research on sepsis and critical illness. Expands institutional biobanks by incorporating datasets and research specimens from adult and pediatric patients with sepsis. Utilizes immunologic assays and machine learning techniques to investigate different subtypes of sepsis.Develops translational rodent models that are relevant to the study of critical illness.Provides resources to educate clinicians, trainees and patients about septic illness." .
SCR:026309 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BayesSpace" ;
definition: "Software R package for clustering and enhancing resolution of spatial gene expression experiments. Clusters low-dimensional representation of gene expression matrix, incorporating spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into \"sub-spots\", for which features such as gene expression or cell type composition can be imputed." .
SCR:026310 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Conditional AutoRegressive Deconvolution" ;
NIFRID:synonym "CARD: Conditional AutoRegressive Deconvolution",
"Conditional autoregressive-based deconvolution" ;
NIFRID:abbrev "CARD" ;
definition: "Software R package for spatial transcriptomics. Deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations." .
SCR:026311 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TSQ_9000" ;
rdfs:label "Thermo Fisher | TSQ 9000 Triple Quadrupole GC-MS/MS system" ;
definition: "Triple quadrupole mass spectrometry system to study liquid, gaseous or solid samples. Mass analyzer enables absolute quantification of low-concentration metabolites. Designed for complex sample matrices in high-throughput applications. ExtractaBrite or AEI configuration are used to maximize uptime between routine maintenance interventions. The wireless ExtractaBrite ion source is heated throughout and includes the first RF region, commonly the first place susceptible to ion burn. This design ensures high matrix tolerance for high throughput applications. The AEI source is also heated throughout, with RF lenses and benefits from an innate ultra-robustness due to a more tightly focused ion beam, limiting ion burn on the source lenses." .
SCR:026312 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_TRACE_1300_GC" ;
rdfs:label "Thermo Fisher | TRACE 1300 Gas Chromatograph" ;
NIFRID:synonym "TRACE 1300 Gas Chromatograph",
"TRACE 1300 GC" ;
definition: "Intuitive single-button gas chromatography system, that provides ease of use with minimal instrument interaction and full data system control. Offers user-exchangeable, instant connect injector and detector modules and fast oven performance with exceptional retention time stability. Used for detecting wide range of compounds and it is sensitive and user friendly." .
SCR:026314 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2561" ;
rdfs:label "University of Alberta Precision Human Health Laboratory Core Facility" ;
NIFRID:synonym "PHHL - Precision Human Health Laboratory",
"University of Alberta PHHL - Precision Human Health Laboratory" ;
NIFRID:abbrev "PHHL" ;
definition: "Core to advance understanding of mechanism of vascular dysfunction in chronic disease, identify how vascular dysfunction contributes to exercise intolerance, evaluate how exercise training improves vascular dysfunction and exercise intolerance using innovative clinical trial designs." .
SCR:026315 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3006" ;
rdfs:label "Medical College of Wisconsin Oxford Instruments Center for Advanced Microscopy Electron Microscopy Core Facility" ;
NIFRID:synonym "MCW-Oxford Instruments Center for Advanced Microscopy- Electron Microscopy Core",
"Medical College of Wisconsin MCW-Oxford Instruments Center for Advanced Microscopy- Electron Microscopy Core" ;
definition: "Institutionally available research service unit managed on behalf of the Medical College by the Department of Cell Biology, Neurobiology and Anatomy. OCAM-EM encompasses both Light and Electron Microscopy services." .
SCR:026316 a owl:NamedIndividual ;
rdfs:label "Feature Representation Enhancement End-to-end Protein Interaction Inference" ;
NIFRID:abbrev "FREEPII" ;
definition: """Software application encompassing autonomous feature extraction and feature representation enhancement for PPIs and protein complexes inference.
FREEPII establishes feature maps that are consistent with model training, and emphasizes learning the feature representation of proteins rather than the feature representation of PPI, reducing the computational complexity from N^2 to N (N: number of proteins).
FREEPII uses protein sequences to expand the information available for calculating data similarity between proteins. Furthermore, it introduces network-level information into the final feature representation to rescale the strength of interactions present in CF-MS data.""" .
SCR:026319 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TNMplot" ;
definition: "Web tool for comparison of gene expression in normal, tumor and metastatic tissues." .
SCR:026320 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FireBrowse" ;
definition: "Portal provides access to cancer genomic data from variety of analyses: clinical, copy number, miR, miRseq, mRNA, mRNAseq, mutation and pathway analyses. Provides comprehensive suite of interdependent analyses of those data, including: correlations, clustering, and GISTIC and MutSigCV. Companion portal to the Broad Institute GDAC Firehose analysis pipeline, and was developed to cull and analyze data generated by The Cancer Genome Atlas (TCGA), which characterizes and identifies genomic patterns in human cancer models." .
SCR:026321 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SqueezeCall" ;
definition: "Software tool as Nanopore basecalling using Squeezeformer network to improve basecalling accuracy over recurrent neural network (RNN)-based model and Transformer-based models." .
SCR:026322 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Collaborative Cohort of Cohorts for COVID-19 Research" ;
NIFRID:abbrev "C4R" ;
definition: "Portal provides information about nationwide study of more than 50,000 individuals to determine factors that predict disease severity and long-term health impacts of COVID-19." .
SCR:026323 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Promega GloMax 96 Software" ;
NIFRID:synonym "GloMax 96 Microplate Luminometer Software",
"GloMax 96 Software" ;
definition: "Promega glomax software for older but still functional luminometer models. GloMax 96 Software requires that Microsoft Excel is also installed on the PC. GloMax 96 Software is compatible with Excel 2003, 2010 and 2013 versions." .
SCR:026324 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2979" ;
rdfs:label "Montana State University Cryo-EM Core Facility" ;
NIFRID:synonym "Montana State University - Cryo-EM Core Facility" ;
definition: "Core provides single particle analysis and cryo-electron tomography. Instrumentation includes 200 kV Talos Arctica with Gatan K3 camera, 120 kV Tecnai Spirit, and Vitrobot Mark IV allowing imaging of biological structures at single nanometer to sub-nanometer resolutions, and thus enable 3D modeling of cells, viruses, proteins, nucleic acid, and other soft matter at the atomic level." .
SCR:026325 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3007" ;
rdfs:label "Montana State University Imaging and Chemical Analysis Laboratory Core Facility" ;
NIFRID:synonym "Montana State University - Imaging and Chemical Analysis Laboratory" ;
NIFRID:abbrev "ICAL" ;
definition: "Facility supports basic and applied research and education in all science, engineering, and STEM disciplines. Specializes in complementary surface, interfacial, and bulk characterization of materials via high-resolution imaging and spectroscopy. The lab promotes interdisciplinary collaboration between research, educational, and industrial fields." .
SCR:026326 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3008" ;
rdfs:label "Montana State University Social Data Collection and Analysis Services Core Facility" ;
NIFRID:synonym "Social Data",
"Social Data Collection and Analysis Services" ;
definition: "Core enables collection of high-quality data for researchers employing variety of social and behavioral methods. This facility provides tools necessary for researchers to study interactions between human systems and other complex phenomena like public health and ecosystems." .
SCR:026327 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3011" ;
rdfs:label "Benaroya Research Institute Cell and Tissue Analysis Group Core Facility" ;
NIFRID:synonym "Benaroya Research Institute Cell and Tissue Analysis Group",
"Cell and Tissue Analysis Group" ;
NIFRID:abbrev "CATA" ;
definition: "Core offers flow cytometry, imaging, and histology resources.Provides expertise in the fields of imaging, histology, and flow cytometry, physical space and instruments, critical support through the whole process, from hands-on training to experiment design and data analysis." .
SCR:026328 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3009" ;
rdfs:label "Montana State University Cellular Analysis Core Facility" ;
NIFRID:synonym "Cellular Analysis Core",
"Montana State University Cellular Analysis Core" ;
NIFRID:abbrev "and single cell RNA sequencing",
"CAC",
"flow cytometric analysis and cell sorting",
"histological samples preparation" ;
definition: "Core provides access to functional, up-to-date equipment for flow cytometric analysis and cell sorting, histological samples preparation, and single cell RNA sequencing which is essential for all researchers in immunology, infectious disease, and cell biology and is highly useful for scientists in other related fields." .
SCR:026329 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FLIR | E6 Pro Infrared Camera" ;
definition: "Thermal Imaging camera. Pro-Series Infrared Camera with Ignite Cloud." .
SCR:026330 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BMG Labtech | CLARIOstar Plus" ;
NIFRID:synonym "BMG LABTECH CLARIOstar Plus" ;
definition: "Multi-mode microplate reader that measures chemical, biological, and physical reactions in microplates. It comes equipped with our LVF Monochromators, filters, and spectrometer. The instrument is upgradable and can be equipped with non-isotopic detection technologies:UV/vis absorbance, Fluorescence intensity, including FRET,Luminescence (flash and glow), including BRET,Fluorescence polarization/anisotropy,Time-resolved fluorescence, including TR-FRET AlphaScreen / AlphaLISA / AlphaPlexTM. Atmospheric Control Unit, temperature incubation, multiple shaking, well scan and reagent injectors make the CLARIOstar Plus the ideal platform for any live cell-based assay." .
SCR:026331 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_iBright_FL1500" ;
rdfs:label "Thermo Fisher: Invitrogen | iBright FL1500 Imaging System" ;
NIFRID:synonym "iBright FL1500 Imaging System" ;
definition: "System to capture images and analyze data from western blots and gels. Supports main imaging applications of fluorescent, chemiluminescent, and colorimetric western blots, in addition to fluorescent stained nucleic acid gels, fluorescent stained protein gels, colorimetric stained protein gels, and colorimetric membrane stains." .
SCR:026332 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3012" ;
rdfs:label "Montana State University Geospatial Core Facility" ;
NIFRID:synonym "Montana State University - Geospatial Core Facility" ;
definition: "Provides equipment and team support to the workflow of all things geo-spatial from primary data collection using suite of different sensors and platforms to analysis that includes:Advanced mapping and geo-spatial analysis that leverage Uncrewed Aerial Vehicle (UAV) or drone-based sensors that use LiDAR, hyperspectral, thermal, orthoimagery, and Structure from Motion; High precision mapping and analysis using GPS and GNSS; Acoustic Doppler Profiles of rivers, reservoirs, and lakes;Data visualization and cartography;Remote sensing using active and passive sensors;Geo-spatial analysis, data development, and management;High Performance Computing infrastructure that leverages all of the above using open source and proprietary software." .
SCR:026333 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3014" ;
rdfs:label "Montana State University Montana Microfabrication Core Facility" ;
NIFRID:synonym "Montana State University - Montana Microfabrication Facility" ;
NIFRID:abbrev "MMF" ;
definition: "Micro and nanofabrication facility that offers range of processing and packaging capabilities including lithography, wet and dry etching, thin film deposition, dicing, wire bonding, metrology, and inspection." .
SCR:026334 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3013" ;
rdfs:label "Montana State University Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "Montana State University - Nuclear Magnetic Resonance Facility",
"Montana State University Nuclear Magnetic Resonance Facility" ;
definition: "Core provides open access availability to NMR spectroscopy instrumentation, training and sample preparation. Facility can be accessed individually or as full service center. NMR Facility has a total space of ~2,500 sq ft. divided among 3 rooms fully constructed with considerations for cooling, in-place floor dampening infrastructure and space for wet lab/sample preparation. Facility specializes in small molecule structure determination, small molecule characterization, biomolecular/protein structure determination, qualitative and quantitative NMR analysis, and small molecule purification from wide variety of sample sources." .
SCR:026335 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BenchMark_XT" ;
rdfs:label "Roche | Ventana BenchMark XT system" ;
NIFRID:synonym "BenchMark XT automated slide preparation system",
"Ventana BenchMark XT system" ;
definition: "Automated slide preparation system to expand test menu, process more slides, and improve turnaround times. Fully automated, random-access platform allows simultaneously run IHC and ISH tests and process patient case all at once. Can be used for CINtec PLUS preparation." .
SCR:026336 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BD Biosciences | PrepStain Slide Processor" ;
NIFRID:synonym "AutoCyte PREP System",
"BD PrepStain",
"BD PrepStain system",
"Becton Dickinson PrepStain Slide Processor" ;
definition: "Slide processor to produce BD SurePath Liquid-based Pap Test slides. Liquid based thin layer cell preparation process intended as replacements for conventional gynecologic Pap smears, for use in screening and detection of cervical cancer, pre-cancerous lesions, atypical cells and all other cytologic categories." .
SCR:026337 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Karma" ;
NIFRID:synonym "Karolinska Mammography Project for Risk Prediction of Breast Cancer" ;
definition: "Karolinska Mammography Project for Risk Prediction of Breast Cancer. Research group at Karolinska Institutet created the world’s best characterised breast cancer cohort with the aim to reduce mortality and incidence in breast cancer through translational research focusing on breast cancer screening and prevention." .
SCR:026338 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "2015 PQStat Statistical Calculation Software" ;
definition: "Software application for statistical calculation." .
SCR:026339 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PhysMAP" ;
definition: "Software R code for multi-modal analysis to delineate cell types using electrophysiology. Interpretable in vivo neuronal cell type identification using multi-modal analysis of electrophysiological data." .
SCR:026340 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3019" ;
rdfs:label "Massachusetts Institute of Technology Koch Institute High Throughput Sciences Core Facility" ;
NIFRID:synonym "High Throughput Sciences",
"High Throughput Sciences (HTS)",
"Massachusetts Institute of Technology Koch Institute High Throughput Sciences" ;
definition: "Core offers automation and screening capabilities. Equipped with environmentally-controlled high-content microscopes, automated liquid handlers, plate washers and readers, and robotic platforms, HTS aims to accelerate experiments from small-scale assays to large screening campaigns." .
SCR:026341 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BD Biosciences | Totalys SlidePrep" ;
NIFRID:synonym "Becton Dickinson Totalys SlidePrep" ;
definition: "Fully automated slide preparation and staining. Processes BD SurePathTM Liquid-based Pap test and Non-Gynaecological samples. Integrates slide creation and staining from enriched cell pellet. Allows for random sample loading." .
SCR:026342 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Manitoba Grex High Performance Computing Core Facility" ;
NIFRID:synonym "Grex High-Performance Computing system at University of Manitoba" ;
NIFRID:abbrev "Grex" ;
definition: "Core offers computing and storage resources, along with support and training. Currently, Grex system consists of over 10,000 CPU cores connected via low-latency InfiniBand interconnect, several GPU compute nodes, 2 Petabytes of high-performance Lustre storage, and tape backup system. System also provides for condominium model of hosting researcher-contributed hardware funded by Canada Foundation for Innovation (CFI) and other granting agencies." .
SCR:026343 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3024" ;
rdfs:label "Northwestern University GIANTFab Core Facility" ;
NIFRID:synonym "GIANTFab",
"The Glovebox Inert Atmosphere (N2) Thin-film Fabrication and Testing (GIANTFab)" ;
definition: "Core provides equipment to manufacture and test thin-film devices without ever exposing them to air or water, allowing measurements of device performance unaffected by environmental degradation." .
SCR:026344 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CyTOF XT" ;
rdfs:label "Standard BioTools | CyTOF XT mass cytometer" ;
NIFRID:synonym "CyTOF XT",
"CyTOF XT mass cytometer" ;
definition: "Fully automated and affordable cytometer to simplify and standardize deep single-cell profiling studies." .
SCR:026345 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3028" ;
rdfs:label "University College London Darwin Research Core Facility" ;
NIFRID:synonym "Darwin Research Facility",
"UCL Darwin Research Facility",
"University College London Darwin Research Facility" ;
definition: "Facility provides diverse range of equipment, expertise and training in field of biochemistry, molecular, structural and cellular biology. Facility consists of several research laboratories and support areas." .
SCR:026346 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SpectraMax_i3x" ;
rdfs:label "Molecular Devices | SpectraMax i3x Multi-Mode Microplate Reader" ;
NIFRID:synonym "Multi-Mode Microplate Reader",
"SpectraMax i3x Multi-Mode Microplate Reader" ;
definition: "Microplate reader can perform wide range of essential cell-based and biochemical assays using included absorbance, fluorescence, and luminescence detection modes." .
SCR:026347 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Qsep100" ;
rdfs:label "BiOptic | Qsep100 Bio-Fragment Analyzer" ;
NIFRID:synonym "Qsep100 Bio-Fragment Analyzer" ;
definition: "Standard-sized automated analyzer with its single-channel design, it can run 1~96 samples. Supports various types of applications, including DNA, RNA and protein fragment analyses and high-voltage fast analysis." .
SCR:026348 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Weizmann Institute of Science Curated Cancer Cell Atlas" ;
NIFRID:synonym "Curated Cancer Cell Atlas" ;
NIFRID:abbrev "3CA" ;
definition: "Collected, annotated and analyzed cancer scRNA-seq datasets. Data from different studies to reveal patterns of transcriptional ITH across tumour samples." .
SCR:026349 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GeneSetCart" ;
definition: "Interactive web-based application to facilitate data integration, discovery, and hypothesis generation across diverse Common Fund programs' datasets, highly processed data can be converted into gene-, metabolite- and drug-set libraries." .
SCR:026350 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TIDE" ;
NIFRID:synonym "Tumor Immune Dysfunction and Exclusion" ;
definition: "Web platform for large-scale public data reuse to model immunotherapy response and resistance. Provides integrated large-scale omics data and biomarkers on published ICB trials, non-immunotherapy tumor profiles, and CRISPR screens." .
SCR:026351 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3016" ;
rdfs:label "Montana State University Animal Resources Center Core Facility" ;
NIFRID:synonym "Montana State University - Animal Resources Center" ;
NIFRID:abbrev "ARC" ;
definition: "AAALAC approved animal research facility to study diverse number of animal species. Core maintains animal housing rooms, observation rooms, and procedure rooms at BSL 1 and 2 containment levels. The ARC is supported by certified veterinarians and animal care technicians who provide technical support and veterinary care." .
SCR:026352 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3050" ;
rdfs:label "University of Luxembourg LCSB Bioimaging Platform Core Facility" ;
NIFRID:synonym "LCSB Bioimaging Platform",
"University of Luxembourg LCSB Bioimaging Platform" ;
definition: "Bioimaging Platform provides access to and support for wide variety of advanced microscopy and flow cytometry instruments, enabling researchers to perform studies from the tissue level and down to sub-cellular scales. Provides access to analytical imaging technologies. As such, the platform comprises of advanced microscopy systems for high resolution studies of fixed and live samples as well as for low-phototoxicity imaging of whole organs and organisms.Bioimaging platform includes seven advanced microscopy systems, two flow cytometers and several high-performance analysis workstations." .
SCR:026353 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3029" ;
rdfs:label "Columbia University Confocal and Specialized Microscopy Shared Resource Core Facility" ;
NIFRID:synonym "Columbia University Confocal and Specialized Microscopy Shared Resource",
"Confocal and Specialized Microscopy Shared Resource" ;
definition: "Advanced microscope systems for multidimensional optical imaging of living and fixed cells and tissues. Microscopy technologies include confocal, super-resolution (Airyscan and SMLM), TIRF, and wide-field microscopy as well as plate reading and laser capture microdissection. Analysis workstation and software are available, with custom pipeline development for processing, analysis, and visualization." .
SCR:026354 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5944" ;
rdfs:label "Field Museum of Natural History Pritzker Laboratory for Molecular Systematics and Evolution Core Facility" ;
NIFRID:synonym "Field Museum of Natural History Pritzker Laboratory for Molecular Systematics and Evolution",
"Field Museum Pritzker Laboratory for Molecular Systematics and Evolution",
"Pritzker Laboratory for Molecular Systematics and Evolution" ;
definition: "Interdepartmental, multiuser core facility dedicated to genetic analysis and preservation of the world's biodiversity. Provides equipment used in molecular biology enabling to pursue study of genetic diversity throughout tree of life and at all taxonomic levels, from populations to classes to phyla of organisms." .
SCR:026355 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3022" ;
rdfs:label "Benaroya Research Institute Human Immunophenotyping Core Facility" ;
NIFRID:synonym "Benaroya Research Institute Human Immunophenotyping Core",
"Human Immunophenotyping Core" ;
NIFRID:abbrev "IHP" ;
definition: "Core provides access to technologies and services enabling study of human immune-mediated diseases. Offers expertise in human immunology along with innovative assays and technology. Core specializes in high-parameter single-cell assays utilizing conventional, spectral, and mass cytometry (CyTOF), which can be paired with genomic and bioninformatic analyses through our connections with other outstanding BRI cores. Other services include cell sorting, short-term in vitro assays, DNA/RNA extraction, qPCR, and ELISA or multiplex protein analysis (Luminex), guidance on study design and training on new technologies, execution, data analysis and interpretation." .
SCR:026356 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HSSM" ;
NIFRID:synonym "Hierarchical Sequential Sampling Models" ;
definition: "Software Python toolbox for fitting Hierarchical Sequential Sampling Models using Bayesian methods." .
SCR:026357 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GxEScanR" ;
definition: "Software R package to run genome-wide association study (GWAS) and genome-wide by environment interaction study (GWEIS) scans using genetic data stored in binary dosage file." .
SCR:026358 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3033" ;
rdfs:label "University of Kentucky Flow Cytometry and Immune Monitoring Core Facility" ;
NIFRID:synonym "UK Flow Cytometry & Immune Monitoring core facility",
"University of Kentucky Flow Cytometry and Immune Monitoring Core (FCIM-UKY)",
"University of Kentucky Flowcytometry and Immune Monitoring Core" ;
NIFRID:abbrev "FCIM",
"FCIM-UKY" ;
definition: "Core supports research requiring flow cytometry techniques in basic and translational research. Provides access to equipment, and technical and scientific expertise for comprehensive analysis of immune responses. Uses standardized and optimized SOPs and study protocols to obtain reproducible and quality results for our collaborating investigators in cost-effective manner." .
SCR:026359 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3034" ;
rdfs:label "University of Kentucky Research Mass Spectrometry and Proteomics Core Facility" ;
NIFRID:synonym "Research Mass Spectrometry and Proteomics Core",
"University of Kentucky Research Mass Spectrometry and Proteomics Core" ;
definition: """Mass spectrometry core lab performing proteomics, small molecule, and lipidomic analyses.
Provides access to advanced analytical equipment for quantitation and structural analysis. Offers assistance in sample preparation, method development, acquisition, and data analysis.""" .
SCR:026360 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_707" ;
rdfs:label "Northwestern University Keck Interdisciplinary Surface Science Core Facility" ;
NIFRID:synonym "Keck Interdisciplinary Surface Science Facility (Keck-II)",
"Northwestern University Keck Interdisciplinary Surface Science Facility (Keck-II)" ;
NIFRID:abbrev "Keck-II" ;
definition: "Core facilitates research, collaboration, education and outreach in all science from soft biological matter to hard physical matter, specializing in surface analysis and nano-scale characterization. Instruments include Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), X-ray Photoelectron Spectroscopy (XPS), Fourier Transform Infrared Spectroscopy (FT-IR), Confocal Raman System, High Resolution Stylus Profilometer, 3D Optical Microscope, Spectroscopic Ellipsometer, and Zetasizer.Staff provides hand-on training, collaboration and assistance." .
SCR:026361 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_314" ;
rdfs:label "Northwestern University Electron Probe Instrumentation Center EPIC Core Facility" ;
NIFRID:synonym "Electron Probe Instrumentation Center - EPIC - part of NUANCE",
"Northwestern University Electron Probe Instrumentation Center - EPIC - part of NUANCE" ;
NIFRID:abbrev "EPIC" ;
definition: "Offers wide range of electron microscopy (both transmission and scanning), accessory instrumentation, and expertise to the scientific and engineering community through education, collaboration, and service. Provides facilities for preparation and examination of many types of bulk and thin specimens (foils/films), fine particles, and replicas, including biological materials, by transmission and scanning electron microscopy." .
SCR:026362 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3023" ;
rdfs:label "Massachusetts General Hospital NGS Core Facility" ;
NIFRID:synonym "Massachusetts General Hospital MGH NGS Core",
"Massachusetts General Hospital NGS Core",
"MGH NGS Core" ;
definition: "Core offers sequencing, upstream library construction (bulk RNA/DNA, single-cell), and post-sequencing analysis. Core uses Illumina NextSeq 2000 sequencers (and a MiSeq). Single-cell (fresh, frozen, FFPE) libraries (3' & 5' RNA-Seq, CITE-Seq, ATAC-Seq, Multiome, FLEX) are made with 10X Chromium X." .
SCR:026363 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mice" ;
NIFRID:synonym "mice: Multivariate Imputation by Chained Equations",
"Multivariate Imputation by Chained Equations" ;
NIFRID:abbrev "MICE" ;
definition: "Software package implements method to deal with missing data. The package creates multiple imputations (replacement values) for multivariate missing data.Various diagnostic plots are available to inspect the quality of the imputations." .
SCR:026364 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3035" ;
rdfs:label "Field Museum of Natural History Biomolecular Clean Laboratory Core Facility" ;
definition: "Facility dedicated to study of degraded and low DNA yield samples, such as environmental DNA, historical DNA, or ancient DNA. Offers positive pressure lab spaces that follow strict decontamination procedures to prevent human, bacterial, and fungal contamination. It is physically isolated from tissue samples or polymerase chain reaction (PCR) products to avoid contamination from samples with higher DNA concentration and quality. The space has dedicated equipment necessary for DNA extraction and PCR-free sample preparation." .
SCR:026365 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nanion | Patchliner" ;
NIFRID:synonym "Patchliner" ;
definition: """Fully automated patch clamp system which records from either 4 or 8 cells simultaneously.
Automated electrophysiology machine.""" .
SCR:026366 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "meryl" ;
definition: "Software application as genomic k-mer counter and sequence utility." .
SCR:026367 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FCS-GX" ;
NIFRID:synonym "Foreign Contamination Screening - GX" ;
definition: "Software Foreign Contamination Screening - GX source code. Part of NCBI’s Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes." .
SCR:026368 a NLX:63400,
owl:NamedIndividual ;
definition: "Standalone tool to compute assembly summary statistics and manipulate assembly sequences in FASTA, FASTQ or GFA [.gz] format. Gfastats stores assembly sequences internally in a GFA-like format. This feature allows gfastats to seamlessly convert FAST* to and from GFA [.gz] files. Gfastats can also build an assembly graph that can in turn be used to manipulate the underlying sequences following instructions provided by the user, while simultaneously generating key metrics for the new sequences." .
SCR:026369 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MitoHiFi" ;
definition: "Software Python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads. Used to find, circularise and annotate mitogenome from PacBio assemblies." .
SCR:026370 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "compleasm" ;
definition: "Software genome completeness evaluation tool based on miniprot." .
SCR:026371 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3036" ;
rdfs:label "Seattle Childrens Research Institute Behavioral Phenotyping Core Facility" ;
NIFRID:synonym "Behavioral Phenotyping Core",
"Seattle Childrens Research Institute Behavioral Phenotyping Core" ;
NIFRID:abbrev "BPC" ;
definition: "Core dedicated to the protocol driven collection, analysis, and reporting of behavioral data using a blend of classic and innovative assays. Supports neuroscience, psychology, pharmacology, genetics, cancer, and development by providing advanced tools and expertise for the precise measurement and interpretation of behavior." .
SCR:026372 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3037" ;
rdfs:label "UCSF Helen Diller Family Comprehensive Cancer Center Flow and Cell Sorting Core Facility" ;
definition: "Provides access and training on two FACS Calibur benchtop cytometers, one FACS Canto II multi-laser digital cytometer, one FACS Aria II cell sorter, one FACS Aria III cell sorter, and one Sony SH800 cell sorter. These systems are primarily used for the rapid analysis and sorting of single-cell suspensions. To analyze the light scatter and fluorescence characteristics of a cell population, one of the benchtop machines is appropriate. For more complex assays requiring more than four differentiating markers, then the high-end multi-laser Canto II system would work well. To rapidly retrieve or sort a particular sub-group of cells from a mixed sample, then a cell sorter would be required." .
SCR:026373 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clearsynth" ;
definition: "Company from India specializes in Innovative Organic Chemistry and Synthesis of Unique Complex Molecules, Stable Isotope Labelled compounds and Metabolites." .
SCR:026374 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Synbio Technologies " ;
definition: "DNA synthesis company provides comprehensive services including gene synthesis, protein expression, gene editing, etc., supporting one-stop solutions for global users." .
SCR:026375 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Dabur Research Foundation" ;
definition: "Dabur Research Foundation (DRF), established in 1979, is Indian Contract Research Organization offering comprehensive preclinical services in Drug Discovery and Development. Focused on identifying potential lead molecules and developing drugs to conducting IND enabling studies." .
SCR:026376 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Delter" ;
definition: "Software tool to filter short artificial deletion variations by Oxford Nanopore Technologies (ONT) R9 and R10 flow cells and chemistries." .
SCR:026377 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PretextGraph" ;
definition: "Software tool to embed bedgraph data into Pretext contact maps." .
SCR:026378 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rapid curation" ;
definition: "Repository of software curation tools. Contains curation tools guide." .
SCR:026379 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID: grid.425274.2; ISNI: 0000 0004 0620 5939; Wikidata: Q3152211;" ;
rdfs:label "Paris Brain Institute" ;
definition: "Institute was created to support and develop research on the brain and nervous system, serving collaborative, interdisciplinary model conducive to innovation and breakthrough discoveries." .
SCR:026380 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_330" ;
rdfs:label "Northwestern University NUANCE SPID Core Facility" ;
definition: "SPID provides imaging instrumentation and support facilities for atomic to molecular imaging. Supports broad range of nanoscale science and technology characterization needs at nanoscale by providing resources coupled with expert staff. Research at SPID encompasses physical and chemical sciences, engineering and life sciences, and has a strong inter-disciplinary emphasis." .
SCR:026381 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Conos" ;
definition: "Software R package for joint analysis of multiple single-cell RNA-seq datasets. Used to wire together large collections of single-cell RNA-seq datasets, which allows for both identification of recurrent cell clusters and propagation of information between datasets in multi-sample or atlas-scale collections." .
SCR:026382 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Northwestern University Program Evaluation Core Facility" ;
NIFRID:synonym "Program Evaluation Core" ;
definition: "Program Evaluation Core staff and faculty collaborate with investigators to design evaluations plans for grant proposals, collect, analyze and interpret data, write reports and co-develop strategies for program improvement." .
SCR:026383 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Kentucky Magnetic Resonance Imaging and Spectroscopy Center Core Facility" ;
NIFRID:synonym "Magnetic Resonance Imaging and Spectroscopy Center (MRISC)" ;
definition: "Service and consultation core supporting basic and clinical research. Provides advanced 3T Siemens PRISMA scanner with high performance gradients, echo-planar whole body imaging and hydrogen spectroscopic capabilities for both human and animal studies. For dedicated animal studies Bruker/Siemens 7T MR scanner has been installed." .
SCR:026384 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ECHO Genome Annotation" ;
definition: "Software comprehensive genome annotation pipeline with precision control through semi-supervised random forest gene model filter." .
SCR:026385 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Protheragen Infectious Diseases" ;
definition: "Commercial company dedicated to development of new products and technologies, with steadfast commitment to continuous innovation. Provides assistance to researchers from pharmaceutical, biotechnology, government, and academic organizations worldwide in expediting the drug discovery and development process for infectious diseases." .
SCR:026386 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "CD Biosynsis" ;
definition: "Biotechnology company specialises in providing protein expression services. Services include all steps from gene expression and purification to protein expression and purification, including selection and optimization of multiple expression platforms including bacterial, yeast, insect cell, and mammalian cell platforms." .
SCR:026387 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Ace Therapeutics" ;
definition: "Ace Therapeutics offers biomarker services for anti-psychotic drug development. Provides psychiatric biomarker testing services. Can perform experiments from variety of biological samples: tissues, cell lines, and RNA." .
SCR:026392 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "High-Precision Optical Fiber-Based Lickometer" ;
definition: "Low-cost open-source lickometer that combines restricted infrared beam defined by optical fibers, with poke design that allows easy access to the tongue while limiting access of other body parts and external light sources. This device also includes features for detecting nose pokes and presenting visual cues during behavioral tasks. Used to study lick microstructure in combination with other techniques, such as imaging of neural activity, in freely moving mice." .
SCR:026393 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3038" ;
rdfs:label "Paris Brain Institute Quantitative Cellular and Molecular Imaging Core Facility" ;
NIFRID:abbrev "ICM.Quant" ;
definition: "Core provides expertise in optical microscopy, electron microscopy, and image analysis for neuroscience research. The platform is open to all researchers. Offers access to advanced technologies, including electron microscopy, confocal microscopy, two-photon imaging, and super-resolution microscopy." .
SCR:026394 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3039" ;
rdfs:label "Paris Brain Institute PRISME Core Facility" ;
definition: "Core facility dedicated to the study of human cognition and normal and pathological human behavior either via computer tests or in simulations, including using virtual reality." .
SCR:026395 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3040" ;
rdfs:label "Ludwig Maximilian University Hospital Munich Flow Cytometry Core Facility" ;
NIFRID:synonym "Core Facility Durchflusszytometrie des Klinikums",
"Core Facility Flow Cytometry of the LMU Clinic" ;
definition: "Core Facility for flow cytometry at the Ludwig-Maximilian-University Hospital Munich. Provides access and services for flow cytometry and cell sorters." .
SCR:026396 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3041" ;
rdfs:label "Salk Institute Single-Cell and Spatial Omics Core Facility" ;
NIFRID:synonym "Single-Cell and Spatial Omics Core",
"Single-Cell and Spatial Omics Core Facility at the Salk Institute" ;
NIFRID:abbrev "OMICS" ;
definition: "Core offers single-cell and spatial omics services. Provides consultation, expert guidance in experimental design, and technologies tailored for innovative research in genomics. Facility is equipped with 10x Genomics Chromium X and Xenium systems, Vizgen MERSCOPE, Bruker/NanoString GeoMx Digital Spatial Profiler, and nCounter MAX." .
SCR:026397 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3042" ;
rdfs:label "University of Louisville Medicinal Chemistry Core Facility" ;
definition: "Core Facility provides essential medicinal and organic chemistry support for drug discovery. The core specializes in the lead optimization of an initial lead compound to improve biological activity and drug-like properties, and to elucidate structure activity relationships. Other services include the design and synthesis of fluorescent and isotopic probes, compound scale up (1 – 5 grams), and custom synthesis." .
SCR:026398 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | Stratagene Mx3000P qPCR cycler" ;
definition: "Real-time polymerase chain reaction (PCR) system used for quantitative PCR (qPCR) to measure and analyze nucleic acids in biological samples. Applications include gene expression analysis, pathogen detection, and DNA methylation analysis." .
SCR:026399 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_uScopeMXII-20" ;
rdfs:label "Microscopes International | uScopeMXII-20 Digital Microscope" ;
NIFRID:synonym "uScopeMXII-20 Digital Microscope" ;
definition: "Small size uScopeMXII-20 digital microscope comes with 20x/0.4NA 160mm conjugate objective. This model is suited to applications where very high depth of field is required. The uScopeMXII-20 has wider depth of field than higher power models of the uScopeMXII. So, tissue samples and smears can be thicker with more of the image in focus. This unit is able to produce very high-quality digital microscope while browsing or scanning an area of interest." .
SCR:026400 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bakta" ;
definition: "Software tool for rapid and standardized annotation of bacterial genomes via alignment free sequence identification. Implemented in Python 3 and runs on MacOS and Linux systems." .
SCR:026401 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoDockTools " ;
NIFRID:synonym "AutoDockTools: the Graphical User Interface for AutoDock" ;
NIFRID:abbrev "ADT" ;
definition: "Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure." .
SCR:026402 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3032" ;
rdfs:label "Children's Hospital of Philadelphia Research Institute CHOP Gastrointestinal Epithelium Modeling Core Facility" ;
NIFRID:synonym "Children's Hospital of Philadelphia Research Institute CHOP Gastrointestinal Epithelium Modeling (GEM) Core",
"CHOP Gastrointestinal Epithelium Modeling (GEM) Core" ;
NIFRID:abbrev "GEM" ;
definition: "Core is component of the GEM Program collaborative research effort focused on accelerating discovery and innovation using patient tissue-derived organoids. GEM Core staff generate and maintain living biobank of tissue-derived organoids with matched original tissue and blood specimens and provide access to specialized training, protocols, and reagents." .
SCR:026403 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sylvan" ;
definition: "Software comprehensive genome annotation pipeline with precision control through semi-supervised random forest gene model filter." .
SCR:026404 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3056" ;
rdfs:label "University of Texas Southwestern Medical Center Dallas Metabolic Phenotyping Core Facility" ;
NIFRID:synonym "University of Texas Southwestern Medical Center Dallas Metabolic Phenotyping Core",
"UTSW Metabolic Phenotyping Core" ;
definition: "Academic core facility provides analytical and phenotypical measures to the scientific community. Provides services related to metabolic disorders (diabetes and obesity), cancer, aging neurological disorders, etc. Provides letters of support for grant proposals and research applications." .
SCR:026405 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3057" ;
rdfs:label "University of Kentucky Light Microscopy Core Facility" ;
definition: "Core facility offers fluorescence, confocal, super resolution, multi-photon, laser capture and atomic force microscopy. Provides central preparatory laboratory and high-end computer workstations for data analysis and image processing. Technical support ranges from investigator training on instrumentation, allowing independent use, to complete processing of samples and final imaging by facility staff. The facility is GRP accredited, undergoes annual compliance checks and provides extensive standard operating procedures for all instrumentation." .
SCR:026407 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WGAND" ;
NIFRID:synonym "Weighted Graph Anomalous Node Detection",
"Weighted Graph Anomalous Node Detection (WGAND)" ;
definition: "Software tool designed to identify anomalous nodes in weighted graphs. By estimating expected edge weights and analyzing deviations, WGAND scores nodes to detect anomalies." .
SCR:026408 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LongReadSum" ;
definition: "Software fast and flexible QC and signal summarization tool for long read sequencing data." .
SCR:026409 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpheroidSegDeDeb" ;
definition: "Software minimal tool for segmentation of irradiated tumor spheroids using optimized U-Net." .
SCR:026410 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PVGA" ;
definition: "Software tool as virus-focused assembler that does both assembly and polishing into unified workflow. Viral genome assembler enables detection of subtle genomic variations that can significantly impact viral function and pathogenicity." .
SCR:026411 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ClipKIT" ;
definition: "Software fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others. Multiple sequence alignment-trimming algorithm for accurate phylogenomic inference." .
SCR:026412 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3058" ;
rdfs:label "Paris Brain Institute Electrophysiology Core Facility" ;
NIFRID:synonym "ePHYS Electrophysiology Platform" ;
NIFRID:abbrev "ePHYS" ;
definition: "Core develops solutions to meet your needs in electrophysiology data. Provides electrophysiology services to the neuroscience scientific community. Core has standard recording equipment such as patch clamp techniques or electroencephalographic (EEG) recordings." .
SCR:026413 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_506" ;
rdfs:label "Massachusetts Institute of Technology MIT BioMicro Center Core Facility" ;
NIFRID:synonym "Massachusetts Institute of Technology MIT BioMicro Center",
"MIT BioMicro Center" ;
definition: "Integrated genomics/bioinformatics facility located at MIT. Provides Illumina HiSeq2000, NextSeq500 and MiSeq sequencing instruments as well as PacBio Sequel and Oxford Minion. Provides services in preparing Illumina libraries for high-throughput sequencing samples using several different methods, supports technologies including Agilent BioAnalyzer, AATI Fragment Analyzer, AATI FemtoPulse, Roche LC480 qPCR machines, automated liquid handling through Tecan Evo150s, TTP Labtech Mosquito HV. Supports 10X Chromium and single cell work using NamoCell single cell dispenser and custom oligo synthesis using Dr.Oligo 192. Supports informatics and bioIT tools. Core administers ~2PB of data storage on several platforms, including 600TB Isilon server. Hosts 400 processor Dell cluster and Dell Quad Core 2950 application server for Illumina sequencing and bioinformatic applications. All application servers and storage servers are interconnected by 1gigabyte private networks or by fiber optic lines and are administered by IT staff that are part of the BioMicro Center. Servers are configurable to provide secure data storage for clinical data if required." .
SCR:026414 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3045" ;
rdfs:label "Northwestern University School of Medicine SBDRC Skin Tissue Engineering and Morphology Core Facility" ;
NIFRID:synonym "Northwestern University SBDRC Skin Tissue Engineering & Morphology (STEM) Core�",
"SBDRC Skin Tissue Engineering & Morphology (STEM) Core" ;
NIFRID:abbrev "STEM" ;
definition: "Core provides services in human skin tissue procurement, isolation, and culture of human and murine skin-derived primary cells, 3D organotypic skin cultures, tissue processing, and basic histologic stains. The Core trains researchers in the development and use of these various techniques." .
SCR:026415 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_511" ;
rdfs:label "Miami University Center for Bioinformatics and Functional Genomics Core Facility" ;
NIFRID:synonym "Center for Bioinformatics and Functional Genomics",
"Miami University Center for Bioinformatics and Functional Genomics" ;
NIFRID:abbrev "CBFG" ;
definition: "Core provides training and equipment. Instruments include Pacific Biosciences VEGA benchtop long-read system, Oxford Nanopore Technologies minION and an Illumina MiSeq Next Generation Sequencing instrumentation, ABI Capillary Electrophoresis Genetic Analyzer (3130xl); an Eppendorf epMotion 5073m NGS liquid handling workstation; Promega MaxwellRSC Nucleic Acid extraction robot; real-time qPCR instruments (Rotor-Gene Q with HRM, Bio-Rad CFX Connect, QuantStudio 7 Flex [384/96 well interchangeable blocks]), and Bio-Rad ddPCR QX200 system, laser Attune NxT Flow Cytometer for analysis, laser BD FACS Melody Flow Cytometer for sorting, UV NanoDrop spectro photometers (ND1000, ND2200), and NanoDrop (ND3300) Fluorospectrophotometer; Promega Quantus, Agilent Bioanalyzer 2100; Covaris M220 Ultrasonic Nucleic Acid Shearer, a Sage BluePippin, seven 96 well gradient capable PCR thermal cyclers, two thermally controlled table top centrifuges capable of accepting 96-well plates used for DNA template preparation; two Eppendorf ThermoMixer C mixing units (384 well PCR to 50 mL tube format), two benchtop micro-centrifuges, Molecular Devices SpectraMax iD5 microplate reader, KTA-FPLC with UV detector and fractions collector, UV-1600PC UV-VIS Spectrophotometer with Sipper module, AlphaInnotechHP Gel Imaging System, Bio-Rad ChemiDoc MP Imaging System, Bio-Rad Dodeca-Cell Criterion PAGE system, several Bio-Rad Mini-Protean Gel Apparatus, Bio-Rad IEF Focusing Cells; numerous power-packs for gel electrophoresis, DNA gel boxes, pipettors, multi-channel pipettors. Provides computers (Linux & Win10), including four Ubuntu O/S based workstations for genome assembly and related bioinformatics analyses. CBFG maintains paid licenses for CLC Genomics Workbench, CLC Main Workbench, BioBam OmicsBox, SnapGene, FlowJo 10, SoftMax 7.1, Biogazelle qBasePLUS, and CANOCO." .
SCR:026416 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2799" ;
rdfs:label "University of Idaho IIDS Genomics and Bioinformatics Resource Core Facility" ;
NIFRID:synonym "IIDS Genomics and Bioinformatics Resource Core",
"University of Idaho IIDS Genomics and Bioinformatics Resource Core" ;
definition: "Core provides access to technology, experience, and expertise in molecular biology methods.Offers expertise in bioinformatics needed to acquire, analyze, and visualize data generated from high throughput technologies used in genomics research. Services include Illumina sequencing,Bioinformatics and statistical analysis,PacBio sequencing,Oxford Nanpore sequencing,High-throughput DNA and RNA library preparation,Double-barcoded amplicon sequencing. GBRC also participates in many of the bioinformatic analyses from the projects including De novo genome and transcriptome assembly, RNAseq differential expression analysis, SNP calling, RAD sequence analysis, Dual-barcoded amplicon community analysis, Phylogenetic analysis, CRISPR transformant profiling,Speed congenics, Novel agriculture virus detection and assembly." .
SCR:026417 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3047" ;
rdfs:label "Northwestern University School of Medicine SBDRC Gene Editing, Transduction and Nanotechnology Core Facility" ;
NIFRID:synonym "GET-IN Core",
"SBDRC Gene Editing",
"Transduction and Nanotechnology (GET iN) Core" ;
NIFRID:abbrev "GET iN" ;
definition: "Core provides services and R&D in cell engineering and gene expression modifications by using retro- and lentivirus, adenovirus, adeno-associated virus, shRNA/MIR and CRISPR-Cas9 genome editing methods." .
SCR:026418 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3044" ;
rdfs:label "Emory University EPC Genomics Core Facility" ;
NIFRID:synonym "EPC Genomics Core" ;
definition: "Core offers assistance in experimental design, sample preparation, library prep, sequencing, data analysis and bioinformatics. Provides experience working with non-human primate genomes and other non-standard genomes in addition to the more commonly studied human and mouse genomes. Provides expertise in the use of transcriptomics and genomics to study immune responses and repertoires.Houses Illumina NovaSeq 6000 and Illumina MiSeq." .
SCR:026419 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3046" ;
rdfs:label "Northwestern University School of Medicine SBDRC Translating Experimental Skin Testing with Immune Tracing, Informatics, and Technology Core Facility" ;
NIFRID:synonym "and Technology (TEST IT�) Core�",
"Informatics",
"SBDRC Translating Experimental Skin Testing with Immune Tracing" ;
NIFRID:abbrev "TEST IT" ;
definition: "Core provides service, equipment, protocols, and training to help investigators differentiate healthy skin from skin with abnormal immune responses at the cellular and molecular level, to enable biomarker identification as well as to increasing our knowledge of skin immune responses." .
SCR:026421 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TAMU College of Medicine Flow Cytometry and Cell Sorting Core Facility" ;
NIFRID:synonym "TAMU College of Medicine Flow Cytometry and Cell Sorting Facility",
"Texas A and M University College of Medicine Flow Cytometry and Cell Sorting Facility" ;
definition: "College of Medicine Flow Cytometry and Cell Sorting Facility (formerly SMACC) at Texas A&M Health provides cell analysis and cell sorting services and is managed by Department of Microbial Pathogenesis and Immunology." .
SCR:026422 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_633" ;
rdfs:label "University of Oklahoma Health Sciences Center OK INBRE Data Science Core Facility" ;
NIFRID:synonym "OK INBRE Data Science Core",
"University of Oklahoma Health Sciences Center OK INBRE Data Science Core" ;
definition: "Core provides data science analysis support, training and promotion of data science education for undergraduate and high school students in the state of Oklahoma. Services include 1) Global analysis of gene expression data using custom spotted microarrays and commercial Affymetrix and Combimatrix arrays to examine gene expression patterns in mice, adenovirus-infected cells, and a variety of bacterial systems. 2) Genome annotation and comparative genomics analysis, including studies on several bacterial and viral pathogens important for human and agricultural disease. Informatics support for genome sequencing projects, annotation support, and post-sequence studies. Bioinformatics educational include analysis of laboratory data for DNA barcoding, instructional materials for protein structure analyses and phylogenetic analyses, and microbial and viral genome sequence annotation and analysis, career counseling to undergraduate students, both individually and in large groups, supervision of undergraduate summer interns and high school interns to enhance interest in pursuing bioinformatics as a career path, providing instructional materials for high school teachers interested in incorporating bioinformatics into their lesson plans." .
SCR:026423 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Tecnai_G2_Spirit_BioTwin" ;
rdfs:label "FEI | Tecnai G2 Spirit BioTwin transmission electron microscope" ;
definition: "Transmission electron microscope designed for general-purpose, high-resolution imaging of both biological and non-biological samples, offering capabilities like bright-field, dark-field, and diffraction modes, typically utilizing LaB6 electron gun and operating within voltage range of 20-120kV; it's particularly well-suited for analyzing the ultrastructure of delicate specimens with high contrast due to its \"BioTwin\" features, allowing for low-dose imaging of beam-sensitive samples like cryo-preserved biological materials." .
SCR:026424 a owl:NamedIndividual ;
rdfs:label "Penn State Institute of Computational and Data Sciences Roar Core Facility" ;
NIFRID:synonym "Roar Core Facility" ;
definition: "Provides advanced cyberinfrastructure resources including large scale compute and data storage. to the Penn State University research community under the operation of the Institute of Computational and Data Sciences" .
SCR:026425 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Penn State University Center for Immersive Experiences Core Facility" ;
definition: "Visualization Hub provides immersive technologies, knowledge, and skills to the Penn State community with the goal to create leadership in immersive experiences by advancing the underlying science and integrating it into the academic spectrum through research, education, and outreach. Provides research and development support for immersive technology projects. Projects can range from developing virtual reality (VR), augmented reality (AR), mixed reality (MR) applications or experiences, access to VR/AR/MR hardware, digital twins, creating 3D models, etc." .
SCR:026426 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pennsylvania State University RISE Core Facility" ;
NIFRID:synonym "Pennsylvania State University Research Innovations with Scientists and Engineers Core Facility",
"Research Innovations with Scientists and Engineers" ;
NIFRID:abbrev "RISE" ;
definition: "Core team of computational scientists and software engineers provide serivces to bring high-performance computing to research projects under the Institute of Computational and Data Sciences at the Pennsylvania State University." .
SCR:026427 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_S220_Focused" ;
rdfs:label "Covaris | S220 Focused Ultrasonicator" ;
NIFRID:synonym "S220 Focused Ultrasonicator" ;
definition: "S220 Focused-ultrasonicator is based on Covaris Adaptive Focused Acoustics technology. Instrument designed for tissue homogenization, cell lysis, DNA or chromatin shearing, and other sample preparation steps. The system is comprised of the Treatment System which delivers the acoustic energy to the sample, the Safety System which protects users from inadvertently contacting the high intensity acoustic energy, and the Computer and Application Software which provides users an interface to control the device." .
SCR:026428 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Observatory Toolbox" ;
definition: "Software MATLAB toolbox for interacting with the Allen Brain Observatory." .
SCR:026429 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3049" ;
rdfs:label "Virginia Commonwealth University VCU Bioimaging and Applied Research Core Facility" ;
NIFRID:synonym "VCU Bioimaging and Applied Research Core (BARC)",
"Virginia Commonwealth University VCU Bioimaging and Applied Research Core (BARC)" ;
NIFRID:abbrev "BARC" ;
definition: "Core offers comprehensive instrumentation and technical support for all aspects of in vitro and in vivo pre-clinical non-human anatomical and molecular imaging. Studies may be conducted on samples prepared to exhibit characteristic features for a particular imaging modality. Within the intact environment, physiological and pathophysiological activity may be observed through imaging or numerous biological pathways and interactions involved in injury and disease progression, such as traumatic brain injury, cardiac disease, tumorigenesis, and therapeutic interventions." .
SCR:026430 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Strainy " ;
definition: "Software tool for phasing and assembly of bacterial strains from long-read sequencing data (either Oxford Nanopore or PacBio). Given reference (or collapsed de novo assembly) and set of aligned reads as input, tool produces multi-allelic phasing, individual strain haplotypes and strain-specific variant calls. Used for phasing and assembly of strain haplotypes from long-read metagenome sequencing." .
SCR:026431 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Polars" ;
definition: "Open-source DataFrame library for data manipulation known for being one of the fastest data processing solutions on single machine. Features well-structured, typed API that is both expressive and easy to use. DataFrame interface on top of OLAP Query Engine implemented in Rust using Apache Arrow Columnar Format as the memory model." .
SCR:026432 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eastern Cooperative Oncology Group Performance Status Scale" ;
NIFRID:synonym "ECOG Performance Status Scale" ;
definition: "ECOG Performance Scale describes patient’s level of functioning in terms of their ability to care for themself, daily activity, and physical ability (walking, working, etc.). Standard criteria for measuring how the disease impacts patient’s daily living abilities. Used to assess the functional status of patient." .
SCR:026433 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WHODrug Global" ;
NIFRID:synonym "WHO Drug Dictionary",
"World Health Organization Drug Dictionary" ;
definition: "International reference guide for medicinal products maintained by the Uppsala Monitoring Centre. With its unique drug code hierarchy and extensive coverage, it provides consistent drug dictionary with exact terminology when coding concomitant medications. Dictionary is used to identify drug names and evaluate medicinal product information, including active ingredients and products’ anatomical and therapeutic classifications, from nearly 150 countries. Data covers both conventional medicines and herbal remedies. Data is continuously updated, with new releases twice a year, on 1 March and 1 September." .
SCR:026434 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID: grid.420224.2",
"ISNI: 0000 0001 2153 0703",
"Wikidata: Q7899169" ;
rdfs:label "Uppsala Monitoring Centre; Uppsala; Sweden" ;
NIFRID:abbrev "UMC" ;
definition: "Uppsala Monitoring Centre, located in Uppsala, Sweden, is the field name for the World Health Organization Collaborating Centre for International Drug Monitoring. UMC works by collecting, assessing and communicating information from member countries' national pharmacovigilance centres in regard to benefits, harm, effectiveness and risks of drugs since 1978." .
SCR:026435 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Response Evaluation Criteria in Solid Tumors" ;
NIFRID:abbrev "RECIST" ;
definition: "Provides methodology to evaluate activity and efficacy of new cancer therapeutics in solid tumors, using validated and consistent criteria to assess changes in tumor burden. RECIST Working Group comprises representatives of the European Organization for Research and Treatment of Cancer (EORTC), National Cancer Institute (NCI) of the United States and Canadian Cancer Trials Group (CCTG), as well as several pharmaceutical companies. Its mission is to ensures that RECIST undergoes continued testing, validation and updating." .
SCR:026436 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NormiRazor" ;
definition: "Web-based tool that screens for experiment-specific reference genes. Tool applying GPU-accelerated computing for determination of internal references in microRNA transcription studies." .
SCR:026437 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ Rapid2" ;
rdfs:label "Magstim | Rapid2 stimulator" ;
NIFRID:synonym "Rapid2 stimulator" ;
definition: "Device to generate repetitive transcranial magnetic stimulation and is used in numerous fundamental and clinical research studies worldwide. Combines stimulation frequencies from 1Hz to 100Hz with touch screen interface which controls every aspect of stimulator’s control and operation." .
SCR:026440 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3059" ;
rdfs:label "Howard Hughes Medical Institute at Janelia Research Campus Viral Tools Shared Resource Core Facility" ;
NIFRID:synonym "Janelia Viral Tools" ;
definition: "Core specializes in custom production with high titer, high standards, and fast turnaround. Provides services from designing viral constructs to troubleshooting experiments. Offers routine adeno-associated virus (AAV), rabies, and lenti/retrovirus vector production. Other viral vectors can be produced on as-needed basis." .
SCR:026441 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "regplot" ;
definition: "Software R package to plot regression nomogram of regression objects. Covariate distributions are superimposed on nomogram scales and the plot can be animated to allow on-the-fly changes to distribution representation and to enable outcome calculation." .
SCR:026444 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "timeROC" ;
definition: "Software R package for estimation of time-dependent ROC curve and area under time dependent ROC curve in the presence of censored data, with or without competing risks. Confidence intervals of AUCs and tests for comparing AUCs of two rival markers measured on the same subjects can be computed, using the iid-representation of the AUC estimator." .
SCR:026445 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NC4gate" ;
definition: "Code for testing and operating NC4gate modules of modular gate system for autonomous control of rodent behavior. Fully customizable gate system that can be used in behavioral experiments involving rodent mazes (T-maze, Y-maze, radial arm, etc.)." .
SCR:026446 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xCell " ;
definition: "Software R package for generating cell type scores and R scripts for development of xCell. Web tool that performs cell type enrichment analysis from gene expression data for immune and stroma cell types. Used for Cell types enrichment analysis." .
SCR:026447 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hdf5r" ;
definition: "Software R package as data model, library and file format for storing and managing large amounts of data." .
SCR:026448 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hgu133plus2" ;
definition: "Software R package for Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data assembled using data from public repositories." .
SCR:026449 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Genexus" ;
rdfs:label "Thermo Fisher | Ion Torrent Genexus Integrated Sequencer" ;
NIFRID:synonym "Genexus Integrated Sequencer" ;
definition: "Ion Torrent Genexus Integrated Sequencer is part of the Ion Torrent Genexus System. Instrument that can automate library construction, templating, and sequencing in single-instrument run." .
SCR:026450 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Optolane | LOAA digital real-time PCR" ;
definition: "Instrument engineered to amplify specific genes (DNA or RNA), enable real-time detection and estimate absolute quantities." .
SCR:026451 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Allegra_X-12R" ;
rdfs:label "Beckman Coulter | Allegra X-12R Refrigerated Centrifuge" ;
NIFRID:synonym "Beckman Coulter Allegra X-12 R" ;
definition: "Benchtop refrigerated centrifuge designed for routine processing, cell isolation, binding studies and separation, and more applications." .
SCR:026452 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Element | AVITI24 system" ;
NIFRID:synonym "AVITI24" ;
definition: "Element AVITI24 system is the benchtop platform enabling high-quality, low-cost sequencing and single cell multiomics in one powerful system." .
SCR:026453 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Element Biosciences" ;
definition: "Biotechnology company in San Diego, California focused on developing disruptive DNA sequencing and other omics technology for research markets." .
SCR:026454 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_API 4000 LC-MS/MS" ;
rdfs:label "SCIEX | API 4000 LC-MS-MS System" ;
NIFRID:synonym "API 4000 LC-MS-MS System" ;
definition: "Liquid chromatography-mass spectrometry (LC-MS/MS) system manufactured by AB Sciex, commonly used in research and analytical labs for high-sensitivity detection and quantification of chemical compounds in a sample, often used in fields like pharmaceuticals, environmental testing, and clinical research. atmospheric pressure ionization method used in this system allows for analysis of wide range of molecules." .
SCR:026455 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3054" ;
rdfs:label "Virginia Commonwealth University VCU Structural Biology Core Facility" ;
NIFRID:synonym "VCU Structural Biology Core" ;
definition: "Provides access to equipment, offering researchers capability to determine 3D structure of macromolecules and macromolecular complexes. Provides services for structure-based drug design, protein-ligand or DNA binding studies, testing mutational effects on target macromolecules, and finding the absolute stereochemistry of chiral compounds. Offers training, technical support, and collaborative opportunities, which are crucial for structural biologists and other researchers studying structure of biological macromolecules and other materials.Core encompasses X-ray crystallography, Cryo-Electron Microscopy (Cryo-EM), and Nuclear Magnetic Resonance (NMR) facilities, and is also closely associated with the School of Pharmacy Molecular Modeling facility." .
SCR:026457 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Overture" ;
definition: "Collection of open-source software used to create platforms for researchers to manage, share and access scientific data." .
SCR:026458 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ionicon PTR-TOF Data Analyzer" ;
NIFRID:synonym "Proton-Transfer-Reaction Time-of-Flight mass spectrometer Data Analyzer",
"PTR-TOF Data Analyzer" ;
definition: "Software tool for analyzing HR PTR-TOF-MS data. GUI leads the user through the data analysis process which involves data selection, definition of the data analysis parameters and options, and an interactive edition of the data output. A series of graphical outputs is generated to allow for immediate and visual quality assurance. Output data are generated both in HDF5 and Excel file format." .
SCR:026459 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PTR-TOF_1000_ultra" ;
rdfs:label "IONICON | PTR-TOF 1000 ultra analyzer" ;
NIFRID:synonym "PTR-TOF 1000 ultra" ;
definition: "IONICON ultra-sensitive PTR-TOF-MS - Trace VOC Analyzer,the PTR-TOF 1000 ultra, is the new benchmark for robust and compact real-time volatile organic compounds analyzer. Based on PTR-TOF 1000 platform, the PTR-TOF 1000 ultra offers outstanding sensitivity." .
SCR:026460 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3060" ;
rdfs:label "Cleveland Clinic Research Flow Cytometry Core Facility" ;
definition: "Core provides investigators with resource for quantitative studies of cells, extracellular vesicles, and single-cell gene transcriptome analyses. Offers sample acquisition and analysis, cell sorting, and consultation for experimental design, interpretation and troubleshooting." .
SCR:026461 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scGCM" ;
definition: "Software tool for integrating single-cell multimodal mosaic data. This framework represents single-cell data as graph structures and utilizes graph structures to preserve both local and global features of cells, maintaining topological structure of the data during dimensionality reduction. Additionally, the framework employs neighborhood graphs and contrastive learning to effectively eliminate batch effects." .
SCR:026462 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpecHLA " ;
definition: "Software tool enables full-resolution Human Leukocyte Antigen typing from sequencing data. Reconstructs entire diploid sequences of HLA genes and infers LOH events. Supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data." .
SCR:026463 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ShatterSeek" ;
definition: "Software package to detect chromothripsis in whole-genome sequencing data." .
SCR:026464 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HMMcopy" ;
definition: "Software R package for copy number prediction with correction for GC and mappability bias for HTS data." .
SCR:026465 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Linetogel | Vu-C Chemiluminescence Imaging System" ;
definition: "High-sensitivity imaging device used to imaging device for detecting and analysis signals in biological samples, commonly for Western blotting and other luminescent assays." .
SCR:026466 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sequali " ;
definition: "Software tool for quality control of short- and long-read sequencing data. Fast sequencing data quality metrics. Features adapter search, overrepresented sequence analysis, and duplication analysis and supports FASTQ and uBAM inputs." .
SCR:026467 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BoostNano" ;
definition: "Software segmentation toolkit to segment the Nanopore RNA signal. Preprocessing ONT-Nanopore RNA sequencing reads." .
SCR:026468 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HERB" ;
definition: "High-throughput experiment- and reference-guided database of traditional Chinese medicine." .
SCR:026469 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3061" ;
rdfs:label "University of Texas Institute for Personalized Cancer Therapy Cancer Genomics Laboratory Core Facility" ;
definition: "Provides services and instrumentation including Illumina Next-Generation Sequencing, Single Cell Analysis and Spatial Transcriptomics. These techniques are developed and optimized by our lab scientists to deliver the highest-possible quality sequencing data from a wide variety of sample types such as peripheral blood, bone marrow, fresh frozen tissue and FFPE-derived tumor samples." .
SCR:026470 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggtext" ;
definition: "Software R package that enhances text rendering in ggplot2 by allowing the use of Markdown, HTML, and rich text formatting for annotations, labels, and titles in plots." .
SCR:026471 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggsci" ;
definition: "Software R package that provides scientific-themed color palettes for ggplot2, offering visually appealing and publication-quality color schemes inspired by scientific journals and data visualization standards." .
SCR:026472 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chronos-Fit software" ;
definition: "Software tool for analysis of biological rhythms, particularly circadian rhythms, using curve fitting methods to model time-series data and determine key parameters such as period, amplitude, and phase." .
SCR:026473 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Heart Rate Variability Analysis Software" ;
NIFRID:synonym "HRV Analysis Software" ;
definition: "Software tool used to assess heart rate variability." .
SCR:026474 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "BrainLab" ;
definition: "Privately held German medical technology company headquartered in Munich, Bavaria. Brainlab develops software and hardware for radiotherapy and radiosurgery, and the surgical fields of neurosurgery, ENT and craniomaxillofacial, spine surgery, and traumatic interventions. Brainlab software and hardware devices create and enhance data to improve critical surgeries, radiosurgery treatments and operating room efficiency." .
SCR:026475 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3065" ;
rdfs:label "Augusta University Therapeutics Core Facility" ;
definition: "Core offers services including assay development, FDA-drug library screening, unbiased compound screening, high-content imaging and screening. Facility can empower researchers to repurpose existing FDA-approved drugs and discover new compounds for drug development. Provides affordable platform for discovering therapeutic targets and interventions, supporting drug development from target identification to screening and validation. Features HTS facilities, including Biomek i7 Liquid Handling system, Pherastar FSX plate reader, ImageXpress Micro Confocal, and Pala cell sorter." .
SCR:026476 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MIIT" ;
NIFRID:synonym "Multi-omics Imaging Integration Toolset" ;
definition: "Software Python framework for integratig spatially resolved multi-omcis data. Framework capable of coordinating different spatial resolutions and sampling organizations between different spatial modalities to create one spatial omics dataset." .
SCR:026477 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GreedyFHist" ;
definition: "Algorithm for registration of stained fresh frozen serial images. Used for registration of stained histology images." .
SCR:026478 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sylph" ;
definition: "Software tool for ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash. Species-level metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. Offers precise, efficient profiling with accurate containment ANI estimation even for low-coverage genomes." .
SCR:026481 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bio2zarr" ;
definition: "Software tool to convert bioinformatics file formats to Zarr." .
SCR:026482 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "vcztools" ;
definition: "Software tool for partial reimplementation of bcftools for VCF Zarr." .
SCR:026483 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3070" ;
rdfs:label "Augusta University Integrated Genomics Shared Resource Core Facility" ;
NIFRID:synonym "Integrated Genomics Shared Resource" ;
definition: "Core offers services from sample processing from both fresh and frozen, as well as fixed cells or tissues to library preparation and next-generation sequencing (NGS) for bulk DNA/RNA sequencing and single-cell/nuclei sequencing. For single-cell studies, core is equipped with Chromium X system from 10X Genomics. Sequencing capabilities include Illumina Novaseq6000 and NextSeq 500. Offers single cell spatial transcriptomics with CosMx SMI platform. Other equipped includes CytAssit instrument from 10X genomics for VISIUM spatial transcriptomic and QIAConnect from Qiagen for nucleic acid and protein extraction." .
SCR:026484 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3071" ;
rdfs:label "Harvard University School of Medicine BIDMC HIV-1 Neutralizing Antibody Core Facility" ;
NIFRID:synonym "Beth Israel Deaconess Medical Center Neutralizing Antibody Core",
"BIDMC HIV-1 Neutralizing Antibody Core" ;
definition: "Core provides in vitro HIV-1 neutralizing antibody assay services. Serves as resource for assessing breadth and potency of HIV-1 neutralizing antibodies, and for characterizing neutralization phenotype of HIV-1 isolates. Investigators send monoclonal antibodies or serum samples from vaccinated or HIV-1-infected individuals to the core for in vitro testing using the validated TZM.bl neutralizing antibody assay. The core also has the capability to phenotype primary HIV-1 isolates for sensitivity to broadly neutralizing antibodies. GCLP-compliant, In vitro testing of monoclonal antibodies or seurm samples, Validated TZM.bl neutralizing antibody assay, Phenotoyping of primary HIV-1 isolates." .
SCR:026485 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3072" ;
rdfs:label "Boston Children's Hospital Cellular Imaging Core Facility" ;
NIFRID:synonym "Boston Children's Hospital Cellular Imaging Core",
"Cellular Imaging Core" ;
definition: "Cellular Imaging Core facility is light microscopy core in Boston Children's Hospital's Neurobiology Program. The Core maintains systems for Widefield, confocal, multiphoton, and lightsheet light microscopy as well as sample preparation and image processes tools and technologies to assist the microscopy community of Boston Children's Hospital in addition to the surrounding greater Boston area. Core services and equipment are available to all upon request, contact core staff for access." .
SCR:026486 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "chopper" ;
definition: "Software tool that combines the utility of NanoFilt and NanoLyse, for filtering sequencing reads based on quality, length, and contaminating sequences, delivers 7-fold speed up compared to the Python implementation, making use of the Rust-Bio library and Rust bindings to minimap2." .
SCR:026487 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Plastic Surgery Home" ;
definition: "Website serves as digital resource for plastic surgery professionals. Educational and resource platform dedicated to plastic surgeons, trainees, and researchers. Provides access to curated content, including links to major plastic surgery societies, journal repositories, clinical resources, and upcoming events. Serves as comprehensive hub for continuous professional development and collaboration in the field of plastic surgery." .
SCR:026488 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RIVET" ;
NIFRID:synonym "Ribosomal Investigation and Visualization to Evaluate Translation" ;
definition: "Software tool to automate statistical analysis of RNA seq data acquired from polysome profile or ribosome footprinting experiments." .
SCR:026489 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "C-ARES" ;
NIFRID:synonym "c-ares" ;
definition: "Software C library for asynchronous DNS requests. Provides set of library functions, datatypes, and enumerations which integrators will use for their implementations." .
SCR:026490 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gettext" ;
definition: "Software tools that provide framework to help other GNU packages produce multi-lingual messages." .
SCR:026491 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "X.Org" ;
definition: "X.Org project provides open source implementation of X Window System. The development work is being done in conjunction with the freedesktop.org community. The X.Org Foundation is the educational non-profit corporation whose Board serves this effort, and whose Members lead this work." .
SCR:026492 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Time Zone Database" ;
NIFRID:synonym "tz data",
"tz database",
"zoneinfo" ;
definition: "Database contains code and data that represent the history of local time for many representative locations around the globe. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight-saving rules." .
SCR:026493 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tibble" ;
definition: "Software package for modern re-imagining of data frame. Provides 'tbl_df' class with stricter checking and better formatting than traditional data frame." .
SCR:026494 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Attune" ;
definition: "Software framework for integrating gene expression and chromatin accessibility, enabling the inference of regulatory mechanisms and the prediction of gene expression from cross-modal data. Repository contains code and tutorials for the following tasks: multimodal pretraining, cross-modal prediction, inferring regulatory network and potential analysis." .
SCR:026495 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Vanquish_Neo_UHPLC" ;
rdfs:label "Thermo Fisher | Vanquish Neo UHPLC System" ;
NIFRID:synonym "Vanquish Neo UHPLC System" ;
definition: "Low flow, high-sensitivity Liquid Chromatography-Mass Spectrometry system delivers retention time precision from nano up to 100 μL/min at pressures up to 1500 bar for reproducible nano-, capillary-, and micro-flow LC-MS." .
SCR:026496 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Annotation Comparison Explorer" ;
NIFRID:synonym "Annotation Comparison Explorer (ACE)" ;
NIFRID:abbrev "ACE" ;
definition: "Web application for comparing cell type assignments and other cell-based annotations (e.g., donor demographics, anatomic locations, batch variables, and quality control metrics). Used for connecting brain cell types across studies of health and Alzheimer's Disease." .
SCR:026497 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CompactTree" ;
definition: "Software lightweight header only C++ library for loading and traversing trees. Used for for loading and traversing trees." .
SCR:026498 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chemical space estimation of plants" ;
definition: "Software repository contains scripts and notebooks for defining the limits, challenges and estimations of plant chemical space using MS data." .
SCR:026499 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "histoCAT" ;
NIFRID:synonym "Histology Topography Cytometry Analysis Toolbox" ;
definition: "Software package to visualize and analyse multiplexed image cytometry data interactively." .
SCR:026500 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NucleAIzer" ;
definition: "Software tool as parameter-free deep learning framework for nucleus segmentation using image style transfer. Cell segmentation tool." .
SCR:026501 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Conserved Unique Peptide Patterns" ;
NIFRID:abbrev "CUPP" ;
definition: "Web application for sequence analysis employing conserved peptide patterns for determination of similarities between proteins." .
SCR:026502 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NucPred" ;
definition: "Web tool for predicting nuclear localization of proteins. Analyses eukaryotic protein sequence and predicts if protein spends at least some time in nucleus or spends no time in the nucleus." .
SCR:026503 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepLoc" ;
NIFRID:synonym "DeepLoc 2.0",
"DeepLoc 2.1" ;
definition: "Web server for prediction of protein subcellular localization and sorting signals. DeepLoc 2.1 additionally classifies input proteins into membrane protein types Transmembrane, Peripheral, Lipid-anchored and Soluble. Used to predict subcellular localization and associated membrane type of eukaryotic proteins" .
SCR:026504 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MULocDeep" ;
definition: "Web service for protein localization prediction and visualization at subcellular and suborganellar levels." .
SCR:026505 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SecretomeP" ;
NIFRID:synonym "SecretomeP 2.0" ;
definition: "Web application for feature-based prediction of non-classical and leaderless protein secretion.Used for prediction of mammalian secretory proteins targeted to non-classical secretory pathway, i.e. proteins without N-terminal signal peptide." .
SCR:026506 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WallProtDB" ;
NIFRID:synonym "WallProtDB-2" ;
definition: "Database resource for plant cell wall proteomics. Aims at collecting cell wall proteomic experimental data. For each experiment, a scheme summarizing the strategy used for protein isolation and identification is provided." .
SCR:026507 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Ion Chef Instrument" ;
definition: "Provides automated library preparation, template preparation, and chip loading for users at any experience level. Simplifies the Ion Torrent next-generation sequencing (NGS) workflow by integrating several manual and instrument steps into single process." .
SCR:026508 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Ion S5 XL System" ;
NIFRID:synonym "Ion S5 XL Sequencing System" ;
definition: "Ion S5 XL next-generation sequencing system enables simple targeted sequencing workflow for your lab with reliable performance and industry-leading speed.Torrent Server direct connection to the Ion S5 XL Sequencer is supported." .
SCR:026509 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ecodist" ;
definition: "Software R package as dissimilarity-based functions for ecological analysis. Used for analyzing ecological data." .
SCR:026510 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "microViz " ;
definition: "Software R package for microbiome data visualization and statistics. Docker image available." .
SCR:026511 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RSeqQC " ;
definition: "Software RNA-seq quality control package. Used for quality control of RNA-seq experiments." .
SCR:026512 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "survimer " ;
definition: "Software R package contains functions for drawing survival curves using 'ggplot2'." .
SCR:026513 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Renishaw WiRE software" ;
definition: "Renishaw windows-based Raman Environment, WiRE, software can control acquisition of Raman data and provide users with dedicated data processing and analysis options." .
SCR:026514 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3073" ;
rdfs:label "Louisiana State University Mass Spectrometry Core Facility" ;
NIFRID:synonym "Louisiana State University Mass Spectrometry Facility",
"LSU Mass Spectrometry Facility" ;
definition: "Core provides analytical support and services. Services include data analysis, sample preparation, proteomics, metabolomics, lipidomics, Maldi and Maldi imaging, Agilent GC-MS, SPE purification." .
SCR:026515 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3074" ;
rdfs:label "Howard Hughes Medical Institute at Janelia Research Campus Immortalized Cell Line Culture Shared Resource Core Facility " ;
NIFRID:synonym "Immortalized Cell Line Culture" ;
definition: "Core offers support for various tasks such as plating, passaging, cryopreserving, transfection, and preparing cells for imaging and other applications. Our facility fosters collaboration, allowing researchers to reserve cell culture hoods and engage with fellow lab and staff members." .
SCR:026516 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3075" ;
rdfs:label "University of Louisville Protein Expression and Purification Core Facility" ;
definition: "Core offers recombinant protein expression and purification in E. coli systems to investigators for functional and structural studies. Services include vector construction, expression optimization, protein purification using FPLC, and isotopically labeled protein expression for NMR. Clients can choose from expression strain delivery, optimized protocols, and/or purified protein, with fast turnaround times and consultation throughout the process." .
SCR:026517 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3076" ;
rdfs:label "University of Louisville Nuclear Magnetic Resonance Spectroscopy Core Facility" ;
definition: "Core Facility houses 600 MHz Bruker Avance Neo NMR spectrometer available for both collaborative and fee-for-service use. The facility is equipped with a 14.1 T Bruker system and a nitrogen-cooled Prodigy probe, enabling a range of 3D experiments on isotopically labeled biomolecules with enhanced sensitivity for challenging samples. Services include biomolecular structure determination, characterization of biomolecular motions, and stable isotope-resolved metabolomics for studying metabolic pathways." .
SCR:026518 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3064" ;
rdfs:label "Beth Israel Deaconess Medical Center Biomarker and Metabolism Research Core Facility" ;
NIFRID:synonym "Biomarker and Metabolism Research Core" ;
definition: "Core provides access to XFe 96 Extracellular Flux Analyzer, seahorse technology, as well as additional services that include technical advice in experimental design, data analysis and basic training. Provides access to electrochemiluminescence immunoassays using MESO QuickPlex SQ 120. You can perform multiplex biomarker and cytokine assays, test for immunogenicity or toxicity, or we can help you develop your own unique assays. Core also provides access to ImageXpress Pico, the next generation of digital microscopy and access to SPECTRAMAX I3X, multi-mode microplate reader." .
SCR:026519 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3010" ;
rdfs:label "Montana State University CBE Bioimaging and Analytical Core Facility" ;
NIFRID:synonym "Montana State University - CBE Bioimaging and Analytical Core",
"Montana State University CBE Bioimaging and Analytical Core" ;
definition: "Core offers imaging and analysis of intact biofilms to capture with ultimate precision the position, interactions, activity, and identification of microbes in real-time from intact samples. With our broad range of analytical capabilities, we can determine how microbes are interacting and altering their environmental conditions. We provide one-on-one training, method development, proposal writing, troubleshooting and data analysis services to help you meet your biofilm-related analytical and imaging needs." .
SCR:026520 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hamamatsu | NanoZoomer-XR Digital slide scanner" ;
NIFRID:synonym "NanoZoomer XR scanner" ;
definition: "High-resolution digital slide scanner designed for wide-field imaging of tissue samples. It captures high-quality digital images of microscope slides at up to 40x optical magnification. NanoZoomer XR scanner is capable of capturing images with a maximum resolution of 0.23 microns per pixel." .
SCR:026521 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | BOND-III Stainer" ;
definition: "Leica Bond III automated IHC – ISH stainer to processes up to 30 simultaneous slides in under 2.5 hours. Used for immunohistochemistry for in situ hybridization slides staining." .
SCR:026522 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Infinite_M_Plex" ;
rdfs:label "Tecan | Infinite M Plex microplate reader" ;
definition: "Multimode microplate reader with monochromator optics. Offers free wavelength selection and scanning capabilities. Used for all standard absorbance, fluorescence and luminescence assays." .
SCR:026523 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Revolve" ;
rdfs:label "ECHO | Revolve Microscope" ;
definition: "4-in-1 digital hybrid microscope, combining four microscopes into one. ECHO Revolve is a hybrid microscope that can be used for viewing glass slides and live samples in fluidic chambers. It can be used for upright or inverted observation methods." .
SCR:026524 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Synapt XS" ;
rdfs:label "Waters | Synapt XS mass spectrometer" ;
NIFRID:synonym "Synapt XS mass spectrometer" ;
definition: "Hybrid Q-TOF mass spectrometer with integrated ion mobility." .
SCR:026525 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker | rapifleX" ;
NIFRID:synonym "rapifleX" ;
definition: "Bruker MALDI-TOF mass spectrometry system. Enables time critical applications and faster decision making processes." .
SCR:026526 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker | amaZon Speed ETD mass spectrometer" ;
NIFRID:synonym "amaZon Speed ETD" ;
definition: "Ion trap mass spectrometer with electron transfer dissociation capabilities. Sets analytical standard for proteomics and small molecule applications." .
SCR:026527 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LCMS-8060NX" ;
rdfs:label "Shimadzu | LCMS-8060NX Triple Quad LC-MS/MS mass spectrometer" ;
NIFRID:synonym "LCMS-8060NX",
"LCMS-8060NX Triple Quad LC-MS/MS",
"Shimadzu LCMS-8060NX" ;
definition: "Triple Quadrupole Mass Spectrometer is liquid chromatograph mass spectrometer (LCMS) for fast, accurate detection, to quantify components of sample or to analyze their structure with increased specificity and sensitivity." .
SCR:026528 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LC-40D XS" ;
rdfs:label "Shimadzu | Nexera HPLC/UHPLC Pump - LC-40D XS" ;
NIFRID:synonym "Nexera HPLC/UHPLC Pump - LC-40D XS" ;
definition: "High-performance liquid chromatography HPLC pump that s used for separation, sensitivity, and resolution. It s part of the Nexera series of HPLC and UHPLC systems from Shimadzu. " .
SCR:026529 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CTO-40S" ;
rdfs:label "Shimadzu | Nexera HPLC/UHPLC Column Oven - CTO-40S" ;
NIFRID:synonym "Nexera HPLC UHPLC Column Oven - CTO-40S" ;
definition: "Oven used to control the temperature of the column in a liquid chromatography LC system.CTO-40S Slim Line column oven is ideal for saving space while maintaining excellent thermal stability." .
SCR:026530 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Meso-Py" ;
definition: "Cost-effective, compact foot-print, and open-source Raspberry Pi-based widefield imaging system. Used for close-proximity dual-brain cortical mesoscale functional-imaging to simultaneously observe activity in two head-fixed animals in staged social touch-like interaction. We provide all schematics, code, and protocols for a rail system where head-fixed mice are brought together to a distance where the macrovibrissae of each mouse make contact." .
SCR:026531 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AIRR Knowledge Commons" ;
NIFRID:synonym "AIRR-Knowledge",
"airr-knowledge.org" ;
definition: "Repository of integrated data and knowledge about adaptive immune receptors, the complex genomic loci encoding AIRs, and the antigens and epitopes bound by AIR." .
SCR:026532 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NetworkDataCompanion" ;
definition: "Software R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo. Streamlines routine steps in TCGA data processing, including filtering and mapping gene and sample identifiers between modalities and allows modality-specific data transformation, such as normalization and cleaning." .
SCR:026533 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MeTPeak" ;
definition: "Software package for finding the location of m6A sites in MeRIP-seq data." .
SCR:026534 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Natural Products Magnetic Resonance Database" ;
NIFRID:abbrev "NP-MRD" ;
definition: "Database and respository for NMR data associated with natural products and specialized metabolites." .
SCR:026535 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Liftoff" ;
definition: "Software genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Aligns genes from reference genome to target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. Used for accurate mapping of gene annotations." .
SCR:026536 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3077" ;
rdfs:label "University of Liverpool GeneMill Core Facility" ;
NIFRID:synonym "GeneMill" ;
definition: "Automation, synthetic biology and protein production facility. As founder member of Global Biofoundry Alliance we are part of UK government initiative to strengthen engineering biology capabilities in the country and beyond. GeneMill offers high-throughout, automated gene cloning, sequence diversity generation and phenotyping. Our portfolio also includes a full protein production service." .
SCR:026537 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3078" ;
rdfs:label "University of Liverpool High Field Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "University of Liverpool High-Field NMR Facility LIV-SRF" ;
definition: "Facility offers NMR technologies to determine content and purity of sample as well as its molecular structure, interactions and chemometrics of biological mixtures." .
SCR:026538 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_AXR_NSPARC" ;
rdfs:label "Nikon | AXR NSPARC super resolution inverted microscope" ;
definition: "Confocal microscope provides enables collection of more data over wide area and down to deep regions in tissues. Its high sensitivity and high-speed scanning reduce phototoxicity to specimen and minimize damage. Equipped with image acquisition/analysis functions utilizing Artificial Intelligence (AI), the AX/AX R can efficiently acquire highly reliable data. Nikon Spatial Array Confocal (NSPARC) detector utilizes detector array to collect two-dimensional image at each scanned point. It adds additional potential to imaging by providing new level of ultra-low noise sensitive spatial detection, enabling improved lateral resolution of 1 airy unit/~230 nm and improved signal-to-noise ratio." .
SCR:026539 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Next Advance | Bullet Blender Homogenizer" ;
NIFRID:synonym "Bullet Blender",
"Next Advance Bullet Blender" ;
definition: "Tissue homogenizer for 24 samples in microcentrifuge tubes with very powerful motor. Cooling with dry ice or liquid nitrogen to maintain 4°C sample temperature. Includes starter kit of beads, scoop and tubes. CE certified." .
SCR:026540 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ timsTOF_Ultra" ;
rdfs:label "Bruker | timsTOF Ultra mass spectrometer" ;
NIFRID:synonym "timsTOF Ultra" ;
definition: """Mass spectrometer used for proteomics research. Offers the ultimate fusion of
trapped ion mobility spectrometry (TIMS) with quadrupole time-of-flight (QTOF) technology.""" .
SCR:026541 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_timsTOF_Ultra_2" ;
rdfs:label "Bruker | timsTOF Ultra 2 mass spectrometer" ;
NIFRID:synonym "Bruker timsTOF Ultra 2",
"timsTOF Ultra 2 mass spectrometer" ;
definition: "Spectrometer timsTOF Ultra 2 is paired with CaptiveSpray Ultra 2 ion source for high sensitivity to work with challenging samples and detect low-abundance peptides. Used to analyze even the smallest amounts and uncover previously unseen peptides." .
SCR:026542 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_timsTOF_SCP" ;
rdfs:label "Bruker | timsTOF SCP mass spectrometer" ;
NIFRID:synonym "Bruker timsTOF SCP",
"timsTOF SCP" ;
definition: "The timsTOF SCP (single-cell proteomics) is mass spectrometer from Bruker. Ultra-high sensitivity instrument for quantitative single cell biology research with unbiased, deep single-cell 4D-Proteomics, immunopeptidomics, epiproteomics and PTM analysis. It features an additional separation in the tims cell where ions get separated according to their ion mobility, leading to collision cross-section values.Allows the analysis of hundreds of samples with minimal sample load (<200 ng) at sequencing speeds exceeding 100 Hz." .
SCR:026543 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_timsTOF_HT" ;
rdfs:label "Bruker | timsTOF HT mass spectrometer" ;
NIFRID:synonym "Bruker timsTOF HT" ;
definition: "Mass spectrometer is equipped with the 4th generation high capacity TIMS-XR analyzer and advanced digitizer technology (ADT). Offers higher dynamic range for unmatched analytical depth and quantitation in high-throughput proteomics experiments." .
SCR:026544 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_timsTOF_Pro" ;
rdfs:label "Bruker | timsTOF Pro mass spectrometer" ;
NIFRID:synonym "Bruker timsTOF Pro" ;
definition: "Mass spectrometry (MS)-based proteomics instrument designed for shotgun proteomics and phosphoproteomics, leveraging Parallel Accumulation Serial Fragmentation (PASEF) technology to enhance speed, sensitivity, and resolution." .
SCR:026545 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_timsTOF_Pro_2" ;
rdfs:label "Bruker | timsTOF Pro 2 mass spectrometer" ;
NIFRID:synonym "Bruker timsTOF Pro 2" ;
definition: "Mass spectrometer used for research, particularly in proteomics and metabolomics, leveraging Trapped Ion Mobility Spectrometry (TIMS) and Parallel Accumulation Serial Fragmentation (PASEF) technologies for enhanced 4D-omics capabilities." .
SCR:026546 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3079" ;
rdfs:label "Rockefeller University Data Science Platform Core Facility" ;
NIFRID:synonym "Rockefeller University Data Science Platform" ;
NIFRID:abbrev "DSP" ;
definition: "Data Science Platform focuses on Artificial Intelligence, Signal Processing, Computer Vision with the aim of advancing the research of Rockefeller Laboratories. DSP owns and operates fully dedicated computing infrastructure, equipped with state of the art GPUs and large storage capabilities." .
SCR:026547 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "targetscore" ;
definition: "Software tool as data-driven network modeling algorithm for drug response analysis in cancer." .
SCR:026548 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mayo Clinic Spatial Biology Core Facility" ;
definition: "Core provides broad range of spatial transcriptomic and targeted proteomics services including: Conventional nCounter analysis to determine RNA abundance, GeoMx Digital Spatial Profiling platform to determine protein and RNA abundance, CosMx Spatial Molecular Imaging platform for single cell spatial analysis of RNA and protein." .
SCR:026549 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Recording Analysis and Visualization Online" ;
NIFRID:abbrev "BRAVO" ;
definition: "Web interface to easily import, visualize, and analyze brain signals. Used for analysis of longitudinal neural recording data." .
SCR:026550 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fluidigm | CyTOF Mass Cytometer" ;
NIFRID:synonym "CyTOF Mass Cytometer" ;
definition: "CyTOF instrument uses atomic mass spectrometry to allow simple, independent detection of up to 33 metal labeled antibodies (and two DNA intercalators) based on currently available reagents. Has capacity to measure 100 independent signals. CyTOF system is inorganic mass spectrometer specifically built for biologists and single cell applications. Inductively coupled plasma mass spectrometer used extensively by analytical chemists and is proven in the quantification of elements and stable isotopes in variety of complex matrices." .
SCR:026551 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CyTOF_2" ;
rdfs:label "Fluidigm | CyTOF 2 mass cytometer" ;
NIFRID:synonym "Fluidigm CyTOF 2" ;
definition: """Time-of-Flight mass spectrometer for high-speed acquisition of highly multi-parametric single cell data. Simultaneously resolves multiple parameters with minimal signal overlap, providing insights into the functional and phenotypic complexity of biological systems at the single-cell level. Analyzes cells labeled with panel of reagents conjugated to stable
metal isotopes using time-of-flight mass cytometry technology. Includes over 120 detection channels and 35 Maxpar metal probes.""" .
SCR:026552 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PathoMAN" ;
NIFRID:synonym "Pathogenicity of Mutation Analyzer" ;
definition: "Web application to automate germline genomic variant curation from clinical sequencing based on ACMG guidelines. Aggregates multiple tracks of genomic, protein and disease specific information from public sources." .
SCR:026553 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MMseq2 " ;
NIFRID:synonym "Many-against-Many sequence searching" ;
definition: "Software suite to search and cluster huge protein and nucleotide sequence sets. Sensitive protein sequence searching for analysis of massive data sets. Used for ultra fast and sensitive search and clustering." .
SCR:026554 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Coding-Non-Coding Index" ;
NIFRID:synonym "Coding-Non-Coding Index (CNCI)" ;
NIFRID:abbrev "CNCI" ;
definition: "Software tool for utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts." .
SCR:026555 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "find_circ" ;
definition: "Software tools to find circRNAs in RNA-seq data. Used to detect head-to-tail spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) in RNA-seq data." .
SCR:026556 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "siFi" ;
NIFRID:synonym "siRNA-Finder" ;
definition: "Software tool for RNAi-target design and off-target prediction. Used for long double-stranded RNAi-target design and off-target prediction." .
SCR:026557 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3093" ;
rdfs:label "Emory University NIH Tetramer Core Facility" ;
NIFRID:synonym "NIH Tetramer Core Facility",
"NIH Tetramer Facility" ;
definition: "Core produces and distributes of MHC/peptide tetramers and related reagents. Production and distribution to the research community of major histocompatibility complex (MHC) tetramers and related reagents for detection of T cell responses to viruses, bacteria, parasites, tumors, auto-antigens, and other model antigens. Reagents are provided to qualified investigators at no cost, except for shipping and handling fees and in cases where investigator is asked to provide the TCF with peptide or other appropriate ligands." .
SCR:026558 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3067" ;
rdfs:label "Mayo Clinic Stem Cell and Organoid Core Facility" ;
NIFRID:synonym "Mayo Clinic Stem Cell and Organoid Core",
"Stem Cell and Organoid Core - Mayo Clinic" ;
definition: "Core provides researchers with access to high-quality human induced-pluripotent stem cell (iPSC) production, expansion, validation, and quality control services, while strictly adhering to approved protocols, ensuring high-quality standards and consistency throughout the process." .
SCR:026559 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3068" ;
rdfs:label "Mayo Clinic Florida Multi-Omics Mass Spectrometry Core Facility" ;
NIFRID:synonym "Mayo Clinic Florida Multi-Omics Mass Spectrometry",
"Multi-Omics Mass Spectrometry" ;
definition: "Core is equipped with instrumentation in mass spectrometry, sample preparation, and automation technology. Bruker timsTOF Ultra 2 ultra-high speed and sensitivity mass spectrometer for single cell and other low input proteomics methods. It comes equipped with the Bruker nanoElute 2 UHPLC and the alternative EvosepOne HPLC for high throughput applications. Sample preparation can be automated using the Opentrons Flex liquid handling robot." .
SCR:026560 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Automated Projection Pursuit" ;
NIFRID:abbrev "APP" ;
definition: "Software tool for automated projection pursuit clustering. Alternative clustering approach that alleviates the curse of dimensionality by sequentially projecting high-dimensional data into a low-dimensional representation." .
SCR:026561 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "phenoimager2mc" ;
definition: "Software tool for formatting PhenoImager TIFF/OME-TIFF metadata for compatibility with MCMICRO workflow." .
SCR:026562 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GTestimate" ;
definition: "Software R package for scRNA-seq normalization. Uses Simple Good-Turing estimator for the per cell relative gene expression estimation." .
SCR:026563 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3094" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Proteomics and Metabolomics Core Facility" ;
NIFRID:synonym "Cleveland Clinic Proteomics and Metabolomics Core Facility",
"Lerner Research Institute Proteomics and Metabolomics Core" ;
definition: "Core provides advanced mass-spectrometric instrumentation and for both proteomics and metabolomic experiments. Performs qualitative and quantitative analysis of proteins and post-translationally modified peptides and both targeted and untargeted LC/GC-MS based metabolomics." .
SCR:026564 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University College London Centre for Cell and Molecular Dynamics Core Facility" ;
NIFRID:synonym "UCL-Zeiss Centre for Cell and Molecular Dynamics Core Facility",
"University College London Centre for Cell and Molecular Dynamics CCMD - UCL-Zeiss Multiscale Imaging Centre UZMIC" ;
definition: "UCL light microscopy platform. Provides wide variety of microscopes available in the Confocal Imaging unit." .
SCR:026565 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_iBright_CL1500" ;
rdfs:label "Thermo Fisher: Invitrogen | iBright CL1500 Imaging System" ;
NIFRID:synonym "iBright CL1500 Imaging System" ;
definition: "System supports the main imaging applications of chemiluminescent and colorimetric western blots, in addition to fluorescent stained nucleic acid gels, fluorescent stained protein gels, colorimetric stained protein gels, and colorimetric membrane stains." .
SCR:026566 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dnaMethyAge" ;
definition: "Software R package to predict epigenetic age and calculate age acceleration from DNA methylation data." .
SCR:026567 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Benchmarking Graph Pipelines" ;
NIFRID:synonym "Benchmarking Pangenome Graph Pipelines",
"Benchmarking Pangenome Graph pipelines" ;
definition: "Software pipelines for benchmarking workflow for evaluating graph-based pangenome construction tools. The repository contains scripts to compare the performance of Minigraph-Cactus, PGGB, Minigraph pipelines using both simulated and real-world datasets. It includes data processing steps, evaluation metrics, and reproducible scripts for analyzing structural variants in pangenomes." .
SCR:026568 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ROGUE" ;
definition: "Software tool as entropy-based metric for assessing purity of single cell populations. Used to accurately quantify purity of identified cell clusters." .
SCR:026569 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PESSA" ;
NIFRID:synonym "Pathway Enrichment Score-based Survival Analysis" ;
definition: "Web tool for pan-cancer survival analysis and visualization by using results from single sample gene set enrichment analysis. Used for pathway enrichment score-based survival analysis in cancer.Users can quickly explore impact of target pathway on survival outcomes in different tumors, assisting clinicians and researchers in further investigating mechanism of tumor development and improving clinical decision-making." .
SCR:026570 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "chromvar" ;
NIFRID:synonym "chromatin Variability Across Regions" ;
definition: """Software R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. Enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility.
Used for analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data.""" .
SCR:026571 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100010960" ;
rdfs:label "UCI Machine Learning Repository" ;
NIFRID:synonym "UC Irvine Machine Learning Repository" ;
definition: "Collection of databases, domain theories, and data generators that are used by machine learning community for empirical analysis of machine learning algorithms. Datasets approved to be in the repository will be assigned Digital Object Identifier (DOI) if they do not already possess one. Datasets will be licensed under a Creative Commons Attribution 4.0 International license (CC BY 4.0) which allows for the sharing and adaptation of the datasets for any purpose, provided that the appropriate credit is given" .
SCR:026572 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ArUco" ;
NIFRID:synonym "Aruco",
"Augmented Reality University of Cordoba" ;
definition: "Automated rodent behavioral scoring system, complete with 3D design files and code/software. System monitors behavioral engagement using open-source software. 3D design files and necessary software has been made available, as well as code that can be used for data analysis." .
SCR:026573 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3081" ;
rdfs:label "University of British Columbia BCCHR Imaging Core Facility" ;
NIFRID:synonym "BCCHR Imaging Core",
"University of British Columbia BCCHR Imaging Core" ;
definition: "Core is multi-user facility located on the 4th floor in the Translational Research Building (TRB) at A4-110. It houses microscopes and image data analysis computers to provide imaging for wide range of samples, including cell structures in tissue sections, and subcellular structures and 3D morphologies of single cells. A full-time technician provides training, consultation, and guidance to researchers, from sample preparation to data analysis." .
SCR:026574 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SEER Explorer" ;
NIFRID:synonym "and End Results Explorer",
"Epidemiology",
"Surveillance" ;
definition: "Web application tool as interactive website for SEER cancer statistics." .
SCR:026575 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HCP Pipelines" ;
NIFRID:synonym "Human Connectome Project Pipelines" ;
definition: "Software package as set of tools, primarily shell scripts, for processing multi-modal, high-quality MRI images for the Human Connectome Project. Minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space." .
SCR:026576 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "r3d100014632" ;
rdfs:label "Health Data Nexus" ;
NIFRID:abbrev "HDN" ;
definition: "Platform for health data sharing and analytics that emphasizes patient privacy and security, provides transparent and speedy access, and simplifies data discovery and analysis. Houses datasets for applied AI learning and research. Repository of freely-available medical research data, managed by the University of Toronto Temerty Centre for AI Research and Education in Medicine." .
SCR:026589 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "kg-microbe" ;
NIFRID:synonym "KG Microbe",
"knowledge graph microbe" ;
definition: "Software tool as framework for knowledge graph construction and the current 4 KGs. Used to extract and integrate diverse knowledge about microbes from variety of structured and unstructured sources." .
SCR:026590 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3096" ;
rdfs:label "Augusta University Georgia Cancer Center Immune Monitoring Shared Resource Core Facility" ;
NIFRID:synonym "Augusta University Georgia Cancer Center Immune Monitoring Shared Resource",
"Immune Monitoring" ;
definition: "Core provides services in Assay Development, Assays Experimental Design, Immune Monitoring, Cytokine Assays, ELISA, multiplex Flow based and Luminex based Bead Arrays, Project Based Flow Cytometry and Data Analysis." .
SCR:026591 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenomicKB" ;
NIFRID:synonym "Genomic Knowledgebase" ;
definition: "Database that uses knowledge graph to consolidate genomic datasets and annotations. Graph database for researchers to explore and investigate human genome, epigenome, transcriptome, and 4D nucleome. Genomic entities and relationships are represented as diverse nodes and edges with properties." .
SCR:026592 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Genomic Literature Knowledge Base" ;
NIFRID:abbrev "GLKB" ;
definition: "Resource that integrates biomedical terms and biomedical relationships. This collection is curated from PubMed abstracts and biomedical repositories, offering unparalleled wealth of knowledge for researchers and practitioners in the field. The database is coupled with RESTful APIs and user-friendly web interface." .
SCR:026593 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PanKbase" ;
definition: "Centralized knowledge base of the human pancreas for diabetes research. Integrates diverse type 1 diabetes (T1D) datasets with expert-curated knowledge in centralized, open-source data hub. Since users will ultimately be able to contribute their own data, this will be repository for reproducible, collaborative research within the pancreas and T1D realms." .
SCR:026594 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PanKgraph" ;
definition: "Knowledge Graph developed for the study of the human pancreas. By leveraging large language models (LLMs) and diverse data types, PanKgraph enables users to uncover biological connections and insights into diabetes pathogenesis. Previously disjointed entities such as genes, single nucleotide polymorphisms (SNPs), and pancreatic expression quantitative trait loci (eQTLs) can now be explored and connected in innovative ways." .
SCR:026595 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Integrated Cell Browser" ;
definition: "Integrated Cell Browser features integrated single-cell RNA sequencing (scRNA-seq) and single cell ATAC-seq data from human donor-specific pancreatic islet cells. The browser enables detailed interrogation of single cell RNA-seq and single cell ATAC-seq data through intuitive visualizations. Within the single-cell browser, users can first identify and filter single-cell datasets and dataset collections. Users can visualize interactive plots of cell type clusters, gene expression, cell type abundance, and marker gene expression. Donors and their data were provided by external programs described here." .
SCR:026596 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "siibra-python" ;
definition: "Software interface for interacting with brain atlases. Python client to brain atlas framework that integrates brain parcellations and reference spaces at different spatial scales, and connects them with broad range of multimodal regional data features. It aims to facilitate programmatic and reproducible incorporation of brain parcellations and brain region features from different sources into neuroscience workflows." .
SCR:026597 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PISAD" ;
definition: "Software reference-free intraspecies sample anomalies detetion tool based on k-mer counting." .
SCR:026599 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3082" ;
rdfs:label "Beth Israel Deaconess Medical Center Preclinical Murine Pharmacogenetics Core Facility" ;
NIFRID:synonym "Beth Israel Deaconess Medical Center Preclinical Murine Pharmacogenetics Facility",
"Preclinical Murine Pharmacogenetics Facility" ;
definition: "Core provides expertise in the design and implementation of preclinical trials to test new drugs, drug combinations and novel therapeutic modalities in mouse models of human diseases." .
SCR:026600 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3083" ;
rdfs:label "Beth Israel Deaconess Medical Center Small Animal Imaging Core Facility" ;
NIFRID:synonym "Beth Israel Deaconess Medical Center BIDMC - Small Animal Imaging Facility",
"BIDMC - Small Animal Imaging Facility",
"Longwood Small Animal Imaging Facility (SAIF)" ;
definition: "Provides small animal imaging services. Facility provides multi-modality imaging, advanced data analysis, image fusion resources, custom chemistry, and satellite animal facility for longitudinal studies." .
SCR:026601 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3086" ;
rdfs:label "University of British Columbia BCCHR Flow Cytometry Core Facility" ;
NIFRID:synonym "BCCHR Flow Core",
"University of British Columbia BCCHR Flow Core" ;
definition: "Facility provides equipment for flow cytometric analysis and full-service cell sorting, as well as flow cytometry training and education for new users." .
SCR:026602 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3084" ;
rdfs:label "Charles University Vinicna Microscopy Core Facility" ;
NIFRID:synonym "Faculty of Science",
"Faculty of Science; Charles University Vinicna Microscopy Core Facility",
"Vinicna Microscopy Core Facility" ;
definition: "Facility is equipped with range of advanced microscopes, from traditional light microscopes to cutting-edge super-resolution and live cell imaging systems.Provides imaging and analysis services." .
SCR:026603 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3088" ;
rdfs:label "University of British Columbia BCCHR Analytical Core for Metabolomics and Nutrition Core Facility" ;
NIFRID:synonym "ACMaN Core",
"Analytical Core for Metabolomics and Nutrition (ACMaN)",
"BCCHR Analytical Core for Metabolomics and Nutrition (ACMaN) Core",
"University of British Columbia BCCHR Analytical Core for Metabolomics and Nutrition (ACMaN) Core" ;
NIFRID:abbrev "ACMaN" ;
definition: "Analytical Core for Metabolomics and Nutrition (ACMaN) is located on the first floor of the Varity Building. ACMaN allows researchers to analyze and track biological compounds, such as nutrients to track how these small molecules change during course of disease or treatment to better understand the disease itself and to develop new diagnostic tools and therapies. ACMaN plays role in research on metabolic diseases, hormones, and the effects of nutrition on childhood development." .
SCR:026604 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3087" ;
rdfs:label "University of British Columbia BCCHR Histology Core Facility" ;
NIFRID:synonym "BCCHR Histology Core",
"University of British Columbia BCCHR Histology Core" ;
definition: "Core is a multi-user facility located on the 4th floor in the Translational Research Building (TRB) at A4-132. Histology facility offers services for processing tissue samples, automated equipment for tissue processing, paraffin embedding, micro-sectioning, and staining. Our technicians offer consultation, experimental design, and troubleshooting and work closely with researchers to get the most optimal tissue sections tailored to each project. The facility also provides training on the microtome and paraffin embedder to allow flexibility in workflow." .
SCR:026605 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3097" ;
rdfs:label "University of Liverpool Centre for Preclinical Imaging Core Facility" ;
NIFRID:synonym "Centre for Pre-Clinical Imaging",
"Centre for Preclinical Imaging-CPI" ;
definition: "Provides access to imaging systems. Offers researchers technologies for multi-modality, non-invasive approaches to imaging on small, live animals, or tissues and organs extracted from animals . Our equipment can be used for pre-clinical models and non-biological samples." .
SCR:026606 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3098" ;
rdfs:label "University of Liverpool Shared Research Histology Core Facility" ;
NIFRID:synonym "University of Liverpool Shared Research Histology Facility" ;
definition: """Facility offers preparation of samples from fresh or fixed tissue through to scanned images.
Provides training to prepare and use equipment to embed, section and hand stain tissues as required. Offers three different types of wax for embedding and sectioning as required.
Fully equipped for methyl methacrylate and glycol methacrylate embedding and sectioning (including larger samples), freeze microtomy and high throughput slide imaging using our Zeiss Axioscan Z1.""" .
SCR:026607 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Drug Target Commons" ;
NIFRID:abbrev "DTC" ;
definition: "Web application as crowd-sourcing platform to improve consensus and use of drug-target interactions. Users can search, view and download bioactivity data using various compound, target and publications identifiers." .
SCR:026608 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford Sciex 7500+ Triple Quadrupole LC/MS system" ;
NIFRID:synonym "Sciex 7500+ Triple Quadrupole LC/MS system" ;
definition: "Sciex 7500+ Triple Quadrupole Liquid Chromatography/Mass Spectrometry System enables rapid, sensitive screening for large panels of analytes, including metabolites, lipids, and environmental contaminants. SCIEX 7500+ system minimizes downstream contamination of the ion optics, maintaining instrument robustness over greater periods than the benchmark triple quadrupole mass spectrometers." .
SCR:026609 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3099" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Microbial Sequencing and Analytics Core Facility" ;
NIFRID:synonym "Microbial Sequencing and Analytics Resource (MSAAR)" ;
NIFRID:abbrev "MSAAR" ;
definition: "Core provides services, from DNA and RNA extraction from diverse sample types such as tissue, stool, and bacterial isolates to next-generation sequencing, including whole-genome sequencing, total RNA-seq, metatranscriptomics, and dual RNA-seq, along with expert bioinformatics support. Core expertise spans 16S rRNA amplicon sequencing, shotgun metagenomics, metatranscriptomics, meta-omics analysis of dual RNA-seq, and single-cell RNA-seq data. Core also assists with experimental design and power calculations to ensure statistically robust results, offering consultation at every stage, from experimental design to data interpretation and troubleshooting." .
SCR:026610 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ssGSEA 2.0" ;
NIFRID:synonym "Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)",
"ssGSEA2.0/PTM-SEA" ;
definition: "Software application as updated version of original ssGSEA R-implementation. Depending on the input dataset and chosen database (gene sets or PTM signatures), the software performs either ssGSEA or PTM-SEA, respectively." .
SCR:026611 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3100" ;
rdfs:label "University of Texas MD Anderson Cancer Center Advanced Microscopy Core Facility" ;
NIFRID:synonym "Advanced Microscopy Core",
"MD Anderson Cancer Center Advanced Microscopy Core",
"University of Texas MD Anderson Cancer Center Advanced Microscopy Core" ;
definition: "Core provides microscopy services to departments at MD Anderson in high resolution and multispectral fluorescence microscopy for users from divisions including Basic Research, Cancer Medicine, Diagnostic Imaging, Surgery, Internal Medicine Pediatrics and Radiation Oncology, among others. Offers microscopy resources and expertise in fluorescence imaging to spatially and dynamically assess cells, tissues and their requisite contents across scales." .
SCR:026612 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "joinet" ;
definition: "Software R package implementing multivariate lasso and ridge regression using stacked generalization. Used for predicting correlated outcomes." .
SCR:026613 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "County Health Rankings and Roadmaps " ;
definition: "Program of University of Wisconsin Population Health Institute, highlights policies and practices that can help everyone be as healthy as possible. Aims to grow shared understanding of health, equity and power of communities to improve health for all." .
SCR:026614 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of California at Irvine Optical Biology Core Facility" ;
NIFRID:synonym "University of California at Irvine Optical Biology Core" ;
definition: "Shared resource facility to provide researchers access to resources, including state of the art instrumentation and technical support, to conduct biomedical research. Provides access to light microscopes (confocal, mesoscale lightsheet, and Super Resolution), as well as software for 3D and 4D analysis." .
SCR:026615 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of California at Irvine Genomics Research and Technology Hub Core Facility" ;
NIFRID:synonym "GRT Hub",
"UCI Genomics Research and Technology Hub",
"UCI GRT Hub",
"University of California at Irvine-Genomics Research and Technology Hub" ;
definition: "Core provides services ranging from DNA/RNA QC analysis, library construction and sequencing on various platforms. Offers several sequencing platforms from Illumina’s MiSeq and NovaSeq to PacBio’s Sequel II System." .
SCR:026616 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of California at Irvine Flow Cytometry Core Facility" ;
NIFRID:synonym "University of California at Irvine Flow Cytometry Core" ;
definition: "Core is part of the UCI Sue and Bill Gross stem cell research center. Provides various fee based services to researchers at UCI towards flow cytometry and cell sorting." .
SCR:026617 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CREsted" ;
NIFRID:synonym "and design",
"Cis-Regulatory Element sequence training",
"explanation" ;
definition: "Software Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences." .
SCR:026618 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pycisTopic" ;
definition: "Software Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data." .
SCR:026619 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Borzoi" ;
definition: "Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences." .
SCR:026620 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tangermeme" ;
definition: "Software application for biological sequence analysis for the modern age." .
SCR:026621 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gReLU" ;
definition: "Software Python library to train, interpret, and apply deep learning models to DNA sequences. Comprehensive framework for DNA sequence modeling and design." .
SCR:026622 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SnapATAC2" ;
definition: "Software Python/Rust package for single-cell epigenomics analysis." .
SCR:026623 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "statannotations" ;
definition: "Software Python package to optionally compute statistical test and add statistical annotations on plots generated with seaborn. Used to add statistical significance or custom annotations on seaborn plots." .
SCR:026624 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PUMATAC" ;
NIFRID:synonym "Pipeline for Universal Mapping of ATAC-seq" ;
definition: "Software pipeline for universal mapping of ATAC-seq." .
SCR:026625 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CreateZoom" ;
definition: "Backend application to process high-resolution histology images to DeepZoomImage format, made of smaller tiles, for use in the QUINT Workflow." .
SCR:026626 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pycistarget" ;
definition: "Software Python tool to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes." .
SCR:026627 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bigtools" ;
definition: "Software library and associated tools for reading and writing bigwig and bigbed files. High-performance BigWig and BigBed library in Rust." .
SCR:026628 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BerryPortraits" ;
NIFRID:synonym "Phenotyping of Ripening Traits" ;
definition: "Open source Python-based image-analysis software that rapidly detects and segments berries and extracts morphometric data on fruit quality traits such as berry color, size, shape, and uniformity. Used for quantifying visual phenotypes of cranberries and other berries." .
SCR:026630 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DeepAnnotation" ;
definition: "Software Python package to perform genomic selection. Predicts phenotypes from comprehensive multi-omics functional annotations with interpretable deep learning framework. Novel interpretable DL-based genomic prediction model that integrates comprehensive species- and tissue-level transcriptional regulatory functional annotations to predict phenotypes." .
SCR:026631 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3110" ;
rdfs:label "Fred Hutchinson Cancer Center Prevention Center Shared Resource Core Facility" ;
NIFRID:synonym "Fred Hutch Cancer Center Prevention Center Shared Resource" ;
definition: "Provides services in the conduct of exercise interventions, nutrition interventions, or prevention-based clinical interventions. Facility offers well-trained, specialized staff and inviting space for study participants to participate in population-based research." .
SCR:026632 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3092" ;
rdfs:label "Texas A and M University System Genomics and Bioinformatics Service Core Facility" ;
NIFRID:synonym "Genomics & Bioinformatics Service",
"Texas A&M University System Genomics & Bioinformatics Service" ;
definition: "Core provides services including Sequencing, Library preparation, Bioinformatics Analysis and Processing. Experienced staff provide expertise to users." .
SCR:026633 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "modeltest" ;
NIFRID:synonym "ModelTest-NG" ;
definition: "Software tool for selecting the best-fit model of evolution for DNA and protein alignments. Used for selection of DNA and Protein evolutionary models." .
SCR:026634 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ScType" ;
definition: "Computational platform, which enables data-driven, fully-automated and ultra-fast cell-type identification based on given scRNA-seq data, combined with comprehensive cell marker database as background information. Deployed as both interactive web-tool and open-source R-package." .
SCR:026635 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3111" ;
rdfs:label "Pennsylvania State University Honey and Pollen Diagnostic Laboratory Core Facility" ;
NIFRID:synonym "Penn State Honey and Pollen Diagnostic Laboratory",
"Pennsylvania State University Honey and Pollen Diagnostic Laboratory" ;
NIFRID:abbrev "PSU HPDL" ;
definition: "Core offers researchers and beekeepers, throughout the world, services to identify floral resources and evaluate characteristics of honey and pollen." .
SCR:026636 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RNAcomposer" ;
definition: "Web application as fully automated RNA structure modeling server. Used for RNA tertiary structure prediction." .
SCR:026637 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hex" ;
NIFRID:synonym "HexServer" ;
definition: "Web FFT-based protein docking server. First Fourier transform (FFT)-based protein docking server to be powered by graphics processors.Interactive protein docking and molecular superposition program. Hex understands protein and DNA structures in PDB format, and it can also read small-molecule SDF files.Hex will run on most Windows-XP, Linux and Mac OS X PCs." .
SCR:026638 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Architect_i2000SR" ;
rdfs:label "Abbott | ARCHITECT i2000SR immunoassay analyzer" ;
NIFRID:synonym "Architect i2000SR" ;
definition: "Analyzer offers maximum throughput of up to 200 tests per hour. Featuring load-up capacity of 135 samples with 35 priority and 100 routine areas. Has 25 refrigerated reagent positions. Designed for efficient and accurate analysis of various biological samples, including serum, plasma, and other bodily fluids." .
SCR:026639 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_cobas_e_402" ;
rdfs:label "Roche | cobas e 402 analytical unit" ;
NIFRID:synonym "cobas e 402",
"cobas e 402 analytical unit" ;
definition: "Fully automated immunology analyzer designed to analyze biological samples like serum, plasma, and other bodily fluids, providing insights into immunological parameters. Has throughput of up to 120 tests per hour, with 9-minute STAT applications for time-sensitive tests. Can be used for testing broad range of parameters, including cytokines, antibodies, antigens, and immune cell populations." .
SCR:026640 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_cobas_e_602" ;
rdfs:label "Roche | cobas e 602 analytical unit" ;
NIFRID:synonym "cobas e 602 analytical modul",
"cobas e 602 analytical unit" ;
definition: "Immunochemistry analyzer as mid-volume throughput immunochemistry module that performs broad range of heterogeneous immunoassay tests using ElectroChemiLuminescence (ECL) technology. Offers Heterogeneous immunoassays, Throughput of up to 170 tests/hour, 25 reagent positions, Reagent cassette loading/unloading during standby, Carryover-free disposable tips, Clot and air bubble detection." .
SCR:026641 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Seahorse_XF96" ;
rdfs:label "Agilent | Seahorse XF96 Analyzer" ;
NIFRID:synonym "Seahorse XF96 Extracellular Flux Analyzer" ;
definition: "Seahorse XF96 Extracellular Flux Analyzer measures the rate of change of analytes dissolved oxygen and pH in media immediately surrounding living cells cultured in a microplate." .
SCR:026642 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioBox" ;
definition: "Platform to help scientists organize all biological knowledge into singular, unified resource that is searchable, accessible and capable of answering the most difficult questions in science. Used for bioinformatics analysis." .
SCR:026643 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scATAC-seq Fragment Tools" ;
definition: "Software tools for manipulating scATAC-seq fragment files." .
SCR:026644 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scPrinter" ;
definition: "Softwre framework for multi-scale footprinting analysis of single-cell ATAC-seq data. Designed to identify and visualize regulatory elements that drive cell-type-specific gene expression programs through footprinting. Uses deep learning model to predict activity of transcription factors from single-cell ATAC-seq data. Provides suite of visualization tools to explore calculated multi-scale footprints." .
SCR:026645 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Breeding Insight" ;
definition: "U.S. Department of Agriculture Agricultural Research Service initiative hosted at Cornell University in Ithaca, New York. Assists USDA-ARS breeders by creating new opportunities in assimilating data-driven tools, technologies, and methods to remove barriers and more easily allow for the use of genomic insights. We integrate phenomics (trait analysis), genomics (genotypic data), data management, and software tools to help breeders increase the rate of genetic gain and create more healthy and nutritious specialty crops and animals. These gains improve on-farm production for many of America’s favorite specialty crops and animals." .
SCR:026646 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Breeze web-tool" ;
NIFRID:synonym "Breeze",
"Breeze 2.0" ;
definition: "Interactive web application for drug screening data analysis. It includes comprehensive quality control statistics, dose-response curve fitting, and calculation of quantitative scoring parameters such as EC50, IC50, drug sensitivity score and AUC. Used to facilitate quality control, dose-response curve fitting, and data visualization." .
SCR:026651 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroDevTime" ;
definition: "Software code for age prediction in fetal brain and organoid single cell data. This repository contains cell type agnostic models to predict the developmental age of brain cell types from single cell RNAseq data. Code contains 4 jupyter notebooks, which apply pretrained models to predict neurodevelopmental age of cell types in new human fetal brain and organoid datasets." .
SCR:026652 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3113" ;
rdfs:label "Northwestern University Evanston Single Cell Genomics Core Facility" ;
NIFRID:synonym "Evanston Single Cell Genomics Core",
"Northwestern University Single Cell Genomics Facility" ;
definition: "Core dedicated to supporting single cell and spatial biology experiments on the Evanston campus. Home of flow cytometry. Offers single cell encapsulation and library preparation services using the 10X Genomics platform. Provides experiments consultations.Shared use, training, and service facility. Instrumentation includes FACSDiscover S8 flow sorter, LSRFortessa flow analyzer, MERSCOPE spatial transcriptomics platform, 10X Genomics Chromium iX, Epredia NX70 Cryostat, QuantStudio 3 real-time PCR, VeritiPro Thermocycler, Agilent Bioanalyzer, Axiovert inverted microscope (DIC, Brightfield, 4 fluorescent channels), Revvity Cellometer K2 automated cell counter, Qubit 4 fluorometer, Nanodrop spectrophotometer. Services include assisted flow cytometry, 10X Genomics library preparation, spatial transcriptomics via MERSCOPE, cell counting, bioanalyzer analysis, bulk library preparation, and low input library preparation." .
SCR:026653 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciLifeLab Precision Medicine Portal" ;
definition: "Swedish national resource supporting precision medicine research in Sweden through access to data sources, customised dashboards and guidance on data management with focus on making data FAIR and reusable." .
SCR:026654 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Axion Biosystems | Maestro Pro System" ;
NIFRID:synonym "Axion Biosystems Maestro Pro™ microelectrode array (MEA)" ;
definition: "System for non-invasive, real-time, and label-free evaluation of cellular function in vitro, particularly for monitoring electrical activity of excitable cells like neurons and cardiomyocytes, as well as tracking cell growth and death. Used in neuroscience to measure electrical activity of network of cultured neurons." .
SCR:026655 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "3D-Hub-O platform" ;
NIFRID:synonym "3D Hub-O organoid platform",
"3D-Hub-O" ;
definition: """3D-Hub-O specializes in production, manipulation and analysis of organoids from normal and tumor tissues. Physiological platform for research on living pathological tissues.
Platform participates in knowledge transfer through customized training of specific organoid culture carried out by platform staff.""" .
SCR:026656 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RWD Life Science | Standard Stereotaxic Holder" ;
NIFRID:synonym "Standard Stereotaxic Holder",
"Standard Stereotaxic Instruments" ;
definition: "Compact stereotaxic instrument designed for use with knock-out and transgenic mice. Instrument includes 100 micron, 3-axes left-hand manipulator arm, mouse snout clamp and tooth bar, dual-sided ear bars, and corner clamp probe holder. Stoelting’s Motorized Stereotaxic Manipulator Arms are designed for fast, accurate positioning during stereotaxic surgery. Motorized manipulator arms employ touchscreen display for easy-to-control movement of each axis. Manual movement is available anytime. Optional Drill feature available." .
SCR:026657 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3103" ;
rdfs:label "North Carolina State University College of Veterinary Medicine Flow Cytometry and Cell Sorting Core Facility" ;
NIFRID:synonym "NCSU-CVM Flow Cytometry and Cell Sorting Core Facility",
"North Carolina State University NCSU-CVM Flow Cytometry and Cell Sorting Core Facility" ;
definition: "Core provides flow cytometry services. Staff members will help with experimental design, instrument training, sample acquisition, data analysis with software provided, and conventional/spectral cell sorting." .
SCR:026658 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3104" ;
rdfs:label "Benaroya Research Institute Genomics Core Facility" ;
NIFRID:synonym "Benaroya Research Institute BRI Genomics Core",
"BRI Genomics Core" ;
definition: "Core provides services for genomics analysis, from sample processing through data generation. Available technologies focus on Illumina RNA and DNA sequencing. RNA-seq can be performed from a variety of sample types, including purified total RNA, cell populations (including low input samples of 50-1000 cells), or single cells (either plate-sorted rare populations or high-throughput 10x single-cell analyses). DNA-seq pipelines can also be performed, including bulk CUT and Tag/CUT and RUN, and ATAC-seq and single cell ATACseq and multiome capture. Custom prepared libraries can also be submitted for sequencing. Core laboratory houses Illumina sequencers, NextSeq2000 instruments and Miseq, plus 10x Chromium X and 10x CytAssist. Additional equipment includes ThermoFisher Kingfisher Flex, for extracting nucleic acid from variety of sample types using magnetic bead technology with throughput of up to 96 samples. Qiagen QIAcube Connect instruments automate extraction of nucleic acid using spin column technology. Ancillary equipment for sample processing includes Formulatrix Mantis Liquid Handler, Agilent TapeStation 4200 and Tecan NanoQuant." .
SCR:026659 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ubibrowser" ;
definition: "Web application as resource of known and predicted human ubiquitin ligase substrate interaction network. E3-substrate interactions are derived from six data sources: mannual cruration, protein ortholog, protein domain, protein motif and network topology.Designed to explore predicted and reported E3-substrate interactions for query E3 or substrate, and ubiquitination sites for substrate protein." .
SCR:026660 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MyVivarium" ;
definition: """Cloud-based lab animal colony management application with realtime ambient sensing.
Platform for managing vivaria. It features cage management, user management, lab management, and real-time environmental monitoring with IoT sensors.""" .
SCR:026661 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RPi-IoT" ;
NIFRID:synonym "Raspberry Pi-enabled IoT" ;
definition: "Stand-alone Raspberry Pi-enabled IoT system to monitor near-realtime sensor data in MyVivarium web app. Used to track environmental conditions of vivaria." .
SCR:026662 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Causallib" ;
definition: "Software Python package for modular causal inference analysis and model evaluations. Used for inferring causal effects from observational data." .
SCR:026663 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nf-test" ;
definition: "Software tool as simple test framework for Nextflow pipelines. Enables pipeline developers to test individual process blocks, workflow patterns and entire pipelines in insolation." .
SCR:026664 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3114" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Cell Culture Core Facility" ;
definition: "Core provides specialized cell culture services , ensures high-quality and contamination-free cultures by employing aseptic techniques and maintaining Mycoplasma and Quarantine facilities. Offers cell banking, with capacity to freeze and store up to 10,000 vials. Facility provides walk-in warm room and cold room, spinner apparatus capable of handling over 20 liters of cells in suspension, and roller bottle machine that accommodates more than 200 roller bottles. Additional equipment includes automated cell counter and ELISA reader." .
SCR:026665 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3115" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Glassware Core Facility" ;
definition: "Core provides glassware washing and sterilization of all types of glassware and pipettes. Facility maintains stock glassware in common storage area. Glassware personnel collect glassware from laboratories daily and cabinets are replenished regularly. Autoclaving of materials is offered on daily basis. Core can accommodate any special requests. Glassware Core maintains stock of all types of sterile laboratory glassware and pipettes in common storage area." .
SCR:026666 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3116" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Hybridoma Core Facility" ;
definition: "Core provides monoclonal antibody production services. Provides consultation to assist investigator in all aspects of monoclonal antibody production. Services are performed under strict quality control guidelines appropriate for antibodies that may have commercial potential." .
SCR:026667 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3117" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Media Preparation Core Facility" ;
definition: "Core offers quality controlled media at economical prices. Media is prepared in large batches ranging from 50L-300L from commercially produced powders. All products go through strict quality control program. Custom plates and media are offered by request and are usually available within 2-4 business days. All other orders placed online can be picked up on the next business day." .
SCR:026668 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3118" ;
rdfs:label "Augusta University Chemical and Biomolecular Analysis Core Facility" ;
definition: "Core focused on metabolomics, lipidomics, medicinal chemistry, and small molecule analysis. Offers services, expertise, and collaboration for the research community. Instrumentation includes high field nuclear magnetic resonance (NMR), liquid chromatography–mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), high-performance liquid chromatography (HPLC), circular dichroism spectrometer (CD), inductively coupled plasma optical emission spectrometry (ICP-OES), and fluorimeter. Consulting is available to assist with experimental design and data interpretation." .
SCR:026669 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MassChroQ" ;
NIFRID:synonym "Mass Chromatogram Quantification" ;
definition: "Software tool that performs alignment, XIC extraction, peak detection and quantification on data obtained from Liquid Chromatography-Mass Spectrometry (LC-MS) techniques. Performs LC-MS data alignment and peptide quantification by peak area integration on extracted ion chromatograms." .
SCR:026670 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MyProms" ;
NIFRID:synonym "myProMS" ;
definition: "Web server for management and validation of mass spectrometry-based proteomic data." .
SCR:026671 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Azure_300" ;
rdfs:label "Azure Biosystems | Chemiluminescent Western Blot Imager Azure 300" ;
definition: "Multichannel, multimodal imager, with visible fluorescence, visible light, and UV excitation channels. The system is fully upgradeable to fluorescent Western Blot Imaging System." .
SCR:026672 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Leica_DMi8" ;
rdfs:label "Leica | DMi8 Inverted Microscope" ;
NIFRID:synonym "Leica DMi8",
"Leica DMi8 microscope" ;
definition: "Leica DMi8 microscope is an inverted light microscope, intended as a general microscope for routine examinations of biological specimens." .
SCR:026673 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scvi-tools" ;
NIFRID:synonym "single-cell variational inference tools" ;
definition: "Software Python library for deep probabilistic analysis of single-cell and spatial omics data. Used for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData." .
SCR:026674 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FACSDiscover_S8" ;
rdfs:label "BD Biosciences | FACSDiscover S8" ;
NIFRID:synonym "BD FACSDiscover S8 Cell Sorter" ;
definition: "Cell Sorter, equipped with 5 lasers (355, 405, 488, 561 and 640 nm excitation wavelengths) and 78 channels which can measure the entire emission spectra of the fluorescent dyes, is the first spectral flow cytometer sorter with sort-capable image analysis." .
SCR:026675 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OncoSim" ;
definition: "Web-based simulation tool that evaluates cancer control strategies. Microsimulation model calibrated to Canadian input data primarily used to inform health economic policy of cancer screening and prevention strategies." .
SCR:026676 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BIGapp" ;
NIFRID:synonym "Breeding Insight Genomics App" ;
definition: "Species-agnostic web-based application for processing genotypic data in no-code RShiny user-friendly interface. Allows users without coding experience to process genetic data in all genome ploidy ranges and for multiallelic data, starting from number of input formats (including VCF). Also allows to perform downstream QC analyses (e.g., PCA) and run genomic analysis (e.g., Linkage mapping, QTL analysis, genome-wide association studies (GWAS), and genomic selection (GS)." .
SCR:026677 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BIGr" ;
NIFRID:synonym "Breeding Insight Genomics R App" ;
definition: "Software R package contains functions developed within Breeding Insight to analyze diploid and polyploid breeding and genetic data. Provides set of functions for analyzing genomic and pedigree data in diploid and polyploid breeding programs. Used to streamline analysis of breeding and genetic data." .
SCR:026678 a owl:NamedIndividual ;
NIFRID:synonym "breeding insight-web" .
SCR:026679 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MINERVA" ;
NIFRID:synonym "Molecular Interaction NEtwoRk VisuAlization" ;
definition: "Standalone web server for visualization, exploration and management of molecular networks encoded in SBGN-compliant format." .
SCR:026680 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rrvgo" ;
definition: "Software R package to reduce and visualize Gene Ontology terms. Used for interpreting lists of Gene Ontology terms." .
SCR:026681 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nnunetv2" ;
definition: "Software application that automatically adapts to given dataset. It will analyze provided training cases and automatically configure matching U-Net-based segmentation pipeline." .
SCR:026682 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Karolinska Institutet Adaptive Immune Receptor Gene Variant Atlas" ;
NIFRID:abbrev "KIARVA" ;
definition: "Immunology database of B and T cell receptor gene variants, providing population frequency data, FASTA downloads and tools to study IG variation at individual and population levels." .
SCR:026683 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Singular Genomics" ;
definition: "Publicly-traded life science technology company, which specializes in advanced next-generation sequencing (NGS) and multiomic technologies." .
SCR:026684 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_G4X" ;
rdfs:label "Singular Genomics | G4X Spatial Sequencer" ;
NIFRID:synonym "G4X Spatial Sequencer" ;
definition: "Ultra high-throughput, spatial sequencing platform, for integrated multiomic analysis of FFPE samples at subcellular resolution. Spatial sequencing platform capable of simultaneous direct RNA." .
SCR:026685 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3119" ;
rdfs:label "Pennsylvania State University Nanofabrication Lab Core Facility" ;
definition: "Fully-staffed, open access nanofabrication lab provides services including Lithography, Etch (Dry/Wet), Deposition and Characterization." .
SCR:026686 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "kent" ;
definition: "UCSC Genome Browser source tree. Stable branch: \"beta\"." .
SCR:026687 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HiGlass" ;
definition: "Web-based visual exploration and analysis of genome interaction maps." .
SCR:026688 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dask" ;
definition: "Software Python library for parallel and distributed computing. Enables parallel and out-of-core computation." .
SCR:026689 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EpiJen" ;
definition: "Web server for multistep T cell epitope prediction. Also considers proteasome cleavage and TAP binding, therefore it is able to mimic the MHC binding machnism in real life. At present only HLA class I alleles are included in the prediction." .
SCR:026690 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EndoMap" ;
NIFRID:synonym "EndoMAP.v1" ;
definition: "Structural interactome viewer. Interactive database of endosomal protein-protein interactions identified by cross-linking mass spectrometry and modeled by AlphaFold multimer. Structural protein interactome of human early endosomes." .
SCR:026691 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Predictomes" ;
definition: "Interactive database of protein protein interactions modeled by AlphaFold multimer. Classifier-curated database of AlphaFold-modeled protein-protein interactions." .
SCR:026692 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mutect2" ;
definition: "Software tool to call somatic short mutations via local assembly of haplotypes. Somatic variant caller that uses local assembly and realignment to detect SNVs and indels." .
SCR:026693 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3109" ;
rdfs:label "Emory University AI Image Extraction Core Facility" ;
NIFRID:synonym "Emory University EU - AI Image Extraction Core",
"EU - AI Image Extraction Core" ;
NIFRID:abbrev "AI2EC" ;
definition: "Core is supported by the Emory University School of Medicine. Enables large-scale, secure image extraction and de-identification to empower clinical, translational, and AI research." .
SCR:026694 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Seahorse_XF_Pro" ;
rdfs:label "Agilent | Seahorse XF Pro Analyzer" ;
NIFRID:synonym "Seahorse XF Pro Analyzer" ;
definition: """Agilent Seahorse XF Pro analyzer measures and reports the oxygen consumption rate (OCR), proton efflux rate (PER) or extracellular acidification rate (ECAR), as well as ATP production rates of live cells in a 96-well format. This analyzer features excellent OCR precision at low rates, verified performance, optimized temperature control, and is automation enabled.
The XF Pro analyzer is also equipped with advanced software, standardized workflows, and advanced data analytics available in the Agilent Seahorse Analytics software. These features greatly simplify the entire XF assay experience, from assay design to data QC and interpretation.""" .
SCR:026695 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nano@stanford" ;
NIFRID:synonym "Nano at Stanford" ;
definition: "nano@stanford is a group of shared labs at Stanford University focused on fabrication and characterization at the nanoscale and microscale. The labs provide access to shared scientific instrumentation, laboratory infrastructure, and expert staff support to enable multidisciplinary research and educate tomorrow’s scientists and engineers." .
SCR:026696 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3131" ;
rdfs:label "University of Michigan Medical School BRCF Vector Core Facility" ;
NIFRID:synonym "University of Michigan BRCF Vector Core" ;
definition: "Vector Core produces gene transfer vectors that facilitate transfer of specific genes into either normal or aberrant cells. Provides intellectual and technical advice to researchers regarding the optimal use of these systems." .
SCR:026697 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3191" ;
rdfs:label "University of Michigan Medical School BRCF Flow Cytometry Core Facility" ;
NIFRID:synonym "University of Michigan BRCF Flow Cytometry" ;
definition: "Flow Cytometry Core provides instrumentation, expertise and services. Samples are prepared by individual investigators, who then deliver to the Core for flow cytometric analysis or cell sorting. The Core also provides assistance in grant and publication preparation, publication-quality graphics, and the development of experimental designs." .
SCR:026698 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pylustrator" ;
definition: "Software application to prepare figures for publication in reproducible way. This means you receive a figure representing your data and alongside a generated code file that can exactly reproduce the figure as you put them in the publication, without the need to readjust things in external programs. Offers interactive interface to find the best way to present your data in a figure for publication. Added formatting an styling can be saved by automatically generated code. To compose multiple figures to panels, pylustrator can compose different subfigures to a single figure." .
SCR:026699 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3120" ;
rdfs:label "Massachusetts Institute of Technology Preclinical Imaging and Testing Core Facility" ;
NIFRID:synonym "Massachusetts Institute of Technology MIT-Preclinical Imaging and Testing Facility",
"MIT-Preclinical Imaging and Testing Facility" ;
definition: "Core assists in evaluating disease and its cure within complete biological system. Combines expertise and instrumentation to assist investigations on the mechanisms of disease development, to enable the evaluations of drug efficacy and resistance, and to provide the means for testing novel strategies and devices for disease detection and drug delivery." .
SCR:026700 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ecosystem for Multi-modal Brain-behavior Experimentation and Research" ;
NIFRID:synonym "Ecosystem for Multi-modal Brain-behavior Experimentation and Research (EMBER)",
"EMBER Archive" ;
NIFRID:abbrev "EMBER" ;
definition: "BRAIN Initiative data archive for multi-modal neurophysiological and behavioral data, supporting the Brain Behavior Quantification and Synchronization (BBQS) Program. Accessible and versatile data archive for storage, processing, and curation of multimodal neurophysiological and behavioral datasets. EMBER extends established BRAIN Initiative data infrastructure, provides new data harmonization and synchronization capabilities, and supports scalable integrations for data coordination and AI driven batch processing to enable the goals of the BBQS program." .
SCR:026701 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ohio State University Pharmacoanalytical Shared Resource Core Facility" ;
NIFRID:synonym "Ohio State University Pharmacoanalytical Shared Resource (PhASR)",
"Pharmacoanalytical Shared Resource" ;
NIFRID:abbrev "PhASR" ;
definition: "Core provides access to expertise and instrumentation for bioanalytical assay development and quantitative sample analysis, experimental design, data analysis and modeling applied in pre-clinical and clinical research involving development of novel therapies for cancer treatment and prevention, chemopreventive or carcinogenic components in food/environmental sources, and biomarkers relevant to drug therapy, nutrients, food products, and dietary patterns." .
SCR:026702 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCENIC+" ;
definition: "Software Python package to build gene regulatory networks using combined or separate single-cell gene expression and single-cell chromatin accessibility (scATAC-seq) data. Used for inferring and analyzing enhancer-driven gene regulatory networks using single-cell multiomic data." .
SCR:026703 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EnsDbHsapiensv79" ;
definition: "Software ensembl based annotation R package. Exposes annotation databases generated from Ensembl. This package loads SQL connection to database containing annotations from Ensembl." .
SCR:026704 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FARDEEP" ;
NIFRID:synonym "Fast And Robust DEconvolution of Expression Profiles" ;
definition: "Software R tool for enumerating immune cell subsets from whole tumor tissue samples. Utilizes adaptive least trimmed square to automatically detect and remove outliers before estimating cell compositions." .
SCR:026705 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OptimJV3" ;
definition: "Software repository provides optimization algorithms applied to Jarvis3 genomic compressor used for compression of genomic sequences." .
SCR:026706 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3127" ;
rdfs:label "Michigan State University Bioinformatics Core Facility" ;
NIFRID:synonym "Michigan State University MSU Bioinformatics Core",
"MSU Bioinformatics Core" ;
definition: "Core brings together expertise from across MSU to support research through advanced omics data analysis, grant proposal assistance, and tailored training for researchers at all career stages." .
SCR:026707 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "popscle" ;
definition: "Software suite of population scale analysis tools for single-cell genomics data." .
SCR:026708 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mallet" ;
NIFRID:synonym "MAchine Learning for LanguagE Toolkit" ;
definition: "Software Java-based package for statistical natural language processing, document classification, clustering, topic modeling, information extraction, and other machine learning applications to text." .
SCR:026709 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tfmodisco-lite" ;
definition: "Software tool as lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments. Rewrite of the original TF-MoDISCo code." .
SCR:026710 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pathogens Portal Netherlands" ;
definition: "Portal provides information, guidelines, data, services, and other resources aimed at supporting the research community in the Netherlands to share data related to pathogens and pandemic preparedness." .
SCR:026712 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "broom.mixed" ;
definition: "Software R package for tidying output of statistical models." .
SCR:026713 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scatac_fragment_tools" ;
definition: "Software tools for working with scATAC-seq fragment files." .
SCR:026714 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GEfetch2R" ;
definition: "Software R package to access and explore existing scRNA-seq data from various public repositories. Supports downloading scRNA-seq data types, including raw data (SRA and ENA), count matrices (GEO, UCSC Cell Browser, and PanglaoDB), and processed objects (Zenodo, CELLxGENE, and HCA). Can access and explore existing scRNA-seq data, load output/downloaded count matrices and annotations to R (SeuratObject/DESeqDataSet), extract a subset of the SeuratObject based on cell metadata and genes, and merge multiple SeuratObjects if applicable. Provides format conversions between different scRNA-seq objects, including SeuratObject, AnnData, SingleCellExperiment, CellDataSet/cell_data_set, and loom." .
SCR:026715 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3134" ;
rdfs:label "University of Michigan School of Nursing Applied Biostatistics Laboratory and Data Core Facility" ;
NIFRID:synonym "School of Nursing Applied Biostatistics Laboratory University of Michigan",
"University of Michigan Applied Biostatistics Lab and Data Core",
"University of Michigan Nursing Applied Biostatistics Laboratory",
"University of Michigan School of Nursing Applied Biostatistics Laboratory" ;
definition: """Core provides training, education, statistics and data management services.
Services include: experimental design of new studies, advising on outcomes selection,
determining or justifying sample size, designing randomization schemes,designing and writing the statistical analysis/modeling section(s), advising on appropriate database design and implementation methods, advising on the use of national data registries, health system data, grant writing on relevant sections within our specialties, creating custom databases and data entry portals for prospective studies, creating custom datasets or extracts from existing data sources for analysis, merging complex or multi-sourced data in concert with research aims and objectives, implementing blind, double-blind and other randomization schemes and more.""" .
SCR:026716 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3133" ;
rdfs:label "University of Michigan College of Pharmacy Biochemical Nuclear Magnetic Resonance Lab Core Facility" ;
NIFRID:synonym "University of Michigan Biochemical Nuclear Magnetic Resonance Lab",
"University of Michigan Biochemical Nuclear Magnetic Resonance Lab Core Facility" ;
definition: "Provides full-service consultation, sample processing and results. After running your samples, we will process your data using Mestranova and give you access to the raw data via email or Dropbox." .
SCR:026717 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3132" ;
rdfs:label "University of Michigan Biointerfaces Institute Nanotechnicum Core Facility" ;
definition: "Nanotechnicum is a Biointerfaces Institute core facility providing Nanoparticle Size analysis and Zeta Potential characterization, Chiral materials spectroscopy, Material Pore Size and Porosity characterization, Materials Thermal analysis, and Biomolecular Binding characterization instrumentation and services. The Biointerfaces Institute offers instrumentation to the University of Michigan’s research community, fellow academic institutions, and industry." .
SCR:026718 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3136" ;
rdfs:label "University of Michigan Biological Mass Spectrometry Core Facility" ;
NIFRID:synonym "University of Michigan Biological Mass Spectrometry Core" ;
definition: "Facility provides specialized MS services. The major areas of focus of the lab are Analysis of intact proteins, multi-protein complexes, and protein structure; Identification and purification of compounds from complex mixtures coupled with quantitative analysis.; Purification using mass directed autopurification liquid chromatography. Users can be trained on the instruments for walk-up use or samples can be submitted for analysis." .
SCR:026719 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3137" ;
rdfs:label "University of Michigan Biomolecular Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "Biomolecular Nuclear Magnetic Resonance (BioNMR) Core",
"University of Michigan BioNMR Core Facility (U-M BioNMR)" ;
NIFRID:abbrev "BioNMR",
"U-M BioNMR" ;
definition: "Core facility primary mission is to provide access to advanced NMR spectroscopic methods and tools to students, postdoctoral fellows, and faculty of the University for the advancement of their research." .
SCR:026720 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3192" ;
rdfs:label "University of Michigan Medical School BRCF Epigenomics Core Facility" ;
definition: "Core provides resources and services to prepare samples for analysis in epigenetic regulation in both genome-wide and locus-specific manners." .
SCR:026721 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3193" ;
rdfs:label "University of Michigan Medical School BRCF Metabolomics Core Facility" ;
NIFRID:synonym "University of Michigan BRCF Metabolomics Core",
"University of Michigan BRCF Metabolomics Core Facility" ;
definition: "Offers full-service sample analysis to measure concentrations of small molecules in biological samples. Services include targeted and untargeted metabolomic screening, method development to explore novel metabolic pathways and systems. Staff helps with interpretation and visualization of your data, and the preparation of grants, proposals, and manuscripts." .
SCR:026722 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3194" ;
rdfs:label "University of Michigan Medical School BRCF Microscopy Core Facility" ;
NIFRID:synonym "University of Michigan BRCF Microscopy Core",
"University of Michigan Medical School BRCF Microscopy Core" ;
definition: "Offers microscopy instrumentation and services. Offers support and training on variety of high-end instrumentation and advanced methodologies for both light and electron microscopy, sample preparation services for electron microscopy, training and assistance with image analysis. Provides support across variety of open-source and commercial image analysis software packages." .
SCR:026723 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3195" ;
rdfs:label "University of Michigan Medical School BRCF Proteomics Resource Core Facility" ;
NIFRID:synonym "University of Michigan BRCF Proteomics Resource Facility",
"University of Michigan Medical School Pathology BRCF Proteomics Resource Core Facility",
"University of Michigan Medical School Pathology BRCF Proteomics Resource Facility" ;
definition: "Core is dedicated to protein analysis and applying mass spectrometry-based proteomic approaches to varied biological questions." .
SCR:026724 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Qploidy" ;
definition: "Software R package for ploidy and aneuploidy estimation using genotyping platform data." .
SCR:026725 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "WISENT Bioproducts" ;
definition: "Biological and life science product supplier." .
SCR:026726 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3196" ;
rdfs:label "University of Michigan Bru-Seq Lab Core Facility" ;
NIFRID:synonym "University of Michigan Bru-Seq Lab" ;
definition: "Core facility provides nascent RNA sequencing using four techniques: Bru-seq, BruChase-seq, BruUV-seq, and BruDRB-seq. This service is all-inclusive, starting with cells and ending with basic data analysis. In addition, users will have access to our exclusive pipeline to perform further data analysis. Our areas of expertise are RNA isolation, cDNA library preparation, and sequencing data analysis." .
SCR:026727 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3197" ;
rdfs:label "University of Michigan Cancer Data Science Shared Resource Core Facility" ;
NIFRID:synonym "University of Michigan Cancer Data Science Shared Resource" ;
definition: "Core is part of the University of Michigan Rogel Cancer Center. Provides Rogel Cancer Center investigators with assistance in all quantitative aspects of cancer research -- including biostatistics, bioinformatics, computational biology, analytics and other emerging data-driven and data-intense endeavors." .
SCR:026728 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3198" ;
rdfs:label "University of Michigan Cardiovascular Regeneration Core Facility" ;
NIFRID:synonym "U-M Cardiovascular Regeneration Core Laboratory",
"University of Michigan Cardiovascular Regeneration Core Laboratory" ;
definition: "Core routinely generates patient-specific human induced pluripotent stem cells (hiPSCs) for basic science research purposes. Focus is on cardiovascular cell differentiation of hiPSCs to generate unlimited supplies of patient specific cardiovascular cells for in vitro research. Basic services include:hiPSC derivation, hiPSC characterization, hiPSC expanstion;hiPSC differentiation to: Cardiomyocytes, Endothelial Cells, Vascular Smooth Muscle Cells, Pancreatic Cells;3D organoids: Cardiac, Pancreatic;Cardiotoxicity Screening-Drug Discovery Projects;Arrhythmia Testing;High Content Time Lapse Imaging." .
SCR:026729 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3135" ;
rdfs:label "University of Michigan Center for Molecular Imaging Core Facility" ;
NIFRID:synonym "University of Michigan Center for Molecular Imaging" ;
definition: "Facility provides imaging instruments and imaging services for research community. Offers imaging systems including IVIS Spectrum bioluminescent/fluorescent imaging system, Bruker 7 Tesla horizontal bore MRI system, 4DMedical Permetium lung CT system, and Bruker SkyScan CT system." .
SCR:026730 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3199" ;
rdfs:label "University of Michigan Central Ligand Assay Satellite Services Laboratory Core Facility" ;
NIFRID:synonym "CLASS Laboratory",
"University of Michigan Central Ligand Assay Satellite Services Laboratory",
"University of Michigan CLASS Laboratory" ;
definition: "Core is unit of Department of Epidemiology at the University of Michigan’s School of Public Health. Offers support for clinical research projects throughout process of gathering samples, storing them, and coordinating the assay of the desired analytes. Offers collection kit designs tailor-made to your research study, with tubes and components labeled clearly with barcoded labels and unique sample IDs. Once collected, samples can be processed and stored in one of our 51 on-site ultra-low freezers or in our liquid nitrogen freezer, where their temperatures will be monitored 24/7. When all of the samples are collected, we can complete any combination of 40 different routine assays on them. We currently offer testing using ELISA plates, open channel chemistry analyzer, and coagulation analyzer." .
SCR:026731 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3200" ;
rdfs:label "University of Michigan Chemistry NMR Core Facility" ;
NIFRID:synonym "University of Michigan Chemistry NMR Facility" ;
definition: "NMR Facility provides qualified students and researchers in the Chemistry Department access to state-of-the-art NMR instrumentation. Provides support for variety of NMR studies including structure, conformation, dynamics, kinetics and reaction mechanisms of small organic and inorganic molecules and pharmaceuticals." .
SCR:026732 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Hi-cGAN" ;
definition: "Software tool to predict Hi-C matrices based on ChIP-Seq data from histones using cGAN approach." .
SCR:026734 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3139" ;
rdfs:label "Pennsylvania State University Environmental Contaminants Analytical Laboratory Core Facility" ;
definition: "Laboratory is equipped with sample preparation and analysis equipment that support established analytical procedures including:Organic fluorine compounds-PFAS screening: EPA 1621; PFAS targeted and non-targeted analysis: EPA 537.1, EPA 1633; Pharmaceuticals and personal care products: EPA 1694; Agricultural chemicals: pesticides, herbicides-targeted and non-targeted analysis: various methods GC-MS/MS and LC-MS/MS; Volatile organic compounds: EPA 8260D (SW-846); Semivolatile organic compounds: EPA 8270E (SW-846); Dioxins and furans: EPA 23; Total petroleum hydrocarbons: EPA 8440; Microplastics and nanoplastics." .
SCR:026735 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3156" ;
rdfs:label "Pennsylvania State University Energy and Environmental Sustainability Laboratories Core Facility" ;
definition: "Fully-staffed, open access, analytical research facilities at Penn State's Institute of Energy and the Environment. Provided services include radiocarbon measurements on carbon-bearing materials using an Accelerator Mass Spectrometer; high-resolution 3D micro/nano computed tomography of biological and synthetic materials; analysis of environmental and biological samples for emerging and legacy contaminants using high resolution mass spectrometry including (Triple Quad GC-MS/MS, Triple Quad LC-MS/MS, Pyrolysis GC-MS, QExactive LC-MS, Combustion Ion Chromatography, DART-MS with Ion Rocket) and a Laser Direct Infrared Chemical Imaging System. Sample Preparation and Analysis. Provides training for researchers and equipment users, method development, data analysis." .
SCR:026736 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Trailmaker" ;
definition: "Data analysis platform, enables scientists without coding or bioinformatics expertise to access and run the end-to-end data analysis workflow. The platform includes the Pipeline module which processes FASTQ files and the Insights module for downstream analysis." .
SCR:026737 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EvaluateMuscleTissueWithElastography" ;
definition: "Software tool that enables the automatic evaluation of muscle tissue on elastography imaging using MATLAB." .
SCR:026738 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CSAW" ;
definition: "Software R package for detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control." .
SCR:026739 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "motifmatchR" ;
definition: "Software R package to quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library." .
SCR:026740 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cs-benchmark" ;
definition: "Software repository for cell segmentation benchmark." .
SCR:026741 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3141" ;
rdfs:label "University of Michigan LSA Chemistry Mass Spectrometry Core Facility" ;
definition: "Core offers mass spectrometry services. Provided instruments include" .
SCR:026742 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Michigan LSA Chemistry X-Ray and Microporous Materials Characterization Core Facility" ;
NIFRID:synonym "University of Michigan LSA Chemistry X-Ray and Microporous Materials Characterization" ;
definition: "Core provides services for X-Ray and microporous materials characterization." .
SCR:026743 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3140" ;
rdfs:label "University of Michigan Pathology Clinical Core Facility" ;
NIFRID:synonym "University of Michigan Clinical Core Facility",
"University of Michigan Pathology Clinical Core Laboratory" ;
definition: "Core provides services in Clinical Chemistry, Clinical Mass Spectrometry , Hematology, Body Fluids, Urinalysis, Quantitative Flow Cytometry, Coagulation, BioChemical Genetics." .
SCR:026744 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3142" ;
rdfs:label "University of Michigan Conlsulting for Statistics, Computing, and Analytics Research Core Facility" ;
NIFRID:synonym "and Analytics Research",
"Computing",
"University of Michigan Conlsulting for Statistics" ;
definition: "Areas of Expertise:CSCAR staff have expertise in the areas of Biostatistical analyses; Formulation of research aims and development of plans for data collection and analysis; expertise in R, Python, SAS, SPSS, Stata, and Fortran. In addition, can advise clients on the use of number of other statistical and technical software packages." .
SCR:026745 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3143" ;
rdfs:label "University of Michigan Medical School CyTOF Core Facility" ;
NIFRID:synonym "CyTOF Core",
"UMICH CyTOF Core",
"University of Michigan CyTOF Core" ;
definition: "CyTOF Core shares equipment and expertise with researchers. Provided instruments include: Helios CyTOF System (Suspension CyTOF), Hyperion CyTOF System (Imaging CyTOF), Attune Flow Cytometer, ÄKTA Pure FPLC, NanoDrop 2000c Spectrophotometer. Offered services include Human immune profiling panel for 29-color analysis of cells in suspension; Mouse immune profiling panel for 16-color analysis of cells in suspension; Custom CyTOF antibody conjugation; Data acquisition of cells in suspension using Helios CyTOF; Image acquisition of tissue sections using Hyperion CyTOF." .
SCR:026746 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3144" ;
rdfs:label "University of Michigan Dental School Histology Core Facility" ;
definition: "Histology core facility at the University of Michigan School of Dentistry provides histological services using standard histological techniques. The core specializes in sectioning of hard (demineralized) tissues." .
SCR:026747 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3145" ;
rdfs:label "University of Michigan Dental School MicroCT Core Facility" ;
NIFRID:synonym "University of Michigan Dental School MicroCT Core" ;
definition: "Core offers services and instruments. Offers Scanco μCT 100 micro-computed tomography system which provides high resolution scans of radio opaque specimens such as bone, contrasted soft tissue, bio materials, etc." .
SCR:026748 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3146" ;
rdfs:label "University of Michigan Dental School Molecular Biology Core Facility" ;
NIFRID:synonym "University of Michigan Dental School Molecular Biology Core" ;
definition: "Molecular Biology Core (MBC) is School of Dentistry core and provides real-time quantitative PCR service (ABI ViiA7, ABI-7500 instruments), methodology, technique and experiment design consultation, analytical software training, data analysis, statistics and result interpretation assistance" .
SCR:026749 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3147" ;
rdfs:label "University of Michigan Digital Pathology Core Facility" ;
NIFRID:synonym "University of Michigan Digital Pathology Core" ;
definition: "Performs scanning on per-request basis; maintains secure database of scanned images and associated metadata; instructs and provides technical support to faculty and staff for DP use; supports of live-view microscopy for frozen sections and testing and validation of new whole-slide imaging solutions." .
SCR:026750 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3148" ;
rdfs:label "University of Michigan Electron Microbeam Analysis Core Facility" ;
NIFRID:synonym "University of Michigan Electron Microbeam Analysis Lab" ;
definition: "EMAL is part of University of Michigan’s School of Earth and Environmental Sciences. Houses CAMECA SX100 electron microprobes, Rigaku X-ray diffractometers, and JEOL JSM-7800FLV field-emission scanning electron microscope. These instruments are used by researchers for chemical and structural characterization of solid materials." .
SCR:026751 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3149" ;
rdfs:label "University of Michigan Medical School Radiology Functional MRI Laboratory Core Facility" ;
NIFRID:synonym "University of Michigan Functional MRI Laboratory" ;
definition: "Interdisciplinary unit organized under University of Michigan's Medical School - Department of Radiology, dedicated to supporting research on structures and functions of brain that underlie cognitive and affective processes, and research on functional MRI and associated research tools. Provides equipped physical facility and intellectual support services for investigators." .
SCR:026752 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3150" ;
rdfs:label "University of Michigan High Temperature Corrosion Core Facility" ;
NIFRID:synonym "University of Michigan High Temperature Corrosion Lab" ;
definition: "Facility to conduct experimental research on corrosion, stress corrosion cracking, and hydrogen embrittlement experiments in high temperature aqueous and gas environments and, in particular, simulated light water reactor environments. Conducts both high and low temperature corrosion, stress corrosion cracking experiments, electrochemical tests and mechanical tests. Consists of refreshed autoclave systems (titanium, Inconel, or stainless steel construction), mounted in constant extension rate machines and constant load machine. Experiments can be done in range of environments, including supercritical water, simulated BWR and PWR water, high temperature steam, and gas environments. Each autoclave is isolated from the other systems with independent water and computer monitoring systems. The lab also contains two full-featured corrosion measurement systems and additional potentiostats." .
SCR:026753 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3151" ;
rdfs:label "University of Michigan HomeLab Core Facility" ;
NIFRID:synonym "University of Michigan HomeLab" ;
definition: "Simulation lab that is designed as home. Provides space to researchers who want to observe participant behavior in more realistic environment. Offers environment that feels authentic and natural to human condition." .
SCR:026754 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3152" ;
rdfs:label "University of Michigan Human Research 3 Tesla Magnetic Resonance Imaging Core Facility" ;
NIFRID:synonym "University of Michigan Human Research 3 Tesla Magnetic Resonance Imaging" ;
definition: "Human Research 3 Tesla Magnetic Resonance Imaging provides high quality anatomic and advanced MR imaging services for IRB-approved research studies and clinical trials with funds allocated for non-standard-of-care research MRI scans." .
SCR:026755 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3153" ;
rdfs:label "University of Michigan Human Stem Cell Gene Editing Core Facility" ;
NIFRID:synonym "University of Michigan Human Stem Cell and Gene Editing (HSCGE) Core",
"University of Michigan Human Stem Cell Gene Editing Core" ;
definition: "Core supports neuroscience research using stem cell and gene editing technologies. Full service facility. Provides neuroscience research community valuable new sources of human pluripotent stem cells (hPSCs) for basic research, drug discovery, or cell therapy. Offers services including derivation of induced pluripotent stem cells from fibroblasts or blood cells, CRISPR/Cas9-mediated gene editing hPSCs, monolayer differentiation of hPSCs, cerebral organoid differentiation of hPSCs, and training for hPSC maintenance." .
SCR:026756 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3154" ;
rdfs:label "University of Michigan Ion Beam Core Facility" ;
NIFRID:synonym "Michigan Ion Beam Laboratory",
"Michigan Ion Beam Laboratory (MIBL)",
"University of Michigan Ion Beam Lab" ;
definition: "Laboratory is part of the Department of Nuclear Engineering and Radiological Sciences in the College of Engineering. MIBL is part of the National Nanotechnology Infrastructure Network. Services involve advancing our understanding of ion-solid interactions. Provides instruments for conducting ion beam surface modification and ion beam surface analysis under range of conditions. Experiments can be conducted at high or low temperature, in ultra-high vacuums, in reactive gas and in short turnaround times." .
SCR:026757 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3155" ;
rdfs:label "University of Michigan Irradiation Materials Testing Core Facility" ;
NIFRID:synonym "University of Michigan Irradiation Materials Testing Lab" ;
definition: "Core provides facility to conduct experimental research on neutron irradiated materials in aqueous environments. The IMTL consists of five refreshed autoclaves that can be mounted in constant extension rate or crack growth rate configurations. Capable of conducting experiments on stress corrosion cracking of neutron irradiated material in supercritical water." .
SCR:026758 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WebAlign" ;
definition: "Web application for 2D image registration to 3D atlas. Used for user guided affine spatial registration (anchoring) of sectional image data, typically high resolution histological images, to 3D reference atlas space. Can generate user defined cut planes through atlas templates that match orientation of cutting plane of 2D experimental images (atlas maps)." .
SCR:026759 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WebWarp" ;
definition: "Web application for nonlinear refinement of image registration after WebAlign." .
SCR:026760 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CFX_Connect" ;
rdfs:label "Bio-Rad | CFX Connect Real-Time PCR System" ;
NIFRID:synonym "CFX Connect Real-Time PCR System" ;
definition: "CFX Connect Real-Time PCR System provides excellent thermal performance for two-target multiplex PCR and routine detection of single fluorophore experiments." .
SCR:026761 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Health Interview Survey" ;
definition: "Provides information about the National Health Interview Survey (NHIS) data collection, its participants, and its protocols. It also provides analytic notes and references. They will help you understand, analyze, and us.e NHIS data." .
SCR:026762 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IPUMS Health Surveys" ;
NIFRID:synonym "Integrated Public Use Microdata Series Health Surveys" ;
definition: "Integrated Public Use Microdata Series Health Surveys provide free individual-level survey data for research purposes from two leading sources of self-reported health and health care access information: the National Health Interview Survey (NHIS) and the Medical Expenditure Panel Survey (MEPS)." .
SCR:026763 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3157" ;
rdfs:label "University of Michigan Isopaleo Lab Core Facility" ;
NIFRID:synonym "Iso Paleo Lab",
"University of Michigan Isopaleo Lab" ;
definition: "Core specializes in precise measurements of rare isotopologues such as “clumped” isotopes of carbonate and CO2 and triple oxygen isotope distributions in waters, carbonates, phosphates and recently organics. Houses Nu Perspective IRMS mass spectrometers, EuroVector EA3000 and HT-PyrOH, NuCarb device for traditional carbon and oxygen isotopes, Thermo Fisher ISQ 7000 GC-MS, fully automated clumped isotope preparation line, semi-automated triple oxygen isotope preparation line, manual water fluorination line, multi-purpose vacuum extraction line, and ovens, balances, glassware, fume hoods, and other equipment used in experiments and sample preparation." .
SCR:026764 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref ;
rdfs:label "University of Michigan Lurie Nanofabrication Core Facility" ;
NIFRID:synonym "Lurie Nanofabrication Facility",
"University of Michigan Lurie Nanofabrication Facility" ;
definition: "Lurie Nanofabrication Facility serves technology educators and creators through broad access to advanced nanofabrication equipment and staff expertise in safe, collaborative environment. Equipment and processes are available for research on silicon integrated circuits, MEMS, III-V compound devices, organic devices and nanoimprint technology. We also encourage researchers from non-traditional disciplines to make use of our processes, such as metal and dielectric coatings, vacuum processes, fabrication of micro and nano components and metrology tools." .
SCR:026765 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3159" ;
rdfs:label "University of Michigan Marine Hydrodynamics Lab Core Facility" ;
NIFRID:synonym "Aaron Friedman Marine Hydrodynamics Laboratory",
"University of Michigan Marine Hydrodynamics Lab" ;
definition: "Research facility dedicated to the study and testing of various marine and hydrodynamic phenomena. It is part of the Department of Naval Architecture and Marine Engineering at the University of Michigan. Conducts research and experiments related to fluid dynamics, ship design, offshore engineering, and other areas relevant to marine and naval architecture." .
SCR:026766 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3160" ;
rdfs:label "University of Michigan Marine Renewable Energy Laboratory Core Facility" ;
NIFRID:synonym "MRELab",
"University of Michigan Marine Renewable Energy Laboratory" ;
definition: "Core dedicated to developing technology to harness abundant, clean, and renewable marine energy in environmentally sustainable way and at competitive cost." .
SCR:026767 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3161" ;
rdfs:label "University of Michigan LSA MCDB Imaging Core Facility" ;
NIFRID:synonym "MCDB Imaging Facility",
"University of Michigan MCDB Imaging Core" ;
definition: "MCDB Imaging Facility in the Biological Sciences Building provides microscopes available to any University of Michigan researcher. Access to scope time granted after appropriate training. Provides microscope equipment, image capture systems, software to assist researchers with their sample imaging." .
SCR:026768 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3162" ;
rdfs:label "University of Michigan MDRC Chemistry Laboratory Core Facility" ;
NIFRID:synonym "MDRC Chemistry Laboratory",
"Michigan Diabetes Research Center Chemistry Laboratory",
"University of Michigan MDRC Chemistry Laboratory" ;
definition: "Core supports investigators interested in assays related to diabetes, heart disease, and hypertension. Analytical methods include general blood chemistry, chemiluminescence, immunoassay, radioimmunoassay, multiplexing, and ELISA." .
SCR:026769 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3163" ;
rdfs:label "University of Michigan MDRC Islet Core Facility" ;
NIFRID:synonym "MDRC Islet Core",
"Michigan Diabetes Research Center Islet Core",
"University of Michigan MDRC Islet Core" ;
definition: "Islet Core provides consultative advice and equipment and services for isolation and study of pancreatic islet structure and function in support of diabetes-related research." .
SCR:026770 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3164" ;
rdfs:label "University of Michigan Center for Materials Characterization Core Facility" ;
NIFRID:synonym "mc2",
"Michigan Center for Materials Characterization",
"University of Michigan Michigan Center for Materials Characterization" ;
definition: "Facility dedicated to micron and nanoscale imaging and analysis of materials. The center, housed in Building 22 of the North Campus Research Complex, provides instruments and professional training." .
SCR:026771 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3165" ;
rdfs:label "University of Michigan Elemental Analysis Laboratory Core Facility" ;
NIFRID:synonym "University of Michigan Elemental Analysis Laboratory",
"University of Michigan Michigan Elemental Analysis Laboratory" ;
definition: "Core accommodates mass spectrometers (ICP-MS) – Quadrupole ICP-MS and High-Resolution ICP-MS. Provides solution-based elemental analysis on variety of materials from rock through to natural waters in concentration ranges from ppm to ppt in biological, environmental, geological and industrial materials." .
SCR:026772 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3166" ;
rdfs:label "University of Michigan Micro and Nano Computed Tomography Advanced Imaging Core Facility" ;
NIFRID:synonym "Nano Computed Tomography Advanced Imaging Core",
"nano-CT facility",
"University of Michigan Micro and Nano Computed Tomography Advanced Imaging Core" ;
definition: "Core provides services for acquiring three-dimensional imaging and quantitative analysis of biological and engineered structures/materials. The core is capable of imaging mineralized tissues (e.g., bone, teeth) and soft tissues (e.g., tendons, ligaments, cartilage, blood vessels, muscle) with the aid of radiographic contrast agents. This core is managed and operated by members of the Orthopaedic Research Laboratories. " .
SCR:026773 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3167" ;
rdfs:label "University of Michigan MicroCT Scanning Laboratory Core Facility" ;
NIFRID:synonym "University of Michigan MicroCT Scanning Laboratory",
"University of Michigan Museum of Zoology MicroCT Scanning Laboratory" ;
definition: "Core allows researchers to generate high resolution tomographic data of bone, fossils, and contrast enhanced tissues. These data can include 3D surface visualizations of anatomy and morphology, that can facilitate morphometric studies, phylogenetics analysis, and biomechanics modelling." .
SCR:026774 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3168" ;
rdfs:label "University of Michigan Morphomic Analysis Core Facility" ;
NIFRID:synonym "University of Michigan Morphomic Analysis Group" ;
definition: "Core identifies bio-markers using medical imaging that provides insight into disease processes, treatment options, and outcome variability." .
SCR:026775 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3169" ;
rdfs:label "University of Michigan ORL Histology Core Facility" ;
NIFRID:synonym "ORL Histology Core",
"University of Michigan ORL Histology Core",
"University of Michigan Orthopaedic Research Laboratories Histology Core" ;
definition: "Core offers instruments including Reichert-Jung Polycut microtome for decalcified or undecalcified samples, Reichert-Jung rotary microtomes for decalcified specimens, diamond band saws, cryostats for frozen sections with special features for bone section, slow speed diamond saws, high speed grinding cutoff wheel, precision grinding and polishing machines (Buehler Automet 300),complete embedding and preparation equipment and supplies for paraffin, methacrylate, epoxy, and other resins for embedding of biologic specimens, automated tissue processor for plastic and paraffin embedding preparation (Leica ASP 300S)" .
SCR:026776 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3170" ;
rdfs:label "University of Michigan Pathology Flow Cytometry Core Facility" ;
NIFRID:synonym "University of Michigan Pathology Flow Cytometry Core Lab" ;
definition: "Core provides instruments including Becton-Dickinson FACSCelesta or ACEA NovoCyte flow cytometer for use after training . Pathology core staff member is assigned to support instruments, answer questions, and, offer on-demand hardware, software, fluidics and technical expertise. Instrument users must ultimately run their own samples and be responsible for technical and scientific legitimacy of their experiments." .
SCR:026777 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3171" ;
rdfs:label "University of Michigan Pharmocokinetic and Mass Spectometry Core Facility" ;
NIFRID:synonym "University of Michigan Pharmocokinetic and Mass Spectometry Core" ;
definition: "Core offers partnership options, including collaboration, fee-for-service and self-service. Helps to discover new medicines, obtain research funding, file patent applications and publish academic research findings. Offers to analyze drug/compound concentration in biological specimens and develop assays. " .
SCR:026778 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3172" ;
rdfs:label "University of Michigan LSA Chemistry Raman Spectroscopy Core Facility" ;
NIFRID:synonym "University of Michigan Raman Spectroscopy Core",
"University of Michigan Raman Spectroscopy Core Facility" ;
definition: """Core offers services and instrumentation including Renishaw inVia microscopes,
High sensitivity ultra low noise RenCam CCD detector,Multiple lasers on hand (532nm, 633nm, 785nm),< 1 cm-1 spectral resolution capability. Supports sampling accessories such as fiber optic probes and temperature control stages (liq. He – 300ºC). Offers Automated XYZ stage with 100nm positioning control and Compositional mapping.""" .
SCR:026779 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Mindray" ;
definition: "Patient monitoring company, which offered wide range of patient monitors in the OR, emergency care, and critical care environments for over 50 years." .
SCR:026781 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3173" ;
rdfs:label "University of Wisconsin-Madison Intellectual and Developmental Disabilities Models Core Facility" ;
NIFRID:synonym "Intellectual and Developmental Disabilities (IDD) Models Core",
"Intellectual and Developmental Disabilities Models Core Facility" ;
definition: "Models Core in Waisman Center provides resources including mouse models of human conditions, along with behavioral testing capabilities to characterize these models and test new therapies; stem cell technologies to support creation of induced pluripotent stem cell lines for IDD conditions as well as specialized genome editing services; microscopy technology and expertise for characterization of both stem cell and mouse models of IDD conditions." .
SCR:026782 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3174" ;
rdfs:label "Wisconsin National Primate Research Center Pathology Services Core Facility" ;
NIFRID:synonym "Wisconsin National Primate Research Center Pathology Services",
"WNPRC Pathology Services" ;
definition: "Pathology Services Core is essential to nonhuman primate colony health and research at the WNPRC. PSU team consists of pathologists with ACVP and/or ACLAM board certification, research program manager, and research specialists. Unit works with clinical veterinary staff to provide rapid diagnosis and effective monitoring and interpretation of acute and chronic conditions affecting colony animals as well as subjects assigned to research studies. Core offers services including clinical pathology testing; cytology evaluation; surgical biopsy evaluation; gross post mortem examination, specialized sample collections; and histology with unbiased interpretation of lesions in reference to spontaneous disease, experimental questions, and research goals. PSU is responsible for collection, banking, and distribution of NHP samples through both Nonhuman Primate Biological Materials Distribution core and National Institute on Aging Nonhuman Primate Tissue Bank." .
SCR:026784 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ERDDAP" ;
definition: "Data server to download subsets of scientific datasets in common file formats and make graphs and maps. This particular ERDDAP installation has oceanographic data (for example, data from satellites and buoys)." .
SCR:026786 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenDAP" ;
definition: "Nonprofit that optimizes access to remote scientific data through free open-source software. Discipline-neutral data access protocol (DAP) to access and to provide data over the internet. OPeNDAP was originally developed by and designed for oceanographers, but today the protocol is applied across many diverse domains in which large, complex, distributed datasets are used. Serves data in format that works well with most end users’ preferred data analysis applications. End user can inspect datasets remotely through web URL or number of data tools." .
SCR:026792 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Varioskan_LUX" ;
rdfs:label "Thermo Fisher | Varioskan LUX Multi-Mode Microplate Reader" ;
definition: "Varioskan LUX is modular, upgradable instrument that offers usability for range of applications. Reader for absorbance, fluorescence intensity, chemiluminescence, AlphaScreen, and time-resolved fluorescence." .
SCR:026793 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "randomForestSRC" ;
NIFRID:synonym "and Classification",
"Fast Unified Random Forests for Survival",
"Regression" ;
definition: "Software R package for random forests regression, classification, survival analysis, competing risks, multivariate, unsupervised, quantile regression, and class imbalanced q-classification. Extreme random forests and randomized splitting. Suite of imputation methods for missing data." .
SCR:026794 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SingleCellExperiment" ;
definition: "Software R package defines S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries." .
SCR:026795 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DDRTree" ;
NIFRID:synonym "DDRTree: Learning Principal Graphs with DDRTree" ;
definition: "Software R package provides implementation of framework of reversed graph embedding which projects data into reduced dimensional space while constructs principal tree which passes through middle of data simultaneously." .
SCR:026796 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BSgenome Mmulatta UCSC rheMac10" ;
definition: "Software R package for full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac10, Feb. 2019) and stored in Biostrings objects." .
SCR:026797 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3175" ;
rdfs:label "Max Planck Institute for Biological Intelligence Imaging Core Facility" ;
NIFRID:synonym "Max Planck Institute for Biological Intelligence Imaging Facility" ;
definition: "Light microscopy facility. Users are supported with experiment design, image acquisition and operation of microscopes and quantitative processing and analysis of images." .
SCR:026798 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gSpreadComp" ;
definition: "Software UNIX-based, modular bioinformatics toolkit designed to streamline comparative genomics for analyzing microbial communities. It integrates genome annotation, gene spread calculation, plasmid-mediated horizontal gene transfer (HGT) detection and resistance-virulence ranking within the analysed microbial community to help researchers identify potential resistance-virulence hotspots in complex microbial datasets." .
SCR:026799 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3176" ;
rdfs:label "Augusta University Medical College of Georgia Cell Imaging Core Facility" ;
NIFRID:synonym "Augusta University Medical College of Georgia Cell Imaging Core" ;
definition: "Core provides imaging and expert technical assistance and instrumentation in support of investigators." .
SCR:026800 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3187" ;
rdfs:label "University of Michigan LSA Biophysics Single Molecule Analysis in Real-Time Center Core Facility" ;
NIFRID:synonym "University of Michigan LSA Biophysics Single Molecule Analysis in Real-Time Center",
"University of Michigan Single Molecule Analysis in Real-Time Center" ;
definition: "Microscopy core facility that provides university researchers with imaging and manipulation tools to detect, track, manipulate, and analyze biomolecules. Offers training and data acquisition support as well as experienced consultation on experimental design and analysis." .
SCR:026801 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3186" ;
rdfs:label "University of Michigan LSA Stable Isotope Core Facility" ;
NIFRID:synonym "University of Michigan Stable Isotope Core Facility",
"University of Michigan Stable Isotope Facility" ;
definition: "Facility performs stable isotope and elemental analyses that support research in climate change, geology, oceanography, and paleontology." .
SCR:026802 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3185" ;
rdfs:label "University of Michigan Thermocron Lab Core Facility" ;
definition: "Provides facilities for (U-Th)/He thermochronology on variety of accessory minerals, including apatite, sphene, monazite and zircon. The low closure temperature of the (U-Th)/He system in these minerals makes it ideal for application to geological problems in geomorphology, surface processes, tectonics, structural geology, basin evolution, and thermal maturation." .
SCR:026803 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3184" ;
rdfs:label "University of Michigan Tissue and Molecular Pathology Shared Resource Core Facility" ;
NIFRID:synonym "Rogel Cancer Center Tissue and Molecular Pathology (TMP) Shared Resource",
"University of Michigan Tissue and Molecular Pathology Shared Resource" ;
definition: "Core consists of services relating to procurement and evaluation of tissue for research: Tissue Procurement, Histology, and Molecular Pathology. Provides pathology-sanctioned procurement of surgically resected neoplastic and non-neoplastic tissue (fresh and frozen), sample processing, embedding, sectioning, routine H and E, special staining, and immunohistochemistry. Molecular Pathology Research Laboratory performs immunohistochemistry, in-situ hybridization, multiplex immunofluorescence, FISH staining, and tissue microarray construction." .
SCR:026804 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3183" ;
rdfs:label "University of Michigan Battery Lab Core Facility" ;
NIFRID:synonym "University of Michigan Battery Lab" ;
definition: "Full-service battery cell fabrication and testing facility open to any academic or industry user.The lab is an IP-protected safe zone to prototype, test, scale-up, and analyze batteries and the materials that go into them." .
SCR:026805 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3182" ;
rdfs:label "University of Michigan LSA Biological Station Core Facility" ;
NIFRID:synonym "University of Michigan Biological Station" ;
definition: "Core mission is to advance environmental field research, engage students in scientific discovery, and provide information needed to understand and sustain ecosystems from local to global scales. Seek solutions to critical environmental challenges." .
SCR:026806 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3181" ;
rdfs:label "University of Michigan College of Pharmacy Vahlteich Medicinal Chemistry Core Facility" ;
NIFRID:synonym "University of Michigan Vahlteich Medicinal Chemistry Core",
"University of Michigan Vahlteich Medicinal Chemistry Core Facility" ;
definition: "Design and synthesize drug-like molecules and diagnostic probes in your biomedical investigations to translate your research in all therapeutic areas and disease states." .
SCR:026807 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3180" ;
rdfs:label "University of Michigan ULAM Animal Surgery Operating Rooms Core Facility" ;
NIFRID:synonym "University of Michigan ULAM Animal Surgery Operating Rooms" ;
definition: """Core is part of Unit for Laboratory Animal Medicine. Provides services to perform sterile, minimally-invasive, and non-sterile surgical procedures on both small and large animals.
Facility personnel are licensed veterinary technicians and AALAS Technologists.ULAM Veterinary Board-Certified Surgeon also oversees daily operations.Users must have an approved animal use protocol from the Institutional Animal Care & Use Committee (IACUC) prior to utilizing ASOR services and facilities.""" .
SCR:026808 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3179" ;
rdfs:label "University of Michigan ULAM ABSL3 Animal Housing Core Facility" ;
NIFRID:synonym "University of Michigan ULAM ABSL3 Animal Housing" ;
definition: "ABSL3 core is specialized in environments designed to facilitate safe research with Risk Group-3 microbial pathogens, which pose significant risk of airborne transmission and serious disease. Core safe for conducting high-level infectious disease research." .
SCR:026809 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "piPipes" ;
definition: "Software set of pipelines to analyze piRNA/transposon from different Next Generation Sequencing libraries (small RNA-seq, RNA-seq, Genome-seq, ChIP-seq, CAGE/Degradome-Seq)." .
SCR:026810 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3177" ;
rdfs:label "Augusta University Medical College of Georgia Electron Microscopy and Histology Core Facility" ;
NIFRID:synonym "Augusta University Electron Microscopy and Histology Core",
"Augusta University Medical College of Georgia Electron Microscopy and Histology Core" ;
definition: "Core offers variety of specimen preparation services for transmission and scanning electron microscopy, vibratome, paraffin, cryostat and JB-4 sectioning.Offers routine staining and various histological special stains, PASH, Masson Trichrome, Van Gieson and many others, immunohistochemical services including immuno-EM studies. Core staff performs all aspects of the ultrastructural procedures from specimen processing to imaging (for Electron Microscopy, TEM and SEM) and processing, sectioning, and staining for light microscopy (paraffin, cryostat, and JB-4)." .
SCR:026811 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3178" ;
rdfs:label "National Academy of Sciences of Armenia Institute of Molecular Biology Sequencing Core Facility" ;
definition: "Sequencing core facility provides access to high-throughput DNA sequencing technologies and related services. Equipped with sequencing instruments, including long-read platforms, Illumina systems, and more. Provides comprehensive suite of tools to support sample preparation and ensure the quality of all sample types." .
SCR:026812 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.418094.0 ISNI 0000 0001 1146 7878 Crossref Funder ID 100008721 Wikidata Q2379496" ;
rdfs:label "National Academy of Sciences of Armenia" ;
definition: "National Academy of Sciences of the Republic of Armenia is the Armenian national academy, functioning as the primary body that conducts research and coordinates activities in the fields of science and social sciences in Armenia." .
SCR:026813 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "singleCellTK" ;
NIFRID:synonym "Single Cell ToolKit" ;
NIFRID:abbrev "SCTK" ;
definition: "Software R package provides interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. Allows users to integrate tools from various packages at different stages of analysis workflow." .
SCR:026814 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eNRSA" ;
NIFRID:synonym "enhancer Nascent RNA sequencing" ;
definition: "Software tool as enhanced version of NRSA for analyzing nascent transcription profiles generated by PRO-seq, GRO-seq, (m)NET-seq, and Butt-seq data." .
SCR:026816 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3190" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Engineering Core Facility" ;
definition: "Core provides mechanical and biomedical engineering expertise and services. Specializes in early-stage development and proof-of-concept prototypes. Utilizes 3D modeling, 3D printing, nitinol shape setting, and laser cutting to design and fabricate custom medical devices, test fixtures, and CT/MRI-based anatomy models." .
SCR:026817 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MarkerDB" ;
NIFRID:synonym "MarkerDB 2.0" ;
definition: "Database that attempts to consolidate information on known clinical and selected set of pre-clinical biomarkers into single resource. Database includes five major types of biomarkers (condition specific, protein, chemical, karyotypic and genetic) and six biomarker categories (diagnostic, risk, prognostic, safety, monitoring, and response). Provides information such as: biomarker names and synonyms, associated conditions or pathologies, detailed disease descriptions, detailed biomarker descriptions, biomarker specificity, sensitivity and ROC curves, standard reference values (for protein and chemical markers), variants (for SNP or genetic markers), sequence information (for genetic and protein markers), molecular 2D and 3D structures (for protein and chemical markers), tissue or biofluid sources (for protein and chemical markers), chromosomal location and structure (for genetic and karyotype markers), clinical approval status and relevant literature references. Users can browse the data by conditions, condition categories, biomarker types, biomarker categories or search by sequence similarity through the advanced search function." .
SCR:026818 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "summarytools" ;
definition: "Software R package for data cleaning, exploring, and simple reporting. At its core reside the following four functions: freq(), ctable(), descr(), and dfSummary(). Used to quickly and neatly summarize data." .
SCR:026819 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pseudo" ;
definition: "Software R package for computing pseudo-observations for censored data regression. Computes pseudo-observations for modeling: competing risks based on the cumulative incidence function, survival function based on the restricted mean, survival function based on the Kaplan-Meier estimator." .
SCR:026820 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3201" ;
rdfs:label "University of Michigan Medical School Microbiome Core Facility" ;
NIFRID:synonym "University of Michigan Medical School Microbiome Core" ;
definition: "Core provides microbial sequencing, high-throughput nucleic acid extraction, microbial cultivation, and strain identification." .
SCR:026822 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DNA Methylation Age Calculator" ;
definition: "Web portal contains information on how to calculate DNA methylation (DNAm) age based on data measured using the Illumina Infinium platform." .
SCR:026823 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tabula-py" ;
definition: "Software tool as simple wrapper of tabula-java to extract table from PDF into pandas DataFrame. Python wrapper of tabula-java, which can read tables in PDF. Also enables you to convert PDF file into CSV, TSV or JSON file." .
SCR:026824 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3202" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Mechanical Prototyping Core Facility" ;
definition: "Mechanical Core provides variety of fabrication, customization and repair services for mechanical devices and equipment. Offers precision machining of metals and plastics, welding of structural and exotic metals, instrument refurbishing and mechanical repair." .
SCR:026826 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "brainageR" ;
definition: "Software R tool for generating brain-predicted age value, using Gaussian Processes regression. Used for generating brain-predicted age value from raw T1-weighted MRI scan." .
SCR:026827 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GCparagon" ;
definition: "Software Python commandline tool for rapid calculation and correction of fragment length specific GC biases in WGS cfDNA sequencing datasets for liquid biopsy applications. Used for evaluating and correcting GC biases in cell-free DNA at fragment level." .
SCR:026828 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AnimalTFBD" ;
NIFRID:synonym "Animal Transcription Factor Database" ;
definition: "Database including classification and annotation of genome-wide transcription factors and transcription cofactors in animal genomes. Annotation and prediction of animal transcription factors." .
SCR:026829 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Ardent Bio" ;
definition: "Provides a range of assay kits, ELISA kits, high-quality antibodies, antigens, recombinant proteins, and DNA/RNA extraction kits all of which undergo stringent quality control measures at every stage of production to ensure they meet the highest standards of precision and reliability." .
SCR:026830 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LabChip_GX_Touch" ;
rdfs:label "Revvity | LabChip GX Touch Nucleic Acid Analyzer" ;
NIFRID:synonym "LabChip GX Touch Nucleic Acid Analyzer" ;
definition: "Automated microfluidic electrophoresis system that rapidly quantifies and sizes DNA and RNA with high sensitivity using minimal sample volume." .
SCR:026831 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ImageXpress_Pico" ;
rdfs:label "Molecular Devices | ImageXpress Pico Automated Cell Imaging System" ;
NIFRID:synonym "ImageXpress Pico Automated Cell Imaging System",
"ImageXpress Pico Imaging System" ;
definition: "Digital microscope, combining high-resolution imaging with analysis. Whether running fluorescence imaging or brightfield assays, automated imager features comprehensive preconfigured protocols for cell-based assays to shorten learning curve." .
SCR:026832 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3203" ;
rdfs:label "Howard Hughes Medical Institute at Janelia Research Campus Molecular Genomics Shared Resource Core Facility" ;
definition: "Core provides services and expert advice on routine and specialized molecular biology techniques including plasmid preps, genome editing, mutation detection, digital PCR and spatial transcriptomics." .
SCR:026833 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VersaTREK" ;
rdfs:label "Thermo Fisher | VersaTREK" ;
NIFRID:synonym "VersaTREK" ;
definition: "Automated microbial detection system. Instrument for detecting bacteria in biologic and non-biologic samples." .
SCR:026834 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "STPoseNet" ;
definition: "Source code for pose recognition model for laboratory mice based on yolov8. Real-time spatiotemporal network model for robust mouse pose estimation." .
SCR:026835 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OLINDA/EXM" ;
NIFRID:synonym "Hermes Medical Solutions OLINDA/EXM",
"OLINDA/EXM 2",
"Organ Level INternal Dose Assessment/EXponential Modeling" ;
definition: "Software to evaluate mean absorbed doses to organs and tumors in radionuclide images, providing simple and fast solution for radionuclide imaging and treatment of new drugs in clinical trials. Calculates radiation doses to organs and the whole body based on established human body models." .
SCR:026836 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpatialDecon" ;
definition: "Software R package for deconvolution of mixed cells from spatial and/or bulk gene expression data. Algorithm for quantifying cell populations defined by single cell sequencing within regions of spatial gene expression studies. Used for mapping cell types in spatial gene expression studies." .
SCR:026837 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Notepad++" ;
NIFRID:synonym "Notepad++7" ;
definition: "Software tool as text and source code editor for use with Microsoft Windows." .
SCR:026838 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "kraken2" ;
definition: "Software tool as second version of Kraken taxonomic sequence classification system." .
SCR:026839 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3204" ;
rdfs:label "University of Bergen Genomics Core Facility" ;
definition: "Provides genomic services to study genome structure, dynamics and function using Illumina next generation sequencing. Offers expert advice on experimental design and bioinformatics analysis, training and assistance on data storage solutions." .
SCR:026840 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3205" ;
rdfs:label "NIH Center for Cancer Research Sequencing Core Facility" ;
NIFRID:synonym "NIH Center for Cancer Research Sequencing Facility" ;
definition: "Provides access to the latest technologies, with consultation and services available throughout the design and execution of sequencing projects." .
SCR:026841 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3206" ;
rdfs:label "University of Queensland Institute for Molecular Bioscience Advanced Microscopy Core Facility" ;
NIFRID:synonym "IMB Advanced Microscopy Facility",
"University of Queensland Institute for Molecular Bioscience Advanced Microscopy Facility" ;
definition: "Microscopy Facility supports cancer research, cell and developmental biology, and cross-disciplinary studies spanning molecular mechanisms to translational applications. Houses imaging platforms including widefield, confocal, multi-photon, super-resolution, spinning disk, and light sheet systems. Enables advanced modalities such as TIRF, FRET, STED, SHG/THG, and FLIM for detailed exploration of cell behaviour and microenvironments. Facility staff offer training, expert consultation, image analysis support, and troubleshooting." .
SCR:026842 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3207" ;
rdfs:label "University of Michigan Rogel Cancer Center Single Cell Spatial Analysis Shared Resource Core Facility" ;
NIFRID:synonym "University of Michigan Health Single Cell Spatial Analysis Shared Resource",
"University of Michigan Rogel Cancer Center Single Cell Spatial Analysis Shared Resource" ;
definition: "Provides expertise through experimental design consultations,cell isolation,single cell analytics (RNA, DNA, protein),biomarker validation,novel statistical and bioinformatics analyses. Services include Single cell targeted gene expression, Single cell RNA Seq, Single cell DNA Seq, Tissue sectioning, Tissue spatial analysis, Spatial transcriptomics and proteomics." .
SCR:026843 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3208" ;
rdfs:label "University of Michigan Bioinnovation in Brain Cancer High-Plex Immunocytochemistry Core Facility" ;
NIFRID:synonym "University of Michigan High-Plex Immunocytochemistry Core",
"University of Michigan Immunocytochemistry Core Facility" ;
definition: "Core utilizes Akoya PhenoCycler-Fusion to enable high-plex spatial phenotyping of whole tissue slides at single-cell resolution." .
SCR:026844 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3209" ;
rdfs:label "University of Michigan Bioinnovations in Brain Cancer Formulation and Translation Core Facility" ;
NIFRID:synonym "University of Michigan Bioinnovations in Brain Cancer Formulation and Translation Core",
"University of Michigan Formulation and Translation Core" ;
definition: "Core offers sample analysis and experiment design, market assessment and FDA regulation, facilitate interactions for intellectual property protection and support submission of translational grant applications within University of Michigan and government agencies." .
SCR:026845 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3210" ;
rdfs:label "University of Michigan Medical School Central Biorepository Core Facility" ;
NIFRID:synonym "University of Michigan Central Biorepository",
"University of Michigan Medical School Central Biorepository" ;
definition: "Core provides annotated biospecimens for basic, clinical, and translational research. Helps researchers access, collect, manage, and protect biospecimens using automated processes and quality control. Offers safe and monitored management of biospecimens including temperature-controlled storage, preparation of derivatives from these specimens, aliquoting, distribution, and production of specimen collection kits." .
SCR:026846 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NemaQuant" ;
definition: "Software Python tool for detecting and counting nematode eggs from microscopy images." .
SCR:026848 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPINA Carb" ;
NIFRID:synonym "Structure Parameter Inference Approach",
"Structure Parameter Inference Approach Carbohydrate Homeostasis" ;
NIFRID:abbrev "SPINA" ;
definition: "Software tool to deliver estimated structure parameters of endocrine feedback control systems in vivo from serum or plasma hormone levels. Used for the evaluation of insulin-glucose homeostasis. Allows for calculating the secretory capacity of pancreatic beta cells (SPINA-GBeta), insulin receptor gain (SPINA-GR) and a static disposition index (SPINA-DI) from fasting concentrations of insulin and glucose. Additionally, HOMA, QUICKI and other calculated parameters are delivered as well. Binaries are available for macOS and Windows. For other operating systems, including Linux, Solaris and BSD, SPINA Carb is available as source code. Building from source requires Lazarus/Free Pascal. A special version of the calculation engine is available for modern S implementations, e.g. R." .
SCR:026849 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3212" ;
rdfs:label "Cleveland Clinic Lerner Research Institute BioRobotics and Mechanical Testing Core Facility" ;
NIFRID:synonym "BioRobotics and Mechanical Testing Core" ;
definition: "Core provides biomechanical testing of biological structures and biomaterials. Allows investigators to conduct research of mechanical properties of existing biological structures and constructs, as well as to quantify potential for new technologies and clinical advancements. Robotic simulators are built around the simVITRO software platform and are designed for in vitro simulation of major joints including knee, spine, foot, ankle, hip, shoulder, elbow, wrist and more. Provides testing capabilities for range of biomechanical modalities and will offer expert advice and support for development of new test protocols, innovative techniques for instrumentation and data collection. Modalities include tissues, joints, and multi-articular units, such as foot or spine segments." .
SCR:026850 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100007311",
"GRID grid.239578.2",
"ISNI 0000 0001 0675 4725",
"Wikidata Q4117596" ;
rdfs:label "Cleveland Clinic" ;
definition: "Cleveland Clinic is renowned for its advancements in cardiac care, including pioneering coronary artery bypass surgery, and its focus on research and education. It's also known for its strong performance in numerous other specialties, including neurosurgery, gastroenterology, and oncology" .
SCR:026851 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ZenCELL_owl" ;
rdfs:label "ZenCELL owl | live cell imaging and analysis system" ;
NIFRID:synonym "innoME GmbH zenCELL owl",
"innoME GmbH ZenCELL owl live cell imaging and analysis system",
"zenCELL owl" ;
definition: """24 channels microscope for incubator with automated remote monitoring of cell
cultures. 24 independent cameras are used to acquire brightfield or darkfield scans and perform image analysis of up to 24 wells of cell culture in parallel automatically. Culture quality and data can be checked from PC. It enables real-time, non-invasive, label-free monitoring of cell growth directly inside standard incubators. The system captures time-lapse images and performs automated quantitative analysis, generating dynamic growth curves and detailed cellular behavior profiles.""" .
SCR:026852 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FerrDb" ;
NIFRID:synonym "FerrDb V2" ;
definition: "Manually curated database of ferroptosis regulators and ferroptosis-disease associations. There are two secondary categories of ferroptosis regulators: (1) genes and (2) substances. Gene regulators include driver, suppressor, marker, and unclassified regulator. Substances cover range of chemical entities, including pure substances (e.g., iron, erastin) and mixtures (e.g., herbal extracts). Substance regulators include inducers and inhibitors. FerrDb V2 is updated database." .
SCR:026853 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioVenn" ;
definition: "Software R and Python package for comparison and visualization of biological identifiers lists using area-proportional Venn diagrams. Also offers option to map Entrez and/or Affymetrix IDs to Ensembl IDs. In SVG mode, text and numbers can be dragged and dropped. Used to create area-proportional Venn diagram of 2 or 3 circles." .
SCR:026854 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "projecTILs" ;
definition: "Software tool to project scRNA-seq data into reference single-cell atlases, enabling their direct comparison in stable, annotated system of coordinates. Predicts effects of cell perturbations and identifies gene programs that are altered in different conditions and tissues. Used for interpretation of cell states using reference single-cell maps." .
SCR:026855 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Orion" ;
rdfs:label "RareCyte | ORION" ;
NIFRID:synonym "Orion Instrument",
"RareCyte Orion" ;
definition: "Benchtop, high-resolution, spectral imaging instrument that integrates quantitative immunofluorescence and brightfield imaging." .
SCR:026856 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3211" ;
rdfs:label "Rush University Medical Center Genomics and Microbiome Core Facility" ;
NIFRID:synonym "Genomics and Microbiome Core Facility",
"RUSH University Genomics and Microbiome Core Facility" ;
definition: "Core provides full service genomics and Next Generation sequencing. Specializes in microbial sequencing." .
SCR:026857 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.240684.c",
"ISNI 0000 0001 0705 3621",
"Wikidata Q1535116" ;
rdfs:label "Rush University Medical Center" ;
definition: "Rush University Medical Center is academic medical center for basic and clinical research, with physicians and scientists involved in hundreds of research projects developing and testing the effectiveness and safety of new therapies and medical devices. Offers residency and fellowship programs in medical and surgical specialties and subspecialties." .
SCR:026858 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "miRTargetLink" ;
NIFRID:synonym "miRTargetLink 2.0" ;
definition: "Web application provides users with visualization interface to explore and analyze interaction networks between miRNAs and target genes." .
SCR:026859 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RectChr " ;
definition: "Software tool for multi-level visualization of genomic statistical variables on rectangular chromosomes." .
SCR:026860 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3128" ;
rdfs:label "University of Nebraska Medical Center Single Cell and Spatial Transcriptomics Core Facility" ;
NIFRID:synonym "University of Nebraska Medical Center UNMC- Spatial Profiling Hub Core Facility",
"UNMC- Spatial Profiling Hub Core Facility" ;
definition: "Core offers spatial omics processing on many different tissue types. Facility provides instrumnets including Bruker's GeoMx DSP ready for launch with anticipated launch of 10x Visium. Offers expert collaboration from project design to data handoff. Core has established workflows with additional shared resources on UNMC campus to allow for expertise throughout entire project." .
SCR:026861 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3223" ;
rdfs:label "Cancer Research Institute IFOM EMSM Electron Microscopy Single Molecules Core Facility" ;
NIFRID:synonym "IFOM EMSM - Electron Microscopy Single Molecules Core Facility" ;
definition: "Facility uses transmission electron microscopy coupled to low angle rotary shadowing to visualize nucleic acids. This technique allows the inspection of the fine ultrastructure of in vivo chromosomal DNA intermediates on properly enriched genomic DNA samples." .
SCR:026862 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3225" ;
rdfs:label "Cancer Research Institute IFOM CERD Cancer Engineering R&D Core Facility" ;
NIFRID:synonym "IFOM CERD - Cancer Engineering R&D Core Facility" ;
definition: "Core focuses on development of innovative biomedical technologies and devices for cancer research as well as biomedical applications using microfabrication and 3D printing." .
SCR:026863 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3224" ;
rdfs:label "Cancer Research Institute IFOM EMCT Electron Microscopy Cells & Tissues Core Facility" ;
NIFRID:synonym "IFOM EMCT - Electron Microscopy Cells & Tissues Core Facility" ;
definition: "Core performs routine transmission and scanning Electron Microscopy and all kinds of immune Electron Microscopy, correlative light electron microscopy, three-dimensional EM (3DEM), quantitative stereological evaluation of data and more." .
SCR:026864 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3222" ;
rdfs:label "Cancer Research Institute IFOM CPM Cellular And Preclinical Models Core Facility" ;
NIFRID:synonym "IFOM CPM - Cellular And Preclinical Models Core Facility" ;
definition: "Specialized laboratory designed for growth, maintenance, and experimentation of living cells under controlled conditions. This facility is used in various fields such as biomedical research, drug development, and supports the culture of primary cells, immortalized cell lines, human-induced pluripotent stem cells (hiPSCs), and organoids, among others." .
SCR:026865 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3227" ;
rdfs:label "Cancer Research Institute IFOM FC Flow Cytometry Core Facility" ;
NIFRID:synonym "IFOM FC - Flow Cytometry Core Facility" ;
definition: "Core Facility provides technology, instrumentation, and expert support for applications, including Immunophenotyping, Cell cycle and proliferation analysis, Metabolic studies, Apoptosis detection, Fluorescent protein expression analysis, Cytokine, chemokine, and intra/extracellular protein detection." .
SCR:026866 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3226" ;
rdfs:label "Cancer Research Institute IFOM ALM Advanced Light Microscopy Core Facility" ;
NIFRID:synonym "IFOM ALM - Advanced Light Microscopy Core Facility" ;
definition: "Core Facility provides technological platforms in the field of light microscopy. A team of highly qualified and experienced professionals supports IFOM's research activities, assisting in sample preparation and acquisition, data post-processing and image analysis." .
SCR:026867 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3228" ;
rdfs:label "Cancer Research Institute IFOM FGS Functional Genomic Screening Core Facility" ;
NIFRID:synonym "IFOM FGS - Functional Genomic Screening Core Facility" ;
definition: "Core specializes in high-throughput CRISPR screening using pooled or arrayed libraries in diverse cellular models. This technology assesses the effects of thousands of genetic perturbations at single-cell resolution with CRISPR knockout (CRISPR KO), CRISPR interference (CRISPRi), and CRISPR activation (CRISPRa). It also utilizes base and prime editing to investigate specific mutations, such as those relevant to cancer development and progression." .
SCR:026868 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "IFOM ETS - The AIRC Institute of Molecular Oncology; Milan; Italy" ;
NIFRID:synonym "AIRC Institute of Molecular Oncology",
"FIRC Institute of Molecular Oncology",
"FIRC Institute of Molecular Oncology - IFOM",
"IFOM Institute of Molecular Oncology" ;
NIFRID:abbrev "IFOM ETS" ;
definition: "Cancer research institute focused on the study of cancer formation and development." .
SCR:026869 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3230" ;
rdfs:label "Northwestern University SynBio Foundry Core Facility" ;
definition: "Core facility for synthetic biology experimentation including pilot-scale fermentation, high throughput automation, biological sample analysis, and cell-free protein synthesis." .
SCR:026870 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3231" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Electronics Core Facility" ;
definition: "Electronics Core is electronics design, development and repair facility which specializes in proof-of-concept design and prototyping, and early stage development of medical devices and laboratory research instrumentation. Services include system design, schematic capture, printed circuit board layout, board fabrication, assembly and testing." .
SCR:026871 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3232" ;
rdfs:label "University College London LMCB Light Microscopy Core Facility" ;
NIFRID:synonym "Light Microscopy Imaging Platform",
"University College London LMCB Light Microscopy Facility" ;
definition: "Core provides imaging systems for advanced microscopy including confocal, multi-photon and super-resolution modalities, enabling users to address research questions in living systems across temporal and spatial scales. Staff offers training to use equipment, expertise about experimental strategy, design, image processing and analysis." .
SCR:026872 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Atlas MxIF" ;
definition: "Software package contains all original code used to process MxIF data." .
SCR:026873 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mollecular Functional Portraits" ;
NIFRID:abbrev "MFP" ;
definition: "Code to analyse data from \"Conserved pan-cancer microenvironment subtypes predict response to immunotherapy\" by Bagaev et al." .
SCR:026874 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "broom" ;
definition: "Software R package to convert statistical analysis objects from R into tidy format. Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once." .
SCR:026875 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggbeeswarm" ;
definition: "Software R package provides two methods of plotting categorical scatter plots such that arrangement of points within category reflects the density of data at that region, and avoids over-plotting. Categorical Scatter (Violin Point) Plots." .
SCR:026876 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Stanford SCG Bioinformatics Cluster" ;
NIFRID:synonym "SCG Cluster",
"Stanford Genomics cluster",
"Stanford SCG Informatics Cluster",
"Stanford University SCG Cluster" ;
NIFRID:abbrev "SCG" ;
definition: "High-performance computing facility. Its resources have been designed to support labs engaged in genetics and bioinformatics research, but are open to anyone on campus. The Stanford SCG Bioinformatics Cluster is optimized to support large memory, single-node threaded applications as well as applications and workflows that require many small files." .
SCR:026877 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PropCIs" ;
definition: "Software R package with various confidence intervals for binomial proportions inside. Confidence intervals are for single, paired and independent proportions. Various confidence interval methods for proportions." .
SCR:026878 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TP53 Database" ;
NIFRID:synonym "NCI TP53 Database" ;
definition: "Database compiles various types of data and information from literature and generalist databases on human TP53 gene variations related to cancer." .
SCR:026883 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Invitrogen | Qubit 4 Fluorometer with WiFi" ;
NIFRID:synonym "Qubit 4 Fluorometer with WiFi" ;
definition: "Qubit fluorometer designed to accurately measure DNA, RNA, and protein quantity, and now also RNA integrity and quality. Qubit 4 Fluorometer was re-engineered to enable data transfer via WiFi as well as to run Qubit RNA IQ assay. Qubit 4 Fluorometer and RNA IQ Assay Kit work together to accurately distinguish intact from degraded RNA in two steps." .
SCR:026887 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | BOND-MAX Fully Automated IHC and ISH Staining System" ;
NIFRID:synonym "BOND-MAX",
"BOND-MAX Fully Automated IHC and ISH Staining System" ;
definition: """Bench-standing IHC/ISH stainer with three-tray system, with 3.5hour run times.
Each tray functions independently, allowing on-demand access and enabling you to load slides as they become available. System accommodates up to 29 antibodies (with detection loaded) and allows for easy swapping of antibodies without interrupting ongoing staining processes.""" .
SCR:026889 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Agilent | Dako Autostainer Link 48" ;
NIFRID:synonym "Autostainer Link 48" ;
definition: "Immunohistochemistry stainer is united with software and connectivity options. Can process 48 slides in less than three hours." .
SCR:026890 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Indica Labs | SlideQC BF slide scanner" ;
NIFRID:synonym "SlideQC BF",
"SlideQC BF slide scanner" ;
definition: "AI-powered scanner for H&E- and IHC-stained whole slide images that enables automated quality control workflow by detecting the most common artifacts generated during process of slide preparation and scanning including air bubbles, dust/debris, folds, out-of-focus areas, and pen marks. It is integrated into the HALO AP diagnostic digital pathology platform." .
SCR:026891 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ IN_Cell_2500HS" ;
rdfs:label "Cytiva | IN Cell 2500HS" ;
NIFRID:synonym "Cytiva IN Cell 2500HS cell analyzer",
"IN Cell 2500HS",
"IN Cell 2500HS widefield cell imaging system" ;
definition: "Fully-automated, widefield cell imaging system. Building on capabilities of earlier IN Cell Analyzer systems, it provides platform to deliver advances in speed, image quality, and throughput. Allows to perform analysis." .
SCR:026895 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_LE220-plus" ;
rdfs:label "Covaris | LE220-plus Focused-ultrasonicator" ;
NIFRID:synonym "LE220-plus Focused-ultrasonicator",
"LE220-plus instrument" ;
NIFRID:abbrev "LE220" ;
definition: "Ultrasonicator is scalable, automated high-performance sample preparation instrument with automated water works to optimize user-to-user reproducibility and remote set-up and scheduling. Designed for integration with high-throughput laboratory automation. Includes integrated AFA ultraCUBE water chiller and water conditioning module." .
SCR:026896 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SemiBin" ;
NIFRID:synonym "SemiBin2" ;
definition: "Software command tool for metagenomic binning with deep learning, handles both short and long reads. Used for metagenomic binning at contig level which uses deep contrastive learning." .
SCR:026897 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CheckM2" ;
definition: "Software tool to predict completeness and contamination of genomic bins. Used for predicting genome quality of metagenome-assembled genomes. Assessing microbial genome quality using machine learning." .
SCR:026898 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BreaKmer" ;
definition: "Software tool to identify genomic structural variation in target regions/genes from reference-aligned high-throughput sequence data. Used to identify structural variation from sequencing data in target regions." .
SCR:026899 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SigProfilerAssignment" ;
definition: "Software tool for assignment of known mutational signatures to individual samples and individual somatic mutations." .
SCR:026900 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Vi-CELL_BLU" ;
rdfs:label "Beckman Coulter | Vi-CELL BLU Cell Viability Analyzer" ;
NIFRID:synonym "Vi-CELL BLU cell analyzer" ;
definition: "Cell counter automates trypan blue dye exclusion method for cell viability that has been performed with light microscope, pipette, and hemacytometer." .
SCR:026901 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Xstrahl | Small Animal Radiation Research Platform (SARRP) system" ;
NIFRID:synonym "Small Animal Radiation Research Platform (SARRP) system" ;
definition: "System used for in vivo radiation therapy and imaging of in vivo radiation therapy and imaging, like mice and rats, in order to study tumor and normal tissue responses to radiation. It combines micro-CT imaging with conformal radiation delivery, allowing researchers to image small tumors and organs, then precisely deliver radiation therapy with sub-millimeter accuracy." .
SCR:026902 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Revvity | SciClone G3 liquid handling workstation" ;
NIFRID:synonym "SciClone G3 liquid handling workstation" ;
definition: "Advanced automated liquid handling platform originally developed by PerkinElmer. Designed and programmed for next generation sequencing (NGS) applications. They feature library of over 120 pre-developed and verified or vendor qualified automated NGS preparation kits." .
SCR:026903 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3235" ;
rdfs:label "Michigan State University Flow Cytometry Core Facility" ;
definition: "Core provides access to analytical flow cytometry instrumentation and cell sorting services, as well as training and experimental consultation." .
SCR:026904 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3236" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Polymer Core Facility" ;
definition: "Engineers in the Polymer Core work closely with physicians, surgeons, and researchers throughout Cleveland Clinic to provide extensive services on medical device design, prototype and evaluation. We help our inventors to “prove the concept” of their novel inventions, which will ultimately benefit our patients. We also help research groups at Lerner Research Institute to fabricate or repair research instruments, which are not commercially available, such as cell culture fixture, test instruments, etc." .
SCR:026905 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3234" ;
rdfs:label "University of New England In Vitro Analytical Core Facility" ;
NIFRID:synonym "In Vitro Analytical Core",
"University of New England In Vitro Analytical Core" ;
definition: "Core provides expertise and instrumentation to study cell-cell interactions and to delineate intracellular pathways in targeted cell types. Provides training, instrumentation, and technical services for development, analysis, and storage of in vitro cell models (such as stably transfected cell lines using genetically encoded biosensors), sample preparation for downstream analyses such as mass spectrometry and RNA-seq." .
SCR:026906 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CausalCoxMGM" ;
definition: "Software tool for analysis of simulated and real-world biomedical datasets." .
SCR:026907 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Medical Imaging and Data Resource Center (MIDRC) data repository" ;
NIFRID:synonym "MIDRC data repository" ;
definition: "Data repository that is hosting medical images." .
SCR:026908 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SeriesZoom" ;
definition: "Software pan-and-zoom type online viewer for viewing collection of high-resolution images in web browser. Images are expected to be in tiled multi-scale representation." .
SCR:026909 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100014588",
"GRID grid.417924.d",
"Wikidata Q158205" ;
rdfs:label "Sanofi-Aventis" ;
NIFRID:synonym "Sanofi",
"Sanofi S.A." ;
definition: "Sanofi-Aventis was the former name of the French multinational pharmaceutical and healthcare company Sanofi, now headquartered in Paris, France. Sanofi S.A. is global healthcare company focused on discovering, developing, and delivering medicines and vaccines." .
SCR:026910 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 501100000046",
"GRID grid.24433.32",
"ISNI 0000 0004 0449 7958",
"Wikidata Q1437507" ;
rdfs:label "National Research Council Canada" ;
definition: "Primary national agency of the Government of Canada dedicated to science and technology research and development. It is the largest federal research and development organization in Canada. Works closely with Canadian firms, helping them bring new technologies to market." .
SCR:026911 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hyperparameterScoringHiC" ;
definition: "Software tool as scoring functions for Hi-C matrix prediction optimization. Regression models for predicted Hi-C data. The input for the regression are human expert rankings and different Hi-C evaluation scores." .
SCR:026912 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bell Jar" ;
definition: "Software mouse brain histology tool for neuroscientists. Semiautomated registration and cell counting tool for mouse neurohistology analysis." .
SCR:026913 a "Resource,",
owl:NamedIndividual ;
rdfs:label "AMICI" ;
NIFRID:synonym "Advanced Multilanguage Interface to CVODES and IDAS" ;
definition: "Software toolbox implemented in C++/Python/MATLAB that provides efficient simulation and sensitivity analysis routines tailored for scalable, gradient-based parameter estimation and uncertainty quantification. Used for high-performance sensitivity analysis for large ordinary differential equation models." .
SCR:026914 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyPESTO" ;
NIFRID:synonym "python Parameter EStimation TOolbox" ;
definition: "Software Python package for parameter inference. Used for parameter estimation for dynamic models." .
SCR:026915 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PEtab" ;
definition: "Repository contains PEtab specifications and additional documentation. Data format for specifying parameter estimation problems in systems biology. SBML and TSV based data format for parameter estimation problems in systems biology. Human- and computer- readable format for representing parameter estimation problems in systems biology." .
SCR:026916 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HYMET" ;
NIFRID:synonym "Hybrid Metagenomic Tool" ;
definition: "Software Hybrid Metagenomic Tool." .
SCR:026917 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "African Genome Variation Database" ;
NIFRID:synonym "African Genome Variation Database (AGVD)" ;
definition: "Database for exploring genomic variation data within African populations." .
SCR:026918 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "African Genomic Medicine Portal" ;
NIFRID:synonym "African Genomic Medicine Portal (AGMP)" ;
definition: "AGMP provides researchers with platform from which they can retrieve existing information regarding genetic associations to disease-related phenotypes in African populations." .
SCR:026919 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "African Population Ontology" ;
NIFRID:abbrev "AfPO" ;
definition: "AfPO is an ontology that can be used in the study of diverse populations across Africa. It brings together publicly available demographic, anthropological and genetic data relating to African people in standardised and structured format. AfPO can be employed to classify African study participants comprehensively in prospective research studies. It can also be used to classify past study participants by mapping them using language or ethnicity identifier or synonyms." .
SCR:026920 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "eLwazi-AfriGen-D Metadata Catalog" ;
NIFRID:synonym "eLwazi Catalogue" ;
definition: "Catalogue provides searchable metadata for datasets generated and used by the DS-I Africa consortium and external organisations/projects across the African continent." .
SCR:026921 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Afrigen-D Imputation Server" ;
definition: "Web portal provides interconnected resources and services for African genomics research data lifecycle management and implementation. African genotype imputation service using diverse African population reference panel. African genomics data hub." .
SCR:026922 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "H3Africa Data and Biospecimen Catalogue" ;
NIFRID:synonym "H3Africa catalogue",
"Human Heredity and Health in Africa catalogue" ;
definition: """Catalogue enables users to search for H3Africa datasets or biospecimens of interest. Catalogue is updated periodically with metadata from studies submitted to H3Africa Archive and corresponding biospecimen metadata uploaded from following biorepositories:
IBRH3AU: Makerere University, Uganda; IHVN: Institute of Human Virology, Nigeria;
CLS: University of the Witswatersrand School of Pathology, South Africa.""" .
SCR:026923 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "United States Core Data Interoperability" ;
NIFRID:abbrev "USCDI" ;
definition: "United States Core Data for Interoperability (USCDI) is standardized set of health data classes and constituent data elements for nationwide, interoperable health information exchange. USCDI is US Government common data elements for patient data." .
SCR:026924 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phenotype Data Collection Toolkits" ;
definition: "Software suite of data collection toolkits that cover range of biomedical research fields. These toolkits provide data collection forms that can be used to build research database and can facilitate phenotype standardisation and harmonisation efforts on African continent and larger user community." .
SCR:026925 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker timsTOF fleX" ;
NIFRID:synonym "Bruker timsTOF fleX with MALDI" ;
definition: "The timsTOF fleX is fully functional high speed, high sensitivity ElectroSpray Ionization (ESI) instrument for all Omics analyses with integrated Matrix-Assisted Laser Desorption Ionization (MALDI) source for fast MALDI Imaging." .
SCR:026926 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BVSim" ;
NIFRID:synonym "Benchmarking Variation Simulator" ;
definition: "Software package provides several functions and parameters for simulating genetic variations. Benchmarking variation simulator mimicking human variation spectrum." .
SCR:026927 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenTOPAS" ;
NIFRID:synonym "TOol for PArticle Simulation",
"TOPAS" ;
definition: "Software Monte Carlo tool for particle simulation. Used for simulation of medical applications of ionizing radiation with the Monte Carlo method. Allows to assemble and control library of simulation objects (geometry components, particle sources, scorers, etc.) with no need to write C++ code and without knowledge of underlying Geant4 Simulation Toolkit." .
SCR:026928 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QCxMS" ;
definition: "Software application as quantum chemical based program that enables users to calculate mass spectra using Born-Oppenheimer Molecular Dynamics. Quantum mechanic mass spectrometry calculation program." .
SCR:026929 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xTB" ;
NIFRID:synonym "eXtended TB",
"eXtended TB (xTB)",
"extended Tight Binding" ;
definition: "Software semiempirical extended tight-binding program package. Provides userfriendly interface for performing geometry optimizations, vibrational frequency calculations, and Molecular Dynamics simulations." .
SCR:026930 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioFile Finder" ;
definition: "Open-source web application created for easy access, collaboration, and sharing of datasets through rich metadata search, filter, sort, and direct viewing in common industry applications or in our web-based 3D Volume Viewer." .
SCR:026931 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3237" ;
rdfs:label "University of Texas MD Anderson Functional Genomics Core Facility" ;
NIFRID:synonym "University of Texas MD Anderson Cancer Center Functional Genomics Core",
"University of Texas MD Anderson Cancer Center Functional Genomics Core Facility" ;
definition: "Core provides researchers with genetic tools, including shRNA, ORF and CRISPR for studying and annotating gene functions in cell-based assays. FGC personnel provides research support for investigators who are interested in genetic screens." .
SCR:026932 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3238" ;
rdfs:label "University of Texas MD Anderson Research Histology Core Facility" ;
NIFRID:synonym "University of Texas MD Anderson Research Histology Core Laboratory" ;
definition: "Core supports basic and clinical research by providing histological and molecular expertise, technical support and consultation to research investigators. Provides histological, molecular and consultation services. Services are performed by American Society of Clinical Pathology certified histologists with expertise in routine histology, whole slide scanning, image and digital analysis, pathology services, immunohistochemistry, tissue microarray, bone histomorphometry, Visium preparations and RNAscope single and co-detection assays." .
SCR:026933 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3214" ;
rdfs:label "IFOM ETS Cogentech QPCR Quantitative PCR Core Facility" ;
NIFRID:synonym "Cogentech QPCR - Quantitative PCR Core Facility",
"Cogentech QPCR Quantitative PCR Core" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 8th,2025. ogentech's Quantitative PCR (QPCR) Core Facility provides services including project design, assay selection and development, data analysis for quantitative analysis of any specific target sequence for gene expression, copy number variation or variant analysis, in low and high-throughput mode. Provides analysis using both Real Time PCR and digital PCR. Special protocols for small amounts of starting material have been implemented. The laboratory is ISO9001 certified." .
SCR:026934 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3213" ;
rdfs:label "IFOM ETS Cogentech HP Histopathology Core Facility" ;
NIFRID:synonym "Cogentech HP Histopathology",
"Cogentech HP- Histopathology Core Facility" ;
definition: "Cogentech's Histopathology (HP) Core Facility provides services including consultation, tissue trimming and embedding, cutting, staining, photographic documentation for the evaluation and characterization of normal and pathological tissues. Provides Optimization of protocols for new stains or biological specimen.The laboratory is ISO9001 certified." .
SCR:026935 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3216" ;
rdfs:label "IFOM ETS Cogentech GU Genomics Core Facility" ;
NIFRID:synonym "Cogentech GU - Genomics Core Facility",
"Cogentech GU Genomics" ;
definition: "Cogentech's Genomic Core Facility (GU) provides professional support for workflow of research projects, from counseling on experimental design to functional interpretation of results. Support includes identification of the most suitable methodology to achieve the experimental aim, quality control of nucleic acid, generation of indexed fragment library, sequencing according to experimental needs and bioinformatic support for selected applications. Customized protocols can be set-up as well. Sequencing data are delivered using a password protected user-friendly web interface. The laboratory is ISO9001 certified." .
SCR:026936 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3218" ;
rdfs:label "IFOM ETS Cogentech BRF Biological Research Core Facility" ;
NIFRID:synonym "Cogentech BRF - Biological Research Facility",
"Cogentech BRF Biological Research" ;
definition: "Cogentech's Biological Research Facility (BRF) provides animal facility in which laboratory mice are maintained and bred for different research programs. The laboratory is ISO9001 certified." .
SCR:026937 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3219" ;
rdfs:label "IFOM ETS Cogentech Proteomics and Metabolomics Core Facility" ;
NIFRID:synonym "Cogentech P&M - Proteomics & Metabolomics Core Facility",
"Cogentech Proteomics and Metabolomics" ;
definition: "Cogentech's Proteomics and Metabolomics Core Facility provides infrastructure for identification, characterization and quantification of proteins, metabolites and lipids.Offers several instrumental platforms for separation of those molecules. Proteomics, metabolomics and lipidomics analysis rely on mass spectrometry coupled with liquid chromatography." .
SCR:026938 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3217" ;
rdfs:label "IFOM ETS Cogentech IGU Integrative Genomics Core Facility" ;
NIFRID:synonym "Cogentech IGU - Integrative Genomics Core Facility",
"Cogentech IGU Integrative Genomics" ;
definition: "Cogentech's Integrated Genomics Core Facility (IGU) consists of units: Molecular Biology and Sequencing, Histopathology and Bioinformatics. Molecular Biology group provides expertise in various fields of application: nucleic acid extraction from different matrices, ddPCR and various types of sequencing (customised gene panels, Lowpass WGS, WES, WGS, total RNA-Seq, mRNA Seq, TCR-Seq, 16S Metagenomic Seq, ATAC-Seq, genome-wide methylation profiling). Bioinformatics unit provides pipelines for analysis of data produced by all sequencing workflows. In addition, it provides its expertise for implementation and development of customised pipelines. Histopathology unit offers services for slide preparation and staining, image digitisation and laser-capture microdissection. The laboratory is ISO9001 certified." .
SCR:026939 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3215" ;
rdfs:label "IFOM ETS Cogentech DSS DNA Sanger Sequencing Core Facility" ;
NIFRID:synonym "Cogentech DSS - DNA Sanger Sequencing Core Facility",
"Cogentech DSS DNA Sanger Sequencing" ;
definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 8th,2025. Cogentech's DNA Sanger Sequencing (DSS) Core Facility offers standard DNA sequencing and assistance for projects using on Sanger sequencing. We also offer the possibility to use fragment analysis for various applications, providing assistance in the pre-and post-analytical phase. The laboratory is ISO9001 certified." .
SCR:026940 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3220" ;
rdfs:label "IFOM ETS Cogentech Cancer Genetic Test Laboratory Laboratory Core Facility" ;
NIFRID:synonym "Cogentech Cancer Genetic Test Laboratory",
"Cogentech CGT lab (Cancer Genetic Test Laboratory)" ;
definition: "Cogentech's CGT lab is offering its diagnostic services for Hereditary Tumors (Cancer Risk) and for Personalized Medicine (Therapy) to clinicians, laboratories and hospitals." .
SCR:026941 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_e-VF_Handheld" ;
rdfs:label "Ugo Basile | Electronic Von Frey - e-VF Handheld" ;
definition: """Electronic von Frey system for rodents. Used for touch sensitivity in unrestrained animals.
The scientist gradually increases the force applied to the animal paw, until the peak detector scores the animal paw withdrawal (or the user scores it manually with the included pedal).""" .
SCR:026942 a owl:NamedIndividual ;
rdfs:label "WaveSeekerNet" ;
definition: "Software application for accurate and rapid prediction of IAV subtypes and host source." .
SCR:026943 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3239" ;
rdfs:label "National Institute on Drug Abuse Confocal and Electron Microscopy Core Facility" ;
NIFRID:synonym "Confocal and Electron Microscopy Core",
"National Institute on Drug Abuse Confocal and Electron Microscopy Core",
"NIDA IRP Confocal and Electron Microscopy Core",
"NIDA IRP Confocal and Electron Microscopy Core (CEMC)" ;
definition: "NIDA IRP Confocal and Electron Microscopy Core serves NIDA-IRP researchers by providing access to confocal and electron microscopic technologies to characterize cellular and ultrastructural properties of organelles, tissue culture and brain tissue. Provides expertise, consultations and training in adaptation and execution of confocal and electron microscopic techniques and procedures." .
SCR:026944 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3242" ;
rdfs:label "North Carolina State University Genomic Sciences Laboratory Core Facility" ;
NIFRID:synonym "NCSU Genomic Sciences Laboratory",
"North Carolina State University NCSU Genomic Sciences Laboratory" ;
definition: "Core provides equipment and infrastructure required to conduct advanced genomics research. Provides access to DNA sequencing, traditional Sanger sequencing and genotyping, and additional equipment services for functional genomic assays and mapping. Provides robotics and instrumentation to facilitate the handling of large numbers of samples, as well as many advanced sequencing and sequencing support applications." .
SCR:026945 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3241" ;
rdfs:label "Boise State University Biomedical Research Institute Biomolecular Research Core Facility" ;
NIFRID:synonym "Biomedical Research Institute Biomolecular Research Core Facility",
"Biomolecular Research Core Facility",
"Biomolecular Research Core Facility (BRCF)" ;
definition: "Biomolecular Research Core Facility (BRCF) has collection of instrumentation for characterization of biomolecules and their role in variety of processes. Instrumentation is accessible to internal and external customers. Available instrumentation focuses on mass spec, histology, imaging, and protein biochemistry." .
SCR:026946 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3240" ;
rdfs:label "National Institute on Drug Abuse Histology and Imaging Core Facility" ;
NIFRID:synonym "Histology and Imaging Core",
"National Institute on Drug Abuse Histology and Imaging Core",
"NIDA-IRP Histology and Imaging Core (HIC)" ;
definition: "NIDA-IRP Histology and Imaging Core serves NIDA-IRP researchers by providing access to existing and emerging neuroanatomical technologies to map and characterize neuronal circuits. Provides expertiese, consultations and training to NIDA-IRP researchers in the adaptation and execution of neuroanatomical techniques and procedures." .
SCR:026947 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Windows Subsystem for Linux (WSL)" ;
definition: "Windows Subsystem for Linux (WSL) is feature of Windows operating system that enables to run Linux file system, along with Linux command-line tools and GUI apps, directly on Windows, alongside traditional Windows desktop and apps. Tool for developers, especially web developers, those working on open source projects, or deploying to Linux server environments." .
SCR:026948 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ubuntu on WSL" ;
NIFRID:synonym "Ubuntu on Windows Subsystem for Linux" ;
definition: "Ubuntu terminal environment on Windows with Windows Subsystem for Linux (WSL). Used to streamline web application development, leverage cutting-edge AI/ML tooling, develop cross-platform applications and manage IT infrastructure without leaving Windows." .
SCR:026949 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KEGGREST" ;
definition: "Software package that provides client interface to Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. Client-side REST access to KEGG." .
SCR:026950 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggVennDiagram " ;
definition: "Software R package to generate Venn diagram.'ggplot2' implement of Venn Diagram." .
SCR:026951 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "apeglm" ;
NIFRID:synonym "Approximate Posterior Estimation for generalized linear model",
"Approximate posterior estimation for GLM" ;
definition: "Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients." .
SCR:026952 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "correctKin" ;
definition: "Software for Kinship coefficient estimation from low coverage ancient (or degraded forensic) genome data. Used to infer relatedness up to the 4th degree from low-coverage ancient human genomes." .
SCR:026953 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gargammel" ;
definition: "Software sequence simulator for ancient DNA. For ancient hominin samples can also simulate various levels of present-day human contamination and microbial contamination." .
SCR:026954 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "grups-rs" ;
definition: "Ancient DNA genetic relatedness estimation software relying on pedigree simulations. Used to compute estimate of relatedness from randomly sampled pseudo-haploidized variant calls, and leverages high-definition pedigree simulations to bypass the use of cohort of individuals." .
SCR:026955 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Kinship_Inference" ;
NIFRID:synonym "KIN" ;
definition: "Software tool to estimate pairwise relatedness from ancient DNA, taking in account contamination, ROH, ascertainment bias. Used to identify identity-by-descent fragments and to estimate degree of relatedness from ancient DNA data." .
SCR:026956 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pcangsd" ;
NIFRID:synonym "PCAngsd" ;
definition: "Software framework for analyzing low-depth next-generation sequencing data in heterogeneous/structured populations using principal component analysis." .
SCR:026957 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ped-sim" ;
NIFRID:synonym "Ped-sim" ;
definition: "Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances." .
SCR:026958 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "READ" ;
NIFRID:synonym "Relationship Estimation from Ancient DNA" ;
definition: "Software tool to infer family relationships for degraded samples. Used to infer degree of relationship (up to second degree, i.e. nephew/niece-uncle/aunt, grandparent-grandchild or half-siblings) for pair of low-coverage individuals." .
SCR:026959 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "READv2" ;
NIFRID:synonym "Relationship Estimation from Ancient DNA version 2" ;
definition: "Software Python3 tool for advanced, user-friendly detection and nuanced analysis of biological relatedness from ancient DNA samples in archaeogenomics. Can classify up to third-degree relatedness and differentiate between two types of first-degree relatedness, full siblings and parent-offspring." .
SCR:026960 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TKGWV2" ;
definition: "Software ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data." .
SCR:026961 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "yFiles Layout Algorithms" ;
NIFRID:synonym "yWorks GmbH yFiles Layout Algorithms" ;
definition: "Software suite of algorithms used for arranging and visualizing graph structures. They provide variety of layout styles, such as hierarchical, organic, tree, circular, and orthogonal, each optimizing for different criteria and visualization needs." .
SCR:026962 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Design and Analysis (DA2) software" ;
definition: "Design and analysis software enables user to set up runs, send plates to the specific instrument, open completed run files, and analyze and review data in integrated and streamlined fashion. Software can be run with security, audit, and e-signature (SAE) enabled. The software also provides suite of analysis modules for secondary analysis and comes with multi-language support." .
SCR:026963 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Countess_3" ;
rdfs:label "Thermo Fisher: Invitrogen | Countess 3 Automated Cell Counter" ;
NIFRID:synonym "Countess 3 Automated Cell Counter" ;
definition: "Automated cell counter was developed using advanced machine-learning image analysis algorithm to deliver accurate cell counts and viability measurements using slide containing cell sample in fewer than 30 seconds. Has automated lighting, focus, capturing, counting, and saving." .
SCR:026964 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VIPERA" ;
NIFRID:synonym "Viral Intra-Patient Evolution Reporting and Analysis" ;
definition: "Software package to automate analysis of evolutionary trajectories over time of series of sequences from same viral infection. Snakemake workflow for SARS-CoV-2 viral intra-patient evolution reporting and analysis." .
SCR:026965 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RNAmut" ;
definition: "Software package for robust identification of somatic mutations in acute myeloid leukemia using RNA-sequencing. Detects clinically important somatic mutations from RNA-seq data on relatively small gene panel (typically less than 100 genes)." .
SCR:026966 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "chevreul" ;
definition: "Software R package and shiny app for processing, plotting, and interactive exploratory data analysis of full-length scRNA-seq as SingleCellExperiments." .
SCR:026967 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3243" ;
rdfs:label "Benaroya Research Institute BRI Biorepository Core Facility" ;
NIFRID:synonym "Benaroya Research Institute BRI Biorepository",
"BRI Biorepository" ;
definition: "BRI is home to rigorously maintained biorepositories containing blood and tissue samples donated by people with immune-mediated diseases and healthy controls.Provides the collection of samples from research participants, sample processing, storage, and sharing." .
SCR:026968 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Implant for Reliable Diaphragm EMG Recordings in Awake, Behaving Rats" ;
definition: "Low-cost implant for reliable diaphragm EMG recordings in awake, behaving rats.Diaphragm EMG implant." .
SCR:026969 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3244" ;
rdfs:label "University of Miami Hussman Institute for Human Genomics Induced Pluripotent Stem Cell Core Facility" ;
NIFRID:synonym "Induced Pluripotent Stem Cell (iPSC) Core" ;
definition: "Core provides standardized services for derivation and characterization of human iPSC lines from peripheral blood and tissue samples. Offerings include PBMC isolation, reprogramming, Sendai virus reprogramming vector removal and analysis, karyotyping, mycoplasma testing, in vitro differentiation of neural and hemopoietic progenitor cells, and immunocytochemical staining of cell type markers and imaging. Core additionally offers hands-on training and consultation to support the use of iPSC technologies in disease modeling." .
SCR:026970 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPEX" ;
NIFRID:synonym "Spatial Expresion Explorer" ;
definition: "Web-based analysis platform offering end to end analytics for spatial omics datasets." .
SCR:026971 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DecisionLinnc Data Science Platform" ;
definition: "Web platform that integrates multiple programming language environments and enables data processing, data analysis, and machine learning through visual interface." .
SCR:026972 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_nanoElute_2" ;
rdfs:label "Bruker | nanoElute 2" ;
NIFRID:synonym "nanoElute 2" ;
definition: "High-performance nanoflow liquid chromatography system with intuitive and flexible user interface, covering broad range of applications from single cell to high throughput routine proteomics." .
SCR:026973 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rnaseq" ;
NIFRID:synonym "nf-core/rnaseq" ;
definition: "Software RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. Can be used to analyse RNA sequencing data obtained from organisms with reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix QC report." .
SCR:026974 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Prosit " ;
definition: "Software tool for proteome-wide prediction of peptide tandem mass spectra by deep learning." .
SCR:026975 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ICGC ARGO Workflows" ;
NIFRID:synonym "ICGC Accelerate Research in Genomic Oncology Workflows" ;
definition: "ICGC-Argo genomic pipeline. Home of the ICGC ARGO (Accelerate Research in Genomic Oncology) Data Platform Scientific Workflows." .
SCR:026976 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gamma Service Medical | Biobeam GM 8000" ;
NIFRID:synonym "Biobeam GM 8000 blood irradiation system",
"Eckert & Ziegler Biobeam GM 8000" ;
definition: "Fully protected Gamma irradiation device for blood irradiation in transfusion medicine and research." .
SCR:026977 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Berthold | Centro LB 960 Microplate Luminometer" ;
NIFRID:synonym "Centro LB 960 Microplate Luminometer" ;
definition: "Instrument for luminescence applications." .
SCR:026978 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | EASY-nLC 1200 System" ;
NIFRID:synonym "Thermo Scientific EASY-nLC 1200 system" ;
definition: "System provides peak performance for nanoflow applications up to 1200 bar. Dual in-line flow sensors before solvent mixing give excellent gradient precision. Its intuitive software facilitates rapid method setup and immediate system control." .
SCR:026979 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PermutMatrix" ;
definition: "Software package for analysing and visualising data. Graphical environment to arrange gene expression profiles in optimal linear order." .
SCR:026980 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Imalytics Preclinical" ;
NIFRID:synonym "Gremse-It Imalytics Preclinical" ;
definition: "Software for interactive segmentation, reconstruction, 3D-visualization, and analysis of biomedical image data sets with user-friendly interface. Used for interactive analysis of biomedical volume data. Used for analysis of passive drug delivery systems, active targeting, biodistribution analysis, probe development, cell labeling, ballistic soap experiments, blood perfusion, dental implants, functional ultrasound, atherosclerotic inflammation, atherosclerotic calcifications, carotid artery stenoses, tissue-engineering, and quantification of body fat." .
SCR:026981 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Pannoramic_1000" ;
rdfs:label "3DHISTECH | PANNORAMIC 1000 Digital Scanner" ;
NIFRID:synonym "Pannoramic 1000 Digital Scanner",
"Pannoramic 1000 Whole Slide Digital Scanner" ;
definition: "Slide digitalization system for high-volume scanning tasks. Its up-to-1200-slide capacity, up-to-100-slides per hour throughput offers for high-volume whole-slide imaging." .
SCR:026982 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "diagram" ;
definition: "Software R package for visualising simple graphs (networks), plotting flow diagrams." .
SCR:026983 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "effectsize" ;
definition: "Software R package for estimation of effect size indices and standardized parameters. Used to work with indices of effect size and standardized parameters, allowing computation and conversion of indices such as Cohen’s d, r, odds-ratios, etc." .
SCR:026984 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mediation" ;
definition: "Software R package for estimation of causal mediation effects. Allows researchers to conduct sensitivity analysis for certain parametric models." .
SCR:026985 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "plyr" ;
definition: "Software R package for splitting, applying and combining data. Used to split up big data structure into homogeneous pieces, apply function to each piece and then combine all the results back together." .
SCR:026986 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "quickpsy" ;
definition: "Software R package to fit psychometric functions for multiple groups.Quickly fits and plots psychometric functions (normal, logistic, Weibull or any or any function defined by the user) for multiple groups." .
SCR:026987 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Beautifulsoup4" ;
NIFRID:synonym "Beautiful Soup" ;
definition: "Software Python PiPy package. It is library that makes it easy to scrape information from web pages. It sits atop HTML or XML parser, providing Pythonic idioms for iterating, searching, and modifying parse tree." .
SCR:026988 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Requests Library Python" ;
NIFRID:synonym "Requests",
"requests" ;
definition: "Software Python package. Requests allows you to send HTTP/1.1 requests extremely easily. There’s no need to manually add query strings to your URLs. Simple, yet elegant, HTTP library." .
SCR:026989 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "The Geoscience Data Exchange" ;
NIFRID:synonym "National Center for Atmospheric Research repository",
"NCAR repository",
"NSF NCAR Research Data Archive" ;
NIFRID:abbrev "GDEX" ;
definition: "Provides data for atmospheric and ocean sciences research. Contains collection of meteorological, atmospheric composition, and oceanographic observations, and operational and reanalysis model outputs, integrated with NSF NCAR High Performance Compute services to support atmospheric and geosciences research. The RDA is managed by the Data Engineering and Curation Services group of the Computational and Information Systems Laboratory at the NSF National Center for Atmospheric Research." .
SCR:026990 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ELOKA" ;
NIFRID:synonym "Exchange for Observations and Local Knowledge of the Arctic" ;
definition: "Project portal to collect, preserve, and exchange local observations and Indigenous Knowledge. Collaborates with Arctic communities and Indigenous organizations, schools, and researchers to create customized data management products. ELOKA provides open and tailored data access, data stewardship for Indigenous communities, and services ranging from advising on data sharing ethics and protocols to handling different data types. Interactive digital atlases showcasing community-based observations of social and environmental change and related geospatial data, such as trail locations, place names, land-use demarcations, or local climate information. Customized websites containing cultural, historical, and/or environmental information significant to partner communities, often in the form of written interview transcripts, audio or video files, photographs, artwork, illustrations, and maps. Data sets of environmental and wildlife observations collected by Indigenous experts. Access to local weather station data, including temperature, snow thickness, and wind data." .
SCR:026991 a "resource",
owl:NamedIndividual ;
rdfs:label "Human Microbiome Compendium" ;
definition: "Microbial ecology dataset describing the composition of publicly available human microbiome samples deposited in INSDC databases (Sequence Read Archive, European Nucleotide Archive, Digital Data Bank of Japan). Genus-level read counts are available for more than 168,000 samples from around the world, with additional curated metadata for samples and projects." .
SCR:026992 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_026993" ;
rdfs:label "Panscan" ;
definition: "Software tool for identifying novel sequences, SVs, and repetitive regions. Used to annotate duplicate genes and visualize complex genomic landscapes. Provides insights into genetic diversity." .
SCR:026995 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GOSemSim" ;
definition: "Software R package for Gene Ontology enrichment analysis. Offers several methods based on information content and graph structure for measuring semantic similarity among Gene Ontology terms, gene products and gene clusters." .
SCR:026996 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "enrichplot" ;
definition: "Software package implements several visualization methods for interpreting functional enrichment results obtained from Over-Representation Analysis and Gene Set Enrichment Analysis." .
SCR:026997 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "InvivoGen" ;
definition: "Biotechnology company in San Diego, California. Provides life scientists with innovative research reagents including immunity and cell culture products." .
SCR:026998 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microscopy_lif_Channel_Masked_Intensity_Quant_MATLAB" ;
definition: "Software application for quantification of masked fluorescence intensity and nuclear count from .lif files in MATLAB." .
SCR:026999 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Microscopy_tif_Channel_Quant_MATLAB" ;
definition: "Software application for quantification of fluorescence channel area in TIFF images using MATLAB." .
SCR:027000 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Orbitrap_Exploris_480" ;
rdfs:label "Thermo Fisher | Orbitrap Exploris 480 Mass Spectrometer" ;
NIFRID:synonym "Orbitrap Exploris 480 Mass Spectrometer" ;
definition: "Orbitrap LC-MS with EASY-IC (Internal Calibration) mass spectrometer for high-resolution, accurate mass analysis of complex samples, providing detailed information about compounds for identification, quantification, and characterization. Liquid Chromatography-Mass Spectrometry combines the separation power of liquid chromatography with the mass analysis capabilities of mass spectrometer. Orbitrap mass analyzer offers high resolution and accuracy, enabling the separation and identification of even closely related compounds. Internal Calibration uses internally generated ions to improve mass accuracy." .
SCR:027001 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BMG Labtech | PHERAstar FSX microplate reader" ;
NIFRID:synonym "PHERAstar FSX",
"PHERAstar FSX microplate reader" ;
definition: """Microplate reader for High-Throughput Screening (HTS) requirements. Performs all leading
detection technologies including UV/vis absorbance, Fluorescence intensity, including FRET, Luminescence (flash and glow), including BRET, Fluorescence polarization/anisotropy,Time-resolved fluorescence (TRF), including TR-FRET, AlphaScreen, AlphaLISA and AlphaPlexTM.""" .
SCR:027002 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_uPMR_790" ;
rdfs:label "United Imaging | uPMR 790 Tesla scanner" ;
NIFRID:synonym "United Imaging uPMR 790",
"uPMR 790" ;
definition: "United Imaging uPMR 790 enables simultaneous PET/MRI imaging with high temporal and spatial resolution. Represents major technological breakthrough in imaging field by combining time of flight (TOF) positron emission tomography (PET) and magnetic resonance imaging (MRI) in one scanner. This system allows simultaneous acquisition of MR and PET images in human subjects." .
SCR:027003 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Analysis of Operant Self-administration Behaviors with Supervised Machine Learning " ;
definition: "Software repository contains protocol for video acquisition and pose estimation analysis using DeepLabCut and Simple Behavioral Analysis." .
SCR:027004 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Quantabio" ;
definition: "Company based in Beverly, Massachusetts, provides advanced DNA and RNA amplification reagents. Offers complete library prep solutions for Illumina NGS platforms, reagents for PCR and RT PCR amplifications." .
SCR:027005 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Gilvasan Pharma GmbH" ;
definition: "Company located in Vienna, Austria, specializes in Austrian quality heparin sodium. Specialized in the distribution of pharmaceuticals in hospitals with special focus on heparin products." .
SCR:027007 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Complete Genomics" ;
definition: "Biotechnology company that has developed and commercialized DNA sequencing platform for human genome sequencing and analysis. The company is a wholly-owned subsidiary of MGI." .
SCR:027008 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cardio-Neuro-Mind Data Platform" ;
NIFRID:synonym "Cardio-Neuro-Mind Data Platform (CNMDP)" ;
NIFRID:abbrev "CNMDP" ;
definition: "Platform to store, analyze, and share large amounts of various types of data to facilitate research, and ultimately, unravel the complex connections between the brain and the heart." .
SCR:027010 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3251" ;
rdfs:label "University College London Genomics Core Facility" ;
NIFRID:synonym "UCL Genomics",
"UCL Genomics Core Facility",
"University College London" ;
definition: "Core facility with expertise in genomic technologies, project design and data analysis. Offers services including nucleic acid extractions; microarray-based methylation, genotyping and pharmacogenomic analyses; short- and long-read sequencing; and single cell and spatial technologies." .
SCR:027011 a owl:NamedIndividual ;
rdfs:label "SEACR" ;
NIFRID:synonym "Sparse Enrichment Analysis for CUT&RUN" ;
definition: "Software tool to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by \"zeroes\" (i.e. regions with no read coverage)." .
SCR:027012 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dREG" ;
definition: "Software tool for detecting regulatory elements using GRO-seq and PRO-seq." .
SCR:027013 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3247" ;
rdfs:label "University of Louisville Sequencing Technology Center Genomics Services Core Facility" ;
NIFRID:synonym "Sequencing Technology Center" ;
definition: "Provides genomic sequencing services including next-generation sequencing (NGS), single-cell analysis, and spatial transcriptomics. Offers advanced short-read and long-read sequencing technologie including our status as a PacBio Certified Service Provider." .
SCR:027014 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3249" ;
rdfs:label "University of California Davis Comparative Pathology Laboratory Core Facility" ;
NIFRID:synonym "VM:Comparative Pathology Laboratory" ;
definition: "Core is veterinary diagnostic laboratory and research pathology core. Provides laboratory animal diagnostics, clinical and health surveillance screening necessary for the care and use of animals in research, and expert pathology support for basic and translational research." .
SCR:027015 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3248" ;
rdfs:label "Baylor College of Medicine BCM Mass Spectrometry Proteomics Core Facility" ;
NIFRID:synonym "BCM Mass Spectrometry Proteomics Core" ;
definition: "Core provides services including project evaluation and design, sample processing and biochemical purifications, mass spectrometry measurements, data processing, and bioinformatics analysis performed by the experienced core personnel." .
SCR:027016 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IgPhyML" ;
definition: "Software phylogenetic inference package for B cell repertoires. It implements codon substitution models designed that incorporate unique features of somatic hypermutation and allow for parameter estimation across lineages to characterize entire repertoires." .
SCR:027017 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RoseTTAFold" ;
definition: "Software package contains deep learning models and related scripts for RoseTTAFold.Used for accurate prediction of protein structures and interactions using 3-track network." .
SCR:027018 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Foldseek" ;
definition: "Software tool for fast and sensitive comparisons of large structure sets. Used for comparisons of large protein structure sets, supporting monomer and multimer searches, as well as clustering. It runs on CPU, supports GPU acceleration for faster searches, and optionally allows ultra-fast and sensitive comparisons directly from protein sequence inputs using a language model, bypassing the need for structures." .
SCR:027019 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FTDock" ;
definition: "Software tool to discrete two molecules onto orthogonal grids and performs global scan of translational and rotational space." .
SCR:027021 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FileZilla" ;
definition: "Open-source, cross-platform FTP application, consisting of FileZilla Client and FileZilla Server. Clients are available for Windows, Linux, and macOS. Both server and client support FTP and FTPS (FTP over SSL/TLS), while the client can in addition connect to SFTP servers. Used to transfer files between local computer and remote server. It facilitates uploading and downloading files, making it popular for managing website files and web hosting." .
SCR:027022 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CARNet TFA Function" ;
NIFRID:synonym "Cerebral Autoregulation Research Network Transfer Function Analysis Function",
"Matlab TFA function" ;
definition: "Software function as Matlab implementation of the TFA as specified in the White Paper (2015). An example of use on the supplied data (tfa_sample_data.txt) is given in tfa_demo.m and results are reported at the end of this report." .
SCR:027023 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "RapidAI" ;
definition: """Health tech company specializing in AI-based neuroimaging software used by physicians in clinical diagnosis and treatment. The company's platform uses AI to create advanced images from non-contrast CT, CT angiography, CT perfusion, and MRI diffusion and perfusion scans.
They provide the RapidAI software platform, which uses AI to analyze medical images for conditions like stroke and aneurysm and it requires paid subscription.""" .
SCR:027024 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VSCapture" ;
NIFRID:synonym "VitalSignsCapture" ;
definition: "Open source software tool developed in C# programming language on the .NET/Mono platform that allows the tool to run on Windows, Macintosh OS X, Linux Ubuntu operating systems. Allows to download or capture data from several medical device interfaces such as Datex AS3 S/5 Anesthesia, Philips Intellivue, GE Dash, Mindray, Spacelabs, Draeger Infinity, Draeger HL7 patient monitors, GE Engstrom, Draeger (Medibus), Maquet (Servo-i & Flow-i), Puritan Bennett ventilators, Covidien BIS Vista cerebral monitor, Fresenius Agilia, Alaris Carefusion, BBraun Spacecom syringe and volumetric pumps, Roche Cobas ASTM ABG analyzers. Requires Visual Studio 2022, .NET 8 or Visual Studio for Mac to compile. Android version requires Xamarin Studio, Android SDK to compile. Support for capture from other monitors is planned in future." .
SCR:027025 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CNSistent" ;
definition: "Software Python package for imputation, consistent segmentation, statistical analysis, and visualization of copy number profiles from heterogeneous datasets." .
SCR:027026 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Click-qPCR" ;
definition: "Web tool for interactive qPCR data analysis. Enables researchers to process, interpret, and visualize their qPCR data. Web-based Shiny application that requires no local installation." .
SCR:027027 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3252" ;
rdfs:label "St.Jude Research Center for Advanced Genome Engineering Core Facility" ;
NIFRID:synonym "Center for Advanced Genome Engineering" ;
NIFRID:abbrev "CAGE" ;
definition: "Genome-editing facility with the mission to provide low-cost, expeditious and collaborative genome-engineering services to St. Jude investigators. Core provides expertise and infrastructure to educate, assist, expedite and perform established and emerging technologies." .
SCR:027028 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SPARC Data Standard" ;
definition: "SPARC data structure is consistent file structure and naming convention, based on the Brain Imaging Data Structure (BIDS) to ensure that the diverse types of data in SPARC is organized in similar manner." .
SCR:027029 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dotmatics ELN and Data Discovery Platform" ;
NIFRID:synonym "Dotmatics Electronic Lab Notebook and Data Discovery Platform" ;
definition: "Software for scientific research and development. ELN captures and manages experimental data, while Data Discovery Platform enables users to explore, analyze, and visualize that data to gain insights." .
SCR:027030 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RFMix" ;
definition: "Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference." .
SCR:027031 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AI-READI" ;
NIFRID:synonym "Artificial Intelligence Ready and Equitable Atlas for Diabetes Insights" ;
definition: "Multidisciplinary data generation project which aims to create and share multimodal dataset optimized for artificial intelligence research in type 2 diabetes. At each release of the AI-READI dataset, two sets will be made available: public access and controlled access set. The public set will be stripped of Protected Health Information (PHI) as well as information related to the sex and race/ethnicity of the participants." .
SCR:027032 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "All of Us" ;
definition: "Portal stores health data from participants from across the United States. Provides interactive Data Browser where anyone can learn about the type and quantity of data that All of Us collects. Users can explore aggregate data including genomic variants, survey responses, physical measurements, electronic health record information, and wearables data." .
SCR:027033 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Helios_NanoLab_600i" ;
rdfs:label "FEI | Helios Nanolab 600i DualBeam" ;
NIFRID:synonym "FEI Helios NanoLab 600i DuaBeam",
"FEI Helios NanoLab 600i DuaBeam Scanning Electron Microscope",
"Helios NanoLab 600i" ;
definition: "Scanning Electron Microscope advanced DualBeam for ultra-high resolution imaging, analysis and fabrication at the nanoscale. Helios NanoLab 600i builds on the success of FEI’s winning DualBeam series offering advances in ion beam, electron beam, patterning and range of features to make milling, imaging, analysis and sample preparation down to nanoscale." .
SCR:027034 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SynProtX" ;
definition: "Software application as deep learning model leveraging large-scale proteomics, molecular graphs, and fingerprints to enhance prediction of synergistic effects in anti-cancer drug combinations." .
SCR:027035 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BostonGene RCC AI TKI IO Hsieh" ;
NIFRID:synonym "RCC.AI_TKI_IO.Hsieh" ;
definition: "Software multimodal AI-models to estimate Tyrosine Kinase Inhibitors and Immune Checkpoint Inhibitors therapy response across renal cell carcinoma." .
SCR:027036 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3254" ;
rdfs:label "University of Massachusetts Chan Medical School Metabolomics Core Facility" ;
NIFRID:synonym "UMass Chan Medical School Metabolomics Core" ;
definition: "Core offers the ability to perform both targeted (including stable isotope tracing studies) and untargeted metabolomics and lipidomics experiments using liquid- and gas-chromatography mass spectrometry (LCMS/MS and GCMS) on a fee-for-service basis. Offers expertise to assist with every stage of the metabolomics/ lipidomics experimental pipeline, including experimental design, method development, data acquisition and processing, data analysis and interpretation. Offers training on data analysis software including both open-source and vendor proprietary analysis software. Offers access to specialized equipment required for metabolomics/ lipidomics sample extraction and preparation, including a Cryomill and Bead Beater for homogenization of tumors, tissue, stool and whole organisms, and a liquid-handling robot for large scale plasma extractions." .
SCR:027037 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Amerigo Scientific VivoMab" ;
definition: "Company specializing in antibodies for multiple applications, integrates research, production, and distribution. Provides antibodies for research and therapeutic applications." .
SCR:027038 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Creative Biolabs Neuros" ;
definition: "Company provides technologies and products in neuroscience research field such as antibodies, proteins, cell lines." .
SCR:027039 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ACQUITY_Premier" ;
rdfs:label "Waters | ACQUITY Premier UPLC System" ;
NIFRID:synonym "ACQUITY Premier UPLC System" ;
definition: "Ultra high pressure liquid chromatography system. System is built with proven ACQUITY technology, which offers true UPLC performance, ultra-low dispersion, and high resolution. Designed with MaxPeak HPS Technology, the ACQUITY Premier System improves peak shape and reproducibility for the most challenging metal-sensitive compounds." .
SCR:027040 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Nebraska-Lincoln Bureau of Sociological Research" ;
definition: "Bureau of Sociological Research has conducted national, regional and local surveys using variety of survey research methods. Our professional staff has experience working with number of contemporary data collection methodologies and our involvement in conferences and organizations related to social research has enabled us to keep abreast of changes and trends in survey methodology." .
SCR:027041 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3255" ;
rdfs:label "Augusta University Small Animal Behavior Core Facility" ;
definition: "Core provides services for researchers in need of behavioral analyses in small animals (specifically mice or rats). Core provides expertise in design and implementation of behavioral experiments as well as data analysis and interpretation. Core is equipped to accommodate behavioral tests relevant to learning and memory, attention, executive function, sensory gating, place/fear conditioning, motor function, nociception, and anxiety and depression-related behaviors etc. Testing facility is operated within centralized animal care program of Division of Laboratory Animal Services." .
SCR:027042 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "3DHISTECH" ;
definition: "European company specializing in digital pathology. Based in Budapest, Hungary, they develop high-performance slide scanners and software tools that digitize and streamline pathology workflows for diagnostics, research, and education" .
SCR:027043 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DFC3000_G" ;
rdfs:label "Leica | DFC3000 G CCD Microscope Camera" ;
NIFRID:synonym "DFC3000 G CCD Microscope Camera",
"Leica DFC3000 G" ;
definition: "Grayscale USB 3.0 microscope camera for routine fluorescence applications. You will receive crisp images due to its unique passive cooling architecture and its highly sensitive CCD sensor. Correlated pixel double sampling together with reduction of ambient temperature of the sensor offers exceptionally clear and noise-free signal. Its CCD sensor is particularly suitable for low light situations such as fluorescence and will capture even smallest amounts of light. Camera produces live images with up to 30 frames per second. The USB 3.0 interface provides for fast data transfer." .
SCR:027044 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_S6_D_Greenough" ;
rdfs:label "Leica | S6 D Greenough stereo microscope" ;
NIFRID:synonym "S6 D Greenough stereo microscope" ;
definition: "Stereo microscope with 6.3:1 zoom and integrated video/photo port allows easy, fast documentation for assembly, quality control, OEM and research applications. Adjustable zoom stops allows fast, easy, repeatable measurements and inspections." .
SCR:027045 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3261" ;
rdfs:label "McLaughlin Research Institute Gene Editing and Mouse Models Assessment Core Facility" ;
NIFRID:synonym "GEMMA Core",
"Gene Editing and Mouse Models Assessment (GEMMA) Core" ;
definition: "GEMMA Core offers transgenic and genotyping services needed for experiments, phenotyping and behavioral services, and mouse colony management services to COBRE faculty. Consultation and training for lab staff is also available." .
SCR:027046 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.280786.3",
"ISNI 0000 0004 1808 0520" ;
rdfs:label "McLaughlin Research Institute" ;
definition: "Independent, non-profit research organization in Great Falls, Montana near the Rocky Mountain Front." .
SCR:027047 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3262" ;
rdfs:label "Augusta University GCC Small Animal Imaging Core Facility" ;
NIFRID:synonym "Augusta University GCC Small Animal Imaging Core",
"GCC Small Animal Imaging Core",
"Small Animal Imaging Resource" ;
definition: "Core provides preclinical imaging and radiation treatment resources for animal research." .
SCR:027048 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3263" ;
rdfs:label "Institute of Molecular Biology of Plants Bioinformatics Core Facility" ;
NIFRID:synonym "CNRS - Bioinformatics Core Facility",
"Institut de Biologie Moléculaire des Plantes",
"Institute of Molecular Biology of Plants IBMP Bioinformatics Core Facility" ;
definition: "Core provides expertise in biological data analysis especially in high-throughput sequencing data analyses, by developing dedicated tools and workflows. Maintains computational and storage infrastructure in bioinformatics and organizes trainings for biologists and/or bioinformaticians." .
SCR:027049 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.462397.d",
"ISNI 0000 0004 0638 2601" ;
rdfs:label "Institut de Biologie Moléculaire des Plantes" ;
NIFRID:synonym "Institute of Molecular Biology of Plants" ;
definition: "Research institute focused on the study of plants at the molecular level.IBMP is a major CNRS center for plant sciences. Located at the Strasbourg site, it collaborates closely with the University of Strasbourg and our international partners in the Upper Rhine Valley region. Conducts research in areas of plant biology, including gene expression and RNA regulation, plant metabolism, organelles, and virology." .
SCR:027059 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eppendorf | Mastercycler X50" ;
NIFRID:synonym "Mastercycler X50" ;
definition: "Thermocycler series with touch screen with precise fingertip control. MC X50 PCR thermocycler enables easy PCR optimization and standardization in routine PCR applications. It is also fitted for NGS." .
SCR:027060 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CyTekBio | Aurora CS system" ;
NIFRID:synonym "Aurora CS system" ;
definition: """Advanced and adaptable cell sorting system employs Full Spectrum Profiling technology to produce high-quality flow cytometric data along with Cytek portfolio of full spectrum instruments. Aurora CS system is the only commercially available spectral cell sorter
that is paired with companion analyzer.""" .
SCR:027061 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3264" ;
rdfs:label "Columbia University Zuckerman Institute Cellular Imaging Core Facility" ;
NIFRID:synonym "Zuckerman Institute Cellular Imaging" ;
definition: "Provides access to imaging technology. Offers combination of both commercial platforms and not-yet commercialized technologies that enable innovative research centered around structural and functional imaging. Optical microscopy and image analysis platform." .
SCR:027063 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "vcf2maf" ;
definition: "Software tool to convert Virtual Contact File into Mutation Annotation Format, where each variant is annotated to only one of all possible gene isoforms." .
SCR:027064 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "almondcv2" ;
definition: "Software repository provides open-source implementation of RGB imaging workflow for morphological and morphometric analysis of fruits and seeds." .
SCR:027065 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Meshlab" ;
definition: "Software application used for processing and editing 3D triangular meshes. Provides tools for editing, cleaning, repairing, inspecting, rendering, texturing, and converting meshes. This makes it suitable for variety of tasks related to 3D data, including preparing models for 3D printing." .
SCR:027066 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CNAqc" ;
definition: "Software package to quality control bulk cancer sequencing data. Used to visualise and manipulate i) somatic mutation data of both single-nucleotide variants and insertion-deletions, ii) allele-specific Copy Number Alterations (CNAs) and iii) tumour purity estimates. Used to validate copy number segmentations against variant allele frequencies of somatic mutations. Provides automatic copy number calling pipeline. Provides also algorithms to phase mutation multiplicities against CNAs and estimate Cancer Cell Fractions (CCFs) with their uncertainty." .
SCR:027068 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioCDQA" ;
definition: "Software retrieval-augmented knowledge mining method with deep thinking LLMs for biomedical research and clinical support. Cross-document question answering dataset addressing current QA limitations, and features Progressive Retrieval-Augmented Reasoning framework that combines advanced retrieval-generation techniques with self-reflection mechanisms and deep-thinking large language models to enhance answer accuracy and contextual relevance.Used to evaluate latent knowledge retrieval and multi-hop reasoning capabilities." .
SCR:027069 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PanGIA" ;
definition: "Software tool for predicting ncRNA-disease associations. Used for identifying association between ncRNAs and diseases." .
SCR:027070 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Farmshare" ;
definition: "Stanford University software shared computing cluster. All Stanford researchers have access to base set of managed computing resources, GPU-based servers, and multi-petabyte, high-performance parallel file system for short-term storage." .
SCR:027071 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Cytek Biosciences" ;
NIFRID:synonym "Cytek® Biosciences Inc." ;
definition: "Leading manufacturer and supplier of flow cytometry products and services. Cytek’s compact, affordable instruments and wide ranging support offerings are used by researchers and clinicians all over the world." .
SCR:027072 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Northern_Lights" ;
rdfs:label "CyTekBio | Northern Lights flow cytometer" ;
NIFRID:synonym "Cytek Northern Lights",
"Cytek Northern Lights™ flow cytometer" ;
definition: "Flow cytometer, with its easy-to-use workflow, is full spectrum flow cytometry solution. Instrument incorporates Cytek’s Full Spectrum Profiling technology allowing for wide array of new fluorochrome combinations without reconfiguring your system for each application. Uses SpectroFlo software.The 1-Laser, 2-Laser, and 3-Laser versions of this model are available." .
SCR:027073 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_M220_Focused" ;
rdfs:label "Covaris | M220 Focused ultrasonicator" ;
NIFRID:synonym "M220 Focused ultrasonicator" ;
definition: "Compact ultrasonicator for DNA shearing for MiSeq and PGM users. AFA technology in the M220 eliminates operator-induced variations, improves performance, increases efficiency, and provides standardized results." .
SCR:027077 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model-Number_ProFlex" ;
rdfs:label "Thermo Fisher: Applied Biosystems | ProFlex PCR System" ;
NIFRID:synonym "ProFlex PCR System" ;
definition: "Thermal cycler with flexible configuration and control features. System with Thermo Fisher Connect to design and upload methods and monitor runs from any smartphone or desktop computer. Has five different blocks that can be changed. Blocks allow up to three experiments to be run simultaneously, completely independently of each other and without interference. Dual 96-well and dual 384-well blocks are available for your high-throughput PCR sequencing needs, and dual flat block is available to support Applied Biosystems OpenArray plate technology for genotyping analysis on the Applied Biosystems QuantStudio 12K Flex Real-Time PCR System." .
SCR:027081 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_7500_Fast_Dx" ;
rdfs:label "Thermo Fisher: Applied Biosystems | 7500 Fast Dx Real-Time PCR Instrument" ;
NIFRID:synonym "7500 Fast Dx Real-Time PCR Instrument" ;
definition: "Real-Time PCR Instrument, with Sequence Detection System (SDS) Software, is 96-well, 5-color real-time PCR instrument available for in vitro diagnostic use. Based on Peltier block technology, instrument is designed to deliver results, in 96-well format. SDS Software allows full control over thermal cycling protocols to further assist in developing or running custom assays." .
SCR:027083 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CytoFLEX_S" ;
rdfs:label "Beckman Coulter | CytoFLEX S V4-B2-Y4-R3 Flow Cytometer" ;
NIFRID:synonym "Beckman Coulter CytoFLEX S",
"CytoFLEX S V4-B2-Y4-R3 Flow Cytometer" ;
definition: "Flow Cytometer has 4 active lasers (405 nm, 488 nm, 561 nm, 638 nm) and 13 channels for fluorescence detection. This instrument can be upgraded with a maximum of 4 Violet, 2 Blue, 4 Yellow Green, and 3 Red channels. It includes 13 repositionable bandpass filters, 450/45, 525/40 (2), 585/42, 610/20 (2), 660/10 (2), 690/50 (2), 712/25, 780/60 (2). The complete system is supplied with computer work station with CytExpert Acquisition software, sheath and waste containers with harness." .
SCR:027084 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CytoFLEX_LX" ;
rdfs:label "Beckman Coulter | CytoFLEX LX N3-V5-B3-Y5-R3-I0 Flow Cytometer" ;
NIFRID:synonym "CytoFLEX LX Flow Cytometer",
"CytoFLEX LX N3-V5-B3-Y5-R3-I0 Flow Cytometer" ;
definition: "Flow Cytometer has 5 active lasers (375 nm, 405 nm, 488 nm, 561 nm, 638 nm) and 19 channels for fluorescence detection. This instrument can be upgraded with a maximum of 3 Near UV, 5 Violet, 3 Blue, 3 Red, and 2 Infrared channels. It includes 21 repositionable bandpass filters, 405/10, 450/45 (2), 525/40 (3), 585/42, 610/20 (3), 660/10 (2), 675/30 (2), 690/50, 710/50, 712/25, 763/43 (3), 840/20, 885/40. The complete system is supplied with computer work station with CytExpert Acquisition software, sheath and waste containers with harness." .
SCR:027085 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3267" ;
rdfs:label "McMaster University Single Cell and Spatial Profiling Core Facility" ;
definition: "Core supports single cell and spatial biology research. Provides services and equipment for analyzing single cells in suspension or tissue sections from mice or humans for discovery and translational research projects. Services include flow cytometry, histology, human immune monitoring, and spatial proteomics and transcriptomics." .
SCR:027086 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pathogens Portal Node Toolbox" ;
definition: "Software package and code for Pathogen Portal node (i.e. a local Pathogens Portal, such as the Swedish and Dutch Pathogens Portals). Allows users to create their own node quickly and easily." .
SCR:027087 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SLAN-96S" ;
rdfs:label "Shanghai Hongshi Medical Technology | SLAN-96S Real-Time PCR System" ;
NIFRID:synonym "SLAN-96S Real-Time PCR System" ;
definition: "High-throughput 96-well qPCR instrument with 4-6 fluorescence channels. Features ±0.1°C temperature precision, rapid thermal cycling (4°C/sec), and low-noise optical system. CE/SFDA certified for clinical diagnostics and research applications. Manufacturer: Shanghai Hongshi Medical Technology Co., Ltd." .
SCR:027088 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GROTIA" ;
NIFRID:synonym "Graph-Regularized Optimal Transport Framework for Diagonal Single-Cell Integrative Analysis" ;
definition: "Software application to preserving local relationships via graph regularization without requiring any prior correspondence information. Achieves global alignment through optimal transport while preserving local relationships via graph regularization." .
SCR:027089 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ContriBOT" ;
definition: "Software text-mining tool that extracts and classifies authorship information from scientific articles." .
SCR:027090 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss | Axio Zoom.V16 for Biology" ;
NIFRID:synonym "ZEISS Axio Zoom.V16 for Biology system" ;
definition: "ZEISS Axio Zoom.V16 microscope system includes fluorescence zoom microscope for large fields. Designed for brightfield and fluorescence microscopy of biological samples. Microscope design is optimized for fluorescence microscopy with specific optical components for light management involving specialized filters and dichroic mirrors." .
SCR:027091 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Variantis" ;
definition: "Web application designed for calculating transition and transversion ratios in DNA sequences. It provides comprehensive matrix for comparative analysis and offers detailed insights into individual nucleotide changes." .
SCR:027092 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3268" ;
rdfs:label "Augusta University Centre for Biotechnology and Genomic Medicine Bioinformatics Core Facility" ;
NIFRID:synonym "Augusta University Centre for Biotechnology and Genomic Medicine Bioinformatics Core",
"CBGM Bioinformatics Core" ;
definition: "Core provides bioinformatics support for genomics, transcriptomics, epigenomics, and other high-throughput data. Offers data analysis, pipeline development, and consultation services to researchers across disciplines, with focus on reproducibility, scalability, and collaboration." .
SCR:027093 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3269" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Genomics Core Facility" ;
definition: "Core provides with easy access to state-of-the-art DNA and RNA services. Offers services, including Illumina microarray-based gene expression profiling, genotyping, and next-generation sequencing (NGS). Equipped with Illumina MiSeq and NovaSeq 6000 platforms, enabling efficient targeted and transcriptome-wide RNA analyses, as well as whole genome sequencing (WGS). Prepares and normalizes libraries for various applications, including RNA-seq, miRNA-seq, DNA-seq, whole-genome sequencing, and single-cell RNA-seq. Additional services include DNA/RNA quality control using Agilent Bioanalyzer and TapeStation systems, and DNA/chromatin shearing using Covaris S2 technology. In collaboration with Genomic Medicine Biorepository, provides DNA and RNA extraction services. Provides letters of support for federal and non-federal grant applications and are open to research collaborations." .
SCR:027094 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Microscopes International" ;
definition: "Microscopes International (often branded as “uScope” by Microscopes International) is a Plano, Texas–based company (est. 2009) specializing in affordable, highly portable digital microscopes and whole‑slide scanning systems for scientific, clinical, and field applications." .
SCR:027095 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_solariX" ;
rdfs:label "Bruker solariX" ;
definition: "Bruker solariX is magnetic resonance mass spectrometry (MRMS) platform, available with high-field magnets ranging from 7 T up to 15 T." .
SCR:027096 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BD Biosciences | Rhapsody Single-Cell Analysis System" ;
definition: """System allows high-throughput capture of multiomic information from single cells using
cartridge workflow and multitier barcoding system. Used for high-throughput, multiomic profiling of single cells. Allows to analyze gene expression at both mRNA and protein levels, as well as other cellular characteristics, using microwell-based system with multitiered barcoding approach.This enables the generation of various next-generation sequencing (NGS) libraries for deeper analysis.""" .
SCR:027097 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DxFLEX" ;
rdfs:label "Beckman Coulter | DxFLEX Flow Cytometer" ;
NIFRID:synonym "DxFLEX Flow Cytometer" ;
definition: "Flow Cytometer designed for clinical applications. Makes multicolor flow cytometry less complex by using avalanche photodiode (APD) detector technology. Streamlines high-complexity testing with 13-color capability and new detector technology for easier compensation. Avalanche photodiode detectors offer advanced sensitivity and improve diagnostic accuracy." .
SCR:027098 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Active Commutator" ;
definition: "Open source active commutator for Open Ephys / Intan electrophysiology systems. Motorized device used in neuroscience research, particularly in studies involving freely moving animals, to manage wires or fibers connecting headstage or other device to external equipment. Addresses common issue of tether tangling during experiments with freely moving subjects. Relies on Hall-Effect sensor detecting rotation of cable, this information is continuously fed to Adafruit microcontroller that operates servo motor to counter-rotate cable as needed, preventing twisting and ensuring clear, uninterrupted data collection. System can also be paused, restarted, and its neutral position recalibrated with simple button presses, allowing for flexible operation." .
SCR:027099 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Leica_M80" ;
rdfs:label "Leica | M80 Stereomicroscope" ;
NIFRID:synonym "M80 Stereomicroscope" ;
definition: "Leica M80 is modular, ergonomic zoom stereomicroscope designed for range of routine applications in life sciences and industrial settings. It features 8:1 zoom range, providing continuous zoom from 7.5x to 60x, and is known for its high resolution, large field of view, and increased depth of focus. M80 is particularly well-suited for tasks like inspection, photography, and measurement of samples such as circuit boards, hairs, fibers, and biological tissues." .
SCR:027100 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3270" ;
rdfs:label "University of Massachusetts Flow Cytometry Core Facility" ;
NIFRID:synonym "UMass Amherst Flow Cytometry Core" ;
definition: "Core facility provides access to technologies in flow cytometry analysis including spectral analysis, high throughput imaging analysis (Amnis) and fluorescence assisted particle sorting (FACS). Instrument training, experiment and panel design, scientific consultation and sample processing are available. Offers training on facility equipment." .
SCR:027101 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_uScopeHXII-20" ;
rdfs:label "Microscopes International | uScopeHXII-20 microscope" ;
NIFRID:synonym "uScopeHXII-20 microscope" ;
definition: "Compact, high-resolution digital microscope and whole slide scanner designed for professionals in fields like pathology, histology, and research. It features 20x Infinity Plan Apochromatic objective with 0.65 numerical aperture, offering balance between magnification and depth of field—ideal for imaging thicker tissue sections and smears with enhanced clarity." .
SCR:027102 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3266" ;
rdfs:label "Beth Israel Deaconess Medical Center BIDMC Tissue Technologies Unit Core Facility" ;
NIFRID:synonym "Beth Israel Deaconess Medical Center BIDMC Tissue Technologies Unit",
"BIDMC-Tissue Technologies Unit" ;
definition: "Core provides research-focus histology, Immunohistochemistry, In-situ Hybridization (ACDBio RNAscope and Basescope) and Highplex Spatial-omics data generation (Akoya CODEX Fusion, 10X Genomics Visium HD, NanoString GeoMX and CosMX). Services also include BSL-2 NHP tissue processing and cryosectioning, tissue microarray (TMA) construction and multiplexing RNAScope and Protein marker staining (PANINI)." .
SCR:027104 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MetaMarkers" ;
NIFRID:synonym "Gillis lab MetaMarkers" ;
definition: "Software R package to efficiently compute robust markers across single-cell datasets. Robust marker signatures from single-cell data." .
SCR:027105 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ethotrack" ;
definition: "Video analysis software designed for the study of animal behavior." .
SCR:027106 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3274" ;
rdfs:label "University of Birmingham Protein Expression Core Facility" ;
NIFRID:synonym "University of Birmingham Protein Expression Facility" ;
definition: "Core, within College of Medicine and Health, offers expert support for all aspects of recombinant protein production. Using range of expression systems, produces proteins suitable for diverse downstream applications." .
SCR:027107 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3272" ;
rdfs:label "University of Birmingham Flow Cytometry Core Facility" ;
NIFRID:synonym "University of Birmingham Flow Cytometry Facility" ;
definition: "Facility supports flow cytometry, cell sorting, and mass cytometry across the University of Birmingham (UoB). Based in the College of Medicine and Health. Also supports instruments at Queen Elizabeth Hospital, Institute of Translational Medicine (ITM), and College of Life and Environmental Sciences. Services range from user training on self-service instruments to expert-supported cell sorting and GCP-compliant mass cytometry in dedicated ITM labs." .
SCR:027108 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3273" ;
rdfs:label "University of Birmingham Microscopy Core Facility" ;
NIFRID:synonym "University of Birmingham Microscopy Facility" ;
definition: "Facility, primarily based in Imaging Suite, offers range of imaging platforms, including widefield and confocal microscopes with fast detectors. Many systems support live imaging, including Selective Plane Illumination Microscopy (SPIM) system ideal for small animal models and spheroids." .
SCR:027109 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UCell" ;
definition: "Software package for evaluating gene signatures in single-cell datasets. UCell signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands less computing time and memory than other available methods, enabling the processing of large datasets in a few minutes even on machines with limited computing power. UCell can be applied to any single-cell data matrix, and includes functions to directly interact with SingleCellExperiment and Seurat objects." .
SCR:027110 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Carina" ;
definition: "Shared on-premises computing cluster with security controls for high-risk data, managed by Stanford Research Computing. Carina contains base set of shared compute and storage resources available to Stanford researchers working with high-risk data (PHI, PII, etc.), with additional dedicated capacity available for purchase." .
SCR:027111 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nero GCP" ;
definition: "Google Cloud Platform projects with security controls for high-risk data, managed by Stanford Research Computing. Nero GCP offers managed GCP projects in several configurations available to and billed directly to Stanford researchers working with high-risk data (PHI, PII, etc.)." .
SCR:027112 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "OncoOmicsDx" ;
definition: "Clinical proteomic for patient care. Molecular diagnostics laboratory operated by OncoPlex Diagnostics, which is mProbe Inc company. The lab is CAP-accredited and CLIA-certified, meaning it meets high standards for clinical quality and regulatory compliance." .
SCR:027114 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioTanon | 5200 Series Automatic Image Analysis System" ;
NIFRID:synonym "Tanon 5200 automatic imaging system" ;
definition: "Tanon series chemiluminescence image analysis system equipped with advanced scientific research-grade cooling CCD and professional lens with fully automatic mechanical one-key switch various shooting modes, can be used for chemiluminescence, multi-color fluorescence, visible light, ultraviolet fluorescence detection to provide sample images." .
SCR:027115 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AlloMate" ;
definition: "Software application that simplifies mate allocation decisions for breeders. Allows to simplify mate allocation by filtering out possible crosses with negative EBVs and by using kinship threshold between parents set by the user." .
SCR:027116 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BayesFactor" ;
definition: "Software R suite of functions for computing various Bayes factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression." .
SCR:027117 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "babelgene" ;
definition: "Software R package to convert between human and non-human gene orthologs/homologs. Integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 , Eyre et al. 2007 , Seal et al. 2011 )." .
SCR:027118 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3276",
"SCR_027541" ;
rdfs:label "McGill University Integrated Core for Animal Modeling MICAM Core Facility" ;
NIFRID:synonym "McGill University Integrated Core for Animal Modeling" ;
definition: "Core offers various services related to animal model generation and maintenance." .
SCR:027119 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PHATE" ;
NIFRID:synonym "Potential of Heat-diffusion for Affinity-based Transition Embedding" ;
definition: "Software tool for visualizing high dimensional data using novel conceptual framework for learning and visualizing manifold to preserve both local and global distances." .
SCR:027120 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "jmotif" ;
definition: "Software R package implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA algorithms facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly), and characteristic pattern discovery along with interpretable time series classification." .
SCR:027121 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CBS StatLine - Lifestyle " ;
definition: "Database of Statistics Netherlands (CBS). Contains lifestyle data of Dutch population living in private households. The numbers can be broken down by various personal characteristics." .
SCR:027122 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Analytik Jena | Real-Time PCR System qTOWER 2.0" ;
NIFRID:synonym "Real-Time PCR System qTOWER 2.0" ;
definition: "Standard RT PCR system allows quantitative PCR in established 96 well format, thus providing open platform for each kind of qPCR plastic ware from 0.2 mL single tubes to 96 well microplates." .
SCR:027123 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3277" ;
rdfs:label "University College London School of Pharmacy Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "UCL School of Pharmacy NMR Facility",
"UCL School of Pharmacy Nuclear Magnetic Resonance (NMR) Facility",
"University College London School of Pharmacy NMR Core Facility" ;
definition: "Core designed for range of solution-state pharmaceutical and biological chemistry applications. Facility is equipped with 600 MHz magnet equipped with high-throughput autosampler and QCI-F cryoprobe optimised for 1H and 19F sensitivity, and 400 MHz magnet dedicated to routine chemistry applications. Facility is also operating ligand-observed 19F-fragment library screening service for drug discovery." .
SCR:027124 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pathos" ;
NIFRID:synonym "Open Science Impact Pathways" ;
NIFRID:abbrev "PathOS" ;
definition: "Horizon Europe project aiming to collect concrete evidence of Open Science effects, study pathways of Open Science practices, from input to output, outcome and impact, including consideration of enabling factors and key barriers." .
SCR:027125 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Korean National Health Insurance Service" ;
NIFRID:abbrev "NHIS" ;
definition: "Healthcare in South Korea is single-payer system organized through National Health Insurance Service (NHIS). Nearly all citizens receive universal medical care through this system. NHIS participates in health screening programmes to offer relevant and useful data for health researchers, especially in the field of non-communicable diseases and health risk factors, and policy-maker." .
SCR:027126 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DoRothEA" ;
definition: "Software R package for storing the regulons. Gene regulatory network containing signed transcription factor (TF) - target gene interactions. DoRothEA regulons, the collection of TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. Confidence level was assigned to each TF-target interaction based on number of supporting evidence." .
SCR:027127 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "decoupleR" ;
definition: "Software R package to infer biological activities from omics data using collection of methods." .
SCR:027128 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3278" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Laboratory Diagnostic Core Facility" ;
NIFRID:synonym "Laboratory Diagnostic Core" ;
definition: "Core has maintained CAP (College of American Pathologists) and CLIA (Clinical Laboratory Improvement Act) accreditations since 2001 and has maintained the required standards for the past 20 years. Core offers automated clinical chemistry, immunology and hematology assays. Tests range from commercially available FDA approved methods to research grade ELISA’s." .
SCR:027129 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DUOTRONIC_III" ;
rdfs:label "PierceDirect | Duotronic III Embalming Machine" ;
NIFRID:synonym "Hygeco Duotronic III Embalming Machine" ;
definition: "Fixation pump for anatomy laboratories. DUOTRONIC III features extra light 1/8 HP motor pump, ensuring considerable outflow without preliminary pressure. The pump is magnetic transmission, centrifugal device equipped with mixing system (based on the principle of the water fountain) allowing homogeneous mixing. Specifications: Stainless steel base with handles; 11 litre tank, graduation in litre; 15 Psi pressure; 220 mono 50 Hz/60 Hz." .
SCR:027130 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GRIDSS" ;
NIFRID:synonym "Genomic Rearrangement IDentification Software Suite",
"GRIDSS2" ;
definition: "Software suite containing tools for detection of genomic rearrangements. Multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using novel positional de Bruijn graph-based assembler. GRIDSS2 is structural variant caller to explicitly report single breakends-breakpoints in which only one side can be unambiguously determined." .
SCR:027131 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AMBER" ;
definition: "Software tool to generate tumor BAF file for use in PURPLE from provided VCF of likely heterozygous SNP sites." .
SCR:027132 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COBALT" ;
NIFRID:synonym "COunt BAm Lines T" ;
definition: "Software tool to determine read depth ratios of supplied tumor and reference genomes." .
SCR:027133 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LINX" ;
definition: "Software annotation, interpretation and visualisation tool for structural variants. Used to aid interpretation of structural variant and copy number data derived from short-read, whole-genome sequencing. Classifies raw structural variant calls into distinct events and predicts their effect on local structure of derivative chromosome and functional impact on affected genes." .
SCR:027134 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JaBba" ;
NIFRID:synonym "Junction Balance Analysis" ;
definition: "Software tool to infer junction-balanced genome graphs with high fidelity. Builds genome graph based on junctions and read depth from whole genome sequencing, inferring optimal copy numbers for both vertices (DNA segments) and edges (bonds between segments)." .
SCR:027135 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MorphoLibJ" ;
definition: "Software integrated library and plugins for mathematical morphology with ImageJ.Collection of generic tools based on Mathematical Morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins." .
SCR:027136 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRISM - Poisson RNA-profile Identification in Scaled Mixtures" ;
NIFRID:synonym "Poisson RNA-profile Identification in Scaled Mixtures" ;
NIFRID:abbrev "PRISM" ;
definition: "Software statistical framework that allows simultaneous extraction of tumor sample composition and cell type and sample specific whole-transcriptome profiles from individual bulk RNA-seq samples." .
SCR:027137 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BAMMtools" ;
NIFRID:synonym "Bayesian Analysis of Macroevolutionary Mixtures tools" ;
definition: "Software R package for analysis and visualization of macroevolutionary dynamics on phylogenetic trees." .
SCR:027138 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ovaHRDscar" ;
definition: "Software R package to quantify allelic imbalances associated with homologous recombination deficiency in ovarian cancer." .
SCR:027139 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "conorm" ;
NIFRID:synonym "count normalization" ;
definition: "Software package for analysis of RNA expresison data. Used to make pythoneer bioinformatician workflow less colluded with R." .
SCR:027140 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Concordance Probability Estimates" ;
NIFRID:synonym "CPE: Concordance Probability Estimates in Survival Analysis" ;
NIFRID:abbrev "CPE" ;
definition: "Software R package used in survival analysis that evaluates predictive accuracy of survival model. Measures how well model can distinguish between pairs of individuals with different survival times. Calculates proportion of all pairs of individuals whose predicted survival times are correctly ordered." .
SCR:027141 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "signifinder" ;
definition: "Software R package designed to streamline collection and use of cancer transcriptional signatures across bulk, single-cell, and spatial transcriptomics data. Used for collection and implementation of public transcriptional cancer signatures." .
SCR:027142 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mvmeta" ;
definition: "Software R package to perform fixed and random-effects multivariate and univariate meta-analysis and meta-regression." .
SCR:027143 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3279" ;
rdfs:label "Dartmouth College Life Sciences Light Microscopy Core Facility" ;
NIFRID:synonym "Life Sciences Light Microscopy Core Facility at Dartmouth College" ;
NIFRID:abbrev "LSLM Facility" ;
definition: "Light microscopy imaging core facility located in the Life Sciences Center at Dartmouth College (Hanover, NH). Facility personnel provide training and imaging guidance. Imaging instruments available to trained users include: laser scanning and spinning disk confocal systems (with super-resolution capability), a TIRF system, and a multiphoton microscope. Image analysis software (e.g. Nikon Elements, ZEN, Arivis Vision 4D, and Imaris Quant) is also available through the facility." .
SCR:027144 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3280" ;
rdfs:label "Tulane University TNBRC Molecular Virology and Sequencing Core Facility" ;
definition: "Core offers advanced services to detect, quantify, and characterize pathogens, as well as assess host immune responses. Supports both standardized and custom assay developments. MVSC is composed of three integrated units: Virology Unit which provides viral stocks for variety of viruses at BSL2 and BSL3, as well as assay services including virus expansion and characterization, viral titer by plaque and TCID50 assays, live virus neutralization and inhibition assays at both BSL-2 and –3. Viruses currently in use by the core include SIV, HIV, Zika, Dengue, SARS-CoV-2, Mayaro, Eastern Equine Encephalitis Virus, Poliovirus, Enterovirus D68, and others. Luminex and Serology Unit Services include antibody detection in serum or plasma by Luminex-based assays and/or ELISA for SPF-agents such as SIV, SRV, STLV, B virus, SFV, CMV, RRV, SVV, SV40, and LCV, and non-SPF infectious agents like measles, Burkholderia pseudomallei, Trypanosoma cruzi, Mycobacterium tuberculosis, and SARS-CoV-2. This unit also offers services for cytokine quantification in body fluids including serum and CSF, as well as tissue culture supernatant. Sequencing Unit provides services related to quantitative PCR and RT PCR detection of viruses such as SIV, Zika, and SARS-CoV-2, as well as next generation sequencing services including whole genome (pathogen or host), epigenetics, targeted amplicons, and 16S and ITS metagenomics. Sequencing unit also performs single cell RNA-seq (10x and Parse) assays as well as NGS based genotyping of NHP, including for major histocompatibility complex (MHC) allelic genotyping." .
SCR:027145 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3281" ;
rdfs:label "Dresden University of Technology Mass Cytometry Core Facility" ;
NIFRID:synonym "Mass Cytometry Core Facility (CyTOF)" ;
definition: "Facility provides customized solutions for complex single cell profiling with up to 45 markers simultaneously. Offers full service and established workflows from panel design, antibody labelling and sample processing to high-dimensional data analysis. Offers expertise in antibody conjugation, sample staining, and data analysis." .
SCR:027146 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ECLIPSE_Ts2R" ;
rdfs:label "Nikon | ECLIPSE Ts2R inverted microscope" ;
definition: "Compact inverted research microscope configurable with wide variety of observation methods such as epi-fluorescence, phase contrast, DIC, and more. The Ts2R features camera port for digital imaging while maintaining compact body." .
SCR:027148 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SPD1030" ;
rdfs:label "Thermo Fisher | SpeedVac SPD1030 Integrated Vacuum Concentrator" ;
NIFRID:synonym "Savant SpeedVac SPD1030 Integrated Vacuum Concentrator",
"SpeedVac SPD1030" ;
definition: "Fully integrated system that combines concentrator, refrigerated cold trap, diaphragm pump and vacuum gauge in single, compact unit. Vacuum concentrator for drying DNA/RNA precipitates, PCR samples, proteins, enzyme, HPLC fractions in plates or tubes in water/ethanol or isopropanol and other organic solvents. SpeedVac SPD1030 System is designed for medium capacity (i.e.,120 x 1.5 mL tubes, other formats)." .
SCR:027149 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3275" ;
rdfs:label "University of Texas at Dallas UTD Genome Center Core Facility" ;
NIFRID:synonym "University of Texas at Dallas UTD Genome Center",
"UTD Genome Center" ;
definition: "Core provides library prep and NGS services using Illumina NextSeq 2000. Our services include sample QC, DNA, RNA bulk sequencing, single cell sequencing, and Sanger sequencing." .
SCR:027150 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gGnome" ;
definition: "Software package provides flexible, queriable R interface to graphs and walks of reference genomic intervals. gGnome is written in R6 object oriented standard and built around GenomicRanges, data.table, and igraph backend, and thus supports agile interaction with graphs consisting of hundreds of thousands of nodes and edges." .
SCR:027151 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "poibm" ;
definition: "Software package for batch correction of heterogeneous RNA-seq datasets through latent sample matching." .
SCR:027152 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "flexmix" ;
NIFRID:synonym "Flexible Mixture Modeling" ;
definition: "Software R package for finite mixtures of regression models using EM algorithm. General framework for finite mixture models and latent class regression in R." .
SCR:027153 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mclust" ;
definition: "Software R package implementing Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation." .
SCR:027154 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "slow5tools" ;
definition: "Software toolkit for converting, compressing, viewing, indexing and manipulating data in SLOW5 format. Used for handling nanopore data in SLOW5 format." .
SCR:027155 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "slow5 format" ;
NIFRID:abbrev "SLOW5" ;
definition: "File format for storing signal data from Oxford Nanopore Technologies sequencing devices. SLOW5 can be encoded in human-readable ASCII format, or more compact and efficient binary format (BLOW5) - this is analogous to the seminal SAM/BAM format for storing DNA sequence alignments." .
SCR:027156 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "slow5lib" ;
definition: "Software library for reading and writing SLOW5 files. Designed to facilitate use of data in SLOW5 format by third-party software packages. Used for efficient parallelization and acceleration of nanopore data analysis." .
SCR:027157 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pyslow5" ;
NIFRID:synonym "slow5 python library" ;
definition: "Software library to read and write slow5/blow5 files. Python wrapper built on top of slow5lib (interfaced using Cython) to allow easy access to SLOW5 for Python programmers." .
SCR:027158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "f5c" ;
definition: "Software ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)." .
SCR:027159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "squigulator" ;
definition: "Software tool for simulating nanopore raw signal data.Takes reference genome, transcriptome, or read sequences, and generates corresponding raw nanopore signal data." .
SCR:027160 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "squigualiser" ;
definition: "Software tool to visualise and analyse nanopore raw signals." .
SCR:027161 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3282" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Electron Microscopy Core Facility" ;
definition: "Transmission (TEM), Scanning (SEM), 2D tile scanning SEM and 3DSEM electron microscopy are available in the Core for imaging and analyzing specimens at the ultrastructural level. Possible samples include fresh tissue specimens, cultured cells growing on a substrate, cells in suspension or subcellular fractions (for purity determinations). Sub-cellular localization of antigens within cells by immunogold labeling can be performed, as well as negative staining for visualizing samples such as microparticles and exosomes. Elemental analysis (EDAX) is also available together with SEM." .
SCR:027162 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3283" ;
rdfs:label "Ohio State University Campus Chemical Instrument Center NMR Core Facility" ;
NIFRID:synonym "Ohio State University Campus Chemical Instrument Center NMR Facility" ;
definition: "Advanced high-field NMR facility combines many capabilities spanning solution and solid state NMR, high sensitivity cryoprobes, ultrafast spinning MAS probes, as well as Dynamic Nuclear Polarization." .
SCR:027163 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cultivarium" ;
definition: "Cultivarium creates tools for life scientists to expand access to novel microorganisms, inspire new research avenues, and push the frontiers of biotechnology. Aggregates information, data, and publications for bacteria, fungi, archaea, and protists." .
SCR:027164 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "EvE Bio" ;
definition: "Focused Research Organization (FRO). Focused on identifying unintended gene product binding partners of pharmaceuticals and other bioactive compounds, to support better drug development and drug repurposing.Along with drug/protein interaction data, includes methods and tools to provide the scale, throughput, and economy that future pharmome mappers will require in order to continue mapping the vast and ever-expanding proteomic/chemical space that is the pharmome." .
SCR:027165 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Forest Neurotech" ;
definition: "Nonprofit startup which focuses on impactful applications and scientific dissemination, ensuring maximum public benefit without commercial constraints. Forest's state-of-the-art tools, research, and discoveries will be shared with the broader scientific community, aligning with its commitment to open science. Company mission is to advance healthcare by making neurotechnology accessible, less invasive, and adaptable across range of neurological conditions." .
SCR:027166 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "E11 Bio" ;
definition: "E11 Bio was launched in 2022 as one of the first Focused Research Organizations (FROs), a novel form of non-profit startup for science. E11 Bio’s mission is to unlock connectomics at the scale of whole mammalian brains by radically cheaper and more accessible technologies." .
SCR:027167 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "African Reproducibility Network" ;
NIFRID:abbrev "AREN" ;
definition: "Organization is part of a strategic global community effort to promote transparent and trustworthy research practices in the academic research systems. Part of the Association of African Universities." .
SCR:027168 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Baobab Africa" ;
NIFRID:abbrev "Bayobab" ;
definition: "Bayobab is a next-generation services company connecting Africa with digital solutions. We see Africa through the eyes of its’ population, a continent brimming with potential and possibility. Until May 2023, the company was known as MTN GlobalConnect. The transition to a new brand is a shift to an open-access business model structured to serve all industry participants and add value to stakeholders and partners." .
SCR:027169 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "RoRi" ;
definition: "RoRI was founded in 2019 with mission to accelerate transformative research on research systems, cultures and decision-making. Headquartered at University College London (UCL), RoRI partners and works closely with expanding international network of research funders, from across Europe, North America, Australia and Africa." .
SCR:027170 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "16SMicrobiomeMLFS" ;
definition: "Code and supporting data for the article: \"Exploring the role of normalization and feature selection in microbiome disease classification pipelines.\"" .
SCR:027171 a owl:NamedIndividual ;
rdfs:label "CLEAR" ;
NIFRID:synonym "CLEAR: Coverage-based Limiting-cell Experiment Analysis for RNA-seq",
"Coverage-based Limiting-cell Experiment Analysis for RNA-seq" ;
definition: "Software workflow that identifies reliably quantifiable transcripts in limiting-cell RNA-seq (lcRNA-seq) data for differentially expressed genes (DEG) analysis. Coverage-based Limiting-cell Experiment Analysis for RNA-seq." .
SCR:027172 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "KEGG enrichment analysis" ;
definition: "Enrichment of related pathways in genes." .
SCR:027173 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TSE Systems | Stellar Telemetry" ;
definition: "System provides flexibility to record data in any environment. Used in implantable physiologic monitoring.Fully implantable Telemetry.Allows monitoring of many animals with just one receiver and facilitates group housing and social interaction." .
SCR:027174 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ScienceDirect" ;
definition: "Database platform that provides access to collection of peer-reviewed scientific literature, including journal articles and book chapters, from Elsevier and other publishers. Scientific Search Engine." .
SCR:027175 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "isoCirc" ;
definition: "Software pipeline to identify high-confidence BSJs and full-length circRNA isoforms from isoCirc long-read data." .
SCR:027176 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nimble" ;
definition: "Software Bayesian statistical modeling R package for hierarchical statistical modeling (aka graphical modeling). It enables writing general models along with methods such as Markov chain Monte Carlo (MCMC), particle filtering (aka sequential Monte Carlo), Laplace approximation and other general methods." .
SCR:027177 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4045" ;
rdfs:label "Adam Mickiewicz University Cytometry Laboratory Core Facility" ;
NIFRID:synonym "AMU CAT - Cytomics and Cell Analysis Core Facility" ;
definition: "Core is utilized in medical biotechnology and in research focused on mammalian cells. Offers analyzing of impact of new drugs and pharmaceuticals on individual cells in vitro. Provides sorting of cell populations with desired characteristics, including fluorescent dye-stained cell sorting (FACS) analysis of cell populations for presence of specific factors, e.g. introduced fluorescent protein, surface markers, DNA content determining the size, granulation and shape of animal and other cells." .
SCR:027178 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4046" ;
rdfs:label "Virginia Commonwealth University Cryo-Electron Microscopy Core Facility" ;
NIFRID:synonym "cryo-Electron Microscopy Facility" ;
definition: "Facility offers sample preparation, visualization and analysis for high resolution 3D reconstruction of frozen-hydrated proteins and macromolecular complexes. Facility is endowed with Thermofisher Scientific Tundra cryo-electron microscope, Vitrobot Mark IV cryo-plunger, Pelco easyGlow glow discharge unit, Denton DV 502B evaporator, and linux server dedicated to image processing." .
SCR:027179 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "napari-k2-WaveBreaker" ;
NIFRID:abbrev "Napari-WaveBreaker; WaveBreaker" ;
definition: "Software Napari plugin for quantifying membrane-associated periodicity and periodic co-localization in super-resolution microscopy images. It uses autocorrelation and cross-correlation analysis to provide unbiased metrics of periodicity and spatial shifts between channels." .
SCR:027180 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Knowledge Platform" ;
definition: "Comprehensive multi-species platform for neuroscience teams to understand brain cells and anatomy. Brain Knowledge Platform includes catalog of relevant data and projects, as well as visualization tools for understanding brain cell types." .
SCR:027181 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "NIS-Elements AR" ;
rdfs:label "NIS-Elements Advanced Research" ;
definition: "Software package for acquisition and device control for advanced research applications. Nikon’s flagship software package features fully automated image acquisition, advanced device control and powerful analysis and visualization tools." .
SCR:027182 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iWorx LabScribe" ;
NIFRID:synonym "LabScribe" ;
definition: "Software package for recording and analysis developed by iWorx. LabScribe has intuitive, user-friendly interface for setting up acquisition screens, calibrating signals and analyzing data. Up to 128 channels of data can be displayed simultaneously at sampling rates as high as 100,000 samples/second." .
SCR:027183 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Med Associates Small Animal Cystometry MED-CMG Software" ;
NIFRID:synonym "Small Animal Cystometry MED-CMG Software" ;
definition: "Med Associates Inc. data acquisition software for recording cystometrigrams from small laboratory animals, such as rats or mice." .
SCR:027184 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Med Associates Cystometry Data Analysis Software" ;
NIFRID:synonym "Cystometry Data Analysis Software" ;
definition: "Med Associates software tool to automatically create graph of cystometrigram of exported data from MED-CMG. Analysis of data is made possible with readouts of bladder pressure, infusion pump, and scale traces to identify void and non-void contractions." .
SCR:027185 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4048" ;
rdfs:label "Washington University in St. Louis Human Cells, Tissues, and Organoids Core Facility" ;
NIFRID:synonym "and Organoids (hCTO) Core",
"Human Cells",
"Tissues" ;
definition: "Core provides training and expertise on culturing human pluripotent cells and their downstream derivatives." .
SCR:027186 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CryoDataBot" ;
definition: "Software pipeline designed to streamline dataset generation for cryogenic electron microscopy (cryoEM)-based atomic model building. Supports large-scale AI training and benchmarking by providing standardized tools for data retrieval, preprocessing, labeling, and quality control. Enables flexible configurations for diverse biomolecular structures, improves modeling reproducibility, and facilitates retraining of AI models such as U-Net and CryoREAD. Python workflow used to curate cryoEM datasets for AI-driven structural biology." .
SCR:027187 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "YSI | 2300 STAT PLUS analyzer" ;
NIFRID:synonym "YSI 2300 STAT PLUS",
"YSI 2300 STAT PLUS Glucose and Lactate Analyzer" ;
definition: "Laboratory instrument intended for use in clinical care and sports medicine applications. Provides measurements of glucose in whole blood, plasma or serum, and of L-lactate in whole blood, plasma, or cerebrospinal fluid (CSF). In whole blood or plasma, glucose and L-lactate can be measured simultaneously." .
SCR:027188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LinkML" ;
NIFRID:synonym "Linked data Modeling Framework",
"LinkML: Linked data Modeling Framework" ;
definition: "Flexible modeling language that allows you to author schemas in YAML that describe the structure of your data. Additionally, it is framework for working with and validating data in variety of formats (JSON, RDF, TSV), with generators for compiling LinkML schemas to other frameworks.Framework that simplifies the process of authoring, validating, and sharing data." .
SCR:027189 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4049" ;
rdfs:label "University of Birmingham Intravital Microscopy Core Facility" ;
NIFRID:synonym "University of Birmingham UOB Intravital Microscopy",
"UOB Intravital Microscopy" ;
definition: "Imaging facility for intravital microscopy. Facility equipment includes widefield, confocal, and multiphoton microscopes. Additional tools, such as laser ablation systems, allow us to probe vascular events such as thrombosis in fine detail. We also have tools for measurement of vascular perfusion, such as full-field laser speckle and laser doppler." .
SCR:027190 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChemPerturbDB" ;
definition: "Artificial Intelligence (AI)-powered website, which provides user-friendly open access analysis of extensive ChemPerturb-seq dataset." .
SCR:027191 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "STAgent" ;
NIFRID:synonym "Spatial Transcriptomics AI Agent" ;
definition: "Software tool as multimodal LLM-based AI agent that enables deep research about spatial transcriptomics data. Integrates multimodal large language models (LLMs) with specialized computational tools to transform weeks-long analysis tasks into minutes of automated processing. Enables autonomous deep research through integrated capabilities, including dynamic code generation for complex analytical workflows, visual reasoning for interpreting spatial patterns, real-time retrieval of relevant peer-reviewd scientific literature, and synthesis of comprehensive, actionable reports." .
SCR:027192 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Metabolic Subphenotype Predictor" ;
definition: "Software repository contains code for Inference of T2D metabolic subphenotypes (MuscleIR, Beta-cell Function, Incretin Effect, Hepatic IR), Identification of dominant metabolic subphenotype, Feature extraction from glucose tiemseries, Extraction of reduced representation of glucose tiemseries,Visualization of metabolic phenotypes based on various glucose-related metrics,Concordance between CGM and Venous glucose values from at home and at clinical setting, Classification of metabolic subphenotypes." .
SCR:027193 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioDare2" ;
definition: "Data analysis resource and repository for biological data related to circadian rhythms, sharing public data from over 10,000 experiments (in 2025). The main features of BioDare2 are: fast analysis of rhythmic data (rhythm detection and period, phase, amplitude), timeseries processing, attractive visualizations, simple data description, data sharing with permalinks, easy data uploads and a modern UI." .
SCR:027194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Palantir" ;
definition: "Algorithm to align cells along differentiation trajectories. Models trajectories of differentiating cells by treating cell fate as probabilistic process and leverages entropy to measure cell plasticity along the trajectory. Generates high-resolution pseudo-time ordering of cells and, for each cell state, assigns probability of differentiating into each terminal state." .
SCR:027196 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoFreeLunch" ;
definition: "Software toolkit for quantitative detection of DNA methylation from nanopore sequencing data without raw signals." .
SCR:027197 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PolyBreedTools_App" ;
definition: "Software application is Shiny app for ancestry estimation using genotypic data. Designed to support any species and ploidy level, it enables users to estimate admixture proportions using reference populations and visualizes ancestry results interactively." .
SCR:027198 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fluidigm | Juno Targeted DNA Sequencing Library Preparation System" ;
NIFRID:synonym "Juno System",
"Juno Targeted DNA Sequencing Library Preparation System" ;
definition: "Juno system used for preparing libraries for next-generation sequencing and IFS preparation for gene expression, genotyping and digital PCR application." .
SCR:027199 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MBI Montreal Biotech | SensoQuest Labcycler Gradient" ;
NIFRID:synonym "Labcycler Grandient" ;
definition: "Thermocycler with gradient function used in PCR (Polymerase Chain Reaction) experiments. It allows for creation of temperature gradient across the sample block, enabling users to optimize annealing temperatures for different reactions simultaneously. Labcycler Gradient with 96 Wells (0.2 ml) Silver Block (± 20 °C)." .
SCR:027200 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher: Sartorius | Secura Semi-Micro Balance" ;
definition: """Semi-micro balance offers four different weighing ranges to fulfill the needs of most 5-digit
weighing applications.""" .
SCR:027201 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Telstar | Boreas Ultra-low temperature freezer" ;
definition: "Ultra-low temperature (ULT) freezer known for Vacuum Insulation Panel insulation and ecological refrigerants. These freezers are designed for the safe and long-term storage of biological and chemical samples at extremely low temperatures, typically down to -86°C." .
SCR:027202 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | Microtome RM2035" ;
NIFRID:synonym "Leica RM 2035 BioCut Manual Microtome" ;
definition: "Leica RM 2035 BioCut Manual Microtome is perfect for manually sectioning paraffin or plastic-embedded specimens." .
SCR:027203 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Vital River Laboratory Animal Technology Inc." ;
definition: "Company specializing in providing laboratory animal models and related services for biopharmaceutical research. It is a subsidiary of Charles River Laboratories, and is known for its expertise in refining breeding practices of specific pathogen-free (SPF) laboratory animals. VRL operates from state-of-the-art facilities and offers a wide range of rodent strains and related services to support research in China and internationally." .
SCR:027204 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "GeneSeed Biotech" ;
NIFRID:synonym "Guangzhou Geneseed Biotech" ;
definition: "Guangzhou Geneseed Biotech. Co.,Ltd., founded in June 2010, is a pioneer in circRNA scientific research and application transformation." .
SCR:027205 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "OBiO Technology" ;
definition: "Established in 2013, OBiO Technology（Shanghai）Corp.,Ltd. is Contract Research Organization and Contract Development and Manufacturing Organization in cell and gene therapy. Provides technical services for the field of Regenerative Medicine and Anti-aging, including cell preparation, production of recombinant proteins/exosomes, and cell storage." .
SCR:027206 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCKANNER" ;
definition: "Web-based software tool to explore current contents of SCKAN, semantic store housing comprehensive knowledge base of autonomic nervous system (ANS) and peripheral nervous system (PNS) nerve to end organ connectivity." .
SCR:027207 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "China National Center for Bioinformation Genome Sequence Archive for Human database" ;
NIFRID:synonym "Genome Sequence Archive for Human (GSA-Human)",
"Genome Sequence Archive for Human database" ;
definition: "Data repository for archiving raw sequence data, which provides data storage and sharing services for worldwide scientific communities. Data repository specialized for human genetic related data derived from biomedical researches." .
SCR:027208 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GevaertLab_DUNE" ;
NIFRID:synonym "Deep feature extraction by UNet-based Neuroimaging-oriented autoEncoder" ;
NIFRID:abbrev "DUNE" ;
definition: "Software tool to extract low-dimensional deep features from multisequence brain MRI data using unsupervised autoencoders." .
SCR:027209 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 501100004332",
"GRID grid.412484.f",
"ISNI 0000 0001 0302 820X",
"Wikidata Q4403855" ;
rdfs:label "Seoul National University Hospital" ;
definition: "Teaching hospital located in Yeongeon-dong, Jongno-gu, Seoul, South Korea. It is general and teaching hospital of Seoul National University's College of Medicine." .
SCR:027210 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LoReC - Coverage" ;
NIFRID:synonym "Long-Read-Checker - Coverage" ;
definition: "Software tool to analyse coverage depths of structural variants or regions/genes of interest from long-read-sequencing datasets obtained by all available technologies as well as short-read sequencing datasets and optical genome mapping. Generates coverage statistics (min, max, Q1, Q3, mean, median) and/or coverage plots based on either the Binary Alignment Map (BAM) file(s) or OGM mapping files (CMAP, XMAP). Software optical mapping, high-throughput and long read coverage comparison and visualization tool." .
SCR:027211 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LoReC - Comparator" ;
NIFRID:synonym "Long-Read-Checker - Comparator" ;
definition: "Software tool as long read, high-throughput sequencing and optical mapping structural variant Comparator. Enables to compare structural variants (SVs) from long-read-sequencing (LRS) datasets obtained by all available technologies as well as short-read sequencing (SRS) datasets and optical genome mapping (OGM). Enables to analyse targeted or whole-genome sequencing datasets using reference genome of interest." .
SCR:027212 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4053" ;
rdfs:label "University of South Carolina Center for Elemental Mass Spectrometry Core Facility" ;
NIFRID:synonym "Center for Elemental Mass Spectrometry",
"Center for Elemental Mass Spectrometry (CEMS)",
"University of South Carolina Center for Elemental Mass Spectrometry (CEMS)" ;
definition: "Core analytical facility with research focus on geochemistry and chemical oceanography. Provides plasma-source mass spectrometers for trace metal and isotope ratio measurements on wide variety of sample types." .
SCR:027213 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4054" ;
rdfs:label "University of South Carolina Mass Spectrometry Core Facility" ;
NIFRID:synonym "USC Mass Spectrometry Core" ;
definition: "Core provides services for EI and CI spectra including high and low resolution analyses available; for GC-MS including positive ion and negative chemical ionization, with high resolution and MS/MS available for high sensitivity work; Electrospray and APCI including low resolution or accurate mass analysis of purified compounds by direct infusion or loop injection analysis; MS/MS available for structural analysis;LC-MS including electrospray and APCI ionization available. Separation by narrowbore or capillary HPLC. MS/MS available for quantitation, peptide microsequencing and protein identification, etc.; MALDI-TOF/TOF including analysis of polymers and biomolecules; ICP-MS including trace elemental detection with high resolution. User training available for students and researchers who will be using the instrumentation for extended projects." .
SCR:027214 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4055" ;
rdfs:label "University of South Carolina Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "University of South Carolina NMR Core" ;
definition: "University of South Carolina NMR Core." .
SCR:027215 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4056" ;
rdfs:label "University of South Carolina College of Pharmacy Microscopy and Flow Cytometry Core Facility" ;
NIFRID:synonym "USC Microscopy and Flow Cytometry Core" ;
definition: "Core advise and assist investigators with advanced microscopy and flow cytometry procedures. Provides training and services in flow cytometry and biological imaging." .
SCR:027216 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bio-Techne | ProteinSimple FluorChem R System" ;
NIFRID:synonym "FluorChem R System" ;
definition: "System was high-performance gel imaging system for chemiluminescence, fluorescence, UV, and visible light applications, but it has been discontinued as of October 15, 2021. ProteinSimple (now part of Bio-Techne) will continue servicing these products through October 15, 2026." .
SCR:027217 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TWOMBLI" ;
NIFRID:synonym "Workflow Of Matrix BioLogy Informatics",
"Workflow Of Matrix BioLogy Informatics (TWOMBLI)" ;
definition: "Software pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. FIJI macro for quantifying pattern in extracellular matrix." .
SCR:027218 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "modelcif" ;
definition: "Software Python package for handling mmCIF and BinaryCIF files compliant with the ModelCIF extension." .
SCR:027219 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "clusterCrit" ;
definition: "Software package for computing collection of clustering validation or quality criteria and partition comparison indices." .
SCR:027220 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCopeLoomR" ;
definition: "Software R package to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers. Can also be used to read data from .loom files." .
SCR:027221 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SeuratObject" ;
NIFRID:synonym "SeuratObject:Data Structures for Single Cell Data" ;
definition: "Software R package defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users." .
SCR:027222 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4057" ;
rdfs:label "University of Nebraska Medical Center Institutional Biospecimen Biobank Core Facility" ;
NIFRID:synonym "Institutional Biospecimen Biobank",
"University of Nebraska Medical Center Institutional Biospecimen Biobank",
"UNMC Institutional Biospecimen Bank (IBB)" ;
definition: "Core to procure and coordinate distribution of fresh frozen human tissue in optimal state of preservation for requesting investigators without impacting diagnostic quality, accuracy and safety in anatomic pathology. Additional services offered include biospecimen DNA or RNA extraction, sectioning of frozen tissues, short-term tissue culture, cytogenetic/molecular cytogenetic analysis, and tissue preparation via investigator-driven protocols." .
SCR:027223 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Another Gtf/Gff Analysis Toolkit" ;
NIFRID:synonym "Another Gtf/Gff Analysis Toolkit (AGAT)" ;
NIFRID:abbrev "AGAT" ;
definition: "Software toolkit containing lots of useful tools for genomics analyses. Used to check, fix, pad missing information (features/attributes) of any kind of GTF and GFF to create complete, sorted and standardised gff3 format." .
SCR:027224 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ZeroShotAMR" ;
definition: "Software repository provides the code for generalizable machine learning models for rapid antimicrobial resistance prediction in unseen healthcare settings." .
SCR:027225 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Dragonfly_600" ;
rdfs:label "Andor | Dragonfly 600 system" ;
definition: "Dragonfly spinning disk confocal microscopy system. Andor Dragonfly 600 series high-contrast multi-dimensional imaging platform for live cell imaging. Andor Dragonfly 620 is spinning disk confocal with many advanced modalities capable of widefield imaging, high-sensitivity or high-contrast spinning disk imaging, TIRF (critical angle, Hi-Lo), STORM (single molecule imaging), photostimulation of specific cellular regions and dual-camera recording." .
SCR:027226 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Leica | TCS SP8 with AOBS" ;
NIFRID:synonym "Leica TCS SP8 with Acousto-Optical Beam Splitter" ;
definition: "Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Leica TCS SP8 system is high precision confocal microscope with Acousto-Optical Beam Splitter that allows for flexible control of the excitation and emission light paths." .
SCR:027229 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hypeR" ;
definition: "Software R package that supports different types of gene set enrichment workflows. Offers multiple enrichment, visualization, and sharing methods in addition to novel features such as hierarchical geneset analysis and built-in markdown reporting." .
SCR:027230 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProteinCartography" ;
definition: "Software pipeline to build similarity maps of protein space. Identifies proteins related to query protein using sequence- and structure-based searches, compares all protein structures, and creates navigable map that can be used to look at protein relationships and make hypotheses about function." .
SCR:027231 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NovelTree" ;
definition: "Software phylogenomic pipeline designed to analyze proteomes from diverse organisms and inferring orthology, gene-family trees, and species tree. Highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionar history. Efficiently performs phylogenetic comparisons at any evolutionary scale." .
SCR:027232 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PreHGT" ;
definition: "Software pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT. Used to quickly screen for transferred genes." .
SCR:027233 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Z2m" ;
rdfs:label "Zeiss | Axio Imager Z2m system" ;
definition: "Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Facility imaging system offers stable imaging conditions, especially crucial for high magnification and time-dependent studies. Z2m model is optimized for materials science applications. It is often used for tasks like 3D subsurface studies of transparent ceramics, metallography, corrosion studies, analysis of thin film uniformity, and inclusion analysis in metals. It is particularly well-suited for situations that require motorized stage to handle large samples." .
SCR:027234 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Olympus_FVMPE-RS" ;
rdfs:label "Olympus | FVMPE-RS imaging system" ;
NIFRID:synonym "Olympus FVMPE-RS",
"Olympus FVMPE-RS multiphoton imaging system" ;
definition: "Multiphoton imaging system for deep imaging in biological tissue. For advanced applications,dual-wavelength excitation extending to 1300 nm is available. Independent control of visible or multiphoton laser light stimulation and ability to synchronize with patch clamp data are also possible. Multiple configurations are available." .
SCR:027235 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TinkerHap" ;
definition: "Software accurate read-based phasing tool that integrates multiple methodologies to enhance phasing accuracy. Used to efficiently phase genomic data by linking sequencing reads across heterozygous sites, extending haplotype blocks, and incorporating pre-phased data when available. Read-based phasing algorithm with integrated multi-method support for enhanced accuracy." .
SCR:027237 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4059" ;
rdfs:label "Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Facility" ;
NIFRID:synonym "Microscopy and Advanced Bioimaging CoRE" ;
definition: "Facility provides access to imaging equipment and analysis tools. It houses widefield, laser scanning confocal, spinning disk confocal, multi-photon, light-sheet, and super-resolution microscopes, along with two transmission electron microscopes and high-content screener. Offers centralized workstation for image processing, high-performance computing capabilities, and data storage. Provides access to several commercial software programs for image analysis and data quantification. Services include consultations for sample preparation, training on the microscopes, full imaging support, and assistance with analysis strategies. Provides several services related to transmission electron microscopy: tissue/cell processing, image acquisition training or assistance, and image analysis support. CoRE scientists can collaborate with investigators to develop novel imaging methods and analysis approaches." .
SCR:027238 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_UltraMicroscope II" ;
rdfs:label "LaVision | BioTec UltraMicroscope II" ;
definition: "Light sheet fluorescence microscope designed for high-resolution, three-dimensional imaging of large, cleared, and fluorescently labeled biological samples. It excels at visualizing entire biological systems like organs, embryos, or even small animals with cellular resolution, making it suitable for studying complex biological structures and processes." .
SCR:027239 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SmartSPIM" ;
rdfs:label "Life Canvas Technologies | SmartSPIM" ;
definition: "High-speed, high-resolution light sheet microscope designed for imaging large, cleared tissue samples. Utilizes patented axially-swept light sheet technology to achieve uniform axial resolution across the entire sample, enabling rapid volumetric imaging. System is particularly well-suited for imaging cleared tissues, including whole organs and even entire juvenile mice, with options for both aqueous and organic clearing methods. Light sheet imaging for rapid volumetric acquisition of intact samples." .
SCR:027240 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4061" ;
rdfs:label "State University of Campinas Institute of Chemistry Laboratory of Mass Spectrometry and Chromatography Core Facility" ;
NIFRID:synonym "LIEM-IQ - Mass Spectrometry and Cromatography Laboratory",
"Universidade Estadual de Campinas (UNICAMP) LIEM-IQ - Mass Spectrometry and Cromatography Laboratory" ;
definition: "Core features several high- and low-resolution mass spectrometers, coupled with liquid and gas chromatographs, as well as an ICP-MS. In addition, we have liquid chromatographs available that operate with other types of detectors. The laboratory collaborates with activities carried out at the Institute of Chemistry, in external academic sectors, and also within private enterprise." .
SCR:027241 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Quanterix_2470" ;
rdfs:label "Quanterix | 2470 Arrayer" ;
NIFRID:synonym "Quanterix Micro Arrays System Model 2470" ;
definition: "Arrayer produces high quality microarrays of DNA, proteins, cell lysates and variety of other samples using its proprietary soft touch deposition technology." .
SCR:027242 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Tecan_D300e" ;
rdfs:label "Tecan | D300e Digital Dispenser" ;
definition: "This instrument is precision liquid handling instrument that enables non-contact, nanoliter-to-microliter scale dispensing of small molecules, biologics, or other reagents directly into assay plates for high-throughput drug screening and dose-response studies." .
SCR:027245 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "chip hgu133plus2" ;
definition: "Software R package for Affymetrix Human Genome U133 Plus 2.0 Array annotation data." .
SCR:027247 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4062" ;
rdfs:label "State University of Campinas Institute of Chemistry Nuclear Magnetic Resonance Laboratory LIRMN-IQ Core Facility" ;
NIFRID:synonym "LIRMN-IQ",
"Universidade Estadual de Campinas (UNICAMP) LIRMN-IQ" ;
definition: "Institutional laboratory of Nuclear Magnetic Resonance (NMR) of the Institute of Chemistry of UNICAMP.The Institutional Nuclear Magnetic Resonance Laboratory has 6 NMR spectrometers, two for solids and four for solution probes, with the possibility of analyzing different nuclei." .
SCR:027248 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zoogle" ;
definition: "Arcadia organisms selection portal. Uses data to suggest model organisms based on relevance to human gene of interest or suggest monogenic diseases to model based on organism of interest." .
SCR:027249 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PrediLnc" ;
definition: "Standalone software and web-based platform for predicting top lncRNA–disease associations using advanced biological feature processing and machine learning. Given input lncRNA or disease, along with associated sequences or target data, PrediLnc uses our custom model GARNet (Graph convolution Attention RNA Network) to return the most relevant predictions.Used for hypothesis generation in biomedical research. LncRNA diseases association predictor." .
SCR:027250 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SLEPLET" ;
definition: "Software Python package for construction of Slepian wavelets in the spherical and manifold (via meshes) settings. Slepian scale-discretised wavelets in Python." .
SCR:027251 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4066" ;
rdfs:label "Weill Cornell Medicine Human Therapeutic Organoid Core Facility" ;
NIFRID:synonym "Human Therapeutic Organoid Core Facility",
"Weill Cornell Medicine Human Therapeutic Organoid Core (HTOC)" ;
definition: "Facility serves as central facility for human organoid technology to accelerate organoid-based scientific discovery. Provides human pluripotent stem cell (hPSC) derived as well as tissue derived cells and organoids." .
SCR:027252 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100020424",
"GRID grid.471410.7",
"ISNI 0000 0001 2179 7643",
"Wikidata Q3567094" ;
rdfs:label "Weill Cornell Medicine" ;
NIFRID:synonym "Cornell University Medical College" ;
definition: "Weill Cornell Medicine, originally Cornell University Medical College, is the medical school of Cornell University, located on the Upper East Side of Manhattan in New York City. " .
SCR:027253 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PanoScore" ;
definition: "PanoScore is a commercial-grade pathology image analysis platform for quantitative tissue segmentation, AI-powered cell phenotyping, and spatial biology research. It supports whole-slide imaging (WSI), multiplex staining analysis (H&E/IHC/IF), and tissue microarray (TMA) processing, enabling reproducible quantification of tumor microenvironments, cell proximity metrics, and biomarker expression." .
SCR:027254 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4064" ;
rdfs:label "Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Mouse Behavior Core Facility" ;
NIFRID:synonym "Mouse Behavior Core" ;
definition: "Mouse Behavior Core provides equipment and software for measuring mouse behavior. The MBC can support mouse phenotyping/drug discovery test batteries as well as more focused behavioral projects." .
SCR:027255 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4065" ;
rdfs:label "Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Genetic Perturbation Screening Core Facility" ;
NIFRID:synonym "The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology - Genetic Perturbation Screening Core" ;
definition: "Core provides guidance in planning and helps with executing gene expression modulation experiments. Currently uses technology based on shRNA for gene knock-down and cDNA libraries for overexpression studies. Core is equipped with genome-wide retroviral shRNA libraries for both human and mouse genomes, Mammalian Gene Collection (MGC) cDNA library, as well as smaller focused sets targeting selected gene families." .
SCR:027256 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "enrichViewNet" ;
definition: "Software package for visualization of functional enrichment results as network graphs." .
SCR:027257 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RPISeq" ;
NIFRID:synonym "RNA-Protein Interaction Prediction" ;
definition: "Web application for RNA-protein interactions prediction." .
SCR:027258 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IntaRNA" ;
NIFRID:synonym "IntaRNA 2.0",
"IntaRNAv2" ;
definition: "Web application for prediction of interactions between two RNA molecules. Used to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions. IntaRNAv2 enables enhanced parameterization as well as fully customizable control over prediction modes and output formats." .
SCR:027260 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CALIMA" ;
NIFRID:synonym "CAlciumIMagingAnalyser",
"CALIMA 1.0",
"CALIMA 2.0" ;
definition: "Standalone software tool to detect cells, to obtain calcium spikes, and to determine underlying network structure of neuronal cell cultures. CALIMA 2.0 is updated version of software tool that detects and analyzes fluorescent signals and correlates cellular activity to identify possible network formation in Brain-on-chip cultures. Used to process calcium fluorescence imaging data." .
SCR:027263 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CNVMetrics" ;
NIFRID:synonym "Copy Number Variant Metrics" ;
definition: "Software R package to calculate similarity metrics to facilitate copy number variant comparison among samples and/or methods." .
SCR:027264 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DCHG-DTI" ;
definition: "Software repository contains the code for paper: Prediction of Drug-Target Interactions Based on Dual-Channel Heterogeneous Graph Neural Networks." .
SCR:027265 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RAIDS (Robust Ancestry Inference using Data Synthesis)" ;
NIFRID:synonym "Robust Ancestry Inference using Data Synthesis",
"Robust Ancestry Inference using Data Synthesis (RAIDS)" ;
NIFRID:abbrev "RAIDS" ;
definition: "Software R package to enable genetic ancestry inference from various cancer sequence sources (RNA, Exome, and Whole-Genome sequences). This package also implements simulation algorithm that generates synthetic cancer-derived data. Used for accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms" .
SCR:027266 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "networkD3" ;
definition: "Software R package creates 'D3' JavaScript network, tree, dendrogram, and Sankey graphs from R." .
SCR:027267 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gtrellis" ;
definition: "Software package to arrange genomic categories and to add self-defined graphics in plot. Genomic plot in trellis layout. Visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple-dimensional data, which are represented as tracks, describe different features from different aspects." .
SCR:027268 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BiomarkerML" ;
definition: "Software cloud-based proteomics ML workflow for biomarker discovery." .
SCR:027269 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4069" ;
rdfs:label "Augusta University Transgenic and Genome Editing Core Facility" ;
definition: "Core provides services in gene editing using CRISPR/Cas9 approach, services on preserving lines by cryopreservation of sperms, and resurrecting mouse lines using in vitro fertilization (IVF) or embryo transfer. Additional services include rederivation to create pathogen-free mouse lines, developing molecular reagents for genetic engineering, and providing expert advice on mouse genetics and breeding schemes." .
SCR:027270 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4070" ;
rdfs:label "Augusta University Human Physiology Core Facility" ;
definition: "Core provides services including body/bone composition, comprehensive assessments of cardiovascular health (conduit vessel, microvascular, and central arterial stiffness), comprehensive assessment of lung health (spirometry, diffusion, lung clearance index, exhaled NO), and metabolic/exercise testing. Expanded core services in humans include oral glucose tolerance testing and continuous glucose monitoring, 24h ambulatory blood pressure monitoring, and assessments of autonomic nervous system, cognitive function, mitochondrial function, intramuscular fat, and electrocardiograms." .
SCR:027271 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4071" ;
rdfs:label "Augusta University Georgia Cancer Center Biorepository Core Facility" ;
NIFRID:synonym "Georgia Cancer Center Biorepository (GCCB)" ;
definition: "Core provides collection, annotation, and storage solutions. This Biorepository is also home to a state-wide resource, the Biorepository Alliance of Georgia for Oncology (BRAG-Onc), which functions to collect samples from 6 participating sites across the State to represent the diversity of cancer patients within the State and to enhance cancer research in Georgia.Tissue specimens are fast-frozen in vapor phase liquid nitrogen to preserve their integrity and stored in large cryofreezers at -170 to -190°C. Blood is routinely separated into serum or plasma and buffy coats prior to freezing. Blood derivatives are stored at -70 to -80°C. The freezers are monitored constantly and are connected to an alarm system to ensure that the low temperatures are maintained." .
SCR:027273 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Celline" ;
definition: "Software Python pipeline for one-step retrieval and integrative analysis of public single-cell RNA sequencing data." .
SCR:027274 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NDC-SOLES" ;
NIFRID:synonym "NDC-Systematic Online Living Evidence Summaries" ;
definition: "Web application to systematically collect, synthesise, and display experimental evidence in genetically-modified animal models of neurodevelopmental conditions." .
SCR:027275 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CMSCaller" ;
definition: "Software R package provides Consensus Molecular Subtype (CMS) classification of colorectal cancer pre-clinical models. Used for consensus molecular subtyping of colorectal cancer pre-clinical models." .
SCR:027277 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4075" ;
rdfs:label "Augusta University Visual Function Assessment Core Facility" ;
definition: "Core provides equipment, expertise, and training for researchers to assess rodent vision in vivo. Offers technical expertise, training, and instrumentation for in vivo visual function assessment in animal models including rodents." .
SCR:027278 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4076" ;
rdfs:label "University of Florida Scripps Institute for Biomedical Innovation and Technology Flow Cytometry Core Facility" ;
definition: "Core provides flow cytometry and cell sorting services." .
SCR:027279 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4077" ;
rdfs:label "University of Florida Scripps Institute for Biomedical Innovation and Technology Metabolic Core Facility" ;
definition: "Core for In Vivo and In Vitro metabolic phenotyping. Provides validated in vitro and in vivo tests. Phenotyping applications span from mitochondrial and cellular metabolism to whole body animal physiology. Provides instrument training, experimental design, data analysis. Studies can be performed by staff, but IACUC-approved Animal Use Protocols are also available to help investigators use resources on their own." .
SCR:027280 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4079" ;
rdfs:label "Florida State University College of Medicine Magnetic Resonance Imaging Core Facility" ;
NIFRID:synonym "Florida State University College of Medicine Magnetic Resonance Imaging Facility" ;
definition: "MRI facility is research-dedicated space that includes 3T Siemens Prisma (whole-body) scanner, an MR-compatible Brain Products system for EEG and psycho-physiological measures, eye tracker, mock scanner, and a MagPro X100 equipped with Localite TMS Navigator for brain stimulation." .
SCR:027281 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Eclipse_50i" ;
rdfs:label "Nikon | Eclipse 50i microscope" ;
NIFRID:synonym "Eclipse 50i" ;
definition: "Eclipse 50i has optical capabilities, utilizing Nikon CFI60 optics, and stress-free design with solid platform for routine digital imaging applications." .
SCR:027282 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BioSpec_70/30_USR" ;
rdfs:label "Bruker | BioSpec 70/30 USR MRI system" ;
NIFRID:synonym "7 Tesla Bruker BioSpec 70/30 USR MRI system",
"Bruker BioSpec 70/30 USR" ;
definition: "High-field, preclinical imaging system primarily used for research on small animals like mice and rats. It enables researchers to conduct detailed anatomical and functional studies, including morphological imaging, functional MRI (fMRI), diffusion tensor imaging (DTI), and MR spectroscopy (MRS). The system's high field strength allows for high-resolution imaging, enabling researchers to visualize intricate anatomical details and subtle changes in tissue and organ function." .
SCR:027283 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_imageBIO266" ;
rdfs:label "ESI | imageBIO266 system" ;
NIFRID:synonym "Elemental Scientific Lasers imageBIO266",
"imageBIO266" ;
definition: "Specialized laser ablation system designed for high-resolution, high-speed bioimaging using LA-ICP-MS (Laser Ablation Inductively Coupled Plasma Mass Spectrometry). Built to analyze elemental composition of biological samples, particularly tissues and cells, with focus on speed and precision." .
SCR:027284 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Axioscan_7" ;
rdfs:label "Zeiss | Axioscan 7 Digital Slide Scanner" ;
NIFRID:synonym "ZEISS Axioscan 7" ;
definition: "High-throughput system designed for automated digitization of microscopy slides, primarily for life science research, clinical diagnosis, and geological applications. It excels at creating high-quality virtual slides from brightfield, fluorescence, and polarization microscopy samples." .
SCR:027285 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AEnet" ;
definition: "Software tool to uncover cellular alternative splicing (AS) heterogeneity and regulatory mechanisms by integrating splicing patterns with gene expression in single-cell RNA-seq (scRNA-seq) data." .
SCR:027286 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CAMPAREE" ;
NIFRID:synonym "Configurable And Modular Program Allowing RNA Expression Emulation" ;
definition: "Software tool as robust and configurable RNA expression simulator. Configurable and modular program allowing RNA expression emulation." .
SCR:027287 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BEERS2" ;
definition: "Software for simulation of RNA-seq reads. Combines flexible and highly configurable design with detailed simulation of entire library preparation and sequencing pipeline and is designed to include effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification." .
SCR:027288 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TEProf3" ;
NIFRID:synonym "TE-derived Promoter Finder 3" ;
definition: "Software pipeline to detect Transposable Elements transcripts. Used to identify TE-derived promoters and transcripts using transcriptomic data from multiple sources, including short-read RNA-seq data, long-read RNA-seq data and single cell RNA-seq data." .
SCR:027289 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Pangenome Reference Consortium" ;
definition: "NIH-funded project that aims to engage scientists and bioethicists in creating human pangenome reference and resource that represents global human genomic variation. In the process of creating the pangenome, the HPRC is developing improved technology for genome assembly and a next-generation tool ecosystem that leverages the pangenome for comprehensive analyses." .
SCR:027290 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Genome Structural Variation Consortium" ;
definition: "Consortium to characterise and improve understanding of full spectrum of human genomic variation. HGSVC utilises the latest sequencing technologies to create high-quality maps of human structural variation, developing new tools for SV discovery and analysis. Consortium involves many groups internationally." .
SCR:027291 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "methylGrapher" ;
definition: "Software methylation analysis pipeline for genome graph. Genome-graph-based DNA methylation analysis using whole genome bisulfite sequencing." .
SCR:027292 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4080" ;
rdfs:label "Mayo Clinic Florida Cytometry and Cell Imaging Core Facility" ;
definition: "Core provides researchers with access to equipment in three main pipelines: Cell and tissue imaging resources, including microscopes and a slide scanner; Flow cytometry, including analytical flow cytometry and cell sorting; Mass cytometry (CyTOF). Provides consultation services including panel and experiment design, sample preparation tips and technical troubleshooting, training for independent use on select equipment, data acquisition and cell sorting." .
SCR:027293 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RagTag" ;
definition: "Collection of software tools for scaffolding and improving modern genome assemblies. Reference-based scaffolder. Used for fast and flexible genome assembly scaffolding and improvement." .
SCR:027295 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " EnsembleTFpredictor" ;
definition: "Software application as ensemble approach to rank putative causal transcription factors that regulate set of query genes by prediction confidence." .
SCR:027296 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gauchian-enrich" ;
definition: "Software variant annotation toolkit for GBA gene variants detected from Illumina/Gauchian tool. Command-line tool designed to annotate tsv files generated by the Illumina/Gauchian tool." .
SCR:027297 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BTE-RAG" ;
definition: "Software application for BTE RAG implementation for DMDB QA datasets. Provides implementation of BTE-RAG framework, designed specifically for retrieval-augmented question answering (QA) in biomedical contexts. BTE-RAG leverages explicit mechanistic knowledge retrieval from BioThings Explorer (BTE) to significantly enhance the accuracy and reliability of large language models (LLMs) on biomedical benchmarks." .
SCR:027298 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HeteroMRI" ;
definition: "Software application for classification of heterogeneous brain MRI data. Used for white matter-related classification of heterogeneous brain FLAIR MRIs." .
SCR:027299 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "GenePharma" ;
definition: "Biotech company founded in Shanghai Hi-Tech Park. Global supplier and service provider of RNAi products and services for RNAi, gRNA, mRNA therapeutics and RNA biomarkers. Provides siRNA chemical synthesis, which include RNA monomer synthesis technology, custom and chemically-modified siRNA oligo synthesis technology, nucleic acid fluorescent labeling technology, and many nucleotide chemical modification technologies." .
SCR:027300 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenMEE" ;
definition: "Open-source, cross-platform software for ecological and evolutionary meta-analysis." .
SCR:027301 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4084" ;
rdfs:label "Howard Hughes Medical Institute at Janelia Research Campus Janelia Experimental Technology jET Core Facility" ;
NIFRID:synonym "HHMI's Janelia Research Campus Janelia Experimental Technology",
"Janelia Experimental Technology (jET)" ;
NIFRID:abbrev "jET" ;
definition: """Core team designs, builds and tests instruments, tools, and software that enable novel scientific investigation. Offers expertise in Data acquisition and analysis; Machine vision and image processing; Precision machining; Embedded systems design and programming;
Laser, microscopy, and optical imaging systems engineering; Custom circuit design; Novel sensor systems; Lab automation, robotics and motion control; Mechanical design, machined and/or fabricated components and assemblies; Process automation.""" .
SCR:027302 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DELAY" ;
NIFRID:synonym "DEpicting LAgged causalitY" ;
definition: "Software application as convolutional neural network for inference of gene-regulatory relationships across pseudotime-ordered single-cell trajectories. Used for depicting pseudotime-lagged causality for accurate gene-regulatory inference." .
SCR:027303 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "chromograph" ;
definition: "Software Camiels scATAC-seq analysis pipeline." .
SCR:027304 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fetal_brain_multiomics" ;
definition: "Software application for supplementary files and notebooks to recreate figures." .
SCR:027305 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCWorkflow" ;
NIFRID:synonym "Microbial Contamination Workflow" ;
definition: "Software application as computational workflow for detecting coordinates of microbial-like or human-like sequences in eukaryotic and procaryotic reference genomes." .
SCR:027306 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4086" ;
rdfs:label "Cancer Research UK Scotland Institute Histology Core Facility" ;
definition: "Offers processing fixed tissue for paraffin-embedded histology, cryo-microtomy, cell pellet processing, H+E staining and special histology stains or cellular material supplied. Immunohistochemistry, immunofluorescence and in-situ hybridisation service is available along with the capability to provide digital scanning and analysis. Many other techniques such as provision of tissue microarrays and other staining techniques such as TUNEL can be provided or set-up as required." .
SCR:027307 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4087" ;
rdfs:label "University College London School of Pharmacy Mass Spectrometry Core Facility" ;
definition: "Core offers services including high throughput, high mass accuracy tandem mass spectrometry coupled with liquid chromatography. Research within the facility ranges from basic biomolecular science and biochemical studies through to proteomics, metabolomics and drug-protein and drug-nucleic acid interactions." .
SCR:027308 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4088" ;
rdfs:label "Oregon State University Electron Microscopy Core Facility" ;
definition: "Core offers negative staining of protein, tissue processing including dehydration, fixation, staining and utra-microtomy, image biological samples at 80 keV on Generation 2 Titan with Rio CMOS side mount camera for low magnification too high magnification shots of cellular structures. Can also rapidly screen grids with Helios STEM in SEM capability. Provides Helios with auto slicenview and fully licensed Avizo for rendering 3D images of cells." .
SCR:027309 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4089" ;
rdfs:label "Augusta University Medical College of Georgia Pathology Research Services Core Facility" ;
definition: "Core offers pathology services to prepare and stain animal and human tissue for basic and clinical research." .
SCR:027310 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4074" ;
rdfs:label "Government of Mexico Science and Technology Center for Research in Optics (CIO) Optical Microscopy Laboratory Core Facility" ;
NIFRID:synonym "Centro de Investigaciones en Optica CIO-Laboratorio de Microscopia Optica",
"CIO-Laboratorio de Microscopia Optica",
"Government of Mexico Science and Technology Center for Research in Optics (CIO) � Optical Microscopy Laboratory",
"Optical Microscopy Laboratory (LMO)" ;
definition: "Core offers services in Confocal/Multiphotonic Microscopy, Raman Microscopy, Fluorescence/Pseudo Dark Field Microscopy,AFM. Available to students and researchers working and interested in research areas including optics, biology, materials, chemistry, and health sciences." .
SCR:027311 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4082" ;
rdfs:label "Weill Cornell Medicine Center for Translational Pathology Core Facility" ;
NIFRID:synonym "Center for Translational Pathology" ;
definition: "Core provides tissue-based and clinical laboratory assays, biospecimens, consultative pathology services, multiparametric imaging, mass spectrometry, molecular pathology, mouse models and advanced cellular therapeutics for basic, translational, and clinical research." .
SCR:027312 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4080" ;
rdfs:label "Mayo Clinic Cytometry and Cell Imaging Core Facility" ;
NIFRID:synonym "Cytometry and Cell Imaging" ;
definition: "Cytometry and Cell Imaging Core provides researchers with access to equipment in three main pipelines:Cell and tissue imaging resources, including microscopes and a slide scanner;Flow cytometry, including analytical flow cytometry and cell sorting.;Mass cytometry (CyTOF).Core provides instrument training, help with experimental design and technical support. Core specializes in antibody-based techniques.Provides expertise in cell sorting, imaging and high-parameter analysis of cells and tissues." .
SCR:027313 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Noldus | UltraVox XT" ;
NIFRID:synonym "UltraVox XT" ;
definition: "System designed for the recording and analysis of animal vocalizations. It supports full-spectrum audio capture from up to four arenas simultaneously using USB microphones, enabling precise, synchronized data collection. The software architecture incorporates advanced analysis capabilities that streamline the identification, quantification, and interpretation of vocal behaviors. UltraVox XT can also process imported audio files, expanding its applicability beyond live recordings. These features make it a versatile tool for animal behavior researchers, with flexibility to meet both current and evolving experimental needs." .
SCR:027314 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SimulAdren" ;
definition: "Software tool as simulation program of hypothalamus-pituitary-adrenal axis (HPA axis, aka corticotropic feedback control) for education and research, based on nonlinear MiMe-NoCoDI model and implemented with CyberUnits Bricks library." .
SCR:027315 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ETHOS-ARES" ;
definition: "Software supporting framework for \"Foundation Model of Electronic Medical Records for Adaptive Risk Estimation\"." .
SCR:027316 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4090" ;
rdfs:label "Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Advanced Light Microscopy Core Facility" ;
definition: "Core offers consultation and training to investigators on range of microscopy techniques, including super-resolution, confocal, multi-photon, and advanced fluorescence imaging and image analysis." .
SCR:027317 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EC-LMGraph" ;
NIFRID:synonym "EC-LMGraph: Enzyme function and Catalytic Site" ;
definition: "Software tool, which combine graph deep learning and protein language model, for accurate enzyme function and catalytic site prediction." .
SCR:027320 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IsoformSwitchAnalyzeR" ;
definition: "Software R package to identify, annotate and visualize isoform switches with functional consequences from both short- and long-read RNA-seq data. Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc." .
SCR:027321 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Orbitrap Ascend MultiOmics Tribrid Mass Spectrometer" ;
definition: "High-resolution mass spectrometer designed for comprehensive multiomics research. It combines a high-performance Orbitrap mass analyzer with a tribrid architecture (quadrupole, linear ion trap, and Orbitrap) for enhanced ion separation, fragmentation, and detection capabilities. This instrument is particularly well-suited for analyzing proteins, lipids, and metabolites in a single experiment, enabling researchers to gain deeper insights into biological systems" .
SCR:027322 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nikon | Crest X-LightV3/DIP SIM spinning disk confocal microscope" ;
NIFRID:synonym "Crest X-LightV3/DIP SIM system" ;
definition: "X-Light V3 in combination with DeepSIM X-Light super-resolution system. Super-resolution microscopy system used to visualize cellular structures and dynamics at nanoscale resolution, typically around 100 nm in XY and 300 nm in Z. It's designed for both live and fixed cell imaging, including complex 3D models like tissues and organoids, and can be seamlessly integrated with existing confocal microscopes like the X-Light V3." .
SCR:027323 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Leica_Cell_DIVE" ;
rdfs:label "Leica | Cell DIVE Multiplex Imaging Solution" ;
NIFRID:synonym "Cell DIVE",
"Cell DIVE Multiplex Imaging Solution" ;
definition: "Cell DIVE Multiplex Imaging Solution is Leica Microsystems’ open, highly customizable platform that combines precision-engineered hardware, iterative staining/dye‑inactivation protocols, and intuitive software to visualize 60+ biomarkers from a single tissue section—delivering crystal-clear, whole‑tissue imaging at the single‑cell level." .
SCR:027324 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4092" ;
rdfs:label "Yale Center for Genome Analysis Core Facility" ;
definition: "Core performs next generation sequencing for RNA and DNA samples, as well as provides support for downstream analysis." .
SCR:027326 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Turtle-Tech | BioDigital-QING Digital PCR System" ;
definition: "BioDigital Qing is a digital PCR system with automated droplet preparation and reagent formulation, enabling all essential steps of digital PCR—including compartmentalization, thermal cycling, and data acquisition—to be completed on a single instrument. Utilizing nucleic acid quantification technology, it allows for absolute quantification without the need for a standard curve. A large volume of reaction mixture is partitioned or digitized into thousands of small, independent reactions, such that each microchamber contains either one or zero target copies. The original concentration is then calculated using statistical methods based on the number of positive and negative microchambers." .
SCR:027327 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EMImR" ;
definition: "Software application for identifying transcriptomic and epigenomic changes." .
SCR:027328 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scimago Journal and Country Rank" ;
definition: "Web portal that ranks journals and countries based on their scientific influence, using data from the Scopus database. Provides bibliometric indicators like the SCImago Journal Rank (SJR) indicator, which measures citation impact, and the h-index, which reflects both the productivity and citation impact of a journal or researcher. Portal allows users to analyze journals by subject area, category, and country, offering a valuable tool for assessing research impact and comparing scientific performance." .
SCR:027329 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MarketScan by Merative" ;
definition: "Employer-sourced medical and drugs claims database of the under-65 working population and their dependents, as well as 65+ with Medicare supplemental insurance paid by employers." .
SCR:027330 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "self-assembling manifold (SAM)" ;
definition: "Software tool to assess gene relevance while enhancing dimensionality-reduction performance. Used to quantify gene relevance and improve dimensionality reduction." .
SCR:027331 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Turtle-Tech | SCI Digital PCR System" ;
definition: "This integrated digital PCR device combines four functions—chip loading, droplet generation, PCR amplification, and signal reading—into one, achieving full process automation and significantly reducing human error. It is compact in size, making it easy to transport and maintain. It is compatible with multiple PCR mixes, has high droplet stability (≥95%), and uses a glass substrate chip to ensure high-quality signal output. It supports single-sample testing, avoiding waste of consumables, and is suitable for flexible and efficient experimental requirements. Translated with DeepL.com (free version)" .
SCR:027332 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Turtle-Tech | SCI Digital PRO Digital PCR System" ;
definition: "Fully automated digital PCR system integrating four functions: chip loading, droplet generation, PCR amplification, and signal reading, enabling ultra-multiplex quantitative detection. The device adopts innovative \"solid oil-water separation\" droplet generation technology, ensuring stable droplets with a high effective ratio. It supports multi-color fluorescence channels and independent temperature control for dual modules, equipped with AI intelligent denoising and recognition functions." .
SCR:027333 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4094" ;
rdfs:label "University of Michigan Human Organoid Core Facility" ;
NIFRID:synonym "formerly the Translational Tissue Modeling Laboratory)",
"Human Organoid Multi-organ Biosample Repository",
"University of Michigan Human Organoid Core (UM-HOC",
"University of Michigan Translational Tissue Modeling Laboratory Core Facility" ;
definition: "Core enables the use of primary human organoids as tissue models for discovery, translation and regenerative medicine by providing:access to high-quality, well-characterized neonatal through adult human organoid lines from multiple organs for investigators studying human development and disease; access to detailed protocols; access to specialized, quality controlled and batch-tested reagents; expertise, guidance and training; help obtaining data;help establishing organoid lines;letters of support for grant submissions." .
SCR:027334 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4095" ;
rdfs:label "University of Michigan Eisenberg Family Depression Center Mobile Technologies Core Facility" ;
definition: "Core provides University of Michigan investigators with guidance and resources needed to utilize mobile technologies and digital mental health measures in their studies. Our experienced faculty and staff offer hands-on consultative services to U-M investigators, regardless of research focus." .
SCR:027335 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4096" ;
rdfs:label "University of Michigan Eisenberg Family Depression Center Data and Design Core Facility" ;
definition: """Core staff provides personalized consultations, knowledge and resources focused on helping investigators leverage secondary data to advance their mental health research.
Offers consultations and guide in areas:Identifying secondary data sources for mental health studies,Data preparation (e.g., merging/appending data, preparing variables for analysis), Developing analysis plan, including pre-registration, Statistical analysis.""" .
SCR:027336 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4097" ;
rdfs:label "University of Michigan AI and Digital Health Innovation Core Facility" ;
definition: "Core with mission to harness data and expertise to power innovations that improve people’s health through unification and enhancement of interdisciplinary efforts at the intersection of artificial intelligence (AI) and health at the University of Michigan. Provides data services, secure computing resources, support to strategically integrate and study AI models in clinical workflows at Michigan Medicine." .
SCR:027337 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4098" ;
rdfs:label "University of Michigan Advanced Research Computing Core Facility" ;
definition: "Core provides access to and support for advanced computing resources including high performance computing, active and archive storage, cloud computing, and secure computing environments for sensitive data." .
SCR:027338 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MRanalysis" ;
definition: "Web-based platform providing integrated and standardized Mendelian Randomization analysis workflow. This includes GWAS data quality assessment, power/ sample size estimation, MR analysis, SNP-to-gene enrichment analysis, and data visualization. Interactive R Shiny application designed for Mendelian randomization analysis." .
SCR:027340 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4100" ;
rdfs:label "University College London LMCB Electron Microscopy Core Facility" ;
definition: "Electron microscopy facility specialising in cell biological electron microscopy for basic and medical research applications." .
SCR:027341 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_VK-X1000" ;
rdfs:label "Keyence | VK-X1000 microscope" ;
NIFRID:synonym "Keyence VK-X1000 3D laser scanning microscope" ;
definition: """Non-contact profile, roughness, and film thickness measurements, nanometer resolution,
material and shape independent with fully automatic measurement and analysis 3D laser scanning microscope.""" .
SCR:027342 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multi Scale Clustering" ;
NIFRID:synonym "Multi-scale Single-cell Clustering (MSC)" ;
NIFRID:abbrev "MSC" ;
definition: "Software R package for multi-scale clustering to perform single-cell transcriptome clustering." .
SCR:027343 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4091" ;
rdfs:label "University of Exeter Centre for Cytomics Core Facility" ;
NIFRID:synonym "UOE-Centre for Cytomics" ;
definition: "Core offers high-dimensional spectral cytometry, conventional flow cytometry, nano cytometry, imaging cytometry, spatial biology, and multi-omics (proteomics and transcriptomics). Provides Cytek Aurora spectral cytometers with up to 64-colour capability, CytoFLEX LX for multiparameter conventional cytometry, and CytoFLEX nano for ultra-sensitive detection of viruses, extracellular vesicles, and submicron particles,FlowCam 8400 imaging system for real-time visualisation and analysis of plankton, microbial communities, and other aquatic particulates.Other instruments include Amnis ImageStreamX MKII, MACSima Imaging Cytomics System.Provides services from immunotherapy development, precision oncology, and regenerative medicine to environmental monitoring, plant sciences, and nanoparticle characterisation. All services are underpinned by advanced AI-driven analytics, leveraging R, Python, TensorFlow, and PyTorch on high-performance computing platforms to integrate and interpret complex datasets." .
SCR:027344 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Biometra TRIO PCR system" ;
NIFRID:synonym "analytikjena Biometra TRIO",
"Biometra TRIO" ;
definition: "PCR system with three different PCR protocols that can be run simultaneously in three different sample blocks." .
SCR:027345 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DMI4000_B" ;
rdfs:label "Leica | DMI4000 B Automated Inverted Microscope" ;
NIFRID:synonym "DMI4000 B Automated Inverted Microscope" ;
definition: "Microscope for scanning cell and tissue cultures. System features fluorescence axis for ultra brilliant fluorescence imaging.Internal filter wheel with motorized excitation manager and FIM (Fluorescence Intensity Manager) enables excitation of fluorochromes in less than 20 milliseconds." .
SCR:027346 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fast Correlation-Based Filter" ;
NIFRID:synonym "Fast Correlation-Based Filter (FCBF)",
"FCBF : Fast Correlation Based Filter for Feature Selection" ;
NIFRID:abbrev "FCBF" ;
definition: "Software R package to select features with high correlation with the target and little correlation with other variables. It does not use the classical Pearson or Spearman correlations, but metric called Symmetrical Uncertainty." .
SCR:027347 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4103" ;
rdfs:label "Emory University EHCF High Containment Core Facility" ;
NIFRID:synonym "Emory High Containment Facility",
"Emory University High Containment Facility" ;
definition: "Core to enhance research capacity for high containment pathogens and strengthen epidemic and pandemic emergency preparedness capabilities. Offers infrastructure, technical support, training, and regulatory compliant environment to investigators." .
SCR:027348 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4105" ;
rdfs:label "Virginia Tech Fralin Life Sciences Institute Advanced Imaging and Microscopy Core Facility" ;
NIFRID:synonym "Facility for Advanced Imaging and Microscopy (FAIM)" ;
NIFRID:abbrev "FAIM" ;
definition: "Light microscopy research resource facility offers confocal, extended and super resolution, and lightsheet imaging options, as well as assistance and training for researchers. The FAIM also has educational resources available for light microscopy basics, and image processing and analysis." .
SCR:027349 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4101" ;
rdfs:label "State University of Campinas Institute of Chemistry Cell Culture Laboratory Core Facility" ;
NIFRID:synonym "LICel-IQ - Cell Culture Laboratory",
"Universidade Estadual de Campinas (UNICAMP) LICel-IQ - Cell Culture Laboratory" ;
definition: "Provides services involving cultivation of mammalian and insect cells, including genetically modified organisms (GMOs). This laboratory is accredited by CTNBio (Brazilian National Technical Council of Biosafety), and its research activities are monitored by CIBio - IQ (Internal Commission of Biosafety)." .
SCR:027350 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4104" ;
rdfs:label "University of North Carolina at Chapel Hill Bioinformatics and Analytics Research Collaborative BARC Core Facility" ;
NIFRID:synonym "Bioinformatics and Analytics Research Collaborative (BARC)",
"University of North Carolina at Chapel Hill Bioinformatics and Analytics Research Collaborative (BARC)" ;
definition: "Provides bioinformatics expertise and analysis for high throughput data. Services include analysis, visualization, interpretation, and management of big data while also offering custom solutions. Offers collaborative environment by hosting workshops, working groups, and seminars, and improve existing tools and/or invent new tools and algorithms." .
SCR:027351 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4102" ;
rdfs:label "Mexican Social Security Institute National Laboratory of Advanced Microscopy IMSS Core Facility" ;
NIFRID:synonym "Laboratorio Nacional de Microscopia Avanzada-IMSS (LNMA-IMSS)" ;
definition: "Core provides optical microscopy and histology services." .
SCR:027352 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Exeter Archival Diabetes Biobank (EADB)" ;
NIFRID:abbrev "EADB" ;
definition: "Exeter Archival Diabetes Biobank (EADB), formerly the Alan Foulis collection. The collection is managed by the University of Exeter Medical School, with images from the biobank made accessible via Pancreatlas. Collection of pancreatic tissues, largely from children who died shortly after a type 1 diabetes (T1D) diagnosis. Provides high-quality digital images of historical, formalin-fixed, paraffin-embedded samples." .
SCR:027353 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH Cardiovascular Repository for Type 1 Diabetes" ;
NIFRID:synonym "NIH CaReT1D" ;
NIFRID:abbrev "CaRe-T1D",
"CaReT1D" ;
definition: "Cardiovascular Biorepository for Type 1 Diabetes Program (CaRe-T1D) to fill a major void of knowledge that exists related to cardiovascular disease in type 1 diabetes." .
SCR:027354 a owl:NamedIndividual ;
rdfs:label "EssSubgraph" ;
definition: "A model algorithm that integrates omics data and network data to predict essential genes." .
SCR:027355 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Olympus_BX41" ;
rdfs:label "Olympus | BX41 Clinical Microscope" ;
NIFRID:synonym "Olympus BX41" ;
definition: "Olympus BX41 is clinical and research grade microscope. Can be customized. Offered as pre-configured with your choice of viewing head - binocular, ergo binocular, or trinocular. This has Plan N 4x, 10x, 40x, 100x oil objectives but others can be provided if needed. Comes with XY mechanical stage with slide holder and focusable condenser." .
SCR:027356 a owl:NamedIndividual ;
rdfs:label "Tissue properties database" ;
definition: "The Tissue Properties database provides comprehensive estimates for tissue material parameter values and also statistical information about the spread and standard deviation per tissue for the different thermal and fluidic parameters. This information is important for assessment of the contribution to the uncertainty in a quantity of interest due to the selection of the material parameters in simulations. For some material parameters, e.g., perfusion, the variation can be large, which in turn can have a severe effect on simulation results." .
SCR:027357 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "SCR_027365" ;
rdfs:label "Dynamont" ;
definition: "Software segmentation/resquiggling tool for ONT signals. Dynamic programming approach to segment ONT signals." .
SCR:027358 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "openMINDS_instances" ;
NIFRID:synonym "openMINDS instance libraries",
"openMINDS instances" ;
definition: "Software application to provide well defined metadata instances for selected schemas of the openMINDS metadata framework." .
SCR:027359 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AIME:Approximate Inverse Model Explanations" ;
NIFRID:abbrev "AIME" ;
definition: "Software tool to address challenges faced by existing methods in providing intuitive explanations for black-box models. Offers unified global and local feature importance by deriving approximate inverse operators for black-box models." .
SCR:027361 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Journey" ;
NIFRID:synonym "TabakaLab:Cell Journey" ;
definition: "Software tool for interactive exploration and analysis of single-cell trajectories in 3D space." .
SCR:027362 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Custom Design and Fabrication | Electronic Cortical Contusion Injury Device" ;
NIFRID:synonym "(ELECTRIC) CORTICAL CONTUSION IMPACTOR (eCCI)" ;
definition: """Electronic CCI device, with adjustable depth, velocity, dwell time, and angle of impact used for neuroscience research.e CCI is constructed with sturdy aluminum frame to maximize rigidity thereby ensuring impact accuracy. The support base, animal platform, and impactor head are anodized to prevent oxidation and to ensure equipment longevity. The assembly includes the base and support frame, adjustable animal positioner with an aluminum animal
platform to be used in conjunction with a variety of stereotactic mounts.""" .
SCR:027363 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VDJtools" ;
definition: "Software tool as comprehensive analysis framework for T-cell and B-cell repertoire sequencing data." .
SCR:027364 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "The International Physical Activity Questionnaire (IPAQ)" ;
NIFRID:abbrev "IPAQ" ;
definition: "International Physical Activity Questionnaire to obtain comparable estimates of physical activity between populations and countries. It was designed for physical activity surveillance so it is particularly useful for large population studies, but can be used with care in other contexts." .
SCR:027366 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4696" ;
rdfs:label "CRUK Scotland Institute Deep Phenotyping Advanced Technology Core Facility" ;
definition: "Core offers comprehensive pathologist-led spatial biology service comprising spatial proteomic, transcriptomic, and multiomic experimental design, including platform and panel selection, assay development, image acquisition, and digital image processing. The facility houses 2x Ventana Discovery Ultra autostainers, 2x 10 x Genomics Xenium platforms, a Lunaphore COMET, an Akoya PhenoImager, an Akoya PhenoCycler, an Olympus VS200 slide scanner and a Visiopharm image analysis suite." .
SCR:027367 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TRIBUS" ;
definition: "Software tool for cell type based analysis of multiplexed imaging data. Interactive knowledge-based classifier for multiplexed images and proteomic datasets that avoids hard-set thresholds and manual labeling. Recovers fine-grained cell types, matching the gold standard annotations by human experts, can target ambiguous populations and discover phenotypically distinct cell subtypes." .
SCR:027368 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4609" ;
rdfs:label "Cancer Research UK Scotland Institute Molecular Technology Service Core Facility" ;
NIFRID:synonym "Scotland Institute Molecular Technology Service Core Facility" ;
definition: "Core provides Next Generation Sequencing (NGS) services and Single Cell services predominantly focussing on single cell RNAseq. Processes samples for variety of cancer associated projects, in both mouse and human derived materials. Offers full end-to-end service, from initial study design and planning, through sample QC, full library preparation, sequencing and data return. Offers range of standard molecular tests covering, plasmid purifications, Sanger sequencing and mycoplasma screening." .
SCR:027369 a owl:NamedIndividual ;
rdfs:label "Giotto" ;
definition: "Giotto Suite is a major upgrade to the Giotto package that provides tools to process, analyze and visualize spatial multi-omics data at all scales and multiple resolutions. The underlying framework is generalizable to virtually all current and emerging spatial technologies. Our Giotto Suite prototype pipeline is generally applicable on various different datasets, such as those created by state-of-the-art spatial technologies, including in situ hybridization, sequencing, and imaging-based multiplexing/proteomics. These technologies differ in terms of resolution (subcellular, single cell or multiple cells), spatial dimension (2D vs 3D), molecular modality (protein, RNA, DNA, …), and throughput (number of cells and analytes)." .
SCR:027370 a owl:NamedIndividual ;
rdfs:label "Thermo Fisher | Orbitrap Exploris 120 high-resolution mass spectrometer" ;
definition: "Orbitrap Exploris 120 LC-MS spectrometry instruments " .
SCR:027371 a owl:NamedIndividual ;
rdfs:label "MarkerView" ;
definition: "Designed with non-statisticians in mind and intuitively developed, MarkerView software does the heavy lifting so you can focus on high-value decisions like reviewing trends and differences in targeted or untargeted mass spec workflows. Distil complex datasets quickly, find statistically significant differences and reveal key insights faster. MarkerView software is now integrated into the SCIEX OS ecosystem." .
SCR:027372 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4695" ;
rdfs:label "Augusta University Bioinformatics Shared Resource Core Facility" ;
definition: "Georgia Cancer Center's Bioinformatics Core provides expertise in integrative computational based analysis solutions to basic, clinical, and translational research applications. Services include study design, analysis, and interpretation that may involve interaction with industry, government, and regulatory agencies in the areas of Clinical trials, Epidemiology, laboratory studies, in addition to data mining using local and national databases for hypotheses generation and scientific investigation." .
SCR:027373 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iDEP: Integrated Differential Expression and Pathway analysis" ;
NIFRID:abbrev "iDEP" ;
definition: "Integrated web application for differential expression and pathway analysis of RNA-Seq data." .
SCR:027374 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nf-core/proteinfamilies" ;
definition: "Software pipeline that generates protein families from amino acid sequences and/or updates existing families with new sequences. It takes a protein fasta file as input, clusters the sequences and then generates protein family Hiden Markov Models (HMMs) along with their multiple sequence alignments (MSAs). Optionally, paths to existing family HMMs and MSAs can be given (must have matching base filenames one-to-one) in order to update with new sequences in case of matching hits." .
SCR:027375 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rfxplot" ;
definition: "Software toolbox for SPM5 which offers plotting effect sizes, fitted responses, and BOLD time courses averaged across subjects from within 2nd level (random effects) analyses. The toolbox offers a large variety of plot configuration both suitable for data exploration and producing high quality figures for publications." .
SCR:027376 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4693" ;
rdfs:label "Cleveland Clinic Bioinformatics and Protein Engineering Core Facility" ;
definition: "Core provides expert support and consulting in advanced bioinformatics analyses and state-of-the-art protein engineering." .
SCR:027377 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4694" ;
rdfs:label "Purdue University College of Agriculture Research Services Core Facility" ;
definition: "ARGE Research Services is dedicated to empowering Purdue Agriculture research by providing expert solutions in conducting team science, implementing best practices for data acquisition, stewardship, and analysis." .
SCR:027378 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker | Avance NMR Spectrometer" ;
definition: "Bruker’s Avance NMR spectrometers are utilized in various scientific fields to elucidate the structure, dynamics, and interactions of molecules. Avance spectrometers are composed of three main hardware components: console, which is the central control unit of the NMR spectrometer, and houses sophisticated electronics for the generation of the pulse sequences and for data acquisition and processing; superconducting magnet to generate homogenous and stable magnetic field to polarize the nuclear spins in the sample; probe for transmitting radiofrequency pulses and detecting the resulting signals from the sample." .
SCR:027379 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XChiMar" ;
NIFRID:synonym "XChiMar pipeline" ;
definition: "Software machine learning-based genotyping correction tool specifically designed to address chimerism-induced errors in next-generation sequencing (NGS) data from Callithrix marmosets. It leverages an XGBoost classifier trained on allele balance metrics to improve variant calling accuracy in chimeric, non-blood tissues such as hair follicles, tail, and ear." .
SCR:027380 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DiscreteGenoGen" ;
definition: "Software tool for simulating synthetic genotype data specifically designed for discrete nature of genotype representation. Implements evaluation framework that integrates metrics from both quantitative genetics and deep learning." .
SCR:027381 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Transformers" ;
definition: "Software framework for machine learning models in text, computer vision, audio, video, and multimodal model, for both inference and training." .
SCR:027382 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "imagecodecs" ;
definition: "Software Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in tifffile, liffile, czifile, zarr, and other scientific image input/output packages." .
SCR:027383 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "imageio" ;
definition: "Software Python library to read and write wide range of image data, including animated images, volumetric data, and scientific formats. It is cross-platform, runs on Python 3.9+, and is easy to install." .
SCR:027384 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 501100018703",
"GRID grid.23636.32",
"ISNI 0000 0000 8821 5196",
"Wikidata Q25188472" ;
rdfs:label "Cancer Research UK Scotland Institute" ;
NIFRID:abbrev "CRUK Scotland Institute" ;
definition: "CRUK Scotland Institute (formerly the CRUK Beatson Institute)* is core-funded by Cancer Research UK and provides environment for its basic and translational scientists to understand the mechanisms that regulate cancer cell proliferation, survival and dissemination; to identify critical components of these pathways as targets for novel cancer therapies; and to help translate this knowledge to patient benefit." .
SCR:027385 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MassImager" ;
definition: "Software for interactive and in-depth analysis of Mass Spectrometry Imaging (MSI) data." .
SCR:027386 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4610" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Center for Therapeutics Discovery Core Facility" ;
NIFRID:synonym "Cleveland Clinic Center for Therapeutics Discovery",
"Cleveland Clinic Center for Therapeutics Discovery (C3TD)" ;
definition: "Core to promote translation of basic science discoveries by Cleveland Clinic researchers into new therapeutics. Through collaboration with investigators we de-risk promising approaches and illuminate fundamental biology using small molecule chemical probes. We have established a pipeline of innovative research programs directed toward improving patient care with a true bench-to-bedside vision. To achieve these goals, we use state of the art technologies in small molecule library screening, fragment-based methods, X-ray crystallography, computational tools, and target validation towards generating starting points for nascent hit-to-lead and lead optimization campaigns." .
SCR:027387 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GHDL" ;
definition: "Software tool to analyse and elaborate sources for generating machine code from your design. Open-source analyzer, compiler, simulator and (experimental) synthesizer for VHDL, a Hardware Description Language (HDL)." .
SCR:027388 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SeSAMe" ;
NIFRID:synonym "SEnsible Step-wise Analysis of DNA MEthylation" ;
definition: "Software R package for reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions." .
SCR:027389 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4607" ;
rdfs:label "State University of Campinas LIAFQ-IQ Laboratory of Physicochemical Analysis Core Facility" ;
NIFRID:synonym "LIAFQ-IQ - Laboratory of Physicochemical Analysis",
"Universidade Estadual de Campinas (UNICAMP) LIAFQ-IQ - Laboratory of Physicochemical Analysis" ;
definition: "Laboratory for Physicochemical Analysis of IQ-UNICAMP houses equipment for a range of analytical techniques:Thermal Analysis comprises techniques that measure the physical or chemical properties of a substance, or its reaction products, under controlled temperature variation;Atomic Spectrometry enables multi-element determination in solution samples;Elemental Analysis is used to determine the Carbon, Hydrogen, and Nitrogen content in solid and viscous samples.Nitrogen Physisorption is a technique used to determine the surface area and pore size of solid materials." .
SCR:027390 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4606" ;
rdfs:label "State University of Campinas LIBio-IQ Biosefaty Laboratories Core Facility" ;
NIFRID:synonym "LIBio-IQ - Biosefaty Laboratories",
"Universidade Estadual de Campinas (UNICAMP) LIBio-IQ - Biosefaty Laboratories" ;
definition: "Core belongs to the Institute of Chemistry of UNICAMP and are structured to accommodate works involving pathogenic bacteria and fungi or genetically modified organisms (GMO). Part of CTNBio (Brazilian National Technical Council of Biosafety) accredited areas and have research activities monitored by CIBio -IQ (Internal Commission of Biosafety)." .
SCR:027391 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4106" ;
rdfs:label "State University of Campinas LISpec-IQ Spectroscopy Core Facility" ;
NIFRID:synonym "LISpec-IQ-Spectroscopy Core Facility",
"Universidade Estadual de Campinas (UNICAMP) LISpec-IQ-Spectroscopy Core Facility" ;
definition: "Institutional Spectroscopy Laboratory is equipped with a comprehensive suite of instruments for spectroscopic analysis. Our capabilities include absorption spectroscopy (UV-Vis, NIR, and IR), Raman scattering, and fluorescence emission spectroscopy." .
SCR:027392 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4608" ;
rdfs:label "State University of Campinas LIRX-IQ X-Ray Institutional Laboratory Core Facility" ;
NIFRID:synonym "LIRX-IQ-X-Ray Institutional Laboratory",
"Universidade Estadual de Campinas (UNICAMP) LIRX-IQ-X-Ray Institutional Laboratory" ;
definition: "Institutional Laboratory of X-ray facility is equipped with instruments that work with following analytical techniques: single crystal X-ray diffraction (SCXRD), X-ray fluorescence (XRF), and small-angle X-ray scattering (SAXS)." .
SCR:027393 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4690" ;
rdfs:label "Washington University School of Medicine Mass Spectrometry Technology Access Center Core Facility" ;
NIFRID:synonym "McDonnell Genome Institute Mass Spectrometry Technology Access Center",
"Washington University School of Medicine McDonnell Genome Institute Mass Spectrometry Technology Access Center" ;
NIFRID:abbrev "MTAC@MGI" ;
definition: "Core services range from simple protein identification to quantification of proteins (relative and absolute) through bottom-up proteomics analyses. Offers intact, native, and top-down proteomics analyses. Provides comprehensive global quantitative analysis of post-translational modifications (PTMs) such as phosphorylation, ubiquitination, acetylation, and methylation, as well as epiproteomics histone PTM assays." .
SCR:027394 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4691" ;
rdfs:label "University of Liverpool Centre for Genomic Research Core Facility" ;
NIFRID:synonym "University of Liverpool Centre for Genomic Research (LIV-SRF)" ;
definition: "Core facility that provides academic and industrial researchers from around the world with affordable multi-platform sequencing, library preparation, data analysis and related services." .
SCR:027395 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4692" ;
rdfs:label "University of Kentucky Animal Behavior and Energy Balance Core Facility" ;
definition: """Core conducts animal behavior tests for investigators at the University of Kentucky.
Ensures that qualified and trained investigators have access to instrumentation and expertise necessary to perform behavior tests. Provides assistance in the design, implementation and analysis of behavioral experiments in rodents and other animals.
Provides equipment for measurement of lean/fat mass and whole body metabolism in mice. Echo MRI is utilized for non-invasive quantitative assessment of lean and fat mass. Sable Promethion Calorimeter indirectly measures oxygen consumption (RER), food and water intake, and physical activity in mice.""" .
SCR:027398 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BRAINCELL-AID" ;
NIFRID:synonym "Brain Cell type Annotation and Integration using Distributed AI" ;
definition: "Web service providing annotations for brain cell type–specific marker gene sets derived from single-cell RNA-seq data spanning the entire mouse brain. It uses a multi-agent AI framework that combines fine-tuned large language models with retrieval-augmented generation, producing biologically grounded annotations supported by peer-reviewed literature." .
SCR:027399 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SEAHORSE" ;
NIFRID:synonym "Serendipity Engine Assaying Heterogeneous Omics Related Sampling Experiments" ;
definition: "Web-based database and search tool for exploratory data analysis in which we have pre-computed statistical associations between available data elements. Large-scale, open-access data sets such as the Genotype Tissue Expression Project (GTEx) and The Cancer Genome Atlas (TCGA) include multi-omic data on large numbers of samples along with extensive clinical and phenotypic information. Allows users to explore significant associations using tabulated summary statistics, data visualizations, and functional enrichment analyses (using RNA-seq data) for identified sets of genes." .
SCR:027401 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "funROI" ;
NIFRID:synonym "FUNctional Region Of Interest" ;
definition: "Software Python toolbox for functional ROI analysis of fMRI data. Provides analytic methods for fMRI data analyses that accommodate inter-subject variability in precise locations of functional activations. Supports several types of analyses, such as parcel generation, fROI definition, effect estimation, spatial correlation estimation, and spatial overlap estimation. The toolbox is compliant with the Brain Imaging Data Structure (BIDS), standardized framework for organizing and sharing neuroimaging data." .
SCR:027402 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "ChemDiv" ;
definition: "Target-to-Clinic Contract Research Organization (CRO) headquartered in San Diego, CA USA. ChemDiv executes pre-clinical discovery chemistry and biology for drug development and clinical trials for international portfolio of companies across the entire range of targets with small molecule and biotech drugs. The company operates multiple research and development (R&D) subsidiaries in Russia, Ukraine and China as well as business operations around the world." .
SCR:027403 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Jeol_JCM-6000" ;
rdfs:label "JEOL | JCM-6000 Benchtop Scanning Electron Microscope" ;
NIFRID:synonym "Jeol JCM-6000" ;
definition: "Compact Benchtop Scanning Electron Microscope. Intuitive operation is achieved via touch panel and new operation screens. The high or low vacuum mode is included in the standard configuration, and EDS can be installed, offering truly multi-functional benchtop SEM." .
SCR:027404 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_XploRA_PLUS" ;
rdfs:label "Horiba | Xplora Plus Confocal Raman Microscope" ;
definition: "Confocal microscope incorporates unique and powerful functions in reliable, high performance system, ideally suited to the research and analytical lab. SWIFT™ Fast Raman images are the fastest fully confocal Raman images available, typically 10x faster than conventional Raman imaging. Has enhanced range of options such as multiple laser wavelengths, EMCCD detection, Raman polarisation and AFM Raman TERS combination." .
SCR:027405 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ClusterGraph" ;
definition: "Software tool for visualization of geometric organization of clusters. Mapper-inspired tool to visualize global layout of clusters." .
SCR:027406 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_4697" ;
rdfs:label "University of Michigan Medical School Hybridoma Core Facility" ;
NIFRID:synonym "UMICH Hybridoma Core" ;
definition: "Core provides research services in custom monoclonal antibody development (mAb) and bulk production of monoclonal antibodies from established hybridomas (somatic cell hybrids). Core has developed monoclonal antibodies against a wide variety of lymphocyte surface antigens, tumor cell antigens, purified proteins, hormones, hormone receptors and recombinant proteins and peptides." .
SCR:027407 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HVRLocator" ;
definition: "Software application to identify spanning hypervariable region(s) from amplicon sequencing variants or SRA public runs (SRR). Aligns query sequences to reference E. coli full-length 16S rRNA gene and identifies spanning region through alignment. Used for identifying hypervariable regions in 16S rRNA big datasets." .
SCR:027408 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DOSE" ;
NIFRID:synonym "Disease Ontology Semantic and Enrichment",
"Disease Ontology Semantic and Enrichment (DOSE)" ;
definition: "Software R package for disease ontology semantic and enrichment analysis." .
SCR:027409 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BlenderNEURON" ;
definition: "Software Python package and addon that takes NEURON simulator model and exports its 3D structure and membrane activity to Blender. Used to integrate NEURON simulator with Blender, allowing 3D visualization, animation, and modeling of NEURON models in Blender." .
SCR:027410 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Combenefit" ;
definition: "Software interactive platform for analysis and visualization of drug combinations. Used for analyzing drug combination effects (e.g., synergy, additivity, or antagonism). Offers advanced data visualization, including 2D/3D heatmaps and dose-response curves, and processes high-throughput data from Excel/CSV files. Users can customize models or extend functionality via Python scripting." .
SCR:027411 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Shapely" ;
definition: "Software Python package for manipulation and analysis of geometric objects in the Cartesian plane." .
SCR:027412 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ARTool" ;
NIFRID:synonym "Aligned Rank Tool" ;
definition: "Software R package for aligned rank transform for nonparametric factorial ANOVAs." .
SCR:027413 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Paintera" ;
definition: "Software general visualization tool for 3D volumetric data and proof-reading in segmentation or reconstruction." .
SCR:027414 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FPulse" ;
definition: "Software application as data acquistion system for patch-clamp recordings, based in CED1401 hardware, and IgorPro." .
SCR:027415 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Noise2Void" ;
NIFRID:synonym "Noise2Void (N2V)" ;
NIFRID:abbrev "N2V" ;
definition: "Software application for denoising from single noisy images." .
SCR:027416 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fedrann" ;
definition: "Software scalable pipeline for overlap detection based on large-scale sequencing data. It is based on three steps: feature extraction, dimenality reduction, and approximate k-nearest neighbor search. Used for effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors." .
SCR:027417 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dusk2Dawn" ;
definition: "Software plugin for 'EEGLAB' MATLAB toolbox, which allows to whole-night sleep EEG using Artifact Subspace Reconstruction (ASR). Used to implement Artifact Subspace Reconstruction cleaning with whole-night sleep EEG. Automatic cleaning of whole-night sleep electroencephalogram using Artifact Subspace Reconstruction." .
SCR:027418 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PeriodAmplitudeAnalysis" ;
definition: "Software application for Period Amplitude Analysis (PAA) for slow wave detection using eeglab." .
SCR:027419 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CORE" ;
NIFRID:synonym "Cores Of Recurrent Events" ;
definition: "Software R package to inference from interval data. Given collection of observed events and geometric association measure between events and explanatory intervals, CORE finds given number of explanatory cores that maximizes the explanation. Combinatorial optimization procedure with depth chosen from considerations of statistical significance." .
SCR:027420 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hictk" ;
definition: "Software blazing fast toolkit to work with .hic and .cool files." .
SCR:027421 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5115" ;
rdfs:label "University of Michigan ISR-VR Lab Core Facility" ;
definition: "Core provides flexible systems with built-in support for biometric data collection, dyadic interactions, and reproducible protocols. Provides access to pipelines that support reproducibility, custom data annotation, and seamless handoff to analysis tools in R, Python, and more. Provides access to IRB-ready templates and documentation, along with tested participant safety protocols and secure data management systems." .
SCR:027422 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5114" ;
rdfs:label "University of Michigan Medical School Nucleic Acid Therapeutics Core Facility" ;
definition: "Nucleic Acid Therapeutics Core accelerates the development of gene-targeted therapies by providing custom oligonucleotide synthesis, expert consultation, and platform for cross-disciplinary collaboration." .
SCR:027423 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProjPrev" ;
NIFRID:synonym "NCI Projected Prevalence",
"Projected Prevalence",
"Projected Prevalence (ProjPrev)" ;
definition: "Software application to apply limited-duration prevalence statistics from SEER*Stat to different population. The population would typically differ in year or geographic area. Enables users to project cancer prevalence data from SEER registries onto larger U.S. or other populations." .
SCR:027424 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Antibody Watch" ;
definition: "Text mining antibody specificity from literature. Helps researchers identify potential problems with antibody specificity. By mining the scientific literature and linking findings to Research Resource Identifiers (RRIDs), it provides alerts on antibodies that may yield unreliable results, supporting reproducibility in biomedical research." .
SCR:027425 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_IVIS_Spectrum_2" ;
rdfs:label "Revvity | IVIS Spectrum 2 In Vivo Imaging System" ;
NIFRID:synonym "IVIS Spectrum 2 In Vivo Imaging System" ;
definition: "In vivo optical imaging system used in preclinical research to non-invasively monitor and quantify biological processes in living animals over time. Designed with innovative camera with patented coating that delivers high sensitivity 2D and 3D bioluminescence and fluorescence imaging capabilities." .
SCR:027426 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Torres CSVmerger" ;
NIFRID:synonym "CSVmerger" ;
definition: "Web tool for merging csv files intended to be submitted to the open data commons databases including: ODC-TBI, ODC-SCI." .
SCR:027427 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VCFPy" ;
definition: "Software Python 3 library with good support for both reading and writing VCF. Reads and writes VCF files in Python." .
SCR:027428 a owl:NamedIndividual ;
rdfs:label "MiGenPro" ;
NIFRID:synonym "Migenpro",
"migenpro" ;
NIFRID:abbrev "Microbial Genome Prospecting (MiGenPro)",
"Semantic Annotation Platform with Provenance (SAPP)",
"SPARQL Protocol and RDF Query Language (SPARQL)" ;
definition: "Software Microbial Genome Processing toolkit. Flexible linked data framework for phenotype-genotype prediction of microbial traits using machine learning." .
SCR:027429 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "memesuite-lite" ;
definition: "Software application as lightweight reimplementation of some of the algorithms in the MEME suite in Python." .
SCR:027430 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Janelia Automatic Animal Behavior Annotator" ;
NIFRID:synonym "Janelia Automatic Animal Behavior Annotator (JAABA)" ;
NIFRID:abbrev "JAABA" ;
definition: "Web application to create variety of automatic behavior classifiers. These classifiers input the animals' trajectories computed by tracking system, and they output time series indicating whether each animal is performing a given behavior in each video frame. Interactive machine learning for automatic annotation of animal behavior. Used to automatically compute interpretable, quantitative statistics describing video of behaving animals." .
SCR:027431 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Caltech FlyTracker" ;
NIFRID:synonym "FlyTracker" ;
definition: "Web application to track the pose (position, orientation, size, wing- and leg positions) of multiple flies and maintain their identities throughout video. Outputs features (such as velocity, facing angle to other fly, and wing angles) useful for behavior analysis." .
SCR:027432 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tempo" ;
definition: "Software application for media browsing, analysis and annotation. MATLAB GUI for browsing, analyzing and annotating time-synchronized media files." .
SCR:027433 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DMC-BrainMap" ;
definition: "Software napari plugin for flexible mapping of various features (cell bodies, axonal densities, injections sites, optical fibers, Neuropixels probes) to standardized reference spaces included in BrainGlobe. Used for anatomical mapping." .
SCR:027434 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DMC-Behavior Platform" ;
definition: "Software DMC-Behavior Platform for standardized auditory decision-making tasks in head-fixed mice." .
SCR:027435 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DMC-FluoImager" ;
definition: "Software Python project for whole slide image acquisition using a fluorescence microscope." .
SCR:027436 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TF-MInDi" ;
definition: "Software Python package for analyzing transcription factor binding patterns from deep learning model attribution scores. It identifies and clusters sequence motifs from contribution scores, maps them to DNA-binding domains, and provides comprehensive visualization tools for regulatory genomics analysis. Used for transcription factor motifs and instances discovery." .
SCR:027437 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5117" ;
rdfs:label "Ottawa Hospital Research Institute Human Pluripotent Stem Cell Core Facility" ;
NIFRID:synonym "Ottawa Human Pluripotent Stem Cell Facility" ;
definition: "Training and support to research with human embryonic and induced pluripotent stem cells (iPSC). Offers opportunity to dissect early human development, generate models of disease, and develop cellular or drug therapeutics." .
SCR:027438 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "USEARCH" ;
NIFRID:synonym "USEARCH12" ;
definition: "Software application that provides search and clustering functionality, typically used with amplicon sequence data. Used to assign sequences to clusters." .
SCR:027439 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Nichirei Biosciences Inc" ;
definition: "Bioscience division of the Japanese conglomerate Nichirei Corporation, specializing in biomedical products for the health and life science industries. The company develops, manufactures, and distributes products for immunohistochemistry (IHC), such as diagnostic and research reagents as well as products for cell biology, rapid diagnostics, functional materials, and natural materials processing. Their products support applications in pathological diagnosis, food safety, and cosmetic ingredients." .
SCR:027440 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100019953",
"GRID grid.471279.e",
"ISNI 0000 0001 2217 1263",
"Wikidata Q7830642" ;
rdfs:label "TOYOBO" ;
definition: "Japanese company that began as a textile manufacturer in 1882 and has expanded to become a global provider of high-function products, including films, functional polymers, industrial materials, and biotechnology products such as enzymes and diagnostic reagents. The company's business is organized around its core technologies in polymerization, modification, processing, and biotechnology, allowing it to contribute to fields like healthcare, environment, and electronics." .
SCR:027441 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LILAC" ;
definition: "Software HLA typing tool to determine HLA-I germline alleles by aligning sequencing reads to HLA-A, HLA-B and HLA-C regions present in the IMGT/HLA database, optimized for cancer genomics analysis with support for tumor-normal paired samples and designed to handle complex scenarios including HLA-Y pseudogene detection and loss of heterozygosity assessment. Open-source integrative framework that characterizes the HLA-I locus, including its tumor status from WGS data." .
SCR:027442 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5119" ;
rdfs:label "University of Luxembourg Model Biobank and Tissue Analytics Platform Core Facility" ;
definition: "Core offers advanced single and combined services including genomics, imaging, metabolomics and lipidomics, in vivo disease modelling, cell-based alternative methods, drug screening, and bioinformatics, providing researchers with essential tools for scientific exploration. Expert staff members offer advice on experimental design, data processing, and troubleshooting, as well as training to facilitate the use of our technologies." .
SCR:027443 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5120" ;
rdfs:label "University of Luxembourg LCSB Bioinformatics Platform Core Facility" ;
definition: """Offers advanced single and combined services including genomics, imaging, metabolomics and lipidomics, in vivo disease modelling, cell-based alternative methods, drug screening, and bioinformatics, providing researchers with essential tools for scientific exploration.
Staff members offer advice on experimental design, data processing, and troubleshooting, as well as training to facilitate the use of our technologies.""" .
SCR:027444 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Childhood Cancer Registry" ;
NIFRID:synonym "National Cancer Institute National Childhood Cancer Registry",
"NCI National Childhood Cancer Registry" ;
NIFRID:abbrev "NCCR" ;
definition: "Platform provides public health surveillance data to better understand the causes, outcomes, effective treatments, and later effects of cancer among children, adolescents, and young adults in the U.S. Developed under the NCI Childhood Cancer Data Initiative (CCDI), the NCCR contributes to the CCDI data ecosystem by serving as a linked infrastructure of central cancer registry data that will integrate various other childhood cancer data—from hospitals, research centers, heath care administrations, and other sources—to enhance access to and utilization of childhood cancer and survivorship data. The NCCR uses the Virtual Pooled Registry Cancer Linkage System to link multiple cancer registries and generate an accurate count of childhood cancer cases by combining information that appears in more than one registry." .
SCR:027445 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GFFx" ;
definition: "Software Rust-Based suite of utilities for ultra-fast genomic feature extraction. Used for ultra-fast and scalable genome annotation access. Can be used both as a command-line tool and as a Rust library." .
SCR:027446 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ion_S5" ;
rdfs:label "Thermo Fisher | Ion S5 System" ;
NIFRID:synonym "Ion S5 Sequencer" ;
definition: "Ion S5 next-generation sequencing system enables simple targeted sequencing workflow for your lab with reliable performance and industry-leading speed. Torrent Server direct connection to the Ion S5 Sequencer is supported." .
SCR:027447 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.34424.35",
"ISNI 0000 0004 0466 6352",
"Wikidata Q5294218" ;
rdfs:label "Donald Danforth Plant Science Center" ;
definition: "Independent, not-for-profit research institute dedicated to plant science located in the Olivette community of Saint Louis County, Missouri, United States." .
SCR:027449 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCP-counter" ;
NIFRID:synonym "Microenvironment Cell Populations-counter" ;
definition: "Software to perform convolution of human bulk transcriptomics and evaluate abundance scores for 10 cell populations. Allows quantification of absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic data." .
SCR:027450 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIRD" ;
definition: "Software tool as network inference in reduced diemnsion. Used to perceive contribution of regulatory components by transforming datasets into networks, using dimensionality reduction and assessing the overlapping structure with AUC metrics." .
SCR:027451 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "National Neighborhood Data Archive" ;
definition: "Open data repository to facilitate research on the relationship between neighborhoods and health, especially within the context of large federally funded surveys and cohort studies. Used to explore topics of interest to neighborhoods and communities. NaNDA measures can be readily linked to survey data, cohort studies, electronic medical records, or other microdata, via geographic identifiers, or combined and explored on their own. NaNDA datasets are created by researchers in the Social Environment and Health program at the University of Michigan Institute for Social Research." .
SCR:027452 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MarmotGraph" ;
NIFRID:synonym "Management Applications for Rich Metadata ObjecTs Graph" ;
definition: "Knowledge graph system developed for managing and organizing rich metadata objects, initially for the Human Brain Project (HBP) and now extended to be a more generic, domain-agnostic solution. It is associated with CSCS (Swiss National Supercomputing Centre) and aims to provide a comprehensive toolset and API for working with knowledge graphs." .
SCR:027453 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NApy" ;
definition: "Software Python tool providing statistical tests for large-scale heterogeneous data with enhanced support for missing data." .
SCR:027454 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DescTools" ;
definition: "Software R package for descriptive statistics and exploratory data analysis. Collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data." .
SCR:027455 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "coin" ;
definition: "Software R package for conditional inference procedures in permutation test framework. Conditional inference procedures for general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems described in." .
SCR:027456 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " pychromVAR" ;
definition: "Software Python package for inferring transcription factor binding variability from scATAC-seq data by implmenting algorithm proposed in chromVAR. It is built on anndata and mudata therefore can work seamlessly with scanpy and muon pipeline." .
SCR:027461 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Aperio_AT2_DX" ;
rdfs:label "Leica | Aperio AT2 DX System" ;
NIFRID:synonym "Aperio AT2 DX System" ;
definition: "400 slide scanner with Aperio ImageScope DX clinical viewing software, and high-performance viewing workstation including color-calibrated medical grade monitors. System can be used standalone, or in conjunction with Aperio Path DX case management software, for streamlined, clinical workflow. Developed from Leica Biosystems,enables to produce consistent, diagnostic quality images, enabling pathologists to diagnose with confidence." .
SCR:027462 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Souporcell" ;
definition: "Software tool to cluster cells using the genetic variants detected within the scRNAseq reads. Robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Used for clustering scRNAseq by genotypes." .
SCR:027463 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Vireo" ;
definition: "Software tool for Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference." .
SCR:027464 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "speckle" ;
definition: "Software R package to analyse differences in cell type proportions in single cell RNA-seq data. Used for analysing single cell data." .
SCR:027465 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CGPipe" ;
definition: "Software minimum viable HPC pipeline. CGPipe is a replacement for the venerable \"make\" that aims to automate the process of running complex analysis pipelines on high-throughput clusters. Make is a standard build tool for compiling software." .
SCR:027466 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GWAS Atlas" ;
definition: "Updated knowledgebase integrating more curated associations in plants and animals. manually curated resource of genome-wide genotype-to-phenotype associations for a wide range of species. Database of publicly available GWAS summary statistics. Each GWAS can be browsed with the manhattan plot, risk loci, MAGMA (i.e. gene-based) results, SNP heritability and genetic correlations with other GWAS in the database. Full summary statistics can be downloaded from the original source following the provided links." .
SCR:027467 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Pannoramic_150" ;
rdfs:label "3DHISTECH | Pannoramic 150 Digital Scanner" ;
NIFRID:synonym "Pannoramic 150 Digital Scanner" ;
definition: """Digital pathology system designed for high-speed, high-resolution brightfield and fluorescence scanning. Equipped with continuously moving stage, advanced Plan-Apochromat optics including 10x objective, and a back-illuminated sCMOS camera.
Capacity:150 slides (6 magazines, 25 slides each) with automatic loading and continuous scanning.Scanning:Dual-mode scanning (brightfield and fluorescence) with area scanning and autofocus.Motorized Camera ChangerIncluded, for seamless transitions between BF and FL imaging modes without manual intervention.Motorized Objective changer
Included when two objectives are selected (supports two objectives).Brightfield Scanning Speed:1 minute 30 seconds for 15 mm x 15 mm area at 0.19 µm/pixel resolution. Fluorescence Scanning Speed:8 minutes 30 seconds for a 15 mm x 15 mm area with 3 fluorescent channels at 20 ms exposure time.Throughput Optimized for high-throughput workflows with fully automated slide handling. Objectives Plan-Apochromat 10x/0.3 NA, 20x/0.8 NA, and 40x Corr/0.95 NA objectives.Brightfield Magnification Up to 103x.
Fluorescence Magnification Up to 98x (with 1.6x adapter). Image Output MRXS format with export options to JPG, JPEGXR, BMP, PNG, TIFF, Roche TIFF, SVS, and DICOM.Slide Compatibility: Slides measuring 75.0-76.2 mm (L) x 25.0-26.0 mm (W) x 0.9-1.2 mm (T) with No. 1 or 1.5 coverslips (0.13-0.19 mm).""" .
SCR:027468 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyTorch Lightning" ;
definition: "Open-source software Python library that provides high-level interface for PyTorch deep learning framework." .
SCR:027469 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5214" ;
rdfs:label "Fred Hutchinson Cancer Center Biostatistics Shared Resource" ;
NIFRID:synonym "Fred Hutchinson Cancer Center Biostatistics Shared Resource Core Facility" ;
definition: "Biostatistics Shared Resource (BSR) provides free, short-term statistical support to Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium investigators, particularly those without dedicated funding. Services include consultations on study design, sample size, power, and analytic methods; assistance with data analysis, interpretation, and manuscripts; and development of statistical sections for grant proposals. While intended as short-term collaborations, BSR projects often lead to funded grants and longer-term partnerships with biostatisticians." .
SCR:027470 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NEXT-scASV" ;
definition: "Software Nextflow pipeline for calling allele-specific variants (ASVs) from 5′ single-cell RNA sequencing data." .
SCR:027471 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HyenaDNA" ;
definition: "Software application as long-range genomic foundation model pretrained on context lengths of up to 1 million tokens at single nucleotide resolution." .
SCR:027472 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nucleotide Transformer" ;
definition: "Genomic language model trained on cross species data." .
SCR:027473 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "create_cisTarget_databases" ;
definition: "Code to create cisTarget databases." .
SCR:027474 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "USDA ERS Rural-Urban Continuum Codes" ;
NIFRID:synonym "U.S. Department of Agriculture's Economic Research Service Rural-Urban Continuum Codes" ;
definition: "Mission of U.S. Department of Agriculture's Economic Research Service is to anticipate trends and emerging issues in agriculture, food, environment, and rural America and to conduct high-quality, objective economic research to inform and enhance public and private decision making. Rural-Urban Continuum Codes distinguish U.S. metropolitan (metro) counties by the population size of their metro area, and nonmetropolitan (nonmetro) counties by their degree of urbanization and adjacency to a metro area. The codes allow researchers, policy makers, and others to view county-level data by finer residential groups—beyond metro and nonmetro—when analyzing trends related to population density and metro influence." .
SCR:027475 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Appalachian Regional Commission Data Reports" ;
NIFRID:synonym "Appalachian Regional Commission (ARC) Data Reports" ;
definition: "Web data report tool uses publicly available data to generate reports for every Appalachian state and county across different topics. Provides detailed information on socioeconomic and demographic factors in Appalachian Region, serving to inform policymakers and regional partners for economic development and decision-making." .
SCR:027476 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Echo_550" ;
rdfs:label "Bechman Coulter | Labcyte Echo 550 acoustic liquid handler" ;
definition: """Non-contact liquid handler that uses Acoustic Droplet Ejection (ADE) technology to precisely transfer nanoliter-sized droplets of liquid for high-throughput applications in pharmaceutical research, drug discovery, and various areas of genomics and biology.
Echo 555 / 550 Liquid Handler: 2.5 nL increment; Flow rate:0.25 – 1 µL/sec; Ideal for reactions of 0.05 – 1 µL; Supports 384 and 1536-well source plate formats; Used for transfer of small molecules for high throughput screening.""" .
SCR:027477 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5216" ;
rdfs:label "Cleveland Clinic Lerner Research Institute Light Microscopy Core Facility" ;
definition: "Core services include: basic light microscopy (determine appropriate staining protocols and offer training and/or assistance in acquiring transmitted and fluorescent digital images with wide-field microscopes); optical sectioning (training and assistance in the use of confocal and multi-photon microscopes); whole slide scanning (brightfield or fluorescence mode). Laser MicroDissection instruments are available for isolating small areas of tissue or single cells. Total Interference Reflection Fluorescence (TIRF) microscopy is available for visualizing and quantifying cellular events localized at the basal plasma membrane. Live cell and tissue imaging can be done on both wide-field and confocal microscopes equipped with environmental chambers for heat/CO2 control.Investigators have access to Image Processing and Analysis workstations with variety of advanced software for extracting quantitative data from their images. They can also generate images and movies for presentations, grants and publications. Core is home to 2 LI-COR Odyssey, laser-based scanning systems for gels, Westerns, in-cell Westerns, ELISA/FLISA, EMSA/Gel Shift, Protein Detection, etc." .
SCR:027478 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5254" ;
rdfs:label "University of Michigan Robert B. Zajonc Experimental Lab Core Facility" ;
definition: "Core provides researchers with facilities to conduct experimental research, particularly within the Research Center for Group Dynamics (RCGD) and across the U-M campus. The labs offer adaptable room configurations, specialized software like E-Prime and z-Tree, and shared access to cutting-edge technology, including a new Virtual Reality (VR) Lab, to support a range of interdisciplinary research projects focused on human social behavior and dynamics." .
SCR:027479 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2951" ;
rdfs:label "Houston Methodist HMRI Neurology Electron Microscopy Core Facility" ;
NIFRID:synonym "HMRI Neurology Electron Microscopy Core Facility" ;
definition: "Core is fee-for-service research laboratory providing internal and external users a wide spectrum of electron microscopy (EM) techniques. As part of the Houston Methodist Research Institute Department of Neurology, we routinely process samples related to the peripheral nervous system but can help with the ultrastructural study of many biological samples." .
SCR:027480 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5158" ;
rdfs:label "Duke University Shared Materials Instrumentation Facility (SMIF)" ;
definition: "Pratt School of Engineering core facility that enables materials, devices, and integrated systems research at Duke University in a variety of fields that include materials, devices, and integrated systems. SMIF is housed in the Fitzpatrick Center for Interdisciplinary Engineering, Medicine and Applied Sciences (FCIEMAS). The facility consists of 7,000 square feet of clean room fabrication space, and nearly 3,000 square feet of specialized laboratory space for characterization and imaging equipment." .
SCR:027481 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2785" ;
rdfs:label "University of Pittsburgh Hillman Cancer Center Translational Oncologic Pathology Services Core Facility" ;
NIFRID:synonym "Translational Oncologic Pathology Services (TOPS)",
"UPMC Hillman Cancer Center Translational Oncologic Pathology Services (TOPS)" ;
definition: "TOPS is a UPMC Hillman Cancer Center managed and regulated resource that provides coordinated collection, processing, annotation, distribution, and storage of patient biospecimens to investigators and their respective collaborators." .
SCR:027482 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100015190",
"GRID grid.63368.38",
"ISNI 0000 0004 0445 0041",
"Wikidata Q7751188" ;
rdfs:label "Houston Methodist" ;
definition: "Houston Methodist Hospital is the flagship quaternary care hospital of Houston Methodist academic medical center.Houston Methodist Hospital is ranked among the country's top hospitals" .
SCR:027483 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SeedGerm-VIG" ;
definition: "Software pipeline to quantify seed vigour in wheat and other cereal crops using deep learning powered dynamic phenotypic analysis." .
SCR:027484 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BEACON" ;
definition: "Software application to perform Bayesian analysis on expression and gene dependency data across different cell lineages. Integrates expression as the dependent variable and gene dependency data as the independent variable. Used to identify cancer gene targets by jointly analyzing global transcriptomic and proteomic profiles with genetic dependency data of cancer cell lines across tissue lineages." .
SCR:027485 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CytoML" ;
definition: "Software R package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R." .
SCR:027486 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HITACHI_H-7650" ;
rdfs:label "Hitachi | H-7650 electron microscope" ;
definition: "Transmission electron microscope developed for the fields of biology and materials science. Equipped with a highly sensitive CCD camera, the H-7650 delivers images with optimal contrast even under low-dose electron beam conditions. As the CCD camera is integrated into the microscope, it can be controlled either manually via the control panel or through a PC. Images displayed on the monitor can be stored in digital formats. With built-in autofocus, other automated functions, and database capabilities, the H-7650 provides users with a user-friendly operating environment during observation." .
SCR:027487 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5305" ;
rdfs:label "University of Ottawa Integrated Neurocognitive and Social Psychophysiology Interdisciplinary Research Environment (INSPIRE) Core Facility" ;
definition: "Multidisciplinary facility designed to explore questions related to human behaviour from various perspectives, including human cognition, social interactions, and psychophysiology." .
SCR:027488 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5306" ;
rdfs:label "University of South Carolina Research Computing Core Facility" ;
definition: "Reporting to the Division of Information Technology, and working in close partnership with the Office of Research, works with researchers to improve their project performance and secure computing resources not only at the university level but beyond, to National Labs and other high profile HPC resources." .
SCR:027489 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ganzfeld_Q450_SC" ;
rdfs:label "Roland | Ganzfeld Q450SC Electrophysiological Test Unit" ;
definition: "Electrophysiological Test Unit for animals. This is usable for Pattern VEP + Pattern ERG + Flash VEP, for scotopic and photopic ERG, EOG fast and slow, mf ERG Flash stimulation and mf VEP Pattern stimulation." .
SCR:027490 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5213" ;
rdfs:label "Mayo Clinic Structural Biology Core Facility" ;
NIFRID:synonym "Mayo Clinic Structural Biology Core",
"Structural Biology Core" ;
definition: "Core offers instrumentation and support for the structural characterization of biological macromolecules to investigators at Mayo Clinic and its partner institutions. Supports cryogenic sample electron microscopy (cryoEM), along with associated services such as training, data collection, processing, analysis, and data storage. Future services will include nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography." .
SCR:027491 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phynteny_transformer" ;
definition: "Software application that predicts bacteriophage gene functions by leveraging gene synteny and genome-wide organizational patterns. Synteny-enhanced annotation of Bacteriophage genes." .
SCR:027492 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100010015",
"GRID grid.44870.3f",
"Wikidata Q3123462" ;
rdfs:label "University of Northampton; Northampton; United Kingdom" ;
definition: "University of Northampton is public university based in Northampton, which offers students undergraduate and postgraduate courses. It was formed in 1975 as Nene College of Higher Education." .
SCR:027493 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5307" ;
rdfs:label "University of Vermont Bioinformatics Shared Resource Core Facility" ;
NIFRID:synonym "Bioinformatics Shared Resource",
"University of Vermont Bioinformatics Shared Resource" ;
definition: "Core offers bioinformatics and data modeling services. Focuses on support for reproducible, well documented, containerized, nextflow pipelines customized to address the specific research questions and biological systems of the investigators. Offers support from preprocessing -omics data, through data integration and manuscript support, based on grant support or a fee-for-service mechanism. Provides training for students and PIs in the form of individual help, seminars, and workshops." .
SCR:027494 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Van Andel Institute Metabolism and Nutrition (MeNu) Program" ;
NIFRID:synonym "Metabolism and Nutrition (MeNu) Program" ;
definition: "Small foundation and think tank that seeks to equip brilliant scientists with leading technology, crucial collaborators and cutting-edge support to accelerate discoveries — transforming bold ideas into breakthroughs in metabolism." .
SCR:027495 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5363" ;
rdfs:label "University of Nevada at Reno Nevada Genomics Center Core Facility" ;
NIFRID:synonym "Nevada Genomics Center Core Facility" ;
definition: "Core to serve academic and industry researchers in their studies on the function and structure of genomes. Offers services for next-generation Illumina sequencing, 10X single-cell library preparation, Sanger sequencing, fragment analysis and nucleic acid quantification and sizing." .
SCR:027496 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hdWGCNA" ;
NIFRID:synonym "hd Weighted Gene Co-expression Network Analysis" ;
definition: "Software R package for performing weighted gene co-expression network analysis in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics." .
SCR:027497 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5361" ;
rdfs:label "Louisiana State University in Shreveport Center for Cardiovascular Diseases and Sciences (CCDS) Surgical Models Core Facility" ;
NIFRID:synonym "Center for Cardiovascular Diseases and Sciences (CCDS) Surgical Models Core" ;
definition: "Core provides centralized service for performing technically challenging mouse models of cardiovascular disease, such as middle cerebral artery occlusion (MCAO) stroke model, coronary artery ligation model of myocardial ischemia, femoral artery ligation model of peripheral artery disease, and partial carotid artery ligation model of disturbed blood flow." .
SCR:027498 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5362" ;
rdfs:label "Louisiana State University in Shreveport Center for Cardiovascular Diseases and Sciences (CCDS) Virus Production Core Facility" ;
NIFRID:synonym "CCDS Virus Production Core",
"Center for Cardiovascular Diseases and Sciences (CCDS) Virus Production Core" ;
definition: "Core provides centralized service for generating AAV particles for cardiovascular studies. The CCDS Virus Production Core offers the production of either pre-made (ex. AAV8-GFP, AAV8 mPCSK9 D377Y) or custom AAVs." .
SCR:027499 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BayesPrism" ;
definition: "Software R package for fully Bayesian inference of tumor microenvironment composition and gene expression deconvolution. Used to analyze bulk RNA-seq data and estimate cell type-specific expression profiles." .
SCR:027500 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Monolith_NT.115" ;
rdfs:label "NanoTemper | Monolith NT.115" ;
NIFRID:synonym "Monolith NT.115" ;
definition: "Instrument used to quantify biomolecular interactions and measure their binding affinity using MicroScale Thermophoresis. Can determine the strength of binding between all types of biomolecules, from single ions to large complexes, in various complex samples and buffer conditions." .
SCR:027501 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tampa General Hospital-University of South Florida Health Precision Medicine Biorepository" ;
NIFRID:synonym "TGH-USF Health Precision Medicine Biorepository" ;
NIFRID:abbrev "PMBioR" ;
definition: "Procures high-quality biologic specimens along with coded clinical and demographic data across broad ethnic, racial, and social demographic of patients. All specimens are systematically collected and processed so that their multi-functional potential for recovering high-quality bioanalytes (including RNA, genomic DNA, protein, enzymes and metabolites) is conserved. All specimens are stored and protected in a database hub to connect researchers conducting variety of scientific projects across multiple medical specialties. Muilti-disciplinary biorepository with capacity for generating specialized bioanalytes." .
SCR:027502 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CBI BrAinPI" ;
NIFRID:abbrev "BrAinPI" ;
definition: "Visualization software tool for viewing large image files in a browser. Works with Brain Image Library, built for BICAN." .
SCR:027503 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5364" ;
rdfs:label "Icahn School of Medicine at Mount Sinai Stem Cell Engineering Core Facility" ;
NIFRID:synonym "Icahn School of Medicine at Mount Sinai Stem Cell Engineering Core",
"Stem Cell Engineering Core" ;
definition: "Core provides services for generation and characterization of induced pluripotent stem cells (iPSCs) from somatic sources such as blood and fibroblasts, along with long-term cryobanking. Offers access to collection of well-characterized iPSC lines derived from both healthy donors and patients with various diseases, representing a range of ethnic backgrounds and sexes.Major focus of core is gene editing in pluripotent stem cells, with expertise in CRISPR-based applications from precise point mutation knock-in (correction or introduction) to the generation of reporter lines (e.g., GFP and other fluorescent reporters) and inducible systems such as Cre-lox, dTAG, and beyond.Core provides guidance and support for the differentiation of iPSCs into multiple cell types, using both monolayer and 3D organoid formats, enabling downstream disease modeling and functional studies." .
SCR:027504 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5418" ;
rdfs:label "Virginia Tech VT Surface Analysis Laboratory Core Facility" ;
NIFRID:synonym "Virginia Tech VT Surface Analysis Laboratory",
"VT Surface Analysis Laboratory" ;
definition: "Core offers contemporary surface analysis techniques, featuring the latest PHI VersaProbe III Scanning XPS Microscope, and expertise." .
SCR:027505 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5417" ;
rdfs:label "Icahn School of Medicine at Mount Sinai Transgenic and Genome Editing Core Facility" ;
NIFRID:synonym "Icahn School of Medicine at Mount Sinai MSSM-Transgenic and Genome Editing CoRE",
"MSSM-Transgenic and Genome Editing CoRE" ;
definition: "Core offers services from consultation until delivery of germline-confirmed genetically engineered mouse models (GEMMs). Uses genome editing tools such as CRISPR/Cas9 to rapidly generate GEMMs with diverse genome modifications such as humanization, large insertion, conditional knockout, base substitution and deletion. Animals produced in the CoRE are thoroughly genotyped by our comprehensive genotyping services. Supports model creation via the traditional transgenesis and the gene targeting in the embryonic stem cells. Other services provided by the CoRE include sperm cryopreservation, in vitro fertilization, rederivation and custom embryology supports." .
SCR:027506 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GPS-Palm" ;
definition: "Software deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins." .
SCR:027507 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Corning Incorporated" ;
definition: "Corning Incorporated is a global manufacturer of laboratory consumables and scientific equipment, widely known for its high-quality cell culture products, microplates, flasks, and filtration systems. Corning Life Sciences provides essential tools for cell biology, genomics, drug discovery, and bioprocessing applications." .
SCR:027508 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Ibidi GmbH" ;
definition: "German manufacturer specializing in advanced cell culture and imaging products, including µ-Slide chambers, microfluidic devices, and reagents for live-cell analysis. Ibidi’s technologies support high-resolution microscopy, cell migration assays, angiogenesis studies, and immunological research." .
SCR:027509 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SteREO_Discovery.V12" ;
rdfs:label "Zeiss | SteREO Discovery.V12" ;
NIFRID:synonym "SteREO Discovery.V12" ;
definition: "Microscope patented optics are setting new standards in modular common main objective stereomicroscopy. Thanks to higher resolution and significantly increased contrast, they provide 20% more image information – in addition to 3D images. The innovative operating concept SyCoP (Systems Control Panel) combines all essential functions of stereomicroscope in single handy operating unit. Used particularly for applications in materials research, quality control, biology and medical research." .
SCR:027510 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cytation_C10" ;
rdfs:label "Agilent | BioTek Cytation C10 Confocal Imaging Reader" ;
NIFRID:synonym "Agilent BioTek Cytation C10 Confocal Imaging Reader",
"Cytation C10" ;
definition: "Imaging reader combines automated confocal and widefield microscopy with conventional multimode microplate reading. Automated water-immersion objectives capture more light, driving lower exposure times and reducing phototoxic impacts on live cells. Spinning-disk confocal module and accompanying disk pinhole options for looking deeper into thick sample biology with improved clarity and detail. High-quality components used in system, including Hamamatsu scientific CMOS (sCMOS) camera, Olympus objectives and laser-based illumination enable excellent image quality. Cytation C10 also includes widefield fluorescence, brightfield, and phase contrast optics. Onboard environmental controls enable live cell assays." .
SCR:027511 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5422" ;
rdfs:label "Concordia University Genome Foundry Core Facility" ;
definition: "Core research facility dedicated to high-throughput DNA assembly, strain engineering, and automation-enabled synthetic biology. Equipped with state-of-the-art robotic platforms and expert technical staff, the Foundry supports academic and industry researchers in the design, construction, and testing of biological systems." .
SCR:027512 a owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 501100002914",
"GRID grid.410319.e",
"ISNI 0000 0004 1936 8630",
"Wikidata Q326342" ;
rdfs:label "Concordia University; Montreal; Canada" ;
NIFRID:synonym "Organization" ;
definition: "Concordia University is a public English-language research university located in Montreal, Quebec, Canada. Founded in 1974 following the merger of Loyola College and Sir George Williams University, Concordia is one of the three universities in Quebec where English is the primary language of instruction." .
SCR:027513 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Van Andel Institute MiND Blood Biorepository" ;
NIFRID:synonym "MiND Biorepository",
"West Michigan Neurodegenerative Diseases (MiND) Program Biobank" ;
definition: "Biorepository that collects and stores donated PBMCs, plasma, and WBC pellets from people with neurodegenerative diseases to support scientific research on Parkinson's disease, dementia, and other neurodegenerative disorders. It functions as a research-focused collection of biospecimens, providing scientists with samples to study the mechanisms and causes of these conditions. Informed consent is obtained through our clinical partners. All donors remain anonymous." .
SCR:027514 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Global Human Settlement Layer" ;
definition: "Project portal from the European Union that creates global geographical data about the evolution of human habitation on Earth. This information is in the form of population density maps, built-up maps, and settlement maps. This information is produced using new geographic data mining tools and knowledge and analytics based on empirical data." .
SCR:027515 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5423" ;
rdfs:label "Science and Technology Facilities Council Central Laser Facility OCTOPUS Microscopy Core Facility" ;
NIFRID:synonym "CLF Octopus Microscopy Facility",
"CLF Optics Clustered to OutPut Unique Solutions Microscopy Facility" ;
definition: "National imaging facility that offers access to single molecule imaging, confocal microscopy, superresolution imaging, light sheet microscopy, optical trapping and cryoscanning electron microscopy. Offers expert guidance and advice for light and electron microscopy experiments alongside advanced instruments for fluorescence and electron microscopy." .
SCR:027516 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Axon Medchem" ;
definition: "Supplier of drug reference standards for life science research, offering collection of small molecule inhibitors and modulators, targeting more than 850 biological pathways, including cell signaling, gene transcription, apoptosis, and CNS function. Provides expert contract research services, specializing in the custom synthesis of bioactive and drug-like molecules." .
SCR:027517 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pore-c Workflow" ;
definition: "Software workflow for analysing Pore-c data for chromatin conformation capture." .
SCR:027518 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chromunity" ;
definition: "Software application for discovery of communities in Pore-C concatemers." .
SCR:027519 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5424" ;
rdfs:label "University Health Network Biospecimen Services Core Facility" ;
NIFRID:synonym "UHN Biospecimen Services" ;
definition: "Core provide services for the enhancement and progression of novel and innovative research and discovery. Provides human biospecimen samples such as: fresh frozen and formalin fixed paraffin embedded (FFPE) tissue, compartmentalized blood components such as serum, plasma, and whole blood peripheral blood mononuclear cells (PBMCs) and other biofluids, including saliva and urine; Tissue microarray (TMA) construction and quantitative image analysis of TMA sections, Laser capture microdissection (LCM), digital slide scanning, quantitative image, and pathological/clinical analysis for various tumour sites and DNA/RNA extraction; support and guidance to researchers and biobanks on accessing, collecting, and using human biospecimens and associated data for health research." .
SCR:027520 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5425" ;
rdfs:label "University Health Network Joint Department of Medical Imaging Research Office JDMI RO Core Facility" ;
NIFRID:synonym "Joint Department of Medical Imaging Research Office (JDMI RO)" ;
definition: "Core services include Imaging Modalities:MRI,PET-MRI,CT,PET-CT,Ultrasound / X-Ray,Interventional / Biopsies;Consultation:Pre-grant submission consultations,Pre-trial launch consultations / site initiation visists,Feasibility assessments MRI physics consultation; Protocol Development / Site Feasibility:Industry site feasibility questionnaires, Protocol development of medical imaging studies and clinical trials; Post-Processing of Images:Tumour measurements, Volumetric measurements." .
SCR:027521 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5426" ;
rdfs:label "University Health Network McCain GU Biobank" ;
NIFRID:synonym "McCain GU Biobank" ;
definition: "Core supports biomarker discovery and enhancing future cancer research in the areas of genomics, proteomics and epidemiology. Provides serialized collections of biospeciments throughout patient prognosis. Clinical time point collections are based on input from our expert surgical, medical, and radiation oncologist teams." .
SCR:027522 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5427" ;
rdfs:label "University Health Network Princess Margaret Cancer Biobank Core Facility" ;
NIFRID:synonym "Princess Margaret Cancer Biobank" ;
definition: "Core offers biobanking services and diverse inventory of biospecimens in the field of Oncology. Offers prospective protocol specific banking tailored to your research needs, including patient eligibility, screening, consenting, biospecimen procurement, handling, and processing, clinical data annotation, short and long-term sample storage, and shipping." .
SCR:027523 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5428" ;
rdfs:label "University Health Network Princess Margaret Living PDX Core Facility" ;
NIFRID:synonym "Princess Margaret Living Biobank (PDX)" ;
NIFRID:abbrev "PMLB PDX Core" ;
definition: "Core provides services for the use of Xenograft (PDX) models listed in open global catalogue of PDX models for comprehensive search and attribute filtering support for clinico-pathological and molecular data. Molecular data and visualization of profiled models could be accessed through the institute's portal." .
SCR:027524 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5429" ;
rdfs:label "University Health Network Princess Margaret Genomics Centre PMGC Core Facility" ;
NIFRID:synonym "Princess Margaret (PM) Genomics Centre" ;
definition: "Core is dedicated to providing access to cost-effective and high quality genomics services including standard and custom-tailored DNA sequencing using Illumina technologies, epigenomics, panel-based profiling (Luminex and Nanostring) and functional genomics. Single cell genomics applications on variety of popular platforms." .
SCR:027525 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5430" ;
rdfs:label "University Health Network Advanced Molecular Diagnostics Laboratory Core Facility" ;
NIFRID:synonym "Advanced Molecular Diagnostics Laboratory (AMDL)" ;
definition: "AMDL is a clinical CAP/CLIA accredited molecular diagnostics laboratory at the Princess Margaret Cancer Centre. Supports clinical trials and translational research projects requiring clinical-grade (CAP/CLIA) molecular testing at Princess Margaret Cancer Centre. AMDL works closely with Molecular Diagnostics lab in Toronto General Hospital to transition protocols into clinical tests." .
SCR:027526 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5432" ;
rdfs:label "University Health Network PMCRT and PGCRL UHN-SickKids Joint Core Facility" ;
NIFRID:synonym "Princess Margaret Cancer Research Tower (PMCRT) and Peter Gilgan Centre for Research and Learning (PGCRL) UHN-SickKids Joint Facility" ;
NIFRID:abbrev "SickKids-UHN" ;
definition: "Facility provides analytical flow cytometers and high-speed cell sorting, as well as training, education and consultation services." .
SCR:027527 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5433" ;
rdfs:label "University Health Network Quantitative Imaging for Personalized Cancer Medicine Advanced Imaging Core Facility" ;
NIFRID:synonym "Quantitative Imaging for Personalized Cancer Medicine (QIPCM) Advanced Imaging Core Lab" ;
definition: "Provides testing and analysis support for clinical trials to improve consistency and reliability in clinical trial data.Helps clinical investigators achieve systematic image collection and improved collaboration. Can help with handling large volume functional and dynamic imaging data." .
SCR:027528 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5434" ;
rdfs:label "University Health Network Biostatistics Core Facility" ;
NIFRID:synonym "Biostatistics@UHN" ;
definition: "Core offers services including Study planning and design; Grant writing and protocol creation; Data collection form design; Data capture instrument construction; Complex data processing and linkage; Quality control involvement; Statistical analysis, figure, and table generation; Manuscript drafting and presentation preparation; Response to manuscript reviews from regulatory agencies and journals." .
SCR:027529 a owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5435" ;
rdfs:label "University Health Network Krembil Discovery Tower Flow Cytometry Core Facility" ;
NIFRID:synonym "Krembil Discovery Tower (KDT) Flow Cytometry Core Facility" ;
definition: "Core offers cell sorting and flow cytometry services. Provided instruments include BD FACS Canto II, Beckman Cytoflex LX, BD FACS ARIA III, AutoMacs Cell Separator." .
SCR:027530 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5436" ;
rdfs:label "University Health Network Princess Margaret Living Biobank PDO Core Facility" ;
NIFRID:synonym "PM Living Biobank",
"Princess Margaret Living Biobank (PDO)" ;
NIFRID:abbrev "PMLB PDO Core" ;
definition: "Core provides services for the use of patient-Derived tumor Organoid (PDO) model.Organoid models are derived from patient-derived xenograft tissues, primary tumors, and metastatic patient tissues. PMLB organoid repository includes models generated from colorectal, pancreatic, and lung cancer tissues." .
SCR:027531 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5437" ;
rdfs:label "University Health Network Spatio-Temporal Targeting and Amplification of Radiation Response Core Facility" ;
NIFRID:synonym "Spatio-Temporal Targeting and Amplification of Radiation Response (STTARR)" ;
definition: "Offers services to support studies in medical fields across oncology, cardiology, metabolic diseases, radiotheranostics and more.Helps with study design to final data analysis, including GLP-compliant histopathology services." .
SCR:027532 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5438" ;
rdfs:label "University Health Network Bioinformatics and High Performance Computing HPC Core Facility" ;
NIFRID:synonym "Bioinformatics and High Performance Computing (HPC) Core" ;
definition: "Core provides services including Basic High-Throughput Sequencing Analysis, Advanced Data Analysis, High Performance Computing." .
SCR:027533 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100009663",
"GRID grid.231844.8",
"ISNI 0000 0004 0474 0428",
"Wikidata Q7894718" ;
rdfs:label "University Health Network" ;
definition: "public research and teaching hospital network in Toronto, Ontario, Canada. It is affiliated with the Temerty Faculty of Medicine at the University of Toronto, and is the largest health research organization in Canada, ranking first in the country for total research funding." .
SCR:027534 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Artificial Social Agent Questionnaire (ASAQ)" ;
definition: "Artificial Social Agent Questionnaire (ASAQ), an instrument for evaluating human interaction with an artificial social agent (ASA), resulted from multi-year efforts involving more than 100 Intelligent Virtual Agent (IVA) researchers worldwide within the OSF work-group of Artificial Social Agent Evaluation Instrument (https://osf.io/6duf7/). It has 19 measurement constructs constituted by 90 items, which capture more than 80% of the constructs identified in empirical studies published in the IVA conference 2013-2018. In addition, a representative item of each construct or dimension was selected to create a 24-item short version of the ASA questionnaire. Whereas the long version is suitable for a comprehensive evaluation of human-ASA interaction, the short version allows quick analysis and description of the interaction with the ASA." .
SCR:027535 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5441" ;
rdfs:label "University Health Network Advanced Optical Microscopy Core Facility" ;
NIFRID:synonym "Advanced Optical Microscopy Facility (AOMF)" ;
definition: "Core offers services in optical microscopy experiments including: confocal, multiphoton, super-resolution, FRAP, FRET, live-cell timelapse, whole-slide scanning, image analysis and more." .
SCR:027536 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5440" ;
rdfs:label "University Health Network Histology Biomarker Lab Core Facility" ;
NIFRID:synonym "Histology Biomarker Lab" ;
definition: "Core provides biospecimen processing and performs automated slide-based biomarker methods (protein/RNA/DNA), implementing good clinical laboratory practices.Offers specialized consultation and perform biomarker development and analyses within clinical study and research program protocols.Provides services to the clinical trials and pre-clinical research community and expertise in biomarker selection, method development, optimization and standardization, and provision of quality consultation on biomarkers for clinical research protocols." .
SCR:027537 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5439" ;
rdfs:label "University Health Network Princess Margaret Flow Cytometry Core Facility" ;
NIFRID:synonym "Princess Margaret Flow Cytometry Facility" ;
definition: "Core offers services in Analytical Flow Cytometry, Fluorescence Activated Cell Sorting, consultation and data analysis. Staff provides training, assisted acquisition, consultation, and data analysis upon request." .
SCR:027538 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Data Kit" ;
NIFRID:synonym "ODK - Open Data Kit" ;
definition: "Software suite of tools designed to build information services for developing regions." .
SCR:027539 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Grobid" ;
NIFRID:synonym "GeneRation Of BIbliographic Data" ;
definition: "Software tool for extracting information from scholarly documents." .
SCR:027540 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_2624" ;
rdfs:label "Icahn School of Medicine at Mount Sinai Metabolomics Core Facility" ;
NIFRID:synonym "ISMMS Metabolomics Core",
"Metabolomics Core" ;
definition: "Core provides mass-spectrometry solutions for small-molecule research. Supports experimental design, ensuring proper handling, appropriate controls, and adequate statistical power, and then executes analyses on Thermo Orbitrap IQ-X and Agilent 6495D LC/MS systems and an Agilent 5977C GC/MS system. Using validated methods annotated against a library of 1,000+ compounds, we maximize metabolite and small-molecule coverage. We also offer untargeted profiling for biomarker and novel metabolite and lipid discovery, as well as stable-isotope tracing for measuring substrate utilization. Results are delivered with custom informatics and statistical interpretation for faster, more approachable insights." .
SCR:027542 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5420" ;
rdfs:label "Science and Technology Facilities Council Octopus Core Facility" ;
NIFRID:synonym "Octopus" ;
definition: "Provides expert advice and guidance for collaborative research projects involving the use of fluorescence and electron microscopy. Access to advanced fluorescence and electron microscopes for external users after a peer-review process." .
SCR:027543 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5431" ;
rdfs:label "Gladstone Institutes Stem Cell Core Facility" ;
NIFRID:synonym "Gladstone Stem Cell Core" ;
definition: "Core offers a fully functional tissue culture facility with specialized instruments, media, reagents, cell lines, and expertise for new or established researchers to perform cutting-edge stem cell research. In addition, our core provides comprehensive human induced pluripotent stem (iPS) cells related training, consultations, and standard and customized scientific services, including derivation of iPS cells, differentiation of iPS cells and genome editing in iPS cells to stem cell researchers." .
SCR:027544 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5421" ;
rdfs:label "Mayo Clinic Antibody Hybridoma Core Facility" ;
NIFRID:synonym "Antibody Hybridoma Core" ;
definition: "Core can generate custom monoclonal antibodies in mouse and hamster systems. Can also produce large amounts of antibodies (of all species) and recombinant proteins in-vitro. Purification is also available for various systems." .
SCR:027546 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5547" ;
rdfs:label "George Washington University Milken Institute School of Public Health Genomics Core Facility" ;
NIFRID:synonym "GW Genomics Core",
"Milken Institute School of Public Health Genomics Core" ;
definition: """Genomics Core team has expertise in bacterial genomics, computational biology, infectious disease, HIV, population and conservation genetics. Offers NGS services. Capable of supporting projects at any stage, from planning to sample processing to sequencing.
keith crandall""" .
SCR:027547 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5546" ;
rdfs:label "University of Connecticut Advanced Light Microscopy Core Facility" ;
NIFRID:synonym "Advanced Light Microscopy Facility",
"University of Connecticut Advanced Light Microscopy Facility" ;
definition: "Facility provides training and access to advanced light microscopy systems at an hourly rate. In addition, we are available to consult with and support users at every stage of a project including: experimental design, sample preparation, image acquisition, analysis, and data preparation." .
SCR:027548 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5601" ;
rdfs:label "University Health Network Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "NMR Core Facility",
"UHN BioNMR Core Facility" ;
definition: "NMR Core Facility is equipped with NMR spectrometers allowing researchers to Characterize bio-molecular structures at the atomic resolution with exquisite details;Identify protein interactions with binding partners in order to understand their architecture;Study protein dynamic;Study protein post-translational modifications acting as molecular switches;Study structure-function relationships of biological proteins to gain insight into biological processes in relation to human disease;Screening of High-throughput drug-like leads for novel therapeutic targets;Study Metabolites of interest.Core facility houses high-field NMR spectrometers equipped with cryogenically cooled probes (1H or 13C optimized) for enhanced sensitivity." .
SCR:027550 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DM2500_P" ;
rdfs:label "Leica | DM2500 P microscope" ;
definition: "General-purpose polarizing microscope designed for all polarization inspection tasks in the petroleum, mining, and structural characterization industries. It is also an all-round instrument suitable for industrial analysis and quality control , such as analyzing glass, plastics, textiles, and fibers, as well as inspecting display panels in the semiconductor industry." .
SCR:027551 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ORCA-Fusion_BT" ;
rdfs:label "Hamamatsu | ORCA-Fusion BT camera" ;
NIFRID:synonym "ORCA-Fusion BT camera" ;
definition: "High-performance scientific CMOS (sCMOS) digital camera designed for low-light microscopy and advanced imaging applications. Its key features include an exceptionally low and uniform readout noise, high quantum efficiency (QE) of up to 95%, and a patented \"Lightsheet Readout Mode\" optimized for light-sheet microscopy. This combination makes it ideal for detecting faint signals with high signal-to-noise ratios in challenging experiments, such as time-lapse, fluorescence, and single-molecule tracking." .
SCR:027552 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Agilent_7000E" ;
rdfs:label "Agilent | 7000E Triple Quadrupole GC/MS system" ;
NIFRID:synonym "7000E Triple Quadrupole GC/MS" ;
definition: "Agilent 7000E triple quadrupole GC/MS instruments incorporate intelligent technology that reduces instrument downtime and improves run times for maximum productivity in analytical labs. Mass spectrometer is used for routine, high-sensitivity analysis of targeted compounds in complex samples, especially for trace-level detection in areas like food safety and environmental testing." .
SCR:027553 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cancer Incidence in Five Continents (CI5)" ;
definition: "Cancer Incidence in Five Continents (CI5) is a collaboration between the International Agency for Research on Cancer (IARC) and the International Association of Cancer Registries (IACR) that produces a benchmark series of data on cancer incidence worldwide. This multi-volume publication, released approximately every five years, compiles standardized data on newly diagnosed cancer cases from population-based cancer registries across the globe. The data provide a unique source of comparable information on the global burden and distribution of cancer and help inform cancer control programs." .
SCR:027554 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NCI Age-Period-Cohort Web Tool" ;
NIFRID:synonym "Age-Period-Cohort (APC) Web Tool" ;
definition: "Web tool, developed by the U.S. National Cancer Institute (NCI), performs statistical modeling of cancer incidence or mortality data using age-period-cohort analysis. It allows users to examine and interpret temporal trends while disentangling the effects of age, calendar period, and birth cohort. The tool supports data import, graphical output, and model fit assessment via interactive web interface." .
SCR:027555 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5603" ;
rdfs:label "Tennessee Tech University Research Computing and Data Core Facility" ;
NIFRID:synonym "Tennessee Technological University Research Computing and Data Core Facility" ;
definition: "Core empowers students, faculty, and staff across all disciplines by providing the tools, training, and equipment for advanced computing for more robust, reproducible research with reduced time to results. Manages the campus cluster, and also facilitate access to larger federally-funded clusters at zero cost. Provided data transfer and network performance monitoring services enable researchers and collaborators to move data quickly." .
SCR:027556 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Tennessee Technological University; Cookeville; United States" ;
definition: "Public research university in Cookeville, Tennessee. It was formerly known as Tennessee Polytechnic Institute, and before that as University of Dixie, the name under which it was founded as a private institution." .
SCR:027557 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5604" ;
rdfs:label "University of Manchester Advanced Metal Development Core Facility" ;
definition: "Core supports all processing of metal related activity and houses equipment in the areas of thermomechanical processing, additive manufacturing, mechanical testing (including testing under a variety of environments), thermomechanical simulation/testing and heat treatment." .
SCR:027558 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DIL_805" ;
rdfs:label "Waters | DIL805 A/D/T Quenching Dilatometer" ;
definition: "805 Series Quenching Dilatometers are the benchmark instruments for scientists and engineers interested in determining dimensional changes and phase transformations of steel alloys. Extremely flexible and configurable, designed to accommodate a wide range of add-on modules enabling it to be tailored to specific user requirements. Quenching, compression, tension, alpha and sub-zero alpha modes all provide highly accurate dimensional change measurements under different conditions and environments.Used for determination of critical parameters in steel manufacturing and heat treatment processes." .
SCR:027559 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenVisR" ;
definition: "Software R package for visualizing genomics data. Provides a user-friendly, flexible and comprehensive suite of tools for visualizing complex genomic data in three categories (small variants, copy number alterations and data quality) for multiple species of interest." .
SCR:027560 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SYSTRONICS_AU- 2704_X" ;
rdfs:label "SYSTRONICS | AU- 2704 X Flashing Xenon Lamp Spectrophotometer" ;
definition: "Double-beam UV-Vis spectrophotometer used for precision measurements in various scientific and industrial applications, such as quality control, environmental monitoring, and biochemical analysis. Its flashing xenon lamp provides a high-intensity, broadband light source for fast, reliable measurements across a wide wavelength range, and its double-beam design ensures accuracy by measuring both the sample and a reference simultaneously." .
SCR:027561 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CAMTHC:Convex Analysis of Mixtures for Tissue Heterogeneity Characterization" ;
NIFRID:synonym "Convex Analysis of Mixtures for Tissue Heterogeneity Characterization" ;
NIFRID:abbrev "CAMTHC" ;
definition: "Software R package for deconvolving tissue heterogeneity using convex analysis of mixture models." .
SCR:027562 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PyReconstruct" ;
definition: "Software successor to the Reconstruct annotation tool. PyReconstruct runs on all major operating systems, breaks through legacy RAM limitations, features intuitive and collaborative curation system, and employs flexible and dynamic approach to image registration. Used to analyze, display, and publish experimental or connectomics data. Suited for generating ground truth to implement in automated segmentation, outcomes of which can be returned to PyReconstruct for proofreading and quality control." .
SCR:027563 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SchemaSheets" ;
definition: "Software tool aimed at data modelers, curators, wrangers, and creators of standards and datamodels. It is aimed at people who prefer to develop these standards using spreadsheet tools over more developer-centric tooling. Human-friendly spreadsheets with machine-actionable models." .
SCR:027564 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bkbit" ;
NIFRID:synonym "Brain Knowledge Base Interaction Toolkit" ;
definition: "Software package contains tools to use the BICAN Knowledgebase Data Models." .
SCR:027565 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5602" ;
rdfs:label "Icahn School of Medicine at Mount Sinai Neuropathology Brain Bank and Research CoRE Facility" ;
NIFRID:synonym "Icahn School of Medicine at Mount Sinai Neuropathology Brain Bank & Research CoRE",
"Neuropathology Brain Bank & Research CoRE" ;
definition: "Provides access to collection of human postmortem brain tissues, including fresh, frozen, and formalin-fixed paraffin-embedded (FFPE) specimens, along with detailed clinical histories and neuropathological assessments. Available histology services include processing and embedding, slide sectioning for FFPE and cryosections, immunohistochemistry (IHC), immunofluorescence (IF), and advanced RNA assays such as RNAscope, BaseScope, and miRscope. High-resolution digital slide imaging is performed using the GT450 scanner. CoRE scientists also collaborate with investigators and trainees to support project development, method optimization and troubleshooting, data analysis." .
SCR:027566 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5608" ;
rdfs:label "University of Bern Translational Research Unit Platform TRU Core Facility" ;
definition: "Core facility offers researchers access to histological services, tissue visualization, slide scanning, digital image analysis, and next-generation tissue microarrays. Our team processes more than 800 projects per year related to patient tissue, patient-related data, clinical studies, and animal models." .
SCR:027567 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SlideTags.wdl" ;
NIFRID:synonym "Slide-tags" ;
definition: "Software pipeline as open-source, cloud-optimized workflow for processing spatial transcriptomics data. It supports data derived from spatially barcoded sequencing technologies, including Slide-tags-based single-molecule profiling. The pipeline processes raw sequencing data into spatially resolved gene expression matrices, ensuring accurate alignment, spatial positioning, and quantification." .
SCR:027568 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "emapper2gbk" ;
definition: "Software tool to convert FastA and Eggnog-mapper annotation files to GenBank files containing GO terms and EC number annotations, suitable for metabolic network reconstruction using Pathway Tools. Used for creation of genbank files from Eggnog-mapper annotation outputs." .
SCR:027569 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5605" ;
rdfs:label "Icahn School of Medicine at Mount Sinai RNA Nanocore Core Facility" ;
NIFRID:synonym "Icahn School of Medicine at Mount Sinai RNA Nanocore",
"RNA Nanocore" ;
definition: "Core Facility at the Icahn Genomics Institute (IGI) offers custom-made lipid nanoparticles and RNA technology to develop new therapeutics and nanomedicines." .
SCR:027571 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5607" ;
rdfs:label "Icahn School of Medicine at Mount Sinai Human Immune Monitoring Center Core Facility" ;
NIFRID:synonym "Icahn School of Medicine at Mount Sinai Mount Sinai Human Immune Monitoring Center",
"Mount Sinai Human Immune Monitoring Center" ;
definition: "Core provides team of experts in the characterization of immune profiles and treatment responses across a diverse range of diseases, such as cancer, autoimmunity, allergy, and neuro-immune disorders. Offers equipment in the field for research at Genomic, cellular and proteomic analysis. Develops assays to balance innovation with protocols and operating procedures to ensure data quality and reproducibility." .
SCR:027572 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5606" ;
rdfs:label "Icahn School of Medicine at Mount Sinai Center for Advanced Genomics Technology Core Facility" ;
NIFRID:synonym "Center for Advanced Genomics Technology",
"Icahn School of Medicine at Mount Sinai Center for Advanced Genomics Technology" ;
definition: "Core has built technology toolbox with access to and application of novel and existing methods in multitude of genomics technologies. These capabilities span bulk, single-cell, spatial, and in situ genomic sequencing methods, all of which are leveraged to generate complementary cross-platform, orthogonally validated datasets to foster novel discovery and advance clinical applicability using human cohorts and model systems" .
SCR:027573 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5613" ;
rdfs:label "Donald Danforth Plant Science Center Data Science Core Facility" ;
definition: "Core Facility provides infrastructure for high-performance computing and data storage (local and cloud). Services include access and training for use of high-performance computing resources, data analysis and visualization, data integration, statistical analysis, and image analysis." .
SCR:027574 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scDenorm" ;
definition: "Software tool that reverts normalised single-cell omics data to raw counts, preserving the integrity of the original measurements and ensuring consistent data processing during integration. Denormalization tool for single-cell transcriptomics data." .
SCR:027575 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "caper" ;
NIFRID:synonym "caper: Comparative Analyses of Phylogenetics and Evolution in R",
"Comparative Analyses of Phylogenetics and Evolution in R" ;
definition: "Software R package used to conduct comparative analyses on phylogenetic data sets." .
SCR:027576 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_KingFisher_Flex" ;
rdfs:label "Thermo Fisher | Kingfisher Flex System" ;
NIFRID:synonym "Thermo Scientific KingFisher Flex" ;
definition: "Automatic Magnetic Bead Cell Isolation System. Benchtop instrument for the purification and extraction of DNA, RNA, proteins, and cells in laboratory settings. It uses magnetic particle technology to handle medium to high throughput processing of 24 or 96 samples per run, providing a more efficient and consistent alternative to manual methods." .
SCR:027577 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "JupyterHub" ;
definition: "Software multi-user server for Jupyter notebooks." .
SCR:027578 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5615" ;
rdfs:label "University of Maryland Baltimore County High Performance Computing Facility" ;
NIFRID:abbrev "UMBC HPCF chip" ;
definition: "Facility maintains and administers the chip high performance computing cluster. The chip cluster is built from more than 150 machines featuring Intel CPUs and NVIDIA GPUs." .
SCR:027579 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5610" ;
rdfs:label "Beth Israel Deaconess Medical Center BIDMC Clinical Research Coordinator Core Facility" ;
NIFRID:synonym "BIDMC Clinical Research Coordinator Core" ;
definition: "Clinical Research Coordinator Core is available to support and collaborate with investigators and their research teams in all phases of clinical research, providing services that include assisting with the organization, implementation and completion of clinical research studies." .
SCR:027580 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ProteoDisco" ;
definition: "Software R package to facilitate proteogenomics studies. Houses functions to create customized protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. Used to generate protein variant sequences based on imported mutations from VCF, MAF and additional files to generate protein-variant database for use in proteogenomics studies." .
SCR:027581 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bactopia" ;
definition: "Software pipeline for complete analysis of bacterial genomes." .
SCR:027582 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5618" ;
rdfs:label "University of Pittsburgh Western Pennsylvania Quantum Information Core Facility" ;
NIFRID:synonym "Western Pennsylvania Quantum Infrastructure Core" ;
definition: "Core is equipped with suite of cryostats and measurement systems for probing electrical, magnetic, and quantum properties at cryogenic temperatures. Sample preparation capabilities include tools for wafer processing, nanomaterial transfer, and inert atmosphere handling. Deposition systems support thin film growth and surface treatment using a variety of techniques. Wirebonding and related sample preparation tools enable precise device packaging and integration, supporting a broad range of experimental workflows in quantum and nanoscale science." .
SCR:027583 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5619" ;
rdfs:label "Oregon Health and Science University Primate Genetics Core Facility" ;
NIFRID:synonym "OHSU Primate Genetics Core",
"OHSU Primate Genetics Core Facility" ;
definition: "Core provides services for comprehensive genetic and genomic analysis of NHPs, including DNA sequencing, nucleic acid extraction, macaque-specific genotyping assays, and NHP DNA Bank distribution services." .
SCR:027584 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5620" ;
rdfs:label "Augusta University Qualitative Research Lab Core Facility" ;
definition: "Core provides services including consultation on research design, training on interviewing, grant development, conducting focus groups, data analysis." .
SCR:027585 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5623" ;
rdfs:label "Medical College of Wisconsin Cancer Center Geospatial, Epidemiology and Outcomes Shared Resource Core Facility" ;
NIFRID:synonym "Epidemiology and Outcomes Shared Resource (GEOSR)",
"MCW Cancer Center Geospatial" ;
definition: "Core provides services including Geospatial Data Technology and Analysis, Epidemiological Information about the Catchment Area, Cancer Outcomes Data and Analysis." .
SCR:027586 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5624" ;
rdfs:label "Fred Hutchinson Cancer Center Collaborative Data Services Core Facility" ;
definition: "Core provides data-related support to cancer researchers by offering services like study design consultation, data management, programming, and access to patient data. Its purpose is to help researchers develop and execute studies, manage data, analyze results, and ultimately accelerate cancer research by making large, complex datasets more accessible and usable. CDS team uses evidence-based standards and effective quality assurance procedures from project design to study end. All CDS study staff are HIPAA-compliant and certified in Human Subjects and Good Clinic Practice training." .
SCR:027587 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5617" ;
rdfs:label "Virginia Tech NMR Spectroscopy Core Facility" ;
NIFRID:synonym "Virginia Tech NMR Facility",
"VT Chemistry NMR Facility" ;
definition: "Facility features 7 state of the art high field NMR instruments ranging from 400 to 600 MHz. The facility provides a diverse selection of probes including room temperature, LN2 cooled probes, 10mm Polymer probes, Diffusion and Solid-State NMR probes. The entire suite of 1D, 2D, Diffusion and Solid-State NMR capabilities are available for a broad range of nuclei." .
SCR:027588 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VenomView" ;
definition: "Open-access, browser-based visualization and summary tool for venom transcriptomic and proteomic data. R Shiny–based interactive application designed as visualization and reporting interface for venom transcriptomic and proteomic data. It enables users to explore annotation metrics, toxin gene families, and quality-control summaries generated by analysis pipelines. While it will eventually serve as part of the VenomsBase front end, VenomView currently operates as standalone prototype. Provides interactive dashboards showing assembly quality, annotation scores, toxin gene families, and functional domains generated by the VenomFlow analysis pipeline. Connected to VenomLanding, VenomView currently features Doryteuthis pealeii (Squid), linking metadata with detailed annotation summaries. The expanded version will include Sepia bandensis (Cuttlefish), Octopus bimaculoides, and arachnid species." .
SCR:027589 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "multiVIB" ;
definition: "Software tool as comprehensive framework for integration of single-cell omics data with probabilistic contrastive learning." .
SCR:027590 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Seurat MapQuery" ;
definition: "Convenience wrapper function around the following three functions that are often run together when mapping query data to a reference: TransferData, IntegrateEmbeddings, ProjectUMAP." .
SCR:027591 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5625" ;
rdfs:label "University of Washington Translational BioImaging Core Facility" ;
NIFRID:synonym "TBIC Translational BioImaging Core",
"The Translational BioImaging Core (TBIC)" ;
definition: "Core has resources available at Fred Hutch and UW in collaboration with multi-disciplinary imaging research groups specializing in respective imaging technologies. Provides services including: support for animal imaging; consultation for appropriate use of imaging; training and education; help with protocol development; infrastructural support; and strategic acquisition of new imaging equipment. Provides animal imaging equipment, including MRI, PET, US and optical to support scientific projects within the UW-FH Cancer Consortium." .
SCR:027592 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_UF-5000" ;
rdfs:label "Sysmex | UF-5000 automated urine particle analyzer" ;
NIFRID:synonym "UF-5000 automated urine particle analyzer" ;
definition: "New type of analyzer that is capable of analyzing the birefringence of particles and the amount of nucleic acid content and size information of the cell, coupled with the complexity of internal structure, using a blue semiconductor laser (488 nm)." .
SCR:027593 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Atellica_UAS_800" ;
rdfs:label "Siemens | Healthineers Atellica UAS 800 Analyzer" ;
NIFRID:synonym "Atellica UAS 800 Analyzer" ;
definition: "Atellica UAS 800 Analyzer is automated urine sediment analyzer designed to minimize the need for manual microscopy." .
SCR:027594 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Method Comparison Regression" ;
NIFRID:synonym "mcr:Method Comparison Regression" ;
NIFRID:abbrev "mcr" ;
definition: "Software R package to quantify relation between two measurement methods. Addresses regression problems with errors in both variables and without repeated measurements." .
SCR:027596 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ViralEmbed" ;
definition: "Software tool as deep learning framework for analyzing viral protein sequences at genomic scale using transformer-based models with sparse attention mechanisms. The tool processes complete viral genomes (up to 61,000 amino acids) to predict protein-protein interactions and identify functional relationships between viral proteins through attention-based contact analysis." .
SCR:027597 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PRECISE-TBI Preclinical CDEs" ;
definition: "Traumatic brain injury (TBI) Common Data Elements (CDEs) created by the PRE Clinical Interagency reSearch resourcE-TBI (PRECISE-TBI) group to harmonize (or merge) language and variables across the preclinical TBI neuroscience landscape." .
SCR:027598 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Olympus_BX43" ;
rdfs:label "Olympus | BX43 clinical microscope" ;
definition: "Olympus BX43 is a popular clinical and research grade microscope that can be configured for many different applications. Modular components enable you to customize the microscope for brightfield, polarization, phase contrast, and fluorescence. BX43 microscope utilizes a high color rendering white LED with a luminosity equivalent to a 30 W halogen lamp. The longlasting LED provides users a consistent color temperature at any brightness level.With an optional low magnification condenser, users can change the objective magnification from 2X to 100X (dry) without changing the condenser or moving the top lens." .
SCR:027599 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5629" ;
rdfs:label "University of Washington Northwest Metabolomics Research Center Core Facility" ;
NIFRID:synonym "Northwest Metabolomics Research Center (NW-MRC)" ;
definition: "Core provides targeted and untargeted measurements of small molecule metabolites utilizing LC-MS, high-field NMR and GC-MS analytical platforms. We also perform quantitative lipidomics and oxylipns metabolic flux analysis, statistical and pathway analysis, and biological interpretation." .
SCR:027600 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5630" ;
rdfs:label "State University of Campinas Gleb Wataghin Physics Institute LAMULT/IFGW Core Facility" ;
definition: "Gleb Wataghin Institute of Physics (IFGW/UNICAMP) hosts a multi-user equipment facility, the LAMULT – an Open Facility-type Multi-user Laboratory that integrates various scientific instruments within single location." .
SCR:027601 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5627" ;
rdfs:label "Liverpool University Biobank Core Facility" ;
NIFRID:synonym "Liverpool University Biobank",
"University of Liverpool Liverpool University Biobank Core Facility" ;
definition: "Core provides facilities including state of the art 2-D barcoded storage and LIMS, sample processing, histology, automated tissue microarray generation and spatial genomics profiling. Research Tissue Bank provides collection of both adult and paediatric biosamples, and is able to confer project-specific approval for their use." .
SCR:027602 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CDEMapper" ;
NIFRID:synonym "CDEMapper 2.0" ;
definition: "Software Common Data Elements (CDEs) mapping tool to bridge the gap between local data elements and National Institutes of Health (NIH) CDEs. Elasticsearch and Large Language Model (LLM)-powered mapping tool designed for biomedical and clinical researchers to efficiently map study variables to the NIH Common Data Elements (CDEs). It integrates essential and advanced services into a user-centered mapping workflow, allowing users to choose different mapping strategies based on their project's needs.Used for enhancing National Institutes of Health common data element use with large language models." .
SCR:027603 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Claude AI" ;
definition: "Generative AI tool capable of creative and analytical tasks like writing, summarizing, coding, and visual analysis. Developed by AI company Anthropic. Claude is known for its ability to process large amounts of text quickly and for its focus on safety through its \"constitutional AI\" training method. Free basic version can be used for Chat on web, iOS, Android, and on your desktop; Generation code and data visualization; Writing, editing, and content creation; Text and images analysis; searching the web. You can Unlock more from Claude with desktop extensions." .
SCR:027604 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5628" ;
rdfs:label "Icahn School of Medicine at Mount Sinai Biorepository and Pathology Core Facility" ;
NIFRID:synonym "Biorepository & Pathology Core",
"Icahn School of Medicine at Mount Sinai Biorepository & Pathology Core" ;
definition: "Core supports tissue and body fluid procurement, storage, and tracking from consented and de-identified collections. Pathologists responsible for procurement can be contacted for consultation to determine investigator requirements for human specimens in translational and basic research and then arrange procurement as feasible. Basic histology services include process, embed, and section fixed and frozen tissues (both animal and human), histochemistry, immunohistochemistry, immunofluorescence, in situ hybridization, laser capture microdissection, special stains for routine light microscopic evaluation. Offers full digital scanning capability with our quantitative and qualitative digital image analysis service (HALO), and support DNA/RNA/miRNA extraction from fluids and tissue specimens (both fixed and frozen) for downstream next generation sequencing and other applications." .
SCR:027605 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5631" ;
rdfs:label "Tulane University School of Medicine Flow Cytometry and Cell Sorting Core Facility" ;
NIFRID:synonym "Tulane University School of Medicine Department of Microbiology/Immunology Flow Cytometry and Cell Sorting Facility" ;
definition: "Tulane University School of Medicine Department of Microbiology/Immunology Flow cytometry and cell sorting shared resource facility. Provides education, training and services, Applications include analysis and sorting of immune subsets and fluorescent-reporter expressing cells, DNA content, multi-plex bead assays and functional assays. Expert assistance with experimental design and data analysis, as well as instrument training, are available at no charge." .
SCR:027606 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Sepax Technologies" ;
NIFRID:synonym "Sepax" ;
definition: "Delaware, USA based leading chromatography product manufacturer and service provider specializing in biological separation areas. We offer unique ranges of HPLC columns for bioanalytical characterization and testing, as well as process media for downstream process and purification of MAb, BsMAb, ADC, Proteins, AAV, VLP, DNA, RNA, and various biologic samples.," .
SCR:027607 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_cobas_u_701" ;
rdfs:label "Roche | Cobas u 701 microscopy analyzer" ;
NIFRID:synonym "cobas u 701 microscopy analyzer" ;
definition: "Fully automated urine microscopy system intended for the in vitro quantitative determination of erythrocytes and leukocytes, semi-quantitative determination of squamous and non-squamous epithelial cells, bacteria, and hyaline casts and qualitative determination of pathological casts, crystals, yeasts, mucus, and sperm in urine." .
SCR:027608 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Integrative Prediction Strategy" ;
NIFRID:synonym "Integrative Prediction Strategy (IPS)" ;
definition: "Software with approach that leverages machine learning and network biology to predict brain gene expression from blood-derived features." .
SCR:027609 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DataCite Commons" ;
definition: "Web discovery, analytics, and reporting tool powered by the links between works, people, and organizations in DataCite DOI metadata. DataCite Commons supports searches for works (with DOIs), people (with ORCID iDs), organizations (with ROR IDs), and repositories. By providing analytics dashboards, DataCite Commons empowers researchers and organizations to gain insights and make informed decisions based on comprehensive and interconnected metadata." .
SCR:027610 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_DYNEX_DS2" ;
rdfs:label "DYNEX | DS2 ELISA System" ;
NIFRID:synonym "DS2 ELISA System" ;
NIFRID:abbrev "DS2" ;
definition: "2-Plate ELISA processing system processes two 96-well microplates and up to 12 different assays simultaneously. Features user-friendly control system, chain of custody management and on-board instrument diagnostics." .
SCR:027611 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "DNA Genotek Inc" ;
definition: "Subsidiary of OraSure Technologies, Inc. focuses on providing biological sample collection products and services for human genomics, microbiome and infectious disease applications. Offers Research Use Only products to collect and preserve large amounts of DNA or RNA from multiple sample types." .
SCR:027612 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5633" ;
rdfs:label "University of Toronto Centre for Immune Analytics Core Facility" ;
NIFRID:synonym "University of Toronto Centre for Immune Analytics" ;
definition: "Core offers specialized services supported by research infrastructure, including flow cytometry, imaging mass cytometry (IMC), single-cell genomic sequencing, and dynamic live cell-culture imaging. Our facility is located in the Medical Sciences Building next to Queen’s Park, a central and convenient location for users across the Greater Toronto Area." .
SCR:027613 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "imcRtools" ;
definition: "Software R package that supports the handling and processing of IMC multiplex imaging data. Used for handling and analysing imaging mass cytometry data." .
SCR:027614 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIAID Data Ecosystem Discovery Portal" ;
NIFRID:synonym "Data Ecosystem Discovery Portal" ;
definition: "Unified search engine for infectious and immune-mediated disease datasets. Enables users to find datasets from biomedical research repositories. It indexes metadata from multiple NIH-funded and generalist repositories. Provides filters, prebuilt queries, and dataset collections to simplify the discovery process for users. The Portal additionally provides documentation and an API for programmatic access to harmonized metadata." .
SCR:027615 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Google Dataset Search" ;
definition: "Search engine for datasets hosted in web-based repositories and marked up according to schema.org. Helps users find datasets on the web. It aggregates information from publisher websites, digital libraries, and other sources, and uses metadata to allow users to filter results by criteria like last updated date, usage rights, download format, and topic. Users can find datasets across a wide variety of disciplines, including scientific, government, and commercial data." .
SCR:027617 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tidygraph" ;
definition: "Software R package as Tidy API for graph manipulation. Graph can be thought of as two tidy data frames describing node and edge data respectively. Used to manipulate these two virtual data frames using API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms." .
SCR:027618 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scStudio" ;
definition: "Web-based application for comprehensive and modular scRNA-seq data analysis. to easily retrieve datasets from repositories housing most publicly available single-cell data. Future expansions of scStudio will integrate additional databases, such as the Human Cell Atlas." .
SCR:027619 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5634" ;
rdfs:label "Georgia Institute of Technology Partnership for an Advanced Computing Environment Core Facility" ;
NIFRID:synonym "Georgia Institute of Technology Partnership for an Advanced Computing Environment",
"Partnership for an Advanced Computing Environment (PACE)" ;
definition: "Core provides high performance computing (HPC) resources with technical support services, infrastructure, software, and more. PACE maintains several computing clusters for Georgia Tech’s faculty, students, and staff." .
SCR:027620 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5635" ;
rdfs:label "Virginia Tech Crystallography Lab Core Facility" ;
NIFRID:synonym "Virginia Tech Crystallography Lab" ;
definition: "Core specializes in single-crystal structure determination of small molecules, inorganic materials, and minerals. The facility houses a Rigaku-Oxford Diffraction Synergy Single-Crystal X-ray Diffractometer equipped with both Cu and Mo sources, variable temperature capabilities (90 – 500 K) and the setup to perform high-pressure diamond-anvil studies." .
SCR:027621 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5636" ;
rdfs:label "Boise State University Biomedical Research Vivarium Core Facility" ;
definition: "Core provides and supports gold standard of high quality mouse, rat and zebrafish care and services. All procedures are conducted according to the National Institutes of Health Guide for the Care and Use of Laboratory Animals. The BRV is accredited at the highest standard of care through the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) International." .
SCR:027622 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5632" ;
rdfs:label "Virginia Tech Department of Chemistry Chromatography Core Facility" ;
NIFRID:synonym "Chromatography Center",
"Virginia Tech Chromatography Center" ;
definition: "Facility enables complete qualitative and quantitative analysis of components within complex sample matrices. Provides services for separating mixtures, and supports critical research across numerous fields, including:Chemistry and Biochemistry, Biology and Medicine, Environmental Science and Toxicology, Food, Nutrition, and Pharmaceutical Development. Provides extraction, separation, detection, and quantification of organic and other complex mixtures from gas, solid, or liquid matrices." .
SCR:027623 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tumor Spheroids MLTimeSeries" ;
definition: "Software tool for predicting long-term relapse of tumor spheroids from early post-treatment brightfield image data. We deploy a dataset consisting of time-series radiomics features for predicting the treatment response of tumor spheroids." .
SCR:027624 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5637" ;
rdfs:label "Lady Davis Institute Cell Imaging Core Facility" ;
NIFRID:synonym "LDI Cell Imaging Core Facility" ;
definition: "Core provides expertise in confocal, live cell, and fluorescent microscopy. Provides services in experimental design, instrumentation, training, technical assistance, and scientific guidance from sample preparation to data analysis and publication." .
SCR:027625 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.414980.0; ISNI 0000 0000 9401 2774; Crossref Funder ID 501100004734; Wikidata Q3145341;" ;
rdfs:label "Jewish General Hospital Lady Davis Institute for Medical Research; Montreal; Canada" ;
definition: "Medical hospital-based research institute in Montreal, Quebec, Canada." .
SCR:027626 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CircaCompare" ;
definition: "Software R package for statistical analyses and comparison of two circadian rhythms. Used to estimate and statistically support differences in mesor, amplitude and phase, between circadian rhythms." .
SCR:027627 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3030" ;
rdfs:label "Montana State University Biophotonics Core Facility" ;
NIFRID:synonym "Montana State University - Biophotonics Facility" ;
definition: "Core provides multiphoton characterization of Genetically-Encoded Probes for the BRAIN Initiative researchers and broader neuroscience community. Services include Measuring of 2-photon absorption spectra in absolute, cross section values; Measuring 3-photon absorption spectra and cross sections; Characterizing multiphoton photobleaching parameters, i.e. quantum yields, nonlinear absorption cross sections:Measuring one-photon absorption, emission, and excitation spectra;Measuring fluorescence quantum yields and lifetimes;Evolving brighter two-photon probes." .
SCR:027628 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Harmonized Ontology of Mammalian Brain Anatomy (HOMBA)" ;
NIFRID:synonym "Harmonized Ontology of Mammalian Brain Anatomy" ;
NIFRID:abbrev "HOMBA" ;
definition: "Harmonized cross-species taxonomy of brain and spinal cord structures. Derived from the Allen Developing Human Brain Atlas (DHBA) ontology, the HOMBA is hierarchical, allowing users to aggregate structures from fine grain parcellations to broad regions. Terminology is harmonized across human, primate, and rodent structures with synonymous terms and includes transient developmental structures. HOMBA is designed for neuroanatomical applications including brain sampling and dissection, tissue block mapping, atlas building, cell-type and pathology localization, and linking cross-species and developmental datasets." .
SCR:027629 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "Allen Institute Taxonomy schema",
"Allen Institute Taxonomy Standard (AIT)" ;
NIFRID:abbrev "AIT" .
SCR:027630 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BuildIndices" ;
definition: "Software workflow is an open-source, cloud-optimized pipeline developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN)." .
SCR:027631 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SWC format" ;
NIFRID:abbrev "SWC" ;
definition: "Software repository contains files needed to build the standard and its supplementary documentation. Changes are automatically pushed and built. Information about the SWC file specification." .
SCR:027632 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HMBA Adult Human Brain Atlas" ;
NIFRID:synonym "HMBA Adult Human Basal Ganglia Atlas" ;
definition: "Three-dimensional (3D) common coordinate framework (CCF) and reference atlas that defines the spatial organization of the basal ganglia of the adult human brain." .
SCR:027633 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HM_450" ;
rdfs:label "Epredia | HM 450 Sliding Microtome" ;
definition: "Automated sliding microtome with additional capability for cutting large and hard specimens. Offers Choice of manual or mechanized operation, Coaxial specimen orientation and memory function for rapid re-orientation of pre-cut blocks, User-friendly control panel for easy operation, Optional retraction to protect specimen." .
SCR:027634 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CytoSPACE" ;
definition: "Software tool for assigning single cells from scRNA-seq to spatial transcriptomics coordinates via optimization framework. Supports high-resolution cell/spot alignment, capacity-constrained/domain-aware placement, and outputs per-cell/per-spot assignments and probabilities for downstream visualization and analysis. Used for optimal mapping of scRNA-seq data to spatial transcriptomics data." .
SCR:027635 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "novoSpaRc" ;
definition: "Software package for flexible spatial reconstruction of single-cell gene expression with optimal transport. Framework for de novo spatial reconstruction of single-cell gene expression. Assigns cells to tissue locations using probabilistic/optimal-transport models, with or without prior marker information, and returns spatial maps and assignment probabilities." .
SCR:027636 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CSOmap" ;
definition: "Software tool for reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly. Infers cellular spatial organization from scRNA-seq by modeling ligand–receptor-mediated self-assembly. It constructs 3D pseudo-space and quantifies cell–cell interactions for downstream visualization and hypothesis testing." .
SCR:027637 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5639" ;
rdfs:label "State University of Campinas Gleb Wataghin Physics Institute OFMEC/IFGW Core Facility" ;
definition: "IFGW hosts a mechanical workshop that produces precision components for advanced research projects." .
SCR:027638 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5640" ;
rdfs:label "State University of Campinas Gleb Wataghin Physics Institute Criogenia/IFGW Core Facility" ;
NIFRID:synonym "IFGW Cryogenics Laboratory" ;
definition: "Core produces and supplies liquid helium and nitrogen to the entire IFGW academic community. Laboratory is equipped with helium liquefier from Linde and nitrogen liquefier from Stirling Cryogenics. In addition, it maintains complex support infrastructure essential for production and distribution of cryogenic liquids." .
SCR:027639 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5641" ;
rdfs:label "State University of Campinas Gleb Wataghin Physics Institute Vidraria/IFGW Core Facility" ;
NIFRID:synonym "IFGW glass workshop" ;
definition: "IFGW glass workshop, equipped with specialized staff, provides expertise in glass forming, welding, and cutting of Quartz and Borosilicate, as well as in design and technical drawing." .
SCR:027641 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HOMBA Macaque Reference Atlas" ;
definition: "Three-dimensional brain reference atlas for macaque basal ganglia created based on annotation of BG structures on Mac25Rhesus template, an averaged MRI template from 25 M. Includes selected published subcortical parcellations to aid in comparing across parcellation schemes. Enables mapping of samples and integration of multimodal data within and across species." .
SCR:027642 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HOMBA Adult Marmoset Basal Ganglia Atlas" ;
definition: "Three-dimensional brain reference atlas based on the RIKEN25v1 MRI-derived template, based on an average of 25 C. jacchus brains resampled to 70 um3 voxel resolution. Includes selected published subcortical parcellations to aid in comparing across parcellation schemes." .
SCR:027643 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5642" ;
rdfs:label "University of Texas MD Anderson Cancer Center Small Animal Imaging Facility" ;
NIFRID:synonym "Small Animal Imaging Facility (SAIF)" ;
definition: "Core provides access to imaging instrumentation and expertise that is necessary to integrate advanced imaging technologies into basic and translational biomedical research. Services include Assistance in experimental design; Developing specialty equipment and innovative procedures for imaging; Preparing animals for studies, inducing and maintaining appropriate anesthesia and immobilization of animals during imaging;Processing and interpreting data for publication or grant preparation." .
SCR:027644 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5644" ;
rdfs:label "Lady Davis Institute Flow Cytometry Core Facility" ;
definition: "Core provides complete flow cytometry analysis and cell sorting services in terms of experimental design, instrumentation, training, technical assistance and scientific guidance from sample preparation to publication." .
SCR:027645 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ImmuCellAI" ;
NIFRID:synonym "Immune Cell Abundance Identifier" ;
definition: "Software tool for comprehensive T‐Cell subsets abundance prediction and its application in cancer immunotherapy." .
SCR:027646 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Dr.Tom multi-omics data mining system" ;
NIFRID:synonym "Dr. Tom Multi-omics Data mining system" ;
definition: "Web application for data visualization and data mining system that offers efficient analysis and discovery by integrating big data with intelligent and intuitive functionality." .
SCR:027647 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bulkAnalyseR" ;
definition: "Software R package for most bulk sequencing datasets. Creates shiny app for interactive data analysis and visualisation. Used for analysing and sharing bulk sequencing results." .
SCR:027648 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Atlantis" ;
definition: "Integrative database for human proteome structural and functional sites. Used for understanding role of specific residues in protein structures, complexes, and interaction networks. Integrates various structural and functional annotation layers for each residue, offering comprehensive understanding of protein functionality." .
SCR:027649 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5638" ;
rdfs:label "Icahn School of Medicine at Mount Sinai Mount Sinai Cryo-EM CoRE Core Facility" ;
NIFRID:synonym "Mount Sinai Cryo-EM CoRE" ;
definition: "Cryo-Electron Microscopy Core facility at ISM offers EM services with state-of art instruments (Vitrobot for sample preparation, Glacios-2 TEM for imaging biological samples at atomic resolution). We offer single particle analysis (SPA) workflow, imaging drug delivery products (ex: liposomes, LNPs, AAVs..)" .
SCR:027650 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PathoFact2" ;
NIFRID:synonym "PathoFact 2.0" ;
definition: "Software integrative pipeline for antimicrobial resistance genes, virulence factors, toxins, and biosynthetic gene clusters prediction in metagenomes. Used for predicting microbiome-based pathogenicity and resistance to better understand and address challenges posed by antimicrobial resistance and infectious diseases." .
SCR:027651 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5643" ;
rdfs:label "Beth Israel Deaconess Medical Center X-ray Crystallography Core Facility" ;
NIFRID:synonym "Structural Biology Core Facility",
"X-ray Crystallography Core (BIDMC)" ;
definition: "Core offers comprehensive protein expression, purification, characterization, and structural biology services, including advanced methods such as Cryo-Electron Microscopy (Cryo-EM) and X-ray Crystallography." .
SCR:027652 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5647" ;
rdfs:label "Cancer Research UK Scotland Institute Mass Spectrometry Core Facility" ;
NIFRID:synonym "Cancer Research UK Scotland Institute Mass Spectrometry Facility",
"CRUK Scotland Institute Metabolomics Facility",
"CRUK Scotland Institute Proteomics Facility" ;
definition: "Core offers proteomics and metabolomics services. Provides support from experimental design to execution, sample processing, data interpretation, and assistance with presentations, manuscript preparation for publication and deposition of data in public repository and data storage on local server. Provides service analysis of post-translational modifications, such as phosphorylation, ubiquitination, acetylation, and others, with precise site localization on either single protein or for entire proteome.Uses Orbitrap Fusion Lumos coupled to Easy-nLC 1200 HPLC system. Facility instruments are operated with various acquisition methods, including classic Data Dependent Analysis (DDA) or more recent Data Independent Analysis (DIA). Acquired data from different methods are used to accurately identify and measure abundance of proteins and peptides employing different quantitation strategies: Label-free, TMT, pulsed-SILAC and Isotope-labelled Iodoacetamide (for Cysteine oxidation).Provides specialized data analysis software like MaxQuant and Mascot for DDA, Spectronaut for DIA of clinical samples and Perseus and Scaffold for data compilation, analysis, and dissemination." .
SCR:027653 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "adaptive_stitching" ;
definition: "Software algorithm for restitching overlapping image crops with intensity adjustment. Crops are intensity corrected and weight adjusted to produce uniform intensity composite image." .
SCR:027654 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Ultra-Mab_Pro" ;
rdfs:label "Resosence Technology | Ultra Mab Pro" ;
NIFRID:synonym "ResoSens Ultra-Mab Pro" ;
definition: "Benchtop plate reader with ResoVu software enables rapid, label-free detection in disposable 96-well plate format. Benchtop system with semi-automated fluidics with Disposable 96-well microarray plate format; User friendly, and easy to operate; Real-time data analysis features." .
SCR:027655 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AutoMorphoTrack" ;
NIFRID:synonym "AMTpackage" ;
definition: "Software Python package for automated detection, morphology classification, tracking, and colocalization analysis of organelles in multichannel fluorescence microscopy data." .
SCR:027656 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5650" ;
rdfs:label "Advanced Cyberinfrastructure Coordination Ecosystem Services and Support Core Facility" ;
NIFRID:synonym "Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support; Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support - ACCESS;" ;
NIFRID:abbrev "ACCESS" ;
definition: "Provides advanced computing systems and services including supercomputer applications, AI and machine learning, big data analysis and storage. Offers suite of cyberinfrastructure coordination services targeted at supporting all areas of science and engineering research and education." .
SCR:027659 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FPNuNet" ;
definition: "Software tool as frequency-aware prompt-guided network for nuclear segmentation and classification in immunohistochemistry images." .
SCR:027660 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ImarisViewer " ;
NIFRID:synonym "3D/4D Microscopy Image Viewer" ;
definition: "Free 3D/4D Microscopy Image Viewer. Used to visualize microscopy images (stacks) in 3D." .
SCR:027662 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mirt" ;
NIFRID:synonym "mirt:Multidimensional Item Response Theory",
"Multidimensional Item Response Theory" ;
definition: "Software package for the R Environment. Used for estimating multidimensional item response theory parameters for exploratory and confirmatory models by using maximum-likelihood meth- ods." .
SCR:027663 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lavaan" ;
NIFRID:synonym "lavaan: Latent Variable Analysis" ;
definition: "Software R package for latent variable analysis. Used to estimate variety of multivariate statistical models. Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models." .
SCR:027664 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ltm:Latent Trait Models under IRT" ;
NIFRID:synonym "Latent Trait Models" ;
NIFRID:abbrev "ltm" ;
definition: "Software R package for analysis of multivariate dichotomous and polytomous data using latent trait models under the Item Response Theory approach." .
SCR:027665 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cmprskcoxmsm" ;
NIFRID:synonym "cmprskcoxmsm: Use IPW to Estimate Treatment Effect under Competing Risks" ;
definition: "Software R package uses inverse probability weighting methods to estimate treatment effect under marginal structure model for the cause-specific hazard of competing risk events. Estimates also the cumulative incidence function (i.e. risk) of the potential outcomes, and provides inference on risk difference and risk ratio." .
SCR:027666 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "biglm" ;
definition: "Software R package for Bounded Memory Linear and Generalized Linear Models. Regression for data too large to fit in memory." .
SCR:027667 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "plotROC" ;
definition: "Software tool for plotting Receiver Operating Characteristic (ROC) curves." .
SCR:027668 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RCy3" ;
NIFRID:synonym "RCy3: Network biology using Cytoscape from within R" ;
definition: "Software R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort.Network biology using Cytoscape from within R." .
SCR:027669 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ontologyIndex" ;
definition: "Software R package enables arbitrary ontologies to be read into R, supports representation of ontological objects by native R types, and provides a parsimonius set of performant functions for querying ontologies." .
SCR:027670 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "celldex" ;
definition: "Software R package provides collection of reference expression datasets with curated cell type labels, for use in procedures like curated cell type labels or deconvolution of bulk RNA-seq." .
SCR:027671 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Solarbio" ;
definition: "Commercial vendor and service provider of laboratory reagents and antibodies located in Beijing, China. Supplier of scientific instrumentation, reagents and consumables, and software services." .
SCR:027672 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5653" ;
rdfs:label "Augusta University Human MRI Imaging Core Facility" ;
definition: "Core dedicated to providing cutting-edge magnetic resonance imaging services for human participants. Provides Human 3 Tesla MRI system from Siemens for human research with proper IRB approval and approved MRI protocols." .
SCR:027673 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5654" ;
rdfs:label "Augusta University Proteomics and Mass Spectrometry Core Facility" ;
definition: "Facility for characterization and expression level quantitation of proteins (isolated or in an extract) and small molecules/metabolites by mass spectrometry (MS) and/or chromatography. Services include protein identification, labeled and label-free comparative proteomics by Orbitrap mass spectometry, protein/small molecule quantification using targeted mass spectometry (PRM and SRM/MRM mass spectometry), high throughput protein immune-protein assays (384-well Luminex/ELISA assay), etc." .
SCR:027674 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5655" ;
rdfs:label "University of Montreal Institute for Research in Immunology and Cancer Genomics Platform Core Facility" ;
NIFRID:synonym "Institute for Research in Immunology and Cancer of the Université de Montréal - Genomics Platform",
"IRIC's Genomics Core Facility" ;
definition: "Facility offers services, combining expert guidance and technologies including Sanger Sequencing, Next-Generation Sequencing, Single-Cell Sequencing, qPCR, Quantity and Quality of DNA and RNA measurement." .
SCR:027675 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5656" ;
rdfs:label "Van Andel Institute MiND iPSC and Screening Platform Core Facility" ;
NIFRID:synonym "MiND iPSC and Screening Platform" ;
definition: "Core provides iPSC cell culture laboratory with access to curated and validated iPSC lines for neurodegeneration research. Provides robotic and fully automated high-content imaging system to perform high-throughput screening on living brain cells (iPSC derived through reprogramming) to understand the mechanisms behind neurodegeneration at the molecular level." .
SCR:027676 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5657" ;
rdfs:label "Institute of Ecology INECOL Advanced Microscopy Unit Core Facility" ;
NIFRID:synonym "Advanced Microscopy Unit (UMA) at INECOL",
"Unidad de Microscopía Avanzada - INECOL (UMA-INECOL)" ;
definition: "Core supports research in various scientific disciplines through advanced microscopy techniques (fluorescence, electron, and optical) and micro-CT. Provides technical services, consultation and training in advanced microscopy." .
SCR:027677 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 501100011109",
"GRID grid.452507.1",
"ISNI 0000 0004 1798 0367" ;
rdfs:label "Institute of Ecology; Xalapa; Mexico" ;
NIFRID:synonym "Instituto de Ecología" ;
NIFRID:abbrev "INECOL" ;
definition: "INECOL focuses on research on natural resources, conservation, and biodiversity, aiming to solve ecological problems and generate scientific knowledge." .
SCR:027678 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PySeq2500" ;
definition: "Software tool to control Illumina HiSeq 2500 System. Open source Python code base and flow cell design that converts Illumina HiSeq 2500 instrument, comprising epifluorescence microscope with integrated fluidics, into open platform for programmable applications without need for specialized engineering or software development expertise.Enables non-specialists to develop and implement fluidics coupled imaging methods in benchtop system." .
SCR:027679 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5651" ;
rdfs:label "University of Missouri Kansas City UMKC Proteomics Core Facility" ;
NIFRID:synonym "UMKC-Proteomics Core Facility" ;
definition: "Federally funded facility committed to advancing scientific research by delivering high-quality proteomic data. Provides proteomics analysis, technology, services, and rigorous quality standards." .
SCR:027680 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5652" ;
rdfs:label "Augusta University High Performance Computing Core Facility" ;
NIFRID:synonym "Augusta University High Performance Computing and Parallel Computing Services Core Facility" ;
definition: "Core provides high memory parallel processing environments and software in support of the university research, academic, and cybersecurity missions. HPC clusters use multiple computers to process data in parallel, greatly reducing the time to solution for most computational science tasks. They also provide storage to manage very large data sets." .
SCR:027681 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RLM" ;
definition: "Software tool to read level DNA methylation analysis of bisulfite converted sequencing data." .
SCR:027682 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Model Passports" ;
definition: "Hub for clinical, genetic and functional datasets of preclinical cancer models.Provides details of cell model relationships, patient and clinical information, as well as access to associated genetic and functional datasets. Passports database contains curated details and standardized annotation for cell models, including cancer organoid cultures. Users can navigate database via tissue, cancer-type, genetic feature and data availability to select model. REST-API provides programmatic data access and exploration." .
SCR:027683 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PrankWeb" ;
definition: "Web application for ligand binding site prediction. Used for prediction of ligand binding sites from protein structure." .
SCR:027684 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "COACH" ;
NIFRID:synonym "COACH server" ;
definition: "Web application for protein-ligand binding site prediction. Starting from given structure of target proteins, COACH will generate complementray ligand binding site predictions using two comparative methods, TM-SITE and S-SITE, which recognize ligand-binding templates from the BioLiP protein function database by binding-specific substructure and sequence profile comparisons." .
SCR:027685 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BioLiP" ;
NIFRID:synonym "BioLiP2" ;
definition: "Semi-manually curated database for biologically relevant ligand-protein binding interactions. Structure data are collected primarily from Protein Data Bank (PDB), with biological insights mined from literature and other specific databases. Database used for serving needs of ligand-protein docking, virtual ligand screening and protein function annotation.BioLiP2 offers significantly greater coverage of nucleic acid-protein interactions, and interactions involving large complexes, integrates structural alignment algorithms with structure prediction techniques, which enables composite protein structure and sequence-based searching." .
SCR:027686 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SeamDock" ;
definition: "Web server for interactive and collaborative online docking to assist small compound molecular docking. In silico assessment of protein receptor interactions with small ligands." .
SCR:027687 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5659" ;
rdfs:label "Brigham and Women’s Hospital NeuroTechnology Studio Core Facility" ;
definition: "Offers advanced instrumentation and expert support to advance understanding of brain function and brain disease by providing researchers with access to cutting-edge technologies. Provides access to advanced instrumentation for optical microscopy, genomics, metabolic imaging and other technologies, as well as image analysis software. Provides expert support and training, data quality and interpretation." .
SCR:027688 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5658" ;
rdfs:label "University of Wisconsin Madison Radiopharmaceutical Analytics and Specimen Research Lab Core Facility" ;
NIFRID:synonym "Radiopharmaceutical Analytics and Specimen Research (RASR) Lab",
"Radiopharmaceutical Analytics and Specimen Research Lab",
"University of Wisconsin Madison Radiopharmaceutical Analytics and Specimen Research Lab" ;
definition: "Core for radioactive sample analysis and storage. Provides next generation in-vivo metabolism and biological assessment of new radiopharmaceuticals in clinical and preclinical studies. Houses analytical instruments dedicated for use with radioactive biospecimens." .
SCR:027689 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5661" ;
rdfs:label "University of Coimbra ViralVector Core Facility" ;
NIFRID:synonym "University of Coimbra ViralVector for Gene Transfer",
"Viral Vectors for Gene Transfer",
"ViraVector",
"ViraVector (VV)" ;
definition: "Portuguese national research infrastructure which provides expert consultation for the safe and effective use of vector technologies, and offers custom design and production services for multiple viral types to the national research community and other stakeholders." .
SCR:027691 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "sandwich" ;
NIFRID:synonym "sandwich:Robust Covariance Matrix Estimators" ;
definition: "Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods." .
SCR:027692 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GCAT Workflow" ;
definition: "Software cancer genome and RNA sequencing data analysis pipeline that detects genomic variants and transcriptomic changes." .
SCR:027693 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "LightGBM",
"lightgbm:Light Gradient Boosting Machine" .
SCR:027694 a NLX:63400,
owl:NamedIndividual ;
NIFRID:synonym "dcurves: Decision Curve Analysis for Model Evaluation" .
SCR:027695 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "probably" ;
NIFRID:synonym "probably: Tools for Post-Processing Predicted Values" ;
definition: "Software R package for conducting recalibration, conversion to hard probabilities, assessment of equivocal zones operations as well as calibration tools and conformal inference techniques for regression models." .
SCR:027696 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "U3-Nomogram" ;
definition: "Software application for C-CAT CALICO database. Used for Germline-focUsed analysis of tUmoUr-detected variants with Nomogram for C-CAT CALICO database." .
SCR:027697 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CIPR-Package" ;
NIFRID:synonym "Cluster Identity PRedictor (CIPR)",
"Cluster Identity PRedictor Package" ;
definition: "Software R package for annotating cell clusters in scRNAseq data." .
SCR:027698 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "storm-control" ;
definition: "Custom software to control MERFISH imaging components. System consists of microscope body coupled with Nikon CFI Plan Apo 60X Lambda D oil immersion objective. Microscope control software." .
SCR:027699 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ ECHO_Revolution" ;
rdfs:label "ECHO | Revolution Microscope" ;
definition: "Automated microscope that can convert between both Upright and Inverted configurations, ideal for imaging well plates and slides.Designed for developmental biology, cell biology, neuroscience, immunology, cancer research, and more, Revolution brings the capabilities of live-cell imaging, timelapse, tiling/mosaic imaging, and multi-well plate screening to the lab." .
SCR:027700 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "PacGenomics" ;
definition: "Company provides medical laboratory services, specializing in genetic and genomic testing." .
SCR:027701 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5663" ;
rdfs:label "Icahn School of Medicine at Mount Sinai Flow Cytometry CoRE Core Facility" ;
NIFRID:synonym "Flow Cytometry CoRE" ;
definition: "Situated within the Icahn School of Medicine at Mount Sinai, our CoRE provides all members of the Mount Sinai Health System community with the instrumentation, expertise, and education required to incorporate flow cytometry and cell sorting into any research project." .
SCR:027702 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5664" ;
rdfs:label "Michigan State University Center for Advanced Microscopy Core Facility" ;
definition: """Core provides instruction and access to scanning electron microscopes, transmission electron microscopes, laser capture microscopes, and confocal laser scanning microscopes.
CAM staff members help with microscopes and microscopy analysis.""" .
SCR:027703 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PCL_detector" ;
definition: "Software tool to detect problematic cell lines during text processing.Based on: SciSpacy NER model \"en_ner_jnlpba_md\" -- DNA, Cell Type, RNA, Protein, Cell Line Cellosaurus (Dump, FEV. 2021) and ICLAC (V10)." .
SCR:027704 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PTC_Tempo_Deepwell" ;
rdfs:label "Bio-Rad | PTC Tempo Deepwell Thermal Cycler" ;
NIFRID:synonym "PTC Tempo Deepwell Thermal Cycler" ;
definition: "Conventional PCR instrument built with fixed 96-deepwell reaction block that accommodates reaction volumes of 10 ul to up to 125 µl." .
SCR:027705 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PLMN score" ;
definition: "Web application to provide comparison of the risk predictions. Used to calculate the risk of lymph node metastasis in patients with T1 colorectal cancer." .
SCR:027706 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5667" ;
rdfs:label "University of Texas Southwestern Medical Center Dallas Histo Pathology Core Facility" ;
NIFRID:synonym "University of Texas Southwestern Medical Center Dallas Histo Pathology Core" ;
definition: "Core offers research histology and anatomic pathology services and customized pathology services. Facilitates morphologic and histologic assessment of murine transgenic and knockout phenotypes as well as experimental procedure-based models of disease for basic and clinical research. We utilize expertise in gross pathology, routine histology, immunohistochemistry, tissue microarray, spatial transcriptomics, spatial proteomics, laser-capture microdissection, materials science, photomicrography, and image analysis." .
SCR:027707 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mitochondria Analyzer" ;
definition: "Software pipeline for multidimensional confocal analysis of mitochondrial morphology, function, and dynamics." .
SCR:027708 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5668" ;
rdfs:label "Tufts University Genomics Core Facility" ;
definition: "Core provides protein sequencing services including Next-Generation DNA Sequencing, Peptide Synthesis, Protein Sequencing, and Mass Spectrometry. Provides expert technical and analytical support." .
SCR:027709 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5669" ;
rdfs:label "Tufts University Laser Cytometry Core Facility" ;
NIFRID:synonym "Tufts University Laser Cytometry Core Facility (TLC)" ;
definition: "Core offers Flow and Laser Cytometry equipment and services including FACS Analysis and Cell Sorting, to the scientific community." .
SCR:027710 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH Brain Development Cohorts (NBDC) Data Hub" ;
definition: "Data platform providing centralized and secure access to rich, longitudinal brain, behavioral, and genomic data from both the Adolescent Brain Cognitive Development (ABCD) and the HEALthy Brain and Child Development (HBCD) Studies. By bringing together data from both studies, the NBDC Data Hub facilitates integrative research on early life and adolescent development, helping researchers explore developmental trajectories across the lifespan." .
SCR:027711 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5670" ;
rdfs:label "Texas A and M University Protein Chemistry Laboratory Core Facility" ;
NIFRID:synonym "Protein Chemistry Laboratory (PCL)",
"Texas A&M University Protein Chemistry Laboratory" ;
definition: "Core provides instrumentation, systems, software, technical expertise and training for the application of novel protein and molecular biology technologies. Provides training and expertise. Offers protein and amino acid services." .
SCR:027712 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "A3D3a MVP" ;
NIFRID:synonym "A3D3a Molecular Vulnerability Picker",
"A3D3a Molecular Vulnerability Picker (MVP)",
"A3D3a_MVP",
"A3D3a’s MVP",
"Adaptive AI-Augmented Drug Discovery and Development Molecular Vulnerability Picker" ;
definition: "Software tool as novel graph-based, cooperativity-led Markov chain model to exploit cooperativity of weak signals within cancer molecular network to enhance the signal of true molecular vulnerabilities. Used to identify molecular vulnerabilities from multimodal patient data." .
SCR:027713 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BayGene Biotech | BG-gdsAUTO710 MINI Chemiluminescence Imaging Analysis System" ;
NIFRID:synonym "BG-gdsAUTO710 MINI system",
"Chemiluminescence Imaging Analysis System (BG-gdsAUTO710MINI)" ;
definition: "Chemiluminescence imaging analysis system designed for Western-Blot membrane imaging. High-megapixel camera provides high resolution images and deep-cooled CCD with low background noise improves image quality even in case of long exposure time. For detection of the very weak bands, you can choose multiple binning options of software, from 1x1 to 4x4 binning modes, which collect more signals as you need." .
SCR:027714 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "shallowHRD" ;
definition: "Software R tool for detection of homologous recombination deficiency from shallow whole genome sequencing. Used to assess Homologous Recombination Deficiency of tumor based on the number of Large-scale Genomic Alterations (LGAs)." .
SCR:027715 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "StarDist" ;
definition: "Software application for object detection with Star-convex Shapes. Used for phase-contrast cell images." .
SCR:027716 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Yellowbrick" ;
definition: "Software application for visual analysis and diagnostic to facilitate machine learning model selection. Visualizing the Scikit-Learn Model Selection Process. Used to evaluate stability and predictive value of machine learning models and improves the speed of the experimental workflow. Provides visual tools for monitoring model performance in real world applications. Provides visual interpretation of the behavior of model in high dimensional feature space." .
SCR:027717 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5673" ;
rdfs:label "Louisiana State University Health Sciences Center Shreveport Metabolomics and Machine Learning Core Facility" ;
NIFRID:synonym "Metabolomics and Machine Learning Core" ;
definition: "Metabolomics and Machine Learning Core provides metabolite profiling and stable-isotope tracing, molecular modeling, and machine learning to integrate datasets across transcriptomic, proteomic, and metabolomic analysis." .
SCR:027718 a owl:NamedIndividual ;
rdfs:label "5PSeq Explorer" ;
NIFRID:synonym "fivepseq-explorer" ;
definition: "Web-based platform for interactive exploration of ribosome dynamics derived from 5′P mRNA degradome sequencing (5PSeq) data. Focused on changes in ribosome dynamics associated to mRNA decay that in some cases can be obscured in conventional ribosome profiling data." .
SCR:027719 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SQuIRE" ;
NIFRID:synonym "Software for Quantifying Interspersed Repeat Expression",
"Software for Quantifying Interspersed Repeat Expression (SQuIRE)" ;
definition: "Software RNA-seq analysis pipeline that provides quantitative and locus-specific picture of Transposable Elements expression." .
SCR:027720 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5674" ;
rdfs:label "Medical College of Wisconsin Echo Core Shared High-Frequency Ultrasound Imaging Core Facility" ;
NIFRID:synonym "Echo Core-Shared High-Frequency Ultrasound Imaging Facility" ;
definition: "Core provides VisualSonics Vevo 3100 high-frequency ultrasound imaging unit, small animal imaging station, micro-injection system, anesthesia unit; Linear array transducers (MX250, MX550D, MX700); VevoLab use." .
SCR:027721 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ccube" ;
definition: "Software R package for clustering and estimating cancer cell fractions (CCF) of somatic variants (SNVs/SVs) from bulk whole genome/exome data. Used for estimating cancer cell fractions ." .
SCR:027722 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ClusterSV" ;
definition: "Software application to group genetic structural variant rearrangements into rearrangement clusters and footprints. Used in the PCAWG-6 project." .
SCR:027723 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DPClust" ;
definition: "Software R package containing methods for sub-clonal reconstruction through SNVs and/or CNAs from whole genome or whole exome sequencing data." .
SCR:027724 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mitoAnalyzer" ;
definition: "Software R package for analysis of mitochondrial DNA using sequencing data. Used for analyzing mtDNA single nucleotide variants and copy number variation. It has two components, mitoCaller and mitoCalc/fastMitoCalc." .
SCR:027725 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HotMaps" ;
NIFRID:synonym "Hotspot Missense mutation Areas in Protein Structures" ;
definition: "Software tool to detect somatic mutation hotspot regions in 3D protein structures." .
SCR:027726 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HRDetect" ;
definition: "Software tool for detection and analysis of homologous recombination events." .
SCR:027727 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "IntOGen" ;
NIFRID:synonym "Intogen Plus",
"IntOGen-mutations platform" ;
definition: "Software tool for automatic and comprehensive knowledge extraction based on mutational data from sequenced tumor samples from patients. Summarizes somatic mutations, genes and pathways involved in tumorigenesis." .
SCR:027728 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mSings" ;
definition: "Software tool for detecting microsatellite instability by next-generation sequencing." .
SCR:027729 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MutPanningV2" ;
NIFRID:synonym "MutPanning" ;
definition: "Software tool designed to detect rare cancer driver genes from aggregated whole-exome sequencing data." .
SCR:027730 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OncodriveCLUSTL" ;
definition: "Software application to detect significant clustering signals across genomic regions. Sequence-based clustering method to identify cancer drivers." .
SCR:027731 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OncodriveFML" ;
definition: "Software tool that estimates accumulated functional impact bias of somatic mutations in any genomic region of interest based on local simulation of the mutational process affecting it." .
SCR:027732 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PCAWG SV Merge" ;
definition: "Software application as PCAWG6 workflow to merge SVs from Sanger (BRASS), Broad Inst (DRanger and SnowMan ) and EMBL/DKFZ (DELLY)." .
SCR:027733 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "smregions" ;
definition: "Software tool to detect linear enrichment of somatic mutations in user-defined regions of interest." .
SCR:027734 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "UTRannotator" ;
definition: "Software tool to annotate high-impact five prime UTR variants either creating new upstream ORFs or disrupting existing upstream ORFs. Annotates variants in 5'untranslated regions (5'UTR) that create or disrupt upstream open reading frames." .
SCR:027735 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xTea" ;
NIFRID:synonym "x-Transposable element analyzer" ;
definition: "Software tool to identify transposable element insertions from paired-end Illumina reads, barcode linked-reads, long reads (PacBio or Nanopore), or hybrid data from different sequencing platforms and takes whole-exome sequencing (WES) or whole-genome sequencing (WGS) data as input." .
SCR:027736 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ActivePathways" ;
definition: "Software R package for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets.Method that first prioritises genes through multi-omics data fusion and then identifies enriched pathways with gene-level evidence from input datasets." .
SCR:027737 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ActiveDriverWGS" ;
definition: "Software R package for discovery of cancer driver genes and non-coding elements in whole genome sequencing data. Cancer driver discovery tool for analysis of somatic mutations derived from whole genome sequencing." .
SCR:027738 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BSgenome Hsapiens UCSC hg38" ;
definition: "Software R package containing the full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31)." .
SCR:027739 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MutationTimeR" ;
definition: "Software R package to time somatic mutations relative to clonal and subclonal copy number states and calculate relative timing of copy number gains." .
SCR:027740 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "peakPick" ;
definition: "Software R package for identifying peaks in data related to genomics, genetics, or epigenetics research." .
SCR:027741 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pscl" ;
NIFRID:synonym "Political Science Computational Laboratory" ;
definition: "Software R package providing classes, methods and test data based on maximum likelihood and Bayesian inference." .
SCR:027742 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "T Cell ExTRECT" ;
NIFRID:synonym "T cell exome T cell Receptor Excision Circle",
"T cell exome TREC" ;
definition: "Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes." .
SCR:027743 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "trackViewer" ;
definition: "Software R package to visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data." .
SCR:027744 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bgsignature" ;
definition: "Software Python package used to compute mutational signatures." .
SCR:027745 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CoMUT" ;
definition: "Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots." .
SCR:027746 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FixVAF" ;
definition: "Software tool as Python script to remove bias from Isaac aligned data by clipping all reads for variant positions by 5 bases and producing a modified vcf file." .
SCR:027747 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Telomerecat " ;
definition: "Software R package for estimating average telomere length (TL) for paired end, whole genome sequencing (WGS) sample.Telomere computational analysis tool." .
SCR:027748 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CancerMine" ;
definition: "Text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer." .
SCR:027750 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "HDL-C" ;
rdfs:label "High-definition likelihood inference of genetic colocalization (HDL-C)" ;
NIFRID:synonym "High-Definition Likelihood Colocalization" ;
definition: "Software tool for optimizing likelihood conditioning on high point estimate of local genetic correlation and assesses statistical evidence that the two traits not only exhibit correlated genetic effects but are likely influenced by shared causal variants.Enhances specificity and interpretability in detecting colocalized signals. This targeted framework improves causal inference in pleiotropic architectures, supporting more informed discovery of biomarkers and therapeutic targets." .
SCR:027751 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "e1071" ;
definition: "Software R package for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, generalized k-nearest neighbour." .
SCR:027752 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SlicerRVXLiverSegmentation" ;
definition: "Software 3D Slicer plugin for Liver Anatomy Annotation by R-Vessel-X." .
SCR:027753 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "kernelshap" ;
definition: "Software package provides different SHapley Additive exPlanations (SHAP) algorithms for calculating SHAP values, including Kernel SHAP. Used for explaining predictions made by complex machine learning models." .
SCR:027754 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ELEXSYS_E_580" ;
rdfs:label "Bruker | ELEXSYS-E580 pulse X-/Q-band system" ;
NIFRID:synonym "Bruker ELEXSYS-E580 EPR Spectrometer" ;
definition: "Bruker ELEXSYS-E580 pulse X-/Q-band instrument offers state-of-the-art capabilities for both standard and cutting-edge EPR spectroscopy across a broad range of sample types and experimental needs. High-performance Electron Paramagnetic Resonance (EPR) spectrometer used for advanced research in chemistry, materials science, biochemistry, and physics, enabling studies of paramagnetic molecules, protein structures, quantum states, and materials by combining X-band (9-10 GHz) and Q-band (34 GHz) frequencies for high-resolution, sensitive pulse techniques." .
SCR:027755 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5680" ;
rdfs:label "Augusta University Statistical Consulting Center Core Facility" ;
definition: "Core offers services including statistical analyses, grant applications, prep for manuscript publications, etc." .
SCR:027756 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5677" ;
rdfs:label "Beth Israel Deaconess Medical Center BIDMC Zebrafish Research Core Facility" ;
NIFRID:synonym "BIDMC Zebrafish Research Core" ;
definition: "Core Facility is a 3,000+ fish tank facility, located in the Slosberg-Landay building, equipped with 48 racks which hold standard sized adult zebrafish tanks, three-rack nursery space for larval fish, and quarantine space containing two stand-alone housing systems. Wild-type lines are maintained inhouse for shared use. Wet lab space is available for breeding and line maintenance; core staff and facility-associated technicians perform daily feeding. The core includes a dedicated procedure room for embryo manipulation." .
SCR:027757 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Simple_Plex_Ella" ;
rdfs:label "Bio-Techne | Simple Plex Ella Automated Immunoassay System" ;
definition: "Benchtop automated Ella platform utilizes microfluidic Simple Plex assay cartridge designed to perform all reagent additions, wash steps, and incubations under precisely controlled conditions to run ELISA assays. Available for plexing up to 8 analytes." .
SCR:027758 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "InstaNovo" ;
definition: "Source code for training and inference of InstaNovo and InstaNovo+. InstaNovo is a transformer neural network with the ability to translate fragment ion peaks into the sequence of amino acids that make up the studied peptide(s)." .
SCR:027759 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Octopus bimaculoides Histotomography Blueprint" ;
NIFRID:abbrev "CephTeam_Octo9" ;
definition: "Resource serves as a 'Digital Specimen' for Digital Organismal Biology, providing interactive Neuroglancer-based visualization and 3D segmentation masks for major organ systems, including the digestive, respiratory, vascular, and nervous systems. It specifically annotates novel neural tracts including the Intermediate Longitudinal Tracts (iLT) and Arm-to-Arm U-Tracts (AAUT) as well as ~300 additional tissue and organ level segmentations. Provides high-resolution (0.7 µm isotropic), whole-organism microCT reconstruction of an intact hatchling Octopus bimaculoides." .
SCR:027760 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5682" ;
rdfs:label "University of Maryland School of Medicine Baltimore Electron Microscopy Core Imaging Facility" ;
NIFRID:synonym "Electron Microscopy Core Imaging Facility (EMCIF)",
"UMB Electron Microscopy Core Imaging Facility" ;
definition: "Core is part of the Center for Innovative Biomedical Resources (CIBR) and is located on the 6th floor of Howard Hall. All services, instrumentation, and training courses are available to anyone, academic or private users, with an interest in electron microscopy.EMCIF services are managed by iLab core facility management program. New users must register in iLab to access instrument and EMCIF services." .
SCR:027761 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5683" ;
rdfs:label "Beth Israel Deaconess Medical Center BILH/BIDMC REDCap Core Facility" ;
NIFRID:synonym "BILH/BIDMC REDCap" ;
definition: "REDCap (Research Electronic Data Capture) is a secure HIPAA compliant web-based data collection application hosted by Research and Academic Computing (ARC), a department of Beth Israel Deaconess Medical Center (BIDMC) which is itself part of Beth Israel Lahey Health (BILH). The function of the REDCap Core is to provide REDCap-related services and support to all BILH users." .
SCR:027762 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sunrise" ;
rdfs:label "Tecan | Sunrise Microplate Reader" ;
definition: "Absorbance microplate reader offers all the functionality needed for photometric applications, including advanced 12-channel optics for fast, multichannel absorbance reading of ELISAs, temperature control function for enzyme kinetic assays, and tunable wavelength function for wavelength scanning." .
SCR:027763 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5684" ;
rdfs:label "Laval University IBIS Imaging and Microscopy Platform Core Facility" ;
NIFRID:synonym "Laval University IBIS Imaging and Microscopy Platform" ;
definition: "IBIS Microscopy platform offers sample preparation and acces to TEM, SEM, STED, confocals and other microscopes." .
SCR:027764 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SYLVER" ;
NIFRID:synonym "SYnthetic Lethal Vulnerabilities Exhibiting Reciprocation" ;
definition: "Web application for identification of candidate synthetic lethal vulnerabilities in cancers." .
SCR:027765 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CBaSE" ;
NIFRID:synonym "Cancer Bayesian SElection estimation" ;
definition: "Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer." .
SCR:027766 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5685" ;
rdfs:label "BIDMC Clinical Research Center Clinical Services Core Facility" ;
NIFRID:synonym "Beth Israel Deaconess Medical Center Clinical Research Center Clinical Services Core Facility" ;
definition: "Offers investigators clinical space, equipment, skilled nursing and nutrition services, project management and study coordinator support, resources for conducting community engagement research, as well as one-on-one consultation with Clinical/Translational Research Navigators." .
SCR:027767 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3107" ;
rdfs:label "BIDMC Division of Digital Psychiatry LAMP platform Core Facility" ;
NIFRID:synonym "Beth Israel Deaconess Medical Center mindLAMP",
"BIDMC mindLAMP",
"mindLAMP" ;
definition: "Core collects data to capture and consider the real-time lived experiences of patients. Uses open-source digital platform and mobile app for neuropsychiatric research and clinical care, to monitor, support, and improve brain health by collecting real-time data (like location, activity, heart rate via sensors), conducting digital assessments (surveys, cognitive tests), and delivering interventions (meditation, journaling, psychoeducation) to patients and clinicians. It helps study behavioral patterns, track symptoms, and personalize mental health treatment through features organized around Learn, Assess, Manage, and Prevent." .
SCR:027768 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scATOMIC" ;
definition: "Software R package to annotate cell types in scRNA-seq of tumour microenvironments." .
SCR:027769 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Score" ;
definition: "Platform provides accurate, machine-executable computational models of how the brain gives rise to the mind. Enables researchers to quickly get a sense of the alignment of their model(s) to neural and behavioral measurements, and provides these models to experimentalists to prototype new experiments and make sense of biological data. All code is open-source and community members may choose to make their data or model weights fully public." .
SCR:027770 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PublicnEUro" ;
definition: "Data repository for Brain Imaging Data: MRI, PET, MEG, EEG, etc .. similar to OpenNeuro where each dataset is shared independently. Platform is GDPR compliant, allowing to share brain imaging data as FAIRly as possibly. The catalogue allows all metadata to be open and thus findable. As EU data have to be protected, we provide the necessary privacy protection by controlling user access." .
SCR:027771 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Austrian NeuroCloud" ;
definition: "Platform for sustainable research data management in cognitive neuroscience. Secure data storage and integrated tools to support maintenance, reuse, and FAIR-aligned management of neurocognitive research data. Data remains curated, documented, and accessible for the long term, supporting reproducibility and future discovery." .
SCR:027773 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Oslo Services for sensitive data (TSD)" ;
NIFRID:synonym "Services for sensitive data (TSD)" ;
definition: "Platform to collect, store and analyze sensitive research data in secure environment. It comprises secure project area and integrated solution for collecting sensitive data (Nettskjema), accessible by anywhere in the world." .
SCR:027774 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "XYomics" ;
definition: "Software R package for analysis of condition-specific sex differences in omics data. Includes functions for differential expression, interaction testing, and gene regulatory network analysis. Used for analysis of sex differences in omics data for complex diseases." .
SCR:027775 a owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5687" ;
rdfs:label "University of Pittsburgh Mouse Embryo Services Core Facility" ;
NIFRID:synonym "Mouse Embryo Services (MES) Core",
"University of PMouse Embryo Services Core" ;
definition: "Core provides services including generation of gene editing mice, transgenic mice, ES cell microinjection into blastocysts to create germline competent chimera, cryopreservation and long-term storage of mouse sperm/embryos, recovery of mouse lines from cryopreserved germplasm, in vitro fertilization for mouse line rescue and re-derivation of pathogen free mouse strains." .
SCR:027777 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5689" ;
rdfs:label "University of California at Irvine FIBRE Core Facility" ;
NIFRID:synonym "UC Irvine FIBRE Core Facility.",
"UCI Facility for Imaging and Brain Research",
"UCI FIBRE" ;
definition: "Facility for Imaging and Brain Research houses 3T Siemens Prisma scanner, mock scanner, and data analysis facilities. Research dedicated MRI scanning facility designed to suit wide range of basic and translational research programs by researchers across the UCI campus and beyond." .
SCR:027778 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AER: Applied Econometrics with R" ;
definition: "Software R package contains functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2." .
SCR:027779 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Revvity Inc." ;
definition: "American company in the life sciences and diagnostics business that is focused on selling to the pharmaceutical and biotechnology industries, especially in relation to approaches making use of new cell therapy or gene therapy developments." .
SCR:027780 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Opera_Phenix_Plus" ;
rdfs:label "Revvity | Opera Phenix Plus High-Content Screening System" ;
definition: "Imaging system is confocal imaging platform designed for high-throughput biological assays. Supports phenotypic screening and imaging of complex biological models, including live cells, primary cells, and microtissues." .
SCR:027781 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bamUtil" ;
definition: "Software set of programs and utilities for working on SAM/BAM files." .
SCR:027782 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SYNAPT_G2-Si" ;
rdfs:label "Waters | SYNAPT G2-Si Mass Spectrometry System" ;
NIFRID:synonym "SYNAPT G2-Si MS System",
"Waters SYNAPT G2-Si MS System" ;
definition: "High-resolution mass spectrometer with ion mobility, designed for deep, accurate analysis of complex samples across life science and analytical chemistry research. System adds Ion Mobility Separation to the original SYNAPT G2's high-resolution QuanTof technology, offering a third dimension of separation (size/shape) for superior selectivity, sensitivity, and structural insight in complex samples, beyond just mass and chromatography. The G2-Si integrates StepWave optics and enhanced data workflows for better performance in proteomics, metabolomics, and biomarker discovery." .
SCR:027783 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Codex" ;
NIFRID:synonym "Codex - Connectome Data Explorer" ;
definition: "Web based platform for exploring full brain connectomic datasets. Used for exploring and analyzing large connectomics datasets." .
SCR:027784 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5690" ;
rdfs:label "Augusta University GCC Biostatistics Core Facility" ;
NIFRID:synonym "Augusta University GCC Biostatistics Core" ;
definition: "Core provides biostatistical review of grant applications, offering clear, practical feedback on feasibility and statistical rigor to investigators and review panels. We support investigators across the research lifecycle, from grant proposal development and clinical protocol design to laboratory, animal, and epidemiologic study planning. Services also include short-term consultations, study monitoring, data analysis, manuscript preparation, and responses to peer review." .
SCR:027785 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100009859",
"GRID grid.51462.34",
"ISNI 0000 0001 2171 9952",
"Wikidata Q1808012" ;
rdfs:label "Memorial Sloan Kettering Cancer Center" ;
definition: "World-renowned institution dedicated to ending cancer through expert, compassionate patient care, pioneering research, and education for adults and children with all types of cancer, combining cutting-edge science with a holistic approach to treatment and support. Its mission focuses on innovative diagnosis and treatment (surgery, chemo, radiation, immunotherapy), supportive care (nursing, counseling, rehab), and training future cancer leaders. " .
SCR:027786 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Perkin_Elmer_Victor_X3" ;
rdfs:label "Perkin Elmer | Victor X3 2030-0030 Multimode Microplate Reader" ;
NIFRID:synonym "Perkin Elmer Victor X3 (2030-0030)" ;
definition: "Multimode microplate reader for luminescence, fluorescence (top/bottom), and absorbance, featuring dual filter wheels, expanded temp control, and integrated software for real-time kinetics." .
SCR:027787 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "neuropythy" ;
definition: "Software neuroscience library for Python, intended to complement the existing nibabel library. Can automatic download data and interpret them into Python data structures." .
SCR:027788 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bioage" ;
definition: "Software R package uses published biomarker algorithms to calculate three biological aging measures: Klemera-Doubal Method (KDM) biological age, phenotypic age, and homeostatic dysregulation. Used to quantify biological aging based on analysis of chronological age and mortality risk." .
SCR:027789 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HDOCKlite" ;
definition: "Software standalone package for protein-protein and protein-DNA/RNA docking based on hybrid algorithm of template-based modeling and ab initio free docking." .
SCR:027790 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PASSer" ;
NIFRID:synonym "Protein Allosteric Sites Server" ;
definition: "Web allosteric site prediction tool. Web server designed for prediction and visualization of protein allosteric sites, which are crucial locations on proteins for regulating their function and key targets for drug development. Helps researchers identify these regulatory sites on proteins, supporting efforts in allosteric drug discovery by analyzing protein structures from Protein Data Bank." .
SCR:027791 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "InterProSurf" ;
definition: "Web server for predicting interacting sites on protein surfaces. Analyzes solvent-accessible residues likely to participate in PPIs.Predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of protein complex." .
SCR:027792 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "FreeSASA" ;
NIFRID:synonym "Solvent Accessible Surface Areas (SASA)" ;
definition: "Software C library for SASA calculations that provides both command-line and Python interfaces in addition to its C API. Used for Solvent-Accessible Surface Area analysis." .
SCR:027793 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NeuroJSON.io" ;
NIFRID:synonym "NeuroJSON" ;
definition: "Web application for human-readable, searchable neuroimaging datasets using universally accessible JSON format and URL-based RESTful APIs. NeuroJSON.io is built upon highly scalable document-store NoSQL database technologies, specifically, open-source Apache CouchDB engine, that can handle millions of datasets without major performance penalties. Provides fine-grained data search capabilities to allow users to find, preview and re-combine complex data records from public datasets before download." .
SCR:027794 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5695" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Bioinformatics Core Facility" ;
definition: "Core provides bioinformatics support services including creating and maintaining repository of bioinformatics pipelines, providing customized data analysis support, assisting computational researchers in their research efforts, and training staff in computational and bioinformatics techniques. Provides bioinformatics software applications and pipelines for experimental assays ranging from standard genomics pipelines like RNAseq and variant detection to the growing demand for single-cell processing workflows and new spatial-based assays in transcriptomics and proteomics. Provides training and consulatation." .
SCR:027795 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5696" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Antitumor Assessment Core Facility" ;
definition: "Core provides support for early discovery and in vivo testing of antitumor detection and therapeutic agents. Provides resources, professional and technical expertise, and advisory services related to evaluation of agents with potential diagnostic or therapeutic activity. ATA Core works closely with investigators to establish preclinical models, including Patient-Derived Xenograft (PDX) and Patient-Derived Organoid (PDO) models, for the design and execution of pharmacokinetic (PK), toxicity, and in vivo efficacy studies. Assists investigators in determining the best formulation, administration route, and treatment schedule for each new compound, either alone or in combination with other agents." .
SCR:027796 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5697" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Biobank and Pathology Core Facility" ;
definition: "Biobank and Pathology Core provides resources for human biospecimen-based research to be used to study causes, detection, prevention, and treatment of cancer.Central facility for the collection, processing, storage, and distribution of fresh, frozen, and FFPE-processed human biospecimens (tissues, blood, bone marrow, urine, and other liquid samples) for research use. Core also serves as national resource, as evidenced by the several hundred samples from multiple tumor types that have been provided to the Cancer Genome Atlas (TCGA) and NCI’s CPTAC proteogenomic consortium. Histology Service within the Core facilitates selection of appropriate specimens for tissue analyses and provides the basic services of cutting, dissecting, and staining of fresh-frozen and formalin-fixed, paraffin-embedded tissues. It includes construction of tissue microarray blocks and laser capture microdissection for isolation of pure cell populations and tumor cell enrichment. The Core’s Immunohistochemistry Service provides immunostaining using optimized antibodies for clinico-pathologic research studies." .
SCR:027797 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5698" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Biotherapeutics Core Facility" ;
definition: "Core provides collaborative process development support to investigators across the Center engaged in new Biotherapeutics initiatives. Core staff are responsible for converting research-lab processes into GMP-compliant manufacturing processes. This includes establishing Standard Operating Procedures (SOPs) and batch records for cell processing, cell engineering, and vector production. Provides full support for cGMP manufacturing of cell products: handling patient cells in cGMP environment, from purification and transduction to expansion and formulation, for use in phase 1 and phase 2 clinical trials. Manufactures vector stocks, oversees biosafety and releases testing of generated projects for human use. This includes analysis of patient cells and vector stocks, assessing characteristics such as phenotype, potency, purity, and stability. Gene transfer and expression analyses are also performed. Core performs analytical post-infusion monitoring. For each trial, the Core develops a comprehensive set of analytical tests to ensure quality and safety of the manufactured drug products." .
SCR:027798 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5699" ;
rdfs:label "Memorial Sloan Kettering Cancer Center- Center of Comparative Medicine and Pathology Core Facility" ;
NIFRID:synonym "Memorial Sloan Kettering Cancer Center- Center of Comparative Medicine and Pathology" ;
definition: "Core supports animal model use in cancer research through teams including Research Animal Resource Center (RARC) and Laboratory of Comparative Pathology (LCP). Animals are employed in the development of new methods for diagnosis and treatment of cancer as well as the elucidation of the basic biological mechanisms resulting in neoplasia. CCMP’s professional and paraprofessional staff (152 FTE) serve as a consultative and technical resource for MSK investigators on all matters related to animal research." .
SCR:027799 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5700" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Genome Editing and Screening Core Facility" ;
definition: "Core Facility provides functional genomics, highthroughput screening (HTS), and high-content screening (HCS) services toward the discovery of novel cancer targets and elucidation of complex, aberrant cellular pathways. Offers assistance and training in range of cloning, customized library design, lentivirus production, assay development, screening, and image analysis considerations to assist researchers in harnessing these powerful target identification tools and drug screening methodologies. Offers CRISPR-mediated transcriptional activation/interference (CRISPRa/CRISPRi) technologies combined with lentivirus delivery systems, customized stable isogenic cell line generation (knockout, HDR-directed knock-in, knockdown, base editing, and prime editing) toward the generation of unique cancer cell line models." .
SCR:027800 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5701" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Immune Monitoring Core Facility" ;
definition: "Core provides laboratory services and translational research to support immune monitoring during cancer immunotherapy. Robust immune monitoring assays are essential for characterizing the immune status in patients receiving novel immune-modulating therapies, and the insights gained from studying the immune response in treated patients may help transition promising therapies from the clinical trial phase to standard of care." .
SCR:027801 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5702" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Integrated Genomics Operation Core Facility" ;
definition: "Core provides services and expertise to Center investigators interested in evaluating gene expression, chromosome structure, and nucleotide sequence on a broad scale. Enables basic, clinical, and translational research projects across the Center. Through its production group, the Core enables genomic and transcriptomic analyses and has the expertise to process challenging samples from all origins (tissue, dissociated single cells and cell pellets, paraffin curls, blood, serum, etc.). Bulk DNA/RNA assays operate in highly automated environment, from sample reception to sequencing library preparation." .
SCR:027802 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5703" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Molecular Cytology Core Facility" ;
definition: "Core delivers specialized histology, microscopy, and cytogenetics services for detection in situ (cells, tissue sections, organoids, and whole mounts) of biomarkers (proteins, glycoproteins, lipids, nucleic acids) and molecular processes in normal and pathological conditions. Performs comprehensive antibody validation on cells and tissues, trains investigators in basic staining principles and assists with experimental assay design and downstream analysis. Core maintains four whole-slide scanners and provides support for quantitative whole-slide analysis. Microscopy and dedicated image analysis staff provide support for simple or complex analysis pipelines." .
SCR:027803 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5704" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Mouse Genetics Core Facility" ;
definition: "Core facilitates the use of mouse molecular genetics at MSK for in vivo studies of gene functions germane to cancer. Provides expertise in generation and effective use of genetically engineered mouse (GEM) models—namely, molecular and cell biology, embryo micromanipulation, and reproductive biology. Molecular and cellular biology services cover design and assembly of genome engineering reagents, such as donor transgenes and CRISPR/Cas9; performing all aspects of gene targeting in mouse embryonic stem (ES) cells; identification and verification of alleles carried by a generated GEM model; and establishment of new ES cells from a variety of GEM lines. Provides consultation and training for the design and production of GEM models, ES cell culture and manipulation, and mouse reproduction and genetic crosses." .
SCR:027804 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5705" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Nuclear Magnetic Resonance (Analytical) Core Facility" ;
definition: "Core provides analytical services, access and education for analytical instrumentation and related shared scientific resources. Instrumentation includes high field nuclear magnetic resonance, mass spectrometry and optical spectroscopic instruments. Facility offers investigators the ability to monitor chemical reactions, analysis for determination of molecular structure, chemical mechanisms, purity, stability, biological uptake and other properties of chemical compounds." .
SCR:027805 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5706" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Patient- Reported Outcomes, Community Engagement, and Language Core Core Facility" ;
definition: "Core supports MSK investigators who wish to capture self-reported information from culturally diverse patients, caregivers, clinical staff, and community members. The faculty of the PRO-CEL Core are nationally recognized social and behavioral scientists and community engagement experts who provide technical assistance to all users throughout multiple stages of research, including grant and protocol development, research study assistant and support staff training, and result dissemination. Provides methodological support for clinical trial, behavioral, and population-based research that seeks to engage community or minority populations." .
SCR:027806 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5707" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Radiochemistry and Molecular Imaging Probes Core Facility" ;
definition: "Core functions include cancer biology, medicine, chemistry, physics, radiochemistry, pharmacology, and engineering.Provides investigators with radionuclides and to incorporate these radionuclides into radiolabeled diagnostic and/or therapeutic pharmaceuticals for both basic research investigations and patient formulations. Core provides services: Cyclotron Radionuclide Production Section, Radiolabeling Section, Development and Clinical Translation Section, and Hyperpolarized Magnetic Resonance Section." .
SCR:027807 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5708" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Research Pharmacy Core Facility" ;
definition: "Core is a full-service facility that prepares agents developed by MSK researchers to be used as investigational drugs in preclinical or clinical studies. The Core comprises three principal groups: the Pharmaceutical Product Facility (PPF) for drug formulation/stability and preparation; the Clinical Grade Production (CGP) Facility for bulk product manufacturing, purification, and vialing; and the Pharmacy Investigational Drug Service (PIDS), which develops, procures, prepares, and validates the preparation, packaging, and distribution of investigational drugs for clinical use. Core services include: formulation, analysis, and evaluation of drug release rates; prediction of interactions; and determinations of compatibility and physical stability of medications. Based on the expertise of the RP Core, MSK has been able to bring into early-phase clinical trials multiple types of pharmacologic agents, including traditional small molecules, radiopharmaceuticals, and vaccines." .
SCR:027808 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5709" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Stem Cell Research Core Facility" ;
definition: "Core stocks, characterizes, and distributes human pluripotent stem cell (hPSC) lines. Performs variety of hPSC-related applications for the stem cell community at SKI and beyond. We are a part of the Starr Foundation-funded Tri-Institutional Stem Cell Initiative that provides shared stem cell expertise and resources among Memorial Sloan Kettering, Weill-Cornell, and Rockefeller University." .
SCR:027809 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5710" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Structural Biology Core Facility" ;
definition: "Core provides expertise, advanced equipment, and leading software to support structural investigations. Core maintains equipment, including Krios cryogenic electron microscopes and computational resources for data collection, processing, and structure determination. These resources include graphical workstations and high-performance Linux cluster, supporting the analysis of large proteins, complexes, and macromolecular assemblies.Core has access to synchrotron beamlines and cryo-EM facilities.Provides training and assistance to users, collaborates with non-structural MSK groups on projects involving macromolecular crystallization and structure determination, offers modeling expertise and guidance, enabling labs to use available structural data in experiment design and interpretation." .
SCR:027810 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5711" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Animal Imaging Core Facility" ;
definition: "Core offers suite of animal imaging modalities, including MRI, PET, CT, SPECT, and ultrasound, all commonly used in clinical settings, enhancing the likelihood that findings in animal models will be translatable to human patients. Key instruments include 7.0T and 9.4T MRI systems, PET/MR, PET/CT, SPECT/CT, and advanced ultrasound systems, alongside specialized equipment including a small animal radiation therapy unit and variety of ancillary tools for advanced imaging analysis." .
SCR:027811 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5712" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Proteomics and Metabolomics Core Facility" ;
definition: "Core provides mass spectrometric sequencing and quantitation of peptides and proteins to support basic, translational, and clinical research programs at MSK. Utilizes modern high-resolution mass spectrometry and nanoscale liquid chromatography in conjuction with biochemical processing of samples with the end goal of determining the identity, relative abundance, and presence of post translational modifications from purified components, cell lysates, tissues, and select fluid such as cerebral spinal fluid. Advice is provided by the Core staff to facilitate the design, execution, and analysis of experiments." .
SCR:027812 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DANCE" ;
NIFRID:synonym "Drosophila Aggression and Courtship Evaluator" ;
definition: "Software pipeline to quantify aggression and courtship behaviors in Drosophila. Codes and classifiers for the DANCE manuscript." .
SCR:027813 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_HP_D300" ;
rdfs:label "HP | D300 Digital Drug Dispenser" ;
definition: """Digital drug dispenser. Enables to eliminate serial dilution from dose-response workflow,
miniaturize qPCR reaction volumes, and easily dispense any volume in any well for a broad array of low-volume dispensing applications. Accurately dispense volumes from picoliters to microliters for faster, more reliable dispensing of small molecules and biomolecules.""" .
SCR:027815 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AGGRC" ;
NIFRID:synonym "Aquatic Germplasm and Genetic Resources Center" ;
definition: "Service resource affiliated with Louisiana State University with core mission to develop and commercialize genetic resources for aquatic species. Provides research, technology development, and services for commercial aquaculture and biomedical use, including large-scale cryopreservation." .
SCR:027816 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5693" ;
rdfs:label "Virginia Tech Flow Cytometry Core Facility" ;
NIFRID:synonym "Flow Cytometry Facility",
"Virginia Tech Flow Cytometry Facility",
"Virginia Tech�s Fralin Life Sciences Institute Flow Cytometry Facility" ;
definition: "Facility offers traditional data acquisition, analysis, and cell sorting as well as imaging cytometry. Provided equipment includes: BD FACSAria Fusion: A cell sorter that can also be used as an analyzer, it is equipped with 488nm, 640nm, and 405nm excitation sources and is equipped to analyze up to fifteen parameters simultaneously. The Fusion is capable of processing up to 70,000 events per second and sorting up to four different cell populations at once. It is also equipped with an Automatic Cell Deposition Unit (ACDU) that allows sorting of cells into plates or onto slides; Amnis ImageStream MarkII: this imaging cytometer combines the speed and objectivity of flow cytometry with the detailed imagery of microscopy to allow you to objectively and quantitatively describe biological processes based on cell size, shape, and fluorescence location, texture, and signal intensity.This open platform enables new methods of research and improves traditional flow and imaging based applications. It is equipped with 405nm, 488nm, and 642nm excitation sources and is able to analyze up to twelve parameters simultaneously. It has 20X, 40X, and 60X objective lenses and Enhanced Depth of Field technology. It can process several thousand cells per second." .
SCR:027817 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Opera_Phenix" ;
rdfs:label "Perkin Elmer | Opera Phenix High Content Screening System" ;
NIFRID:synonym "Opera Phenix HCS",
"PerkinElmer Opera Phenix HCS" ;
definition: "Fully automated, high-content imaging and analysis platform designed for high-throughput biological screening and detailed cellular phenotyping. It’s widely used in research settings for applications that require both high resolution and high throughput microscopy across a range of complex biological models." .
SCR:027818 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QlDataReader" ;
definition: "Software tool to convert the .eeg/.qle data recorded by Quanlan devices into .edf format." .
SCR:027819 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MicroSEC" ;
definition: "Software pipeline for filtering sequence errors found in formalin-fixed and paraffin-embedded (FFPE) samples." .
SCR:027820 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciLifeLab Serve" ;
definition: "Web platform for sharing machine learning models and data science applications. Users can interact with the deposited models and applications through a public URL or fetch the models and apps to run them locally on their own computer." .
SCR:027821 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5713" ;
rdfs:label "Memorial Sloan Kettering Cancer Center Biostatistics Core Facility" ;
definition: "Core provides expertise on study design and statistical analysis. Devoted to developing and understanding ways to derive scientific inferences from quantitative data and to developing methods for achieving this aim. The staff are highly trained in this field and experienced in all of the specialized areas of statistical techniques including clinical trials methodology, survival analysis, epidemiologic methods, analysis of genomics data, statistical genetics, methods for diagnostic medicine, health services research, survivorship, evidence-based medicine and psychometric methods." .
SCR:027822 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5714" ;
rdfs:label "University of Cologne Center for Genomics (CCG) Core Facility" ;
NIFRID:synonym "Cologne Center for Genomics (CCG)",
"University of Cologne Center for Genomics (CCG)" ;
definition: "Represents central facility and does not operate for profit, engaging in academic research collaborations and service provision on collaborative basis. Provides infrastructure for all kinds of sequencing, gene mapping and whole genome association studies in complex diseases as well as the validation of copy number variations." .
SCR:027823 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Accu-Cut_SRM_500" ;
rdfs:label "Sakura | Accu-Cut SRM 500 Rotary Microtome" ;
definition: "Compact, manual rotary microtome designed for preparation of thin sections of human and animal tissue samples of varying hardness, as far as they are suitable for manual cutting. Microtome for parafin sectioning. Can be used for all applications as diagnostic aid related to in vitro examination within the histopathological process." .
SCR:027824 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Olympus_BX40" ;
rdfs:label "Olympus | BX40 Microscope" ;
definition: "Durable, modular, upright compound microscope known for clinical, educational, and research use, offering brightfield and phase contrast, UIS optics, and ergonomic features for comfortable, long-term observation, making it popular for routine pathology (like Mohs surgery) and teaching labs. As an earlier BX model, it's reliable, configurable with different heads (binocular, trinocular) and accessories, and often updated with modern LED lighting, providing excellent cost-performance for detailed specimen viewing." .
SCR:027825 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Chord chart" ;
definition: "Circular plot used to visualize flows, relationships, or connections between different groups or entities, showing the strength (weight) of these links with arc sizes and colors, ideal for network analysis, migration data, or interaction matrices." .
SCR:027826 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NiPoppy" ;
definition: "Software lightweight Python framework and command-line tool for organizing, processing, and managing neuroimaging-clinical datasets, designed to make studies more reproducible and adhere to FAIR data principles (Findable, Accessible, Interoperable, Reusable). Provides standardized workflow to handle raw data (like DICOMs), apply containerized processing pipelines (e.g., fMRIPrep), extract analysis-ready features (IDPs), and track processing status, extending the Brain Imaging Data Structure (BIDS) standard for both imaging and clinical data. Includes three components: protocol for data wrangling to standardize generation of analysis-ready datasets; specification for dataset organization that extends the Brain Imaging Data Structure (BIDS) standard; command-line interface and Python package that provide user-friendly tools for applying the framework." .
SCR:027827 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5715" ;
rdfs:label "Lahore University of Management Sciences Syed Babar Ali School of Science and Engineering High Performance Computing Core Facility" ;
NIFRID:synonym "LUMS High Performance Computing Centre (LUMSHPCC)",
"LUMS High-Performance Computing (HPC) facility" ;
definition: "LUMS High-Performance Computing (HPC) facility is specialized computational research core providing high-density processing power and large-scale data storage. It serves as a central hub for faculty and students to execute data-intensive simulations, machine learning workflows, and complex modeling across various scientific disciplines." .
SCR:027828 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100010139",
"GRID grid.440540.1",
"ISNI 0000 0001 0720 9374",
"Wikidata Q13139758" ;
rdfs:label "Lahore University of Management Sciences; Lahore; Pakistan" ;
NIFRID:abbrev "LUMS" ;
definition: "Private research university in Lahore, Punjab, Pakistan. Founded in 1985, it is ranked as one of the most prestigious modern universities in Pakistan. In 1984, Syed Babar Ali recognized the shortage of qualified managers in the country." .
SCR:027829 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Totem" ;
definition: "Software package to facilitate inference of tree-shaped trajectories from single-cell data. These include linear, bifurcating, multifurcating, and other tree-shaped trajectories. Totem uses Slingshot to find linear curves through the lineages of the tree." .
SCR:027830 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LIANA+" ;
definition: "Software framework that adapts and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data. All-in-one framework for cell-cell communication inference." .
SCR:027832 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Functional" ;
definition: "Software application for vendor-neutral, open-source acquisition and reconstruction protocols for fully harmonized multi-site functional MRI studies." .
SCR:027833 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VPixx | TRACKPixx3 2 kHz binocular eye tracker" ;
NIFRID:synonym "TRACKPixx3",
"Vpixx Technologies TRACKPixx3" ;
definition: """Device for 2 kHz eye/gaze-tracking solution supporting both monocular and binocular tracking with single mechanical configuration. Interchangeable lenses support tracker distances from 60 cm to over 160 cm for fMRI applications. TRACKPixx3 does not require a dedicated PC to process eye images and generate gaze information. All image processing is performed within TRACKPixx3 hardware. Gaze data can be logged within the TRACKPixx3 and retrieved by the testing PC with a simple low-latency USB interface.
TRACKPixx3 video feed can be accessed directly through a console display for real-time visualization and adjustment of the tracker. These video feeds can also be accessed through the USB interface for remote control of the TRACKPixx3.""" .
SCR:027834 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Rediscover" ;
definition: "Software R package to identify mutually exclusive mutations. Used to identify mutually exclusive genomic events. Implements exact and approximate computations of the Poisson-Binomial." .
SCR:027835 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpatialProteomics" ;
definition: "Software graphical and containerized spatial proteomics workflow. End-to-end containerized spatial proteomics analysis workflow with QuPath integration. Consists of cell segmentation, batch correction, unsupervised clustering, validation of clusters on the image, and cell type clustering results visualization." .
SCR:027836 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Baby Open Brains" ;
NIFRID:synonym "Baby Open Brains (BOBs) Dataset",
"BOBs" ;
definition: "Open source resource of manually curated and expert reviewed infant brain segmentations hosted on OpenNeuro.org. and OSF.io. Anatomical MRI data was segmented from 71 infant imaging visits across 51 participants, using both T1w and T2w images per visit. Images showed dramatic differences in myelination and intensities across 1–9 months, emphasizing the need for densely sampled gold-standard segmentations across early life. This dataset provides a benchmark for evaluating and improving pipelines dependent upon segmentations in the youngest populations. As such, this dataset provides a vitally needed foundation for early-life large-scale studies such as HBCD." .
SCR:027837 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Reproducible Brain Charts" ;
definition: "Open data resource for mapping brain development and its associations with mental health. Integrates data from 5 large studies of brain development in youth from three continents (N = 6,346). Bifactor models were used to create harmonized psychiatric phenotypes, capturing major dimensions of psychopathology. Neuroimaging data were carefully curated and processed using consistent pipelines in a reproducible manner." .
SCR:027838 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "QLAnalyser" ;
definition: "Software electrophysiological data analysis toolkit developed by Quanlan Technology for beginner neuroscience researchers and clinical electrophysiologists." .
SCR:027840 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MelOD" ;
NIFRID:synonym "Melanoma Omics Dashboard",
"Melanoma Omics Dashboard for Multimodal Data Exploration" ;
definition: "Platform provides suite of powerful tools to explore, visualize, and make sense of complex data that can help accelerate discoveries in melanoma research. By integrating data from multiple studies, including transcriptiomics, single-cell RNA-Seq, and proteomics (with more to come), MelOD allows for comprehensive examination of the molecular landscape of melanoma." .
SCR:027841 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GE | Signa Explorer 1.5 T MRI scanner" ;
NIFRID:synonym "1.5 T Signa Explorer MRI scanner (GE Healthcare)",
"Signa Explorer 1.5 Tesla MRI scanner" ;
definition: "MRI scanner as medical imaging system used for detailed scans of the brain, spine, joints, heart, and other organs, focusing on high image quality, fast scans (using technologies like HyperSense), enhanced patient comfort (with Silent Suite for noise reduction and free-breathing options), and operational efficiency, making it suitable for diverse clinical needs like neuroimaging, orthopedics, and cardiovascular studies. It's designed to handle a broad range of applications and improve workflow, even for patients with MRI-conditional metal implants." .
SCR:027842 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Medical College of Wisconsin Tissue Bank" ;
NIFRID:synonym "MCW Tissue Bank" ;
definition: "College of American Pathologists-accredited biorepository that collects, processes, securely stores, and distributes human biospecimens (tissues and blood products) for medical research. Tissue Bank that is a CAP-accredited biorepository supporting four human consent programs. Provides fresh and frozen tissue and biological materials with known preanalytical variables to researchers as well as provides specialized processing and imaging services." .
SCR:027843 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Semi-Automated MEA Spike Sorting (SAMS)" ;
NIFRID:synonym "Semi-Automated MEA Spike Sorting" ;
definition: "Software MATLAB-based application for spike sorting multi-electrode array (MEA) recordings. Used for efficient, reproducible spike sorting in high-throughput neuronal culture experiments. SAMS performs batched automated spike sorting processes and also allows the users to review and correct any clusters or spike assignments." .
SCR:027844 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mplab x ide" ;
NIFRID:synonym "MPLAB X IDE",
"MPLAB X Integrated Development Environment (IDE)" ;
definition: "Software program from Microchip, serving as a comprehensive, expandable platform for developing Microchip microcontroller applications, with many integrated tools like MPLAB Code Configurator (MCC) and MPLAB XC Compilers (free versions). Incorporates tools to discover, configure, develop, debug and qualify embedded designs for most of microcontrollers and digital signal controllers. MPLAB X IDE works seamlessly with the MPLAB development ecosystem of software and tools." .
SCR:027845 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tracker" ;
NIFRID:synonym "Tracker Video Analysis and Modeling" ;
definition: "Software video analysis and modeling tool developed within the Open Source Physics (OSP) Java framework. Allows frame-by-frame tracking of anatomical landmarks and articulated structures from video recordings, enabling the extraction of time-dependent kinematic variables such as displacement, velocity, and acceleration. Tracker is well suited for biomechanical analyses of articulated systems, as it supports joint-based rotations, reference-frame definition, and the export of quantitative motion data for further post-processing." .
SCR:027846 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cajun Ejector" ;
NIFRID:synonym "NIAID 3D Cajun Ejector",
"NIH 3D Cajun Ejector",
"Shipping Dewar Positional Cooling Device (SDPCD)" ;
definition: "Shipping Dewar Positional Cooling Device (SDPCD) is 3-D printable vertical cooling device that can assist cryopreservation with various standard cooling rates by use with existing standard nitrogen vapor shipping dewars for on-site sperm cryopreservation for aquatic species.Device could hold 22 French straws (0.25-mL or 0.5-mL) and a quick-release ring design could eject straws directly into a canister inside a dewar by pressing a button after freezing. The final prototypes produced cooling rates of 1 to 68°C/min for 0.25-mL straws, and 3 to 37°C/min for 0.5-mL straws with a material cost of 3.5 USD for a single device" .
SCR:027847 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurobagel" ;
definition: """Open source software ecosystem designed to facilitate harmonization, search, and discovery of neuroimaging study cohorts across decentralized datasets. Allows researchers to find participants across different studies based on specific clinical, demographic, and imaging criteria without needing to merge all the original data into a single central database.
Provides tools to connect a local neuroimaging dataset with others in decentralized framework using linked data principles.You can contribute to Neurobagel by enhancing its tools (annotation, querying), improving documentation, adding new features/models, fixing bugs, or sharing your own data/expertise to help researchers find and harmonize brain imaging cohorts through standardized metadata and knowledge graphs.""" .
SCR:027848 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ReproSchema" ;
definition: "Software standardized framework for creating, sharing, and reusing cognitive and clinical assessments. Standardized form generation and data collection schema to harmonize results by design across projects. Used for enhancing research reproducibility through standardized survey data collection." .
SCR:027849 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nested containment list" ;
NIFRID:synonym "Nested Containment List",
"Nested Containment List (NCList)" ;
NIFRID:abbrev "NCList",
"NCLS" ;
definition: "Software library for nested containment list data structure for interval overlap queries, like interval tree. It is a static interval-tree that is fast for both construction and lookups." .
SCR:027850 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "lda" ;
definition: "Software application for topic modeling with latent Dirichlet allocation." .
SCR:027851 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Zeiss | Axioskop 40 Microscope" ;
definition: "Upright light microscope used in research, education, and routine lab work for detailed sample observation, documentation, and analysis in fields like pathology, histology, cytology, and materials science, supporting various techniques like brightfield, fluorescence, and polarization microscopy for capturing sharp digital images." .
SCR:027852 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NanoSight_NS300" ;
rdfs:label "Malvern Panalytical | NanoSight NS300" ;
NIFRID:synonym "Marvel Panlytical NanoSight NS300",
"NanoSight NS300 system" ;
definition: "Particle analysis system that uses Nanoparticle Tracking Analysis (NTA) to measure the size distribution, concentration, and aggregation of nanoparticles (10-2000 nm) in liquid, crucial for research in exosomes, drug delivery, protein aggregation, and colloidal systems. It visualizes individual particles' Brownian motion with lasers and a camera, calculating hydrodynamic diameter and concentration, and includes fluorescence detection for specific labeled particles." .
SCR:027853 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5722" ;
rdfs:label "University of Massachusetts Amherst Electron Microscopy Core Facility" ;
NIFRID:synonym "UMass Amherst Electron Microscopy Core Facility" ;
definition: "EM Core Facility offers instrumentation and training for range of Electron Microscopy applications. Instrumentation includes Thermofisher Tundra cryo-TEM, Tecnai T12 TEM, Magellan 400 SEM, JEOL JEM-2200FS, Vitrobot Mark IV, (cryo)microtomes, and other auxiliary equipment." .
SCR:027854 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scHiCluster" ;
definition: "Software Python package for single-cell chromosome contact data analysis. It includes the identification of cell types (clusters), loop calling in cell types, and domain and compartment calling in single cells. Facilitates visualization and comparison of single-cell 3D genomes." .
SCR:027855 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "demuxlet" ;
definition: "Software tool that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). Genetic multiplexing of barcoded single cell RNA-seq." .
SCR:027856 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "STICR" ;
definition: "Code to conduct combinatorial barcoding. scRNA-seq-compatible tracer for identifying clonal relationships." .
SCR:027857 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5725" ;
rdfs:label "University of Michigan MCity Core Facility" ;
NIFRID:abbrev "MCity" ;
definition: "Core for building and testing mobility innovation is part of the University of Michigan Transportation Research Institute. Helps advance safe and efficient transportation and mobility solutions. Makerspace for mobility and transportation innovators. Offers open-source tools, remote or on-site testing." .
SCR:027859 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5726" ;
rdfs:label "University of Michigan M-Air Core Facility" ;
NIFRID:synonym "M-Air" ;
definition: "Core for testing advanced air mobility (AAM), focusing on drones and electric aircraft, especially Beyond-Line-of-Sight (BVLOS) autonomous flight, to accelerate innovation and commercialization in the industry. It serves as a real-world \"skyway\" for researchers and companies to test new technologies like electric vertical takeoff and landing (eVTOL) aircraft, support Michigan Medicine's air transport, and foster aerospace startups, building on U-M's existing robotics and autonomous vehicle testing facilities." .
SCR:027860 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5727" ;
rdfs:label "University of Michigan Mixed Methods Program Core Facility" ;
definition: "Provides mixed methods consulting services. Located in the Department of Family Medicine, team advises researchers at all levels in the health and social sciences who are developing proposals for funding, revising a manuscript, completing a research project or requiring Mixed Methods training." .
SCR:027861 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5718" ;
rdfs:label "Van Andel Institute Spatial Collaborative Services Core Facility" ;
NIFRID:synonym "Van Andel Institute Spatial Collaborative Services" ;
definition: "Spatial Collaborative Services combines expertise and technology from VAIs Genomics Core and Optical Imaging Core to offer investigators a seamless pipeline for spatial imaging. Services include consultation, histology preparation, sequencing and imaging based spatial platforms." .
SCR:027862 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GLM utilities" ;
definition: "Software tools for fitting Generalized Linear Models (GLMs) with time dependence (a.k.a. filters)." .
SCR:027863 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5728" ;
rdfs:label "Augusta University Medical Sculpture Core Facility" ;
definition: "Department of Medical Illustration’s Medical Sculpture Core advances education and research capabilities in medical sculpture. The space serves as an AU Core Research Lab to provide expertise in medical sculpture, volumetric visualization, and 3D printing. This lab space will offer educational and research opportunities for students to develop medical models such as surgical simulation models and patient education models. The research will improve surgical and medical training and provide insight into materials and technology to improve patient care." .
SCR:027864 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PIANO:Probabilistic Inference Autoencoder Networks for multi-Omics" ;
NIFRID:synonym "piano" ;
NIFRID:abbrev "PIANO" ;
definition: "Software novel variational autoencoder framework for inferring integrated latent space representations for single cell transcriptomics data that uses a negative binomial generalized linear model for stronger batch correction, and code compilation for ten times faster training than existing tools. Enables superior analyses of multiple atlases, solving challenging integration tasks across sequencing platforms, development, and species, while simultaneously preserving desired biological signals." .
SCR:027865 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5729" ;
rdfs:label "Massachusetts General Hospital Brigham Center of Excellence for Molecular Imaging Core Facility" ;
NIFRID:synonym "Mass General Brigham Center of Excellence for Molecular Imaging",
"Massachusetts General Hospital Brigham Center of Excellence for Molecular Imaging" ;
definition: "Core facility that provides microscopy training, imaging solutions, image processing and analysis services, and consultation. Offers imaging techniques and expertise, including spinning disc confocal microscopy, two-photon confocal microscopy, super resolution microscopy, total internal reflection microscopy, wide field microscopy, fluorescence spectroscopy, photo-manipulation techniques (e.g. FRAP, photoablation, optogenetics, and optical tweezers) and live cell imaging." .
SCR:027866 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "gspread" ;
definition: "Software python library for working with Google Sheets allowing users to open spreadsheet by title, key or URL. It also allows to read, write, and format cell ranges and more." .
SCR:027867 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "treeshap" ;
NIFRID:synonym "TreeSHAP" ;
definition: "Software R package to calculate the SHapley Additive exPlanations (SHAP) values in polynomial (instead of exponential) time. Supports models produced with xgboost, lightgbm, gbm, ranger, and randomForest packages." .
SCR:027868 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_ID: 5730" ;
rdfs:label "Northwestern University Metabolomics Core Facility" ;
NIFRID:synonym "Metabolomics Core Facility (MCF)",
"Metabolomics Core Facility of Northwestern University" ;
definition: "Metabolomics Core at Robert H. Lurie Comprehensive Cancer Center of Northwestern University provides LCMS based metabolomics services including identification, semi-quantification and quantification of metabolites and integrative genomics services related to metabolism." .
SCR:027869 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5731" ;
rdfs:label "Northwestern University Immunotherapy Assessment Core Facility" ;
NIFRID:synonym "Northwestern University Immunotherapy Assessment Core" ;
definition: "Core provides services for dissection of the immune response both phenotypically, functionally and transcriptionally at the single cell or population level. Technologies like single cell RNAseq (10x Genomics Chromium platform), multispectral fluorescent tissue imaging of FFPE tissues (Vectra 3 Imaging System, Akoya Biosciences), high-performance electrochemiluminescence plexing immunoassays (QuickPlex 120, MSD), and automated multiplexed single-cell and bulk protein analysis system (IsoLight, IsoPlexis) are available to investigators, providing immune cell (and beyond) characterization at the highest resolution. Other services also include project consultation, sample preparation, controlled rate freezing and cryopreservation/storage, as well as a comprehensive range of standardized and customizable immunological assays." .
SCR:027870 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Canterbury Research Compute Hub" ;
definition: "Platform is part of Research Computing and Services where researchers can perform compute-intensive tasks. It’s accessed through online user interface called Open OnDemand (via HPCNow!). The platform is run by Slurm, a job scheduler that manages and allocates resources, optimising resource use and power consumption. UC-RCH is housed in primary data centre on Dovedale, featuring 9 physical nodes and connecting to a virtual cluster with virtual machines and containers." .
SCR:027871 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "blaseRtools" ;
definition: "Software R tools for Blaser Lab Data Analysis. Package includes commonly used functions for R analysis in the Blaser Lab." .
SCR:027872 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5732" ;
rdfs:label "Michigan Technological University Materials Characterization and Fabrication Core Facility" ;
NIFRID:synonym "Materials Characterization and Fabrication Facility(MCFF)",
"Michigan Technological University Materials Characterization and Fabrication Facility(MCFF)" ;
definition: "Core facility provides tools for imaging, analysis, environmental testing, and micro/nanofabrication. Offers data, expertise, and hands-on training. From advanced materials to environmental systems, MCFF is the hub where discovery meets precision." .
SCR:027873 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5733" ;
rdfs:label "Washington State University WSU Spokane Research Histology Core Facility" ;
NIFRID:synonym "WSU Spokane Histology Service Center" ;
definition: "Provides histology services from sample collection to data analysis.Training is available so that research staff understand the process. Contact us before you start your experiment so we can help you integrate histology with any other tissue-dependent assays you intend to perform." .
SCR:027874 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5734" ;
rdfs:label "Washington State University WSU Spokane Proteomics/Metabolomics Core Facility" ;
NIFRID:synonym "Proteomics/Metabolomics Service Center" ;
definition: "Facility offers proteomics and metabolomics services.Provides training and instrumentation, such as the Orbitrap Q Exactive HF mass spectrometer from Thermo Fisher Scientific and advanced nano-LC systems." .
SCR:027875 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Spectroscopic Imaging, VIsualization, and Computing (SIVIC)" ;
NIFRID:abbrev "SIVIC" ;
definition: "Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies." .
SCR:027876 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Atellica_IM_1300" ;
rdfs:label "Siemens | Atellica IM 1300 Analyzer" ;
definition: "Mid-volume, automated immunoassay system used in clinical labs to perform a wide range of tests for diagnosing and monitoring diseases, detecting infections, checking hormone levels, and assessing cardiac health, by analyzing biological samples like blood for specific proteins, hormones, and other markers with high reliability and efficiency, often integrated into the larger, flexible Atellica Solution for automated workflows." .
SCR:027877 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Purdue University Research Repository (PURR)" ;
NIFRID:abbrev "PURR" ;
definition: "Provides online, collaborative working space and data-sharing platform. Provides services with data management planning, boilerplate text for proposal, sample plans and individual consultation. Each dataset gets DOI. PURR publishes and archives digital datasets from researchers across campus and welcomes all kinds of open data from images and videos to spreadsheets and source code." .
SCR:027878 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Photoline" ;
NIFRID:synonym "PhotoLine" ;
definition: "Software versatile all-purpose image and graphics editor for Windows, macOS, and Linux (via Wine) that combines raster (bitmap) and vector editing, making it a strong, affordable alternative to Adobe Photoshop, with features like layers, masks, color management (CMYK, Lab, 16-bit), batch processing, and web tools, presented in a comprehensive yet sometimes retro-looking interface . You can edit images or optimize them for the web, but you can also prepare print-ready PDF data." .
SCR:027879 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OMIQ" ;
definition: "Cloud-based data science platform for flow cytometry and single-cell analysis, streamlining complex workflows from raw data to insights, enabling collaboration, and ensuring reproducibility with automated tasks, machine learning, and integration for classical and high-dimensional cytometry data. Modern Cloud Software for classical and advanced Flow Cytometry analysis." .
SCR:027880 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "V-Dem Research Institute Academic Freedom Index" ;
NIFRID:synonym "Academic Freedom Index",
"V-Dem Institute Academic Freedom Index",
"V-Dem Project" ;
definition: "V-Dem Institute is an independent research institute that serves as the headquarters of the V-Dem Project a database that seeks to conceptualize and measure democracy. Provides interactive map for comprehensive overview of academic freedom in 179 countries and territories in 2024. Based on assessment of the de facto protection of academic freedom as of December 2024, users can compare countries and investigate developments within countries over time." .
SCR:027881 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5736" ;
rdfs:label "University of St Andrews Mass Spectrometry and Proteomics Core Facility" ;
NIFRID:synonym "St Andrews University Mass Spectrometry and Proteomics Facility" ;
definition: "Core provides services in mass spectrometry including protein identification and analysis, measuring the intact mass of proteins and quantitative proteomics." .
SCR:027882 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SpatialInferCNV" ;
definition: "Software R package to infer genome-wide copy-number variations (CNVs) from spatially resolved in situ mRNA profiles. SpatialInferCNV will generate CNV calls in each spatial region represented by barcoded spots." .
SCR:027883 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellNEST" ;
NIFRID:synonym "Cell Neural Networks on Spatial Transcriptomics (CellNEST)" ;
definition: "Software tool to decipher patterns of communication. Used to relay-network communication detection that identifies putative ligand–receptor–ligand–receptor communication. Detects T cell homing signals in human lymph nodes, identifies aggressive cancer communication in lung adenocarcinoma and colorectal cancer, and predicts new patterns of communication that may act as relay networks in pancreatic cancer." .
SCR:027884 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Brain Initiative Cell Atlas Network Data Catalog" ;
NIFRID:synonym "BICAN Data Catalog" ;
definition: "Database of complete listing of data sets generated by the Brain Initiative Cell Atlas Network (BICAN). Used to find, access, and use data from the BRAIN Initiative's efforts to map brain cell types, integrating molecular, anatomical, and functional data from mouse, primate, and human brains. Its purpose is to provide a comprehensive, open-access \"parts list\" of the brain, accelerate neuroscience discovery, and help understand brain disorders by offering links to raw data, visualizations, and tools for a vast array of cell types and circuits." .
SCR:027885 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BRAIN Armamentarium AAV Collection" ;
definition: "Collection of molecular genetic reagents to gain access to many different brain cell types. Provides scientists with advanced genetic tools, primarily AAV (Adeno-Associated Virus) vectors with cell-type specific \"enhancers,\" to precisely target, map, monitor, and manipulate specific cell types and circuits in the brain and spinal cord." .
SCR:027887 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BICAN Basal Ganglia Epigenome Explorer" ;
definition: "Portal that allows users to explore taxonomy-guided genome selections, visualize epigenetic assays, and analyze chromatin data across basal ganglia cell populations identified by the BRAIN Initiative Cell Atlas Network (BICAN) with an interactive research platform. The portal allows for investigation of several key epigenetic assays including associated with active enhancers and promoters, repressed genes, and constitutive heterochromatin. Used to analyze complex genomic and epigenomic data from the brain, helping identify specific cell types, understand gene regulation, and map disease-related molecular events, ultimately aiding in understanding neurological disorders like Alzheimer's, autism, and depression by revealing what goes wrong at the cellular level, leading to better gene therapies." .
SCR:027888 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VPixx | VIEWPixx system" ;
NIFRID:synonym "VIEWPixx" ;
definition: "Specialized monitor engineered for scientific rigor, replacing consumer displays with research-grade control and synchronization for visual experiments. Features high-performance industrial LCD glass, and a panel controller which has been custom designed to support vision research. Includes an array of peripherals which often need to be synchronized to video during an experiment, including stereo audio stimulator, button box port for precise reaction-time measurement, triggers for electrophysiology equipment, and complete analog I/O subsystem." .
SCR:027889 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Open Data Commons Data Quality APP (ODCdqa)" ;
NIFRID:synonym "ODC Data Quality App" ;
NIFRID:abbrev "ODCdqa" ;
definition: "Web application for facilitating compliance with the minimal data standards (MDS) set by the open data commons for SCI and TBI." .
SCR:027890 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MPBoot" ;
definition: "Software application for fast phylogenetic maximum parsimony tree inference and bootstrap approximation." .
SCR:027891 a owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5739" ;
rdfs:label "Paris Brain Institute iPSC Core Facility" ;
NIFRID:synonym "CELIS-iPS core facility",
"ICV-iPS core facility",
"ICV-iPS platform at the Paris Brain Institute (ICM)",
"iPS cell culture facility of the Paris Brain Institute" ;
definition: "As part of the cellular engineering and vectorology core facility (ICV), the iPSC core facility (ICV-iPS) proposes the generation and the genetic engineering of human induced pluripotent stem cells to internal research teams, external academic teams, and industrial partners. Services include generation of human iPSc with Sendai virus, full molecular and functional characterization of iPSc clones, genetic engineering of human iPSc with CRISPR/Cas9 system and theoretical and practical learning sessions on human iPSc culture. The core facility provides also access to L2 cell culture box dedicated to human iPSc culture." .
SCR:027892 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TElocal " ;
definition: "Software package for quantifying transposable elements at a locus level for RNAseq datasets. TElocal base algortihm is derived from the published TEtranscripts tool." .
SCR:027893 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Collection of Alternative Methods for Regulatory Application (CAMERA)" ;
NIFRID:synonym "Collection of Alternative Methods for Regulatory Application" ;
NIFRID:abbrev "CAMERA" ;
definition: "Interactive database and user interface providing online access to validated alternative methods for U.S. regulatory and other contexts of use. Central hub and unified resource of validated alternative methods that enhances accessibility to validation study reports, data, protocols / SOPs, and information on regulatory guidance.Users can filter searches by alternative method types, defined approaches, Test Method Endpoint, and regulatory guidance." .
SCR:027894 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5740" ;
rdfs:label "University of Victoria Biology Electron Microscopy Laboratory Core Facility" ;
NIFRID:synonym "UVic-Biology Electron Microscopy Laboratory" ;
definition: "Electron microscopy core provides microscopy and image analysis, applications development, and services." .
SCR:027895 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCAN-B MutationExplorer" ;
NIFRID:synonym "Sweden Cancerome Analysis Network–Breast (SCAN-B) MutationExplorer" ;
definition: "Web application to explore somatic mutations in large breast cancer RNA-sequencing datasets, particularly from the Sweden Cancerome Analysis Network–Breast (SCAN-B) project, helping to link genetic alterations to clinical features, patient outcomes (like survival), and potential drug targets, adding a dimension to gene expression analysis for guiding treatment." .
SCR:027896 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CircleSim" ;
definition: "Software command-line tool designed to simulate circular DNA and RNA sequences and generate corresponding sequencing reads. This tool can be helpful for researchers working with circular DNA (like eccDNA) or RNA, providing an easy way to simulate the coordinates of these molecules and generate sequencing files for further analysis." .
SCR:027897 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5743" ;
rdfs:label "Donald Danforth Plant Science Center Field Research Site Core Facility" ;
NIFRID:synonym "Field Research Site" ;
definition: "Field Research Site is a core facility providing scientists with advanced field research infrastructure and crop management capabilities. Offers diverse agricultural practices including full tillage, no-till systems, irrigation, precision spraying, and plot planting for row crops and specialty crops. On-site resources include multiple drying rooms, walk-in freezers, and dedicated processing spaces for soil, tissue, and seed samples." .
SCR:027898 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human brain stimulated-echo diffusion MRI with the diffusion time of 1 second" ;
definition: "This dataset includes human brain stimulated-echo (STE) diffusion MRI (dMRI) images acquired at the long diffusion time of 1 second from 10 healthy volunteers and an ex vivo brain hemisphere, as described by Aganj et al (MRM 2026). Also included are MPRAGE T1 images for all scans and standard dMRI images for the 10 in vivo scans. All images have been anonymized, and the T1 images have been de-faced." .
SCR:027899 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5744" ;
rdfs:label "University of Puerto Rico Center for Microbiome Sciences Core Facility" ;
NIFRID:synonym "COBRE Puerto Rico Center for Microbiome Sciences",
"Puerto Rico Center for Microbiome Sciences" ;
definition: "Core lab aids researchers in the design, compliance, methods, extractions, data analyses and training in microbiome research and innovation. Premier resource center, equipped with instrumentation, analytical capabilities, and training opportunities in microbiome." .
SCR:027900 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_EZ–Retriever_IR" ;
rdfs:label "BioGenex | EZ - Retriever� IR - Antigen Retrieval System" ;
NIFRID:synonym "EZ–Retriever IR System" ;
definition: "Automated, microwave-based instrument designed to perform rapid deparaffinization, rehydration, and antigen/nucleic acid retrieval on formalin-fixed, paraffin-embedded (FFPE) tissue sections. It handles up to 96 slides in 30 minutes, utilizing infrared (IR) technology for consistent, high-throughput staining." .
SCR:027901 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lunaphore | COMET system" ;
definition: "Ultra-rapid, high-throughput, high insight system for multiplex immunofluorescence (IF) and biomarker discovery. System enables to perform highly-multiplexed imaging of entire cross sections with sub-cellular resolution. Fully automated workflows for tissue staining and imaging. A full-stack hyperplexing solution capable of visualizing up to 40 markers." .
SCR:027902 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5745" ;
rdfs:label "Cancer Research UK Cambridge Institute Flow Cytometry and Mass Cytometry Core Facility" ;
NIFRID:synonym "CRUK Cambridge Institute Flow Cytometry and Mass Cytometry Core Facility" ;
definition: "Core provides cell analysis, sorting instruments and expertise in regular fluorescence, spectral, and flow cytometry. Offers educational and cytometric services including stem cell analysis, immunophenotyping, cell cycle analysis, translocation and co-localisation of cell activation markers, chromatin density, and apoptotic and necrotic analyses. Performs cell sorting, expertise in experimental design and provides equipment training for all users." .
SCR:027903 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5746" ;
rdfs:label "University of Texas MD Anderson Cancer Center Mass Spectrometry Imaging Core Facility" ;
NIFRID:synonym "MDACC Mass Spectrometry Imaging Core",
"University of Texas MD Anderson Cancer Center Mass Spectrometry Imaging Core" ;
definition: "Core has personnel with expertise in all aspects of Mass Spectrometry Imaging. Provides spatial mapping of biomolecules from tissue sections using Matrix Assisted Laser Desorption/Ionization (MALDI) and Secondary Ion Mass Spectrometry (SIMS)." .
SCR:027904 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Qlucore Omics Explorer " ;
definition: "Bioinformatics software program for multi-omics data analysis and visualization. It is developed and maintained by Qlucore AB (Lund, Sweden). Delivers flexible and easy-to-use visualization of big data for fast analysis and results." .
SCR:027905 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cas13design" ;
definition: "Web-based, and open-source platform designed to predict and optimize CRISPR-Cas13 guide RNAs (gRNAs) for targeting and knocking down specific RNA molecules. It is specifically used to select the most efficient guide RNAs for RfxCas13d to maximize RNA degradation (knockdown) efficacy, with applications in transcriptome engineering, functional genomics, and antiviral therapy." .
SCR:027906 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dlmoR" ;
definition: "Software R package for estimating dim-light melatonin onset (DLMO), implementing the hockey-stick method. Establishes a reproducible and sustainable foundation for melatonin-based circadian phase estimation and a modular platform for incorporating future quantitative approaches to DLMO detection." .
SCR:027907 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Leica_MZ_FLIII" ;
rdfs:label "Leica | MZ FLIII fluorescence stereomicroscope" ;
definition: "Fluorescence stereomicroscope offers 3D image, larger panoramic field of view, more intense fluorescence, and longer working distances. Living objects can be observed spatially in large fields of view." .
SCR:027908 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5751" ;
rdfs:label "Medical College of Wisconsin Translational Metabolomics Shared Resource Mass Spectrometry Core Facility" ;
definition: "Mass Spectrometry Core provides comprehensive LC-MS and MALDI imaging MS based analytical support for proteomics, lipidomics, metabolomics, glycomics, and spatial omics. Offers expertise in experimental design, optimized sample preparation, data acquisition, data analysis, and investigator training for NIH funded and translational research projects." .
SCR:027909 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell Annotation Schema" ;
NIFRID:synonym "CAS schema" ;
definition: "General, open-standard schema for cell annotations and related metadata. Provides programmatically accessible standard designed to record additional metadata about individual cell type annotations, including marker genes used as evidence and details of automated annotation transfer. Standard is represented as JSON schema as this allows all metadata to be gathered in a single, compact validatable file - which includes a link to a cell by gene matrix file of annotated data. However, the schema is designed so that it can be decomposed into individual tables suitable for use in dataframes/TSVs and flattened onto obs in AnnData format." .
SCR:027910 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scrattch taxonomy" ;
definition: "Software R package from the Allen Institute designed to build, standardize, and analyze single-cell RNA-seq-based cell type taxonomies. It utilizes a structured Allen Institute schema (AIT) to organize cell annotations and metadata, enabling hierarchical, data-driven cell type classification" .
SCR:027911 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5748" ;
rdfs:label "UC Davis Health Comprehensive Cancer Center Molecular Pharmacology and Chemical Biology MPCBSR Core Facility" ;
NIFRID:synonym "UC Davis Molecular Pharmacology and Chemical Biology Shared Resource" ;
definition: "Molecular Pharmacology and Chemical Biology Shared Resource (MPCBSR) provides services for the assessment of new therapeutics, including clinical trial specimens and determination of clinical PK/PD and potential drug-drug interactions (DDI), pharmacological studies on novel therapeutics in preclinical models, including DM/PK/PD, on-target mechanisms, biomarkers, and combination effects, and chemical synthesis of new compounds and drug delivery nanomaterials for improved therapy." .
SCR:027912 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5750" ;
rdfs:label "UC Davis Health Comprehensive Cancer Center Mouse Biology Shared Resource MBSR Core Facility" ;
NIFRID:synonym "UC Davis Mouse Biology Shared Resource" ;
definition: "Mouse Biology Shared Resource (MBSR) provides knockout, transgenic, and humanized murine cancer models and related services for advancing translational cancer research. Additionally, the MBSR offers services to enhance the use of existing mouse models or to facilitate the development of new mouse models for cancer research, including genetic alteration (e.g., CRISPR/Cas9-mediated gene targeting, transgenesis), surgical manipulation (e.g., patient-derived xenografts (PDX), cell-derived allografts (CDA) and xenografts (CDX)), and environmental challenges (e.g., diet, chemotherapeutic agents). can produce a wide range of allele-speci?c mouse models and offers innovative technologies to phenotype mouse models that mimic human conditions." .
SCR:027913 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BrainKB" ;
definition: "Knowledge base platform that provides scientists worldwide with tools for searching, exploring, and visualizing Neuroscience knowledge represented by knowledge graphs (KGs). Provides tools that enable scientists to contribute new information (or knowledge) to the platform and is expected to be a go-to destination for all neuroscience-related research needs. Allows making predictions and new inferences in addition to querying and viewing information." .
SCR:027914 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MEtabolomes, TRaits, and INteractions-Knowledge Graph" ;
NIFRID:abbrev "METRIN-KG" ;
definition: """Software pipeline for generating knowledge graph integrating emi, trydb, globi datasets.
Code for constructing a knowledge graph that integrates enriched metabolite data from Experimental Natural Products Knowledge Graph (ENPKG), LOTUS (available through Wikidata), plant trait data from TRY, and biotic interaction data from Global Biotic Interactions (GloBI). It performs taxonomic alignment against Wikidata records and generates Resource Description Framework (RDF) triples representing taxonomic relationships, traits, and species interactions. The resulting knowledge graph is queryable via a SPARQL (SPARQL Protocol and RDF Query Language) endpoint.""" .
SCR:027915 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Earth Metabolome Initiative Ontology" ;
definition: "Standardized, open-source framework of classes and properties designed to annotate and interlink data regarding metabolites, species taxonomy, ecological traits, and environmental interactions. It powers the METRIN-KG knowledge graph, mapping the chemical diversity of Earth's species to support biodiversity conservation. Knowledge representation schema designed to capture, contextualize, and structure chemical diversity data across all known species. It reuses and harmonizes several existing ontologies, while introducing over 100 new concepts and relations to enable interoperability and data reuse." .
SCR:027916 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "peakachu" ;
definition: "Software supervised learning framework for chromatin loop detection in genome-wide contact maps." .
SCR:027917 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Fit-Hi-C" ;
definition: "Software tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C." .
SCR:027918 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ABC-Enhancer-Gene-Prediction" ;
definition: "Software tool for cell type specific enhancer-gene predictions using ABC model." .
SCR:027919 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "4D-BioReconX" ;
definition: "Software bioinformatic framework for reconstructing 4D spatial transcriptomics atlas and spatiotemporal analyses+." .
SCR:027920 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_SmartClear_II_Pro" ;
rdfs:label "Life Canvas Technologies | SmartClear II Pro" ;
NIFRID:synonym "SmartClear II Pro" ;
definition: "Instrument to increase the rate of tissue clearing. Provides optimal imaging and staining quality. Delipidates for best antibody diffusion and minimal light scatter, and ensures maximum preservation of fluorescent protein signals with optimized buffers that maintain pH. Nanoporous membranes prevent common issues including tissue damage, contamination, browning, black precipitates, and deformation." .
SCR:027921 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5765" ;
rdfs:label "University of Liverpool Micro-X-ray-CT Shared Research Core Facility" ;
NIFRID:synonym "Micro X-ray Computed Tomography Shared Research Facility (XCT-SRF)",
"University of Liverpool Micro-X-ray-CT SRF" ;
definition: "Micro X-ray Computed Tomography Shared Research Facility (XCT-SRF) provides access to an X-ray microscope and micro-CT instrument, and expertise in experiment planning, sample preparation, and data analysis and visualisation. The facility is capable of 3D imaging and analysing a wide range of material samples, with a focus on supporting research in healthcare, manufacturing, and energy applications." .
SCR:027922 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5766" ;
rdfs:label "Mississippi State University Institute for Imaging and Analytical Technologies I2AT Core Facility" ;
NIFRID:synonym "Institute for Imaging and Analytical Technologies I2AT Core Facility" ;
definition: "Core facility that provides instrumentation and related services including SEM, TEM, AFM, XRD, polishing and related sample prep equipment, Surface Imaging, Surface Roughness, Hardness and Electric Properties, Fluorescence Imaging, Surface Elemental Information, High Resolution Imaging of Ultrathin Sections or Nanoparticles, Phase Determination and Phase Orientation." .
SCR:027923 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Miltenyi | Biotec MACSima System" ;
NIFRID:synonym "MACSima System" ;
definition: "Fully automated high-content imaging platform that uses cyclic immunofluorescence to enable high-plex spatial profiling of hundreds of protein markers and dozens of RNAs on the same tissue section, accelerating spatial biology and multiomics research workflows." .
SCR:027924 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5764" ;
rdfs:label "Medical College of Wisconsin Cancer Center Structural Biology Shared Resource Core Facility" ;
NIFRID:synonym "MCW- Structural Biology Shared Resources" ;
definition: "SBSR core consists of the Protein Purification unit and the Structure Determination unit. Protein Purification unit produces homogeneous, high-quality proteins well suited for downstream biophysical studies and structure determination. Structure Determination unit employs X-ray crystallography, Cryo-EM, and advanced AI-assisted analytical tools for structure determination and imaging." .
SCR:027925 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SMIntegration" ;
NIFRID:synonym "Spatial Multi-omics Integration" ;
definition: "Software open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Enables to explore gene-metabolite co-regulation mechanisms through an intuitive web interface, revealing spatial heterogeneity in tissue development and disease progression." .
SCR:027926 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Benthic Terrain Modeler" ;
NIFRID:synonym "Benthic Terrain Modeler (BTM)" ;
definition: "Software set of tools useful in the analysis of benthic terrain. Includes tools for geomorphology and classification." .
SCR:027927 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Coral Point Count" ;
NIFRID:abbrev "CPCe" ;
definition: "Windows-based software (PC use only) that provides a tool for the determination of coral cover using transect photographs. A specified number of spatially random points are distributed on a transect image and the features underlying the points are user-identified. Coverage statistics are then calculated and the results sent to Excel spreadsheets automatically. CPCe can be used for image calibration and area analysis of benthic features. Excel sheets are automatically generated to summarize the area calculations for each image." .
SCR:027928 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Reef Life Survey" ;
definition: "Web interactive digital tool for tracking the health of vital reef ecosystems all around the world. Reef Life Survey program uses scientists and citizen scuba divers to survey fishes on coral and rock reefs throughout the world. Marine life monitoring programm." .
SCR:027929 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CATAMI" ;
NIFRID:synonym "Collaborative and Automated Tools for Analysis of Marine Imagery" ;
definition: "CATAMI web site provides a location of the deposit and access of various underwater imagery, including data from Baited Remote Underwater Video (BRUV), Autonomous Underwater Vehicles (AUV), Diver Operated Video (DOV) and Towed Imagery (TI). CATAMI Classification Scheme provides standardised vocabulary for identifying benthic biota and substrata from underwater imagery." .
SCR:027930 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MarLIN BIOTIC" ;
NIFRID:synonym "Biological Traits Information Catalogue",
"Marine Life Information Network Biological Traits Information Catalogue" ;
definition: "Database developed by the Marine Life Information Network (MarLIN) in collaboration with the Marine Biological Association (MBA) and Plymouth Marine Laboratory. It provides detailed, searchable, and downloadable functional trait information on marine benthic invertebrates and plants to support ecological research. The database emphasizes species found around the coasts and seas of the British Isles." .
SCR:027932 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "polytraits" ;
definition: "Database on biological traits of polychaetes (bristle worms, Polychaeta: Annelida). It covers information about morphological, behavioural, reproductive and larval characteristics of polychaete taxa which has been collected from the literature." .
SCR:027933 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Arctic Traits Database" ;
definition: "Provides morphological, life-history, and behavioral trait data for Arctic benthic invertebrate taxa. It facilitates trait-based ecological research in the Arctic by offering standardized, fuzzy-coded data (scores 0-3) on 19 traits (80 categories), with species names synchronized with the World Register of Marine Species (WoRMS)." .
SCR:027934 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "mFD" ;
NIFRID:synonym "mFunctional Diversity" ;
definition: "Software R package to compute and illustrate the multiple facets of Functional Diversity. Provides graphical functions based on the ggplot library to illustrate FD values through customizable and high-resolution plots of species distribution among functional entities or in a multidimensional space. All functions include internal validation processes to check for errors in data formatting which return detailed error messages. Used to compute a global assessment of functional diversity by gathering computation of alpha and beta functional indices." .
SCR:027935 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "piecewiseSEM" ;
NIFRID:synonym "piecewise Structural Equation Modeling",
"piecewiseSEM: Piecewise Structural Equation Modeling" ;
definition: "Software R package for performing Piecewise Structural Equation Modeling, designed to fit complex causal networks by breaking them into smaller, manageable \"pieces\" (individual regressions) rather than using global covariance estimation. Used to analyze complex, direct/indirect ecological and evolutionary data." .
SCR:027936 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ViewnVivo" ;
rdfs:label "Optiscan | ViewnVivo" ;
NIFRID:synonym "ViewnVivo" ;
definition: "Miniaturized, hand-held, real-time fluorescence confocal endomicroscope designed for preclinical research, allowing researchers to visualize live tissue at cellular and subcellular levels in vivo. It is primarily used to observe dynamic, 3D biological processes, such as tumor progression, drug interactions, and cell-to-cell interactions in animal models." .
SCR:027939 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCIPI" ;
definition: "Software hepatocyte ploidy identification pipeline on the stereo-cell platform for accurate liver polyploidy classification via fluorescence staining and deep learning tools." .
SCR:027940 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Developmental Human Brain Atlas Ontology (DHBA)" ;
definition: "Machine-readable framework designed to standardize, organize, and annotate the anatomical structures, developmental stages, and spatial relationships of the human brain during development. It is primarily derived from the Allen Developing Human Brain Atlas (BrainSpan) to provide a structured, hierarchical taxonomy for researchers. Application ontology built by combining ontologised versions of the Allen Institute Developing Human Brain Atlas (DHBA) StructureGraph mapped to Uberon." .
SCR:027941 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MCdiffusion_wObstacles" ;
definition: "Software code for Monte Carlo diffusion simulation. Monte Carlo diffusion with reflecting or absorbing obstacles in 2 and 3D." .
SCR:027942 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Diffusion-Model" ;
NIFRID:synonym "DifFlux",
"Diffusion Flux",
"Diffusion Flux Model" ;
definition: "Software code for simulating diffusion in brain extracellular space images." .
SCR:027943 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Webilastik" ;
definition: "Software tool is revision of classic ilastik. Used for interactive (supervised) pixel-level image classification and segmentation." .
SCR:027944 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "WebNutil" ;
NIFRID:synonym "webnutil" ;
definition: "Software Python library for spatial analysis of histological brain section images using a reference brain atlas. Implements the core quantification algorithms from the QUINT workflow, designed to replicate and extend the Quantifier feature of the Nutil software." .
SCR:027945 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LLM-scCurator" ;
definition: "Software data-centric, backend-agnostic framework for zero-shot cell-type annotation. Data-centric marker distillation for zero-shot cell-type and spatial annotation with LLMs." .
SCR:027946 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5758" ;
rdfs:label "Louisiana State University Health Sciences Center Shreveport hiPSC and Cell Models Core Facility" ;
NIFRID:synonym "hiPSC & Cell Models" ;
definition: "Core enables generation of genetically defined human iPSC-derived hepatocytes, CRISPR/Cas9 mediated gene editing, and primary mouse hepatocyte isolation." .
SCR:027947 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cross-enhancer Ranking Pipeline" ;
NIFRID:synonym "Cross-enhancer Ranking Pipeline (CERP)" ;
NIFRID:abbrev "CERP" ;
definition: "Software pipeline for identifying enhancers in bulk or single-nucleus ATAC-seq and multiomic data with a high degree of accuracy for prioritizing testing of promising candidate cell type enhancers for targeting homologous cell types across mammalian species." .
SCR:027948 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GBM-TIME multi-dimensional transcriptomics workflow" ;
definition: "Software pipeline for dissecting glioblastoma risk signatures in the tumor immune microenvironment based on single-cell, bulk, and spatial transcriptomic data." .
SCR:027949 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SurvivalVolume" ;
definition: "Software tools for parsing measurement with threshold over time data (eg tumour treatment studies) and generating interactive and static plots." .
SCR:027950 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cancer Treatment Response gene signature DataBase" ;
NIFRID:synonym "CTR-DB 1.0",
"CTR-DB 2.0" ;
NIFRID:abbrev "CTR_DB" ;
definition: "Data resource for clinical transcriptomes with cancer treatment response, and meanwhile supports various data analysis functions, providing insights into the molecular determinants of drug resistance. CTR-DB 2.0 is updated cancer clinical transcriptome resource, expanding primary drug resistance and newly adding acquired resistance datasets and enhancing the discovery and validation of predictive biomarkers." .
SCR:027951 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "compartmap" ;
definition: "Software tool for reconstruction of higher order chromatin from scRNA-seq and scATAC-seq. Chromatin compartment inference from single-cell RNA- and ATAC-seq." .
SCR:027952 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Azure_c600" ;
rdfs:label "Azure Biosystems | c600 Imaging System" ;
NIFRID:synonym "Azure c600 Imaging System",
"Azure c600 Western Blot Imaging System" ;
NIFRID:abbrev "AZURE c600" ;
definition: "Benchtop instrument designed for life science research, specifically for imaging, detecting, and quantifying protein and nucleic acids on gels and blots. It enables multi-channel analysis, including laser infrared (IR) fluorescence, RGB visible fluorescence, and chemiluminescence, allowing for multiplexed Western blots." .
SCR:027954 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5769" ;
rdfs:label "Penn State College of Medicine GPCR Assay Service Center Core Facility" ;
NIFRID:synonym "GPCR Assay Service Center",
"Penn State College of Medicine GPCR Assay Service Center" ;
definition: "Core to accelerate scientific discovery in G protein-coupled receptors (GPCRs) physiology and pharmacology. Provides services to identify signal transduction processes that are specific to their GPCR of interest (such as opioid, cannabinoid and muscarinic) that is either natively present or expressed heterologously in cell systems. Assists investigators with drug development studies. Support researchers with assay development and optimization, pilot data, and grant assistance. Houses instrumentation used." .
SCR:027955 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Wallac_Victor2_1420" ;
rdfs:label "Wallac | Victor2 1420 Multilabel Counter" ;
NIFRID:synonym "PerkinElmer Victor2 1420 Multilabel Counter",
"PerkinElmer Wallac Victor2 1420 Multilabel Counter" ;
definition: "Microplate reader designed for academic, clinical, and industrial laboratories to detect light-emitting or absorbing markers with Manufacturer/Brand: PerkinElmer (formerly Wallac Oy). It supports over 10 non-radioactive technologies, including fluorescence, luminescence, time-resolved fluorometry, and absorbance in various plate formats (1-864 wells). Accepts microtitration plates (up to 1536 wells), Petri dishes, slides, and filters.Equipped with shaking, scanning, and optional temperature control/liquid dispensers for kinetic studies. Operates as a stand-alone unit or integrates with robotic systems for high-throughput screening." .
SCR:027956 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5770" ;
rdfs:label "University of Pittsburgh McGowan Institute Histology Core Facility" ;
definition: "Core offers full histology services including processing and embedding, cutting, staining, and immunohistochemistry. Our services can be customized to fit the needs of any research program." .
SCR:027957 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5771" ;
rdfs:label "University of Pittsburgh Rangos Histology Core Facility" ;
definition: "Core provides histological services in order to facilitate productivity and success of investigators based in the Rangos Research Center and researchers in other units of the University of Pittsburgh and UPMC, as well as clients in other academic institutions in the Pittsburgh area." .
SCR:027958 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5772" ;
rdfs:label "University of Coimbra Department of Chemistry NMR Core facility" ;
definition: "Core offers access to Nuclear Magnetic Resonance (NMR) spectroscopy studies. Facility houses three solution-state FT-NMR instruments operating at proton frequencies of 400, 500 and 600 MHz, a TD-NMR 20 MHz relaxometer and an EPR spectrometer. UC-NMR Core Facility provides researchers and institutions with expertise, services and tools to carry out research requiring solution Nuclear Magnetic Resonance spectroscopy." .
SCR:027959 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChronoRoot2" ;
NIFRID:synonym "ChronoRoot 2.0" ;
definition: "Software open AI-Powered Platform for 2D Temporal Plant Phenotyping." .
SCR:027960 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5773" ;
rdfs:label "Charité Berlin University of Medicine Transgenic Technologies Core Facility" ;
NIFRID:synonym "Transgenic Technologies Charité-Universitätsmedizin Berlin" ;
definition: "Core provides services supporting generation, modification, cryopreservation, and rederivation of genetically modified rodent models for biomedical research, generates genetically modified mouse models via both targeted and random mutagenesis using tools such as CRISPR/Cas9 in zygotes or embryonic stem (ES) cells, provides cryopreservation and rederivation of existing animal models to preserve hygienic integrity. Services for rodent transgenic model development include: Pronuclear Injection and amp; Viral Transgenesis with introduction of genetic constructs into zygotes using microinjection or lentiviral systems; ES Cell-Based Techniques: use of embryonic stem cell manipulation for genetic targeting; Embryo Transfer: transferring manipulated embryos into recipient females; In Vitro Fertilization (IVF): assisted reproductive technology to generate embryos for manipulation or cryopreservation; Cryopreservation: freezing of embryos and sperm for archiving or rederivation of lines as required. Facility’s expertise includes quality control of cryopreserved material to ensure viability upon thawing." .
SCR:027961 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5774" ;
rdfs:label "Charité Berlin University of Medicine Cryo-Electron Microscopy Core Facility" ;
NIFRID:synonym "Charité Universitätsmedizin Berlin cryo-Electron Microscopy (CFcryo-EM)",
"Cryo-Electron Microscopy of Charité - Universitätsmedizin Berlin" ;
definition: "Facility for high resolution imaging of biological samples at cryogenic temperatures. Amongst other applications such as single particle data collection, our high-end instrumentation is suited to perform in situ structural biology by combining cryoCLEM, lamella FIB-milling, and cryo-electron tomography." .
SCR:027962 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5775" ;
rdfs:label "Charité Berlin University of Medicine Virchow Clinic Campus Experimental Hybrid Operating Room Core Facility" ;
NIFRID:synonym "CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN - CAMPUS VIRCHOW KLINIKUM Experimenteller Hybrid-OP FEM CVK",
"Experimenteller Hybrid-OP FEM CVK" ;
definition: "Core offers large-animal experimental hybrid operating room equipped for cardiological and cardiothoracic interventions, including advanced angiography and multimodal intraprocedural imaging, to support patient-oriented preclinical research and education. Facility enables design, conduct, and veterinary-supervised aftercare of acute and chronic large-animal studies and hands-on training courses on implants, ventricular assist devices, artificial hearts, and percutaneous procedures for structural heart valve disease at phantom models and large-animal models. Core functions and services Performance of animal experimental studies and training courses in an experimental hybrid OR environment. Consultation on study design, model selection, and preparation of animal experiment applications for regulatory approval. Provision of anesthesia and surgical assistance, including perioperative and intensive care support. Specialist veterinary support for acute and chronic studies, ensuring animal welfare and scientific quality. Housing and husbandry for large laboratory animals such as sheep, pigs, and minipigs as part of the experimental program. Equipment and technology Hybrid operating room with Philips Allura Clarity FD20 angiography system tailored to cardiology and cardiac surgery interventions. Comprehensive software tools including Echo-, Heart-, and Vesselnavigator for image-guided procedures. EPIQ7 and CX50 ultrasound systems supporting TTE, TEE, ICE, and IVUS imaging modalities for structural and interventional procedures. Carto-3, OPTIS Integrated System, and XperCT platforms for 3D mapping and intravascular or intracardiac imaging. Heart–lung machine and ECMO systems for cardiopulmonary support during complex experimental interventions. Organizational context and availability Located at Campus Virchow-Klinikum as part of the Forschungseinrichtungen für Experimentelle Medizin and operated in cooperation with the Deutsches Herzzentrum Berlin. Provides core facility research infrastructure of the Charité faculty for translational cardiovascular research and advanced training in a large-animal setting. Certified according to ISO 9001:2015, indicating a documented quality management system for its services." .
SCR:027963 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Xevo_TQ_Absolute" ;
rdfs:label "Waters | Xevo TQ Absolute Triple Quadrupole Mass Spectrometer" ;
NIFRID:synonym "Waters Xevo TQ Absolute",
"Xevo TQ Absolute Triple Quadrupole Mass Spectrometer" ;
definition: "High-sensitivity, compact benchtop tandem quadrupole mass spectrometers designed for trace-level quantification in complex samples. Primarily used for PFAS testing, pharmaceutical bioanalysis, clinical diagnostics, and environmental contaminant analysis, offering enhanced performance for negative ion-mode compounds. Used for quantifying drug residues, metabolites in biological samples, and impurities, with specific IVD models available for clinical settings. Equipped with StepWave XR technology to handle high-throughput, complex matrix samples with minimal maintenance." .
SCR:027964 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LLM-PathwayCurator" ;
definition: "Software quality-assurance layer for pathway enrichment interpretation that converts enrichment term lists into context-conditioned, evidence-linked, schema-bounded claims and assigns PASS/ABSTAIN/FAIL via predefined, rule-based audit gates (stability, context validity stress tests, evidence-link integrity, and contradiction checks), producing decision-grade reports with audit logs. The LLM is confined to proposal-only steps; final decisions are mechanical and reproducible." .
SCR:027965 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_554" ;
rdfs:label "Charité Berlin University of Medicine Viral Core Facility" ;
NIFRID:synonym "Charité - Viral Core Facility",
"Viral Core Facility (VCF) of the Charité – Universitätsmedizin Berlin",
"Viral Core Facility of the Charité - Universitätsmedizin Berlin" ;
definition: "Core provides comprehensive services for generation of viral particles from existing vectors or newly created vectors." .
SCR:027966 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Neurosynth Compose" ;
definition: "Web-based platform for flexible and reproducible neuroimaging meta-analysis. Enables to create customized, reproducible neuroimaging meta-analyses with no code/low code solutions. It integrates a regularly updated centralized literature database (NeuroStore) with tools for systematic study curation and annotation following PRISMA guidelines, allowing users to search across tens of thousands of indexed fMRI studies or import external study lists. Analyses can be executed locally or in the cloud using the NiMARE Python library, and results can be interactively reviewed, shared, and archived, facilitating transparent meta-analyses and collaborative knowledge building." .
SCR:027967 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5768" ;
rdfs:label "Mayo Clinic Precision Mouse Engineering Core Facility" ;
NIFRID:synonym "Precision Mouse Engineering Core - Mayo Clinic" ;
definition: "Core generates transgenic and gene-targeted mice for researchers at Mayo Clinic's campuses in Arizona, Florida and Minnesota to enable researchers to observe how genes, or mutant variations of genes, are expressed. Provides services to all Mayo Clinic faculty and staff engaged in research. Also, services are offered to non-Mayo investigators and research collaborators." .
SCR:027968 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5767" ;
rdfs:label "Mayo Clinic Biomedical Imaging Resource Core Facility" ;
NIFRID:synonym "Biomedical Imaging Resource - Mayo Clinic" ;
definition: "Mayo Clinic's Biomedical Imaging Resource Core in Rochester, Minnesota, focuses on supporting and advancing research in biomedical imaging and visualization sciences. Provides guidance on protocol design, routine image analysis, and custom software and hardware solutions. Also, media and model production resources are available to investigators for the creation of high-quality visualizations and physical models of research data.Core provides services to all Mayo Clinic faculty and staff engaged in research. Also, services may be available on a limited basis to investigators and research collaborators outside Mayo Clinic. Before scheduling, contact the core to design optimal settings for the specified imaging task." .
SCR:027969 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_3126" ;
rdfs:label "University of Louisville Proteomics Technology Center PTC Core Facility" ;
NIFRID:synonym "Proteomics Technology Center (PTC)",
"University of Louisville Proteomics Technology Center (PTC)" ;
definition: "Core provides comprehensive proteomic analyses using LC-MS platforms, supporting post-translational modifications, protein-protein interactions, spatial proteomics, and single-cell workflows with bioinformatics." .
SCR:027970 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Canvas Copy Number Variant Caller" ;
NIFRID:synonym "Canvas",
"Illumina Canvas" ;
NIFRID:abbrev "canvas" ;
definition: "Software tool for calling copy number variants (CNVs) from human DNA sequencing data. It can work either with germline data, or paired tumor/normal samples. Its primary input is aligned reads (in .bam format), and its primary output is a report (in a .vcf file) giving the copy number status of the genome." .
SCR:027971 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5778" ;
rdfs:label "Charité Berlin University of Medicine iPATH.Berlin Core Facility" ;
NIFRID:abbrev "iPATH.Berlin" ;
definition: "Core provides immunopathological services from sample embedding and staining to microscopic evaluation. Full service for histopathology includes tissue embedding, staining of tissue sections and microscopic analysis: preparation of paraffin blocks,cutting of cryo and paraffin sections,histochemistry,immunohistochemistry/-fluorescence/multiplexing, in-situ hybridization,Scoring/quantification,storage." .
SCR:027972 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Doric | Fiber Photometry Console" ;
definition: """FPGA-based data acquisition unit designed for real-time monitoring of neural activity in behaving animals. It synchronizes excitation light sources (LED drivers) with detection (photodetectors) to record fluorescence signals, typically using lock-in amplification to filter noise and separate multiple wavelengths (e.g.,
).""" .
SCR:027973 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Doric | LED Driver" ;
definition: "Specialized, high-performance power supplies and controllers designed for neuroscience research, specifically to drive Connectorized LEDs and fiber-coupled light sources. They offer 1, 2, or 4 independent channels for controlling light intensity, modulation (CW, TTL, analog), and complex, software-defined, or automated pulse sequences required for optogenetics and photometry experiments." .
SCR:027974 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Doric | 6 ports Fluorescence Mini Cube (iLFMC6)" ;
definition: "Specialized, compact, all-in-one fiber photometry system designed to monitor neural activity or neurotransmitter levels in freely moving animals. By combining multiple built-in LEDs (405-440 nm, 460-490 nm, etc.) and photodetectors, it enables simultaneous, multi-wavelength measurement of calcium indicators (e.g., GCaMP) and red fluorophores alongside isosbestic controls to correct for movement artifacts." .
SCR:027975 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Phy" ;
definition: "Software open-source Python library providing graphical user interface for visualization and manual curation of large-scale electrophysiological data. It is optimized for high-density multielectrode arrays containing hundreds to thousands of recording sites." .
SCR:027976 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dupRadar" ;
definition: "Software R package for assessment of PCR artifacts in RNA-Seq data. Used for duplication rate quality control for RNA-Seq datasets." .
SCR:027977 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Leica_DM6000_B" ;
rdfs:label "Leica | DM6000 B histology microscope" ;
definition: "Upright microscope designed for histology and pathology. With motorized z-focus, motorized and coded 7x nosepiece, fully automated transmitted light axis, and fully automated 5x or 8x fluorescence axis, the automated Leica DM6000 B research microscope provides all transmitted light contrast methods including the world’s first fully automated Differential Interference Contrast (DIC)." .
SCR:027978 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ChemiScope_6200" ;
rdfs:label "Clinx ChemiScope 6200 imaging analyzer" ;
NIFRID:synonym "ChemiScope 6200" ;
definition: "Imaging system used in laboratories for chemiluminescence and fluorescence imaging, specifically for detecting and analyzing protein bands (Western blot), DNA/RNA gels, and RGB fluorescence. It features a cooled CCD camera for detecting low-abundance samples." .
SCR:027979 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Hitachi_HT7800" ;
rdfs:label "Hitachi | HT7800 Transmission Electron Microscope" ;
definition: "120 kV Transmission Electron Microscope (TEM) designed for high-contrast, high-resolution imaging in biological and materials science, often operated in, lighted rooms. It features a proprietary dual-mode objective lens for switching between wide-field and high-resolution views, along with automated, user-friendly software for navigation and image acquisition." .
SCR:027980 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggcor" ;
definition: "Software extended tools for correlation analysis and visualization." .
SCR:027981 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "smetana" ;
NIFRID:synonym "Species METabolic interaction ANAlysis" ;
definition: "Software tool to analyse interactions in microbial communities. Species metabolic interaction analysis (SMETANA) of microbial communities." .
SCR:027982 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "micom" ;
definition: "Software Python package to study microbial communities using metabolic modeling. Metagenome-scale modeling to infer metabolic interactions in the gut microbiota." .
SCR:027983 a NLX:63400,
owl:NamedIndividual ;
rdfs:label " CellCards" ;
definition: "Web service provides functional annotation of cell types within the lung and combines functional and single cell data for a rigorous catalogue of cell lineages." .
SCR:027984 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5779" ;
rdfs:label "Medical College of Wisconsin Cancer Center Translational Metabolomics Shared Resource, Redox and Bioenergetics Core Facility" ;
definition: "Redox and Bioenergetics core provides instrumentation, cutting-edge techniques, and expertise dedicated to investigating cancer cell metabolism and redox signaling, and to design custom probes for reactive oxygen species (ROS) for MCWCC members." .
SCR:027985 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5780" ;
rdfs:label "Charité Berlin University of Medicine Animal Behavior Phenotyping Core Facility" ;
NIFRID:synonym "Charité Berlin University of Medicine Animal Behavior Phenotyping Facility (ABPF)" ;
definition: "Core offers broad spectrum of behavioral tools to characterize novel animal models, including assays of cognition, exploratory behavior, social interaction, motivation, anxiety‑related behavior, and motor performance. In addition to classical tests such as the Barnes maze, elevated plus maze and open field, the facility develops and implements novel, high‑throughput and ethologically relevant approaches to monitor rodent behavior with particular emphasis on social interactions." .
SCR:027986 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5781" ;
rdfs:label "Charité Berlin University Medicine Research Institutes for Experimental Medicine Core Facility" ;
NIFRID:synonym "Forschungseinrichtungen für Experimentelle Medizin (FEM)" ;
definition: "Core research service unit at the Charité – Universitätsmedizin Berlin specializing in laboratory animal husbandry, breeding, and experimental usage for biomedical research. Provides infrastructure for animal-based studies, ensures compliance with animal welfare regulations (e.g., training, veterinary oversight), and supports the creation of genetically modified models." .
SCR:027987 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Broad Institute Genomics Platform" ;
NIFRID:synonym "Broad Institute Genomics Platform Core Facility" ;
definition: "Facility that generates, analyzes, and interprets high-throughput genomic data to understand the genetic basis of disease. Genomics Platform has played leadership role in the design, data generation, and methods development in support of major genomic resource projects.Through the Broad Clinical Labs (BCL), formerly known as the Clinical Research Sequencing Platform (CRSP), it supports clinical trials, diagnostic testing, and major initiatives, including COVID-19 testing. Offers services including Nucleic Acid Extractions, Single Cell Sequencing (using 10x Genomics products), and GWAS Arrays." .
SCR:027988 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Integra_ASSIST PLUS" ;
rdfs:label "Integra Biosciences | ASSIST PLUS Pipetting Robot" ;
definition: "Pipetting Robot enables automated pipetting with mounted any of INTEGRA’s 25 multichannel electronic pipettes or D-ONE single channel pipetting modules onto the ASSIST PLUS pipette holder. Provides different pipetting programs." .
SCR:027989 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5782" ;
rdfs:label "Charité Berlin University of Medicine Advanced Medical Bioimaging Core Facility" ;
NIFRID:synonym "Advanced Medical Bioimaging AMBIO Core Facility",
"AMBIO",
"Charité Berlin University of Medicine Advanced Medical Bioimaging AMBIO Core Facility" ;
definition: """Core for advanced fluorescence bioimaging. Provides both the infrastructure and expertise necessary for researchers with diverse backgrounds to efficiently perform advanced fluorescence microscopy imaging projects on the molecular, cellular and tissue level.
AMBIO services include individual user training and assistance, and if necessary supervised image acquisition and guidance for data analysis.""" .
SCR:027990 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CrossExpression" ;
definition: "Software package to discover genes that coordinate their expression across spatially adjacent cells. Used for analysis of spatial transcriptomic data allowing in-depth analyses how genes coordinate their expression in space to perform tissue-level functions. Facilitates analysis and exploration of cross-expression patterns." .
SCR:027991 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Hitachi_SU8100" ;
rdfs:label "Hitachi | SU8100 scanning electron microscope" ;
NIFRID:synonym "Hitachi SU8100" ;
definition: "High-performance Field Emission Scanning Electron Microscope (FE-SEM) designed for ultra-high-resolution imaging and elemental analysis of nanostructures, semiconductor devices, and beam-sensitive materials. It features cold field emission technology for superior, low-voltage, high-resolution imaging (approx. 1.1 nm at 1kV)." .
SCR:027992 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "survivalAnalysis" ;
definition: "Software package to provide interface for the most frequent tasks of survival analysis, with focus on the needs of clinical oncology. The syntax follows the tidyverse philosophy and is made to be used in a pipeline." .
SCR:027993 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Poly Pipeline" ;
definition: "Software data analysis pipeline for spatial transcriptomics data tailored to polyploid organisms." .
SCR:027994 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "compareGroups" ;
definition: "Software R package to create tables displaying results of univariate analyses, stratified or not by categorical variable groupings." .
SCR:027995 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CDC Research Data Center United States Cancer Statistics" ;
NIFRID:synonym "US Centers for Disease Control and Prevention Restricted access United States cancer statistics" ;
definition: "Portal provides detailed, non-public data on cancer incidence, such as precise county-level data, specific site factors, and prognostic measures. The restricted access U.S. Cancer Statistics (USCS) dataset provides researchers access to cancer incidence and population data for all 50 states, the District of Columbia, and Puerto Rico. These statistics combine cancer registry data from CDC's National Program of Cancer Registries and the National Cancer Institute's Surveillance, Epidemiology, and End Results program." .
SCR:027996 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CDC Research Data Center" ;
NIFRID:synonym "CDC National Center for Health Statistics Research Data Center",
"CDC NCHS Research Data Center",
"Centers for Disease Control and Prevention NCHS Research Data Center" ;
NIFRID:abbrev "CDC RDC" ;
definition: "Secure facility that provides qualified researchers with access to restricted-use, non-public health data. It protects participant confidentiality while allowing analysis of detailed survey data, such as specific geographic locations or sensitive health info. Provides access to restricted data from the National Center for Health Statistics and from other federal government agency surveys and studies. Access is granted only to approved researchers under strict supervision, and all results undergo disclosure review before leaving the RDC." .
SCR:027997 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CDC Federal Statistical Research Data Center" ;
NIFRID:synonym "Federal Statistical Research Data Centers (FSRDCs)" ;
definition: "Federal Statistical Research Data Centers (FSRDCs) are secure, specialized facilities operated by the U.S. Census Bureau in partnership with leading research institutions across the U.S.. They provide authorized researchers access to restricted-use, non-public microdata from federal agencies for statistical purposes while ensuring strict confidentiality and data protection. There are more than 30 FSRDC sites located throughout the United States. Researchers can access detailed, non-public data from the Census Bureau, Bureau of Labor Statistics, National Center for Health Statistics, and other agencies. Using FSRDC location to access NCHS restricted data involves additional requirements and costs. If you access National Center for Health Statistics (NCHS) data through FSRDC site, you will interact with both your assigned NCHS RDC analyst and the location's FSRDC administrator over the course of your project. Each of these people have their own roles and responsibilities." .
SCR:027998 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Shanghai Xinruan | Sleep Deprivation Device" ;
definition: "Device to systematically deprive mice/rats of sleep for a certain period each day. Uses feedback control by monitoring animal activity levels. It can activate the deprivation lever after the animal enters a specific sleep stage to deprive or break sleep. It has three working modes: feedback adjustment (software control mode), programmable adjustment (external control mode), and independent touch screen adjustment (standard mode). It can be used to create animal models of sleep deprivation or sleep breaking, and features precise adjustment and low physical exertion." .
SCR:027999 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Tiangen Biotech | TGem Ultra Full Wavelength Spectrophotometer" ;
NIFRID:synonym "Ultra Full Wavelength Spectrophotometer" ;
definition: "TGem Ultra is an all-in-one full-wavelength ultraviolet-visible spectrophotometer with a wavelength range of 185-910 nm. The base can detect trace samples of 0.5–2 µl with very high accuracy and repeatability. The flagship version (OSE-260-06) also features a cuvette detection mode, suitable for measuring samples with low concentrations, high volatility, or low surface tension that do not easily form a liquid column. It can also be used for measuring bacterial concentrations and analyzing enzyme kinetics." .
SCR:028000 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5783" ;
rdfs:label "University of Louisville KY INBRE Data Science Core Facility" ;
NIFRID:synonym "Predictive Analytics and Data Science (PADS) Hub" ;
definition: "Specialized, collaborative unit providing bioinformatics, biostatistics, and data analysis services to researchers across Kentucky. It enhances biomedical research capacity through expert support in experimental design, grant application assistance, and high-throughput data analysis, primarily serving faculty and students at member institutions." .
SCR:028001 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NanoZoomer_2.0-RS" ;
rdfs:label "Hamamatsu | NanoZoomer 2.0-RS" ;
definition: "Compact, benchtop whole-slide scanner designed for high-speed, high-resolution digitization of glass slides, primarily used in research pathology, education, and tele-pathology. It converts slides into digital images (NDPI format) for viewing, analysis, and archiving, offering Z-stack imaging for thick tissues and optional fluorescence capabilities." .
SCR:028002 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5784" ;
rdfs:label "Arizona State University Knowledge Enterprise Eyring Materials Center Core Facility" ;
NIFRID:abbrev "ASU KE EMC" ;
definition: "Facility supporting analytical needs for materials. Provides advanced facilities and equipment for materials characterization, surface, optical and structural analysis, elemental composition, and high-resolution electron microscopy. The center supports materials analysis across a broad range of scientific disciplines, including physics, chemistry, life sciences, earth and space sciences, environmental sciences, and engineering. Offers electron microscopy, X-ray diffraction, ICP-MS, spectroscopy, and related techniques." .
SCR:028003 a owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5786" ;
rdfs:label "National Institute for Scientific Research Advanced Laser Light Source Core Facility" ;
NIFRID:synonym "Advanced Laser Light Source",
"Advanced Laser Light Source (ALLS)",
"National Institute for Scientific Research Advanced Laser Light Source (ALLS)" ;
NIFRID:abbrev "ALLS" ;
definition: "Canadian national user facility located at INRS-EMT in Varennes, Quebec, designed to develop and apply high-power, ultrafast lasers for advanced scientific research. It produces intense, synchronized light pulses spanning from THz to hard X-rays for dynamic imaging, materials science, and medical applications. Home of the most powerful laser in Canada with 750 TW and high repetition rate laser systems to explore novel phenomena in matter with ultrafast tools." .
SCR:028004 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100012943",
"GRID grid.418084.1",
"ISNI 0000 0000 9582 2314",
"Wikidata Q3152403" ;
rdfs:label "National Institute of Scientific Research INRS" ;
NIFRID:synonym "Institut National de la Recherche Scientifique" ;
definition: "Specialized research and graduate training university in Quebec, Canada, founded in 1969. It is the only institution in Quebec dedicated exclusively to graduate studies (master's and doctoral level) and applied research in four key strategic sectors: water/environment, energy/materials/telecommunications, urbanization/culture, and health/biotechnology." .
SCR:028005 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tximeta" ;
NIFRID:synonym "Tximeta" ;
definition: "Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility." .
SCR:028006 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BISCUIT" ;
NIFRID:synonym "BISulfite-seq CUI Toolkit",
"BISulfite-seq CUI Toolkit (BISCUIT)" ;
definition: "Software application for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Used to perform alignment, DNA methylation and mutation calling, and allele specific methylation from bisulfite sequencing data. Analyzing sodium bisulfite conversion-based DNA methylation/modification data." .
SCR:028007 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DMRcate" ;
definition: "Software application for de novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions." .
SCR:028008 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "rGREAT" ;
NIFRID:synonym "Genomic Regions Enrichment of Annotations Tool" ;
definition: "Software R package for functional enrichment on genomic regions. Functional enrichment analysis directly performed on genomic regions." .
SCR:028009 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Flexible Procedures for Clustering" ;
NIFRID:synonym "flexible procedures for clustering",
"fpc: Flexible Procedures for Clustering" ;
NIFRID:abbrev "fpc" ;
definition: "Software R package for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Standardisation of cluster validation statistics by random clusterings and comparison between many clustering methods and numbers of clusters based on this. Cluster-wise cluster stability assessment" .
SCR:028010 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Random Number Lab" ;
definition: "Web interactive set of tools for sampling and randomization of data sets and generation of random patterns. The tools include randomization and permutation of data (even stratified random sampling) and random assignments for studies, generation of random numbers following specific probability distributions, generation of random and quasi-random point distributions and sampling patterns, noise in one or two dimensions with adjustable spectral properties, random walks and Lévy flights. Own data tables can be provided for random sampling in a privacy-friendly way, as data processing takes place directly in the browser and no data is transferred to anywhere else. Random Number Lab also offers some educational material and worksheets and can be used for scientific and educational purposes." .
SCR:028011 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5777" ;
rdfs:label "Medical College of Wisconsin Cancer Center Cell Therapy Shared Resource Core Facility" ;
NIFRID:synonym "MCW Cancer Center Cell Therapy Shared Resource",
"MCW Cancer Center Cell Therapy Shared Resource (CTSR)",
"Medical College of Wisconsin Cancer Center Cancer Center Cell Therapy Shared Resource" ;
definition: "Core provides services including processing and production of cell therapy products for clinical use, expertise in translation of cellular therapies to the clinic, and instrumentation supporting the development of novel immunotherapy strategies and insights on mechanisms of action for effective therapies." .
SCR:028012 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "C elegans codon adapter" ;
definition: "Web optimization tool for codon adaptation-based control of protein expression in C. elegans." .
SCR:028013 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Flux" ;
definition: "Open-source machine-learning software library and ecosystem written in Julia. Machine learning library for the Julia programming language providing tools for building neural networks including layers, optimizers, and automatic differentiation." .
SCR:028014 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MLUtils" ;
definition: "Software library within Julia ML ecosystem (JuliaML) designed for managing machine learning pipelines. Utilities for machine learning in Julia including data splitting, shuffling, batching, and preprocessing operations." .
SCR:028015 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Clustering Julia" ;
definition: "Software Julia package for data clustering. Clustering algorithms for the Julia programming language including k-means, hierarchical clustering, DBSCAN, and affinity propagation." .
SCR:028016 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "hoodscanR" ;
definition: "Software R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. Spatial cellular neighbourhood scanning in R." .
SCR:028017 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5787" ;
rdfs:label "University of Technology of Compiègne INGESYSBIO meta-platform Core Facility" ;
NIFRID:synonym "INGESYSBIO meta-platform",
"Université de Technologie de Compiègne (UTC) INGESYSBIO meta-platform" ;
definition: "Specialized research and technical core at the Université de Technologie de Compiègne (UTC), specifically within the BMBI (Bio-Mechanics and Bio-Engineering) CNRS lab, dedicated to the engineering of biological systems. Designed to support training, research, and development activities in the healthcare field, acting as a bridge between engineering and biology. Integrates complementary technological facilities dedicated to the engineering, production, culture, and characterization of biological systems, ranging from simple models to complex structures. It brings together expertise covering the entire experimental workflow, from the design and fabrication of technological devices and biological supports to their cultivation, monitoring, and functional analysis." .
SCR:028018 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100012945",
"GRID grid.6227.1",
"ISNI 0000 0001 2189 2165",
"Wikidata Q622906" ;
rdfs:label "University of Technology of Compiegne; Compiegne; France" ;
definition: "French public engineering school and research university founded in 1972, located in Compiègne. It combines the structure of a university with a Grande École, offering specialized, interdisciplinary programs in engineering, technology, and biotechnology, often blending French and North American educational styles." .
SCR:028019 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5788" ;
rdfs:label "Cancer Research UK Cambridge Institute Microscopy Core Facility" ;
definition: "Core provides expertise, training and instrumentation for a range of advanced light microscopy techniques across scales and for a variety of samples. We offer wide-field, confocal, high-content, light sheet and multi-photon imaging systems for cell and tissue studies." .
SCR:028020 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5789" ;
rdfs:label "Berlin Center for Advanced Neuroimaging Core Facility" ;
NIFRID:synonym "Berlin Center for Advanced Neuroimaging (BCAN)" ;
definition: "Joint facility of the Charité - Universitätsmedizin Berlin and the Humboldt Universität zu Berlin. Research dedicated neuroimaging facility with two state of the art Siemens 128-channel 3 Tesla MRI systems equipped for cognitive, neurological and psychiatric experiments." .
SCR:028021 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5790" ;
rdfs:label "University of Montreal CRCHUM Metabolomics Core Facility" ;
NIFRID:synonym "CRCHUM Metabolomics Core" ;
definition: "Core facility specializes in the analysis of key metabolites for metabolic diseases. Develops and performs targeted methods for quantifying water-soluble and lipid metabolites." .
SCR:028022 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "METAFlux" ;
definition: "Software tool that predicts cancer metabolic fluxes from bulk RNA-seq and scRNA-seq data to address these analytic gaps. Used for characterizing metabolic circuits and output non-degenerative fluxes using cancer gene expression data." .
SCR:028023 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xPONENT" ;
NIFRID:synonym "xPONENT for Luminex FlexMap 3D system" ;
definition: "Software essential for running the FLEXMAP 3D w/xPONENT 4.3 platform. Used to control instrument operations, manage data acquisition, and perform analysis for high-throughput multiplex assays. It enables automated maintenance, 96/384-well plate compatibility, and, in many cases, diagnostic, IVD, or research-use-only testing. Intended to measure and sort multiple signals generated in an in vitro diagnostic assay from a clinical sample." .
SCR:028024 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Luminex_200" ;
rdfs:label "Thermo Fisher | Luminex 200 Instrument System" ;
NIFRID:synonym "Luminex 200 Flow Cytometry System" ;
definition: "Luminex 200 Instrument System is a high-throughput, flow cytometry-based, multiplexing analyzer designed for labs to simultaneously detect and quantify up to 100 different proteins or nucleic acids (analytes) from a single, small-volume biological sample. It is primarily used for research (RUO), including biomarker studies, drug discovery, and immunology." .
SCR:028025 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MKL Julia" ;
NIFRID:synonym "MKL.jl" ;
definition: "Software package that allows users to use the Intel MKL library for Julia's underlying BLAS and LAPACK, instead of OpenBLAS, which Julia ships with by default. Julia interface to Intel Math Kernel Library for accelerated linear algebra." .
SCR:028026 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SeekGene | SeekOne Digital Droplet System" ;
NIFRID:synonym "SeekOne DD",
"SeekOne Digital Droplet (SeekOne DD) System" ;
definition: "Automated instrument for single cell partitioning, capture, and labeling based on principle of microfluidics. In addition to general sample types, the DD system is particularly suitable for highly fragile cells, such as brain tissue, retinal tissue, and all tissues from aged individuals." .
SCR:028027 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "SeekGene" ;
definition: "Chinese biotechnology company based in Beijing that designs and manufactures single cell sequencing technology used in scientific research. Company specializing in high-throughput single-cell multi-omics technology, providing tools, kits, and platforms for single-cell DNA methylation, RNA sequencing, and immune repertoire profiling. Founded in 2018, it offers the SeekOne™ Digital Droplet System." .
SCR:028028 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SeekGene | SeekMate Tinitan Fluorescence Cell Counter" ;
NIFRID:synonym "SeekMate Tinitan Fluorescence Cell Counter" ;
definition: "Fluorescence cell analyzer designed for cell counting and viability detection. It can analyze up to 6 samples per run and supports both bright-field and fluorescence counting modes." .
SCR:028029 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BiOptic_Qsep400" ;
rdfs:label "BiOptic | Qsep400 Bio-Fragment Analyzer" ;
definition: "BiOptic Qsep400 is high-throughput, 4-channel automated capillary gel electrophoresis system designed for fast, accurate size and concentration analysis of DNA, RNA, and protein samples. It acts as a rapid quality control tool for NGS libraries, PCR fragments, and antibody purity in high-volume research and clinical labs." .
SCR:028030 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OpenCloning" ;
definition: "Web application to plan and document cloning and genome engineering. Open source and open access tool, FAIR data principles compatible, designed to simulate and/or document genetic manipulation processes used in every day synthetic biology and molecular biology." .
SCR:028031 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mammalian Adipose Tissue Knowledge Portal" ;
NIFRID:abbrev "MATKP" ;
definition: "Open community portal for multi-species mammalian adipose biology. Aggregates data for adipose tissues and cell types, genes active within them, and their relationship to human phenotypes. Plans to offer reproducible analysis pipelines, wet lab and computational protocols, datasets, analyses, and visualizations for epigenomic, transcriptomic, proteomic, metabolomic, and imaging data. Designed to aggregate and harmonize multi-species (human and mouse) transcriptomic, genetic, and epigenomic data. Enables to explore adipose biology, cell-type-specific gene expression, and metabolic disease mechanisms through interactive tools like Single Cell Browsers." .
SCR:028033 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pydna" ;
NIFRID:synonym "Pydna" ;
definition: "Software simulation and documentation package for DNA assembly strategies using Python." .
SCR:028034 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AlphaFold3" ;
definition: "Software package provides implementation of the inference pipeline of AlphaFold 3." .
SCR:028035 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Pharmaron" ;
definition: "Contract Research, Development, and Manufacturing Organization (CRDMO) supporting the life sciences industry. Founded in 2004, it provides comprehensive services for small molecules, biologics, and cell and gene therapies (CGT) from discovery to commercialization. Offers integrated R&D, laboratory services, and manufacturing." .
SCR:028036 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Closed-Loop Somatosensory Stimulation " ;
definition: "Code to support closed-loop control of cutaneous optical stimulation in freely behaving mice, enabling controlled somatosensory input during movement in naturalistic settings." .
SCR:028037 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5793" ;
rdfs:label "Rush University Imaging Research Core Facility" ;
NIFRID:synonym "Rush Imaging Research Core",
"Rush Imaging Research Core (RIRC)" ;
definition: "Core that provides magnetic resonance imaging (MRI) services and image analysis. Facility contains 3 Tesla Siemens Prisma MRI scanner, variety of head and body receive coils (including 64-channel head coil), and extensive list of pulse sequences and packages providing advanced, accelerated whole-body imaging capabilities. Houses Nordic Neuro Lab hardware and software for functional MRI stimulus delivery, collecting subject feedback, and eye tracking." .
SCR:028038 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.262743.6; ISNI 0000 0001 0705 8297 ; Crossref Funder ID 100008616; Wikidata Q750639" ;
rdfs:label "Rush University; Chicago; USA" ;
definition: "Private university in Chicago, Illinois, United States. Founded in 1972, it is the academic arm of Rush University Medical Center." .
SCR:028039 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5724" ;
rdfs:label "University of Toronto Centre for Analysis of Genome Evolution and Function CAGEF Core Facility" ;
NIFRID:synonym "University of Toronto UofT - Centre for the Analysis of Genome Evolution and Function",
"UofT - Centre for the Analysis of Genome Evolution and Function" ;
definition: "Provides genomics, proteomics, and bioinformatic services, including next-generation-based genome, microbiome and metagenome sequencing, gene expression and transcriptome analysis, and proteome analysis. CAGEF has established internationally-recognized genomics expertise in the analysis of non-standard species, systems, and environments, with particular experience in microbial, plant, and environmental genomics and metagenomics." .
SCR:028040 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DropSift" ;
definition: "Software package as nucleus caller for single-nucleus RNA sequencing data. Distinguishes between nuclei and empty droplets by combining summary metrics of cell barcodes—such as total UMI counts, fraction of intronic reads, and percentage of mitochondrial reads. It also incorporates gene expression to learn signatures characteristic of empty droplets." .
SCR:028041 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bican-mccarroll-manuscript1" ;
definition: "Scripts used to process data for the first McCarroll lab BICAN manuscript" .
SCR:028042 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "GeminiBio" ;
definition: "West Sacramento-based biotechnology company founded in 1985 that specializes in manufacturing cell culture and process liquid solutions for the biotech, cell therapy, and gene therapy industries. They operate cGMP-compliant facilities providing products like human serum, buffers, and media to support drug development from research to commercial production." .
SCR:028043 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Scisco Genetics" ;
definition: "Seattle-based biotechnology company founded in 2006 that provides high-resolution, Next Generation Sequencing (NGS)-based genotyping services and kits for complex immune regions. They specialize in HLA, KIR, MIC A/B, and Fc receptor typing to support transplant programs, disease research, and clinical laboratories." .
SCR:028044 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Greiner Bio-One " ;
definition: "Global medical technology company specializing in high-quality plastic laboratory products for diagnostics, biotechnology, and pharmaceutical industries. With over 60 years of experience, they produce VACUETTE® blood collection systems, CELLSTAR® cell culture products, and specialized labware for sample storage." .
SCR:028045 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University Health Network Princess Margaret Cancer Centre Leukemia Tissue Bank" ;
definition: "Non-profit, specialized repository in Toronto that collects, stores, and distributes high-quality biospecimens—such as blood and bone marrow—from patients with hematologic malignancies. It supports worldwide research on leukemia and blood disorders to improve diagnosis and treatment." .
SCR:028046 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5795" ;
rdfs:label "University Health Network Princess Margaret Cancer Centre Integrative Immune Analysis Core Facility" ;
NIFRID:synonym "Princess Margaret Cancer Centre Centre for Integrative Immune Analysis" ;
definition: "Core provides specialized, high-dimensional immune profiling for clinical and translational studies. It enables researchers to analyze immune responses using advanced flow cytometry, CyTOF, genomics, and cytokine analysis, helping to improve cancer treatments and patient outcomes." .
SCR:028047 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5796" ;
rdfs:label "University of Michigan Medical School National Center of Rabbit Models for Translational Research Core Facility" ;
NIFRID:synonym "National Center of Rabbit Models for Translational Research" ;
definition: "Core dedicated to developing, characterizing, and distributing gene-edited rabbit models for biomedical studies. Team specializes in rabbit embryology, molecular biology, and animal reproduction, including developing Rabbit Gene Editing Technology (RbGET) workshops. Provides services including generating novel, customized gene-edited models (knockout/knock-in), and conducting preclinical, proof-of-concept studies to support drug development." .
SCR:028048 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5797" ;
rdfs:label "Paris Brain Institute Cellular Engineering and Vectorology ICV Core Facility" ;
NIFRID:synonym "Cellular Engineering and Vectorology Platform - Cell Culture and Cytometry",
"Plateforme Ingénierie Cellulaire et Vectorologie - Culture Cellulaire et Cytométrie" ;
definition: """Core facility provides infrastructure and services to academic researchers, biotech companies and industry partners that need vectors or cell culture models for their studies.
Focuses on generating cell models, genetic modification, viral vector development, and advanced flow cytometry analysis.""" .
SCR:028049 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Java Maths" ;
definition: "Open-source, lightweight Java library providing comprehensive set of self-contained mathematics and statistics components. It fills gaps in the Java standard library, offering tools for numerical analysis, linear algebra, probability distributions, statistics, and optimization, following best practices for software development." .
SCR:028050 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "AqNWB" ;
definition: "Software C++ API for acquiring neurophysiological data directly into the NWB (Neurodata Without Borders) format. Our goal is to provide a lightweight API to integrate with existing acquisition systems." .
SCR:028051 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pathway Subtyping Framework" ;
definition: "Software disease-agnostic Python framework for discovering molecular subtypes using pathway-level analysis and Gaussian mixture model clustering with built-in validation gates." .
SCR:028052 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5799" ;
rdfs:label "Michigan State University Mass Spectrometry and Metabolomics Core Facility" ;
NIFRID:synonym "Michigan State University Mass Spectrometry and Metabolomics Core",
"MSU Mass Spectrometry and Metabolomics Core" ;
definition: "Open-access research facility that provides advanced analytical services and hands-on training in high-resolution LC–MS/MS, GC–MS, MALDI imaging, and targeted quantitative metabolomics services supporting biomedical, agricultural, and environmental research." .
SCR:028054 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5801" ;
rdfs:label "Charité Berlin University of Medicine Central Radionuclide Laboratory Core Facility" ;
NIFRID:synonym "Charité Central Radionuclide Laboratory",
"Charité Central Radionuclide Laboratory Core Facility",
"Zentrales Radionukli Labor (ZRNL)" ;
definition: "Specialized, centralized facility that handles, manages, or researches radioactive isotopes for medical or scientific purposes. provides support for handling radionuclides, acquiring, disposing of radioactive substances, laboratory decontamination, activity measurements, and radiation safety advice." .
SCR:028055 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CivicDb" ;
NIFRID:synonym "CIViCdb",
"Clinical Interpretation of Variants in Cancer" ;
definition: "Open-access, community-driven knowledgebase designed to crowdsource and curate evidence on the clinical significance of cancer-related genomic variants. It helps researchers and clinicians interpret tumor DNA mutations to guide precision medicine." .
SCR:028056 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HistoAtlas" ;
definition: "Pan-cancer morphology atlas linking histological features to molecular and clinical outcomes. Structured way to explore cancer morphology at scale and connect tissue organization with patient outcomes and molecular signatures, enabling translational researchers to systematically discover and evaluate pathology-based biomarkers." .
SCR:028057 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "singscore" ;
definition: "Software R package which implements simple single-sample gene signature scoring method that uses rank-based statistics to analyze sample's gene expression profile. Scores expression activities of gene sets at single-sample level. Single sample scoring of molecular phenotypes." .
SCR:028058 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5806" ;
rdfs:label "Georgia Institute of Technology AI Makerspace Core Facility" ;
NIFRID:synonym "Georgia Tech AI Makerspace",
"Georgia Tech AI Makerspace Core Facility" ;
definition: "Advanced computing cluster for student learning and exploration in machine learning. Provides over 300 NVIDIA GPUs for students to learn machine learning skills and develop projects. Part of the Partnership for an Advanced Computing Environment facility. Student-focused supercomputing hub created in partnership with NVIDIA to provide hands-on experience with advanced AI tools. Empowers students to develop, train, and deploy AI models, fostering innovation in engineering, AR/VR, and other fields while preparing them for industry roles." .
SCR:028059 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5807" ;
rdfs:label "University of Manchester BioAutomation and Biofoundry Core Facility" ;
definition: "Facility accelerates synthetic biology research by automating design-build-test-learn (DBTL) cycles. It enables high-throughput, reproducible strain engineering, metabolic engineering, and protein production, serving academic and industrial partners. Lab automation facility supporting Engineering biology/Synthetic biology pipelines i.e. Directed evolution of proteins and DNA pathway assembly." .
SCR:028060 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5802" ;
rdfs:label "University of Louisville Computing and Research Advanced Computing Core Facility" ;
NIFRID:synonym "University of Louisville Advanced Computing Core",
"University of Louisville Computing and Research" ;
definition: "Core to extend the scope of the resources and services provided by the Research Computing team to enable cutting-edge research at UofL and beyond. Provides high-performance computing (HPC) services, including the \"Zurada\" system, to accelerate research, AI development, data analysis, and complex simulations for researchers across the university. It supports data-intensive workflows with specialized NVIDIA GPUs and high-speed storage." .
SCR:028061 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "quantreg" ;
definition: "Software R package for conducting quantile regression analysis, which estimates relationship between variables across various points (quantiles) in distribution, rather than just average. Used to analyze non-normal data, handle outliers, and model extreme outcomes, such as 90th percentile. Used for conditional quantile functions: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also now included." .
SCR:028062 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5813" ;
rdfs:label "Cancer Research UK Cambridge Institute Research Instrumentation and Cell Services Core Facility" ;
definition: "Core houses range of high-end equipment, specialised cell services and technical expertise required for day-to-day experiments. Provides access to equipment and specialised cell services. Offers technical and scientific support and training for equipment, cell and tissue culture. Provides access, tracking and storage of cell lines and routine cell culture quality control testing (mycoplasma/sterility testing and cell line authentication)." .
SCR:028063 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.266820.8; ISNI 0000 0004 0402 6152; Crossref Funder ID 100009368; Wikidata Q1112515;" ;
rdfs:label "University of New Brunswick; Canada" ;
definition: "Public research university with two primary campuses in Fredericton and Saint John, New Brunswick. University founded in 1785, holding the title of Canada's oldest English-language university ranked as the top university in Atlantic Canada and a leader in engineering, computer science, and entrepreneurship." .
SCR:028064 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5814" ;
rdfs:label "University of New Brunswick Microscopy and Microanalysis Core Facility" ;
NIFRID:synonym "UNB Microscopy and Microanalysis Facility" ;
definition: "Provides high-resolution imaging and elemental analysis services. Supports diverse studies through electron microscopy, X-ray micro CT, and confocal microscopy, focusing on material science and biological research." .
SCR:028065 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Brain Variation Project" ;
NIFRID:synonym "Human Brain Variation Project (McCarroll",
"Macosko)" ;
definition: "Project provides data currently generated with support from the NIH Brain Initiative Cell Atlas Network (BICAN). Broad Institute collaboration supported by the NIH BRAIN Initiative, to create comprehensive atlas of cellular variation in the healthy human brain. It maps data from millions of cells across diverse individuals to understand how brain biology differs, helping researchers distinguish healthy variation from disease states." .
SCR:028066 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5815" ;
rdfs:label "Paris Brain Institute Vectorology Core Facility" ;
definition: "Vectorology Core Facility (part of the Cellular Engineering and Vectorology platform) provides specialized, high-level expertise, tools, and services for designing, producing, and validating viral vectors used in neuroscience research and gene therapy development. It supports academic and industrial partners by generating modified, safe viral vectors (e.g., AAV, lentivirus) for gene transfer and cellular, including human iPS, engineering." .
SCR:028067 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5816" ;
rdfs:label "University of Oklahoma Protein Production and Characterization Core Facility" ;
definition: "Offers access to instrumentation, training, and services for protein expression, purification, and biophysical characterization. In addition to instrument access, PPCC personnel offer advice, hands-on training, education, and collaboration. Provides a range of protein purification and characterization equipment." .
SCR:028068 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5817" ;
rdfs:label "University of Pittsburgh Rangos Animal Imaging Core Facility" ;
NIFRID:synonym "Animal Imaging Core (AIC)" ;
definition: "Core provides multi-modal imaging services for academic investigators, national collaborators, and industrial partners.It facilitates longitudinal studies in animal models using MRI, PET, CT, and ultrasound, offering services such as image acquisition, analysis, and consultations for research, therapy assessment, and disease progression tracking." .
SCR:028069 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5810" ;
rdfs:label "Washington University in St. Louis Washington University Center for Cellular Imaging Core Facility" ;
NIFRID:synonym "Washington University Center for Cellular Imaging (WUCCI)" ;
definition: "Core offers access to advanced imaging technologies, expert consultation, training, and collaborative partnerships across the School of Medicine and Washington University research community. Provides access to light and electron microscopy platforms, guidance in experimental design, sample preparation, data acquisition, quantitative image analysis, expertise, and training to enable investigators to explore cellular and tissue architecture across scales." .
SCR:028070 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CNprep" ;
definition: "Software R package for DNA copy number data evaluation using both their initial form (copy number as a noisy function of genomic position) and their approximation by a piecewise-constant function (segmentation), for the purpose of identifying genomic regions where the copy number differs from the norm. Pre-Process DNA Copy Number (CN) Data for Detection of CN Events." .
SCR:028071 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Discover Echo Inc" ;
definition: "San Diego biotechnology company that focuses on creating user-friendly, high-resolution imaging solutions for life science research, including confocal, fluorescence, and brightfield microscopy. Specializes in developing hybrid, digital microscopes that revolutionize life science research by replacing traditional eyepieces with high-resolution iPad displays. Their microscopes, such as the Revolve and Rebel, combine upright and inverted configurations, offering versatility for fluorescence, brightfield, and tissue culture imaging." .
SCR:028072 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Pittsburgh Federal Statistical Research Data Center" ;
definition: "Research facility jointly operated by the University of Pittsburgh and Carnegie Mellon University in partnership with the U.S. Census Bureau. It provides qualified researchers with access to restricted-use microdata from federal statistical agencies in a highly controlled environment, ensuring strict confidentiality through dedicated workstations without internet or external device access. By enabling analysis of detailed federal data, the center supports advanced research in fields such as economics, public health, business, social policy, political science, and demography, allowing investigators to address questions that cannot be answered with public datasets." .
SCR:028073 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5820" ;
rdfs:label "University of Pittsburgh Hillman Cancer Center Translational Pathology Imaging Laboratory Core Facility" ;
NIFRID:synonym "UPMC Hillman Cancer Center Translational Pathology Imaging Laboratory (TPIL)" ;
definition: "Facility permits interrogation of protein biomarkers in tissue through next-generation, quantitative histopathologic technologies. Utilizes Akoya Bioscience’s PhenoImager platform which includes multiplex IF reagent kits, multispectral imaging on the PhenoImager HT, and image analysis with inForm software." .
SCR:028074 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5821" ;
rdfs:label "University of Oklahoma Biomolecular Structure Core Facility" ;
definition: "Offers access to instrumentation, training and services for structure determination of macromolecular molecules using single crystal X-ray diffraction and/or cryo-EM Single Particle Analysis (SPA). Instrumentation is available for initial crystallization trials, optimization of crystallization, single crystal X-ray diffraction and data collection at synchrotron radiation facilities, as well as electron microscopy grid preparation for cryo-EM (SPA), screening and data collection using a Thermo Scientific Tundra Cryo-TEM and assistance for data collection at national laboratories." .
SCR:028075 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Intrinsic Physiology Feature Extractor" ;
NIFRID:synonym "Allen Intrinsic Physiology Feature Extractor (IPFX)" ;
NIFRID:abbrev "IPFX" ;
definition: "Software Python package for computing intrinsic cell features from electrophysiology data. Used to compute intrinsic cell features from intracellular electrophysiology data." .
SCR:028076 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OME-Zarr" ;
definition: "OME-Zarr is the emerging community standard image file format for cloud (S3 object store) compatible image data storage. Thus it is important to know how to access S3 hosted OME-Zarr in various image analysis and visualisation platforms." .
SCR:028077 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Developing Human Brain Atlas version 2 (DHBAv2)" ;
NIFRID:abbrev "DHBAv2" ;
definition: "Three-dimensional (3D) common coordinate framework (CCF) and reference atlas that defines the spatial organization of cortical and subcortical structures in the adult human brain. This atlas modifies and expands the Allen Human Reference atlas (2020). This atlas parcellates the MNI152 ICBM2009b symmetric template, an averaged template from 152 young adult brains (mean age: 25.02 years, range: 18-44 years, 86 male, 66 female). The template has been sampled to 500 um3 voxel resolution and symmetrized along the right-left axis. This atlas includes annotations for all subcortical and cortical structures using a unified ontology developed for cross-species comparisons, the Harmonized Ontology of the Mammalian Brain Anatomy (HOMBA)." .
SCR:028078 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5811" ;
rdfs:label "Cornell University NMR Core Facility" ;
NIFRID:synonym "Cornell University NMR Facility" ;
definition: "Facility provides access to nuclear magnetic resonance spectroscopy for all. Houses spectrometers ranging in field strength from 400 to 600 MHz, including two 500 MHz Brukers equipped with nitrogen-cooled Prodigy CryoProbes. New users may operate a particular spectrometer independently once they complete the required training and demonstrate the knowledge required for operating each instrument." .
SCR:028079 a owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5812" ;
rdfs:label "Cornell University Chemistry MS Core Facility" ;
NIFRID:synonym "Cornell University Chemistry MS Facility" ;
definition: "Core specializes in the analysis of small organic and organometallic analytes. Provides access to mass spectrometers for all." .
SCR:028104 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Edges" ;
definition: "Software tool to find combinations of objects within categories. Can be utilized in bioinformatic analyses to transform two-mode target-pathway relationships to one-mode target-target relationships to generate combination of target genes within related pathways." .
SCR:028105 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BRCA Exchange Knowledgebase for Clinical Cancer Genetics" ;
NIFRID:synonym "BRCA Exchange" ;
definition: "Web application to search data on BRCA1/2 genetic variants and corresponding clinical data from around the world. Used to search for BRCA1 or BRCA2 variants." .
SCR:028106 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BoneBase" ;
NIFRID:synonym "UConn Health's BoneBase" ;
definition: "Bioinformatics knowledge base and datacenter focusing on skeletal phenotypes. Provides searchable bone phenotyping data for knockout mouse lines, interactive histomorphometry plots, and raw data, supporting research into skeletal genetics, disease mechanisms, and personalized skeletal health treatments." .
SCR:028107 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OAI Knowledge base" ;
NIFRID:synonym "Osteoarthritis Initiative Knowledge base" ;
definition: "Centralized, annotated repository for the Osteoarthritis Initiative (OAI) study, designed to accelerate research by organizing and linking extensive clinical, imaging (MRI/X-ray), and biomarker data. It aims to help researchers analyze knee osteoarthritis prevention, treatment, and progression." .
SCR:028108 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GEO SPACE" ;
definition: "NIEHS funded biomedical knowledgebase to provide a curated collection of geospatial datasets and associated information. It enables, data discoverability, data harmonization and data re-uses of GeoSpatial datasets in the USA. GeoSpace has three core modules." .
SCR:028109 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HIV Pharmacology" ;
NIFRID:synonym "HIV Pharmacology Data Repository (PDR)" ;
definition: "Web-based resource for preserving and sharing pharmacokinetic data generated through preclinical and clinical HIV research." .
SCR:028110 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Scooby" ;
definition: "Software aplication to predict scRNA-seq coverage and scATAC-seq insertion profiles along the genome at single-cell resolution. It leverages the pre-trained multi-omics profile predictor Borzoi as a foundation model, equips it with a cell-specific decoder, and fine-tunes its sequence embeddings." .
SCR:028112 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5823" ;
rdfs:label "George Washington University McCormick Bioinformatics Core Facility" ;
NIFRID:synonym "McCormick Bioinformatics Core (MBC)" ;
definition: "Core provides advanced computational analysis and consultation for high-throughput genomics and multi-omics research. Supports investigators across GW and external collaborators with experimental design, data processing, statistical analysis, and biological interpretation of next-generation sequencing datasets. Offers expertise in bulk and single-cell transcriptomics, epigenomics, variant analysis, and integrative multi-omics approaches. Develops and maintains reproducible computational pipelines and collaborates closely with researchers to translate complex genomic data into actionable biological insights." .
SCR:028113 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoWGS " ;
definition: "Nextflow pipeline to process whole genome long-read sequencing data generated in the context of ASAP project." .
SCR:028114 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5824" ;
rdfs:label "Yale University Wu Tsai Institute Microscopy Shared Core Facility" ;
NIFRID:synonym "Wu Tsai Institute Microscopy Shared Facility" ;
definition: "Provides optical microscopy tools to advance research in human cognition. Offers both commercial turnkey microscopes and in-house developments based on emerging techniques." .
SCR:028115 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bonito" ;
definition: "Software application as open source research basecaller for Oxford Nanopore reads." .
SCR:028116 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Rwanda African Center of Excellence in Data Science Core Facility" ;
NIFRID:synonym "African Center of Excellence in Data Science (ACE-DS)",
"African Centre of Excellence in Data Science (ACE-DS)",
"University of Rwanda African Center of Excellence in Data Science" ;
NIFRID:abbrev "ACE-DS" ;
definition: "Core mission is to train post-graduate students with combined expertise in statistics, economics, business, computer science, and engineering to use big data and data analytics to solve development challenges.ACE-DS has established a high-performance computing cluster comprising of one master node and four data nodes, all of which are equipped with NVIDIA GPUs for graphic acceleration.Data nodes are equipped with 32*2 cores of Intel(R) Xeon(R) Gold 6226R processors, which provide a total of 640GB of RAM per node, making 10GB/core. Additionally, each of the data nodes has 50TB of storage, all of which is GPU-enabled.For moderate workloads, there are workstations available that feature an i9 processor, 64GB of RAM, and 10TB of storage.Provides desktop computers that users can utilize for their data science and artificial intelligence work." .
SCR:028117 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Sokoine University of Agriculture Southern African Centre for Infectious Disease Surveillance Core Facility" ;
NIFRID:synonym "SACIDS Foundation for One Health",
"Southern African Center for Infectious Disease Surveillance (SACIDS)",
"Southern African Centre for Infectious Disease Surveillance (SACIDS)" ;
NIFRID:abbrev "SACIDS" ;
definition: "One Health virtual research and training core to strengthen Africa's capacity to detect, identify, and monitor infectious diseases in humans and animals, serving the East and Southern African region." .
SCR:028118 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mzuzu University African Centre of Excellence in Neglected and Underutilised Biodiversity Core Facility" ;
NIFRID:synonym "African Center of Excellence in Neglected and Underutilised Biodiversity",
"African Center of Excellence in Neglected and Underutilised Biodiversity (ACENUB)",
"African Centre of Excellence in Neglected and Underutilised Biodiversity",
"African Centre of Excellence in Neglected and Underutilised Biodiversity (ACENUB)" ;
NIFRID:abbrev "ACENUB" ;
definition: "Research and training hub to enhance food security and nutrition in Africa.Offers postgraduate training, conducting research on nutrient-dense crops, promoting indigenous knowledge, and strengthening partnerships with agricultural industries. Focuses on exploiting neglected, indigenous, and underutilized biodiversity through sustainable, nutrient-dense cropse, value addition, and postgraduate training to improve livelihoods." .
SCR:028119 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Haramaya University Africa Center of Excellence for Climate Smart Agriculture and Biodiversity Conservation Core Facility" ;
NIFRID:synonym "Africa Center of Excellence for Climate Smart Agriculture and Biodiversity Conservation (Climate SABC)" ;
NIFRID:abbrev "ACE Climate SABC" ;
definition: "Core to develop climate-smart agricultural practices, enhance biodiversity conservation, and build regional capacity to adapt to climate change.Serves as centralized facility offering specialized laboratory equipment, technologies, and modern teaching aids to support research activities." .
SCR:028120 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nelson Mandela African Institution of Science and Technology Africa Centre for Research, Agricultural Advancement, Teaching Excellence and Sustainability Core Facility" ;
NIFRID:synonym "Africa Centre for Research",
"African Center for Research Agricultural Advancement",
"Agricultural Advancement",
"Teaching Excellence and Sustainability (CREATES)" ;
NIFRID:abbrev "CREATES" ;
definition: "Serves as a regional hub for developing sustainable agricultural solutions, bio-nanoscience, and climate resilience technologies in East and Southern Africa.Includes bio-repository for research and data repository to predict risks from climate variability. Works with partners such as the UNESCO National Commission in Tanzania and Ifakara Health Institute (IHI) to support malaria medicine discovery and regional nano-hubs." .
SCR:028121 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lilongwe University of Agriculture and Natural Resources Africa Center of Excellence in Aquaculture and Fisheries Science Core Facility" ;
NIFRID:synonym "Africa Center of Excellence in Aquaculture and Fisheries Science (AQUAFISH)" ;
NIFRID:abbrev "AQUAFISH" ;
definition: "World Bank-funded initiative established to strengthen the aquaculture and fisheries sector in Eastern and Southern Africa.Services are focusing on fish breeding, biotechnology, feeds (like black soldier fly), and integrated fish-animal-crop systems to boost production." .
SCR:028122 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Eduardo Mondlane University Regional Center of Excellence in Engineering and Petroleum and Gas Technology Studies Core Facility" ;
NIFRID:synonym "African Centers of Excellence Regional Center of Excellence in Engineering and Petroleum and Gas Technology Studies",
"Regional Center of Excellence in Engineering and Petroleum and Gas Technology Studies (CS-OGET)" ;
NIFRID:abbrev "CS-OGET" ;
definition: "Regional hub for research, specialized training, and consultancy in petroleum engineering, downstream hydrocarbons processing, and environmental management. As a key provider of technical expertise for the region, it drives innovation through MSc and PhD programs, professional training, and industrial research." .
SCR:028123 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Rwanda African Center of Excellence in Energy for Sustainable Development Core Facility" ;
NIFRID:synonym "African Center of Excellence in Energy for Sustainable Development",
"University of Rwanda African Center of Excellence in Energy for Sustainable Development (ACE-ESD)" ;
NIFRID:abbrev "ACE-ESD" ;
definition: "World Bank-funded hub at the College of Science and Technology in Kigali.Provides interdisciplinary research and training in smart electrification, rural energy access, and sustainable energy management.Acts as a research hub for grid innovation and incubation, supported by international partnerships, including Italian research centers.Provides specialized training for experts in public, private, and academic institutions on topics like microgrid and smartgrid design." .
SCR:028124 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Nelson Mandela African Institution of Science and Technology African Centre of Excellence Water Infrastructure and Sustainable Energy Futures Core Facility" ;
NIFRID:synonym "Water Infrastructure and Sustainable Energy Futures",
"Water Infrastructure and Sustainable Energy Futures (WISE Futures)" ;
NIFRID:abbrev "WISE Futures" ;
definition: "Specialized research and training hub aimed at improving water resources, sanitation, and sustainable energy security across East and Southern Africa. Provides technical support, laboratory services (like Material Characterization), and consultancy to address regional development challenges." .
SCR:028125 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Addis Ababa University Center for Innovative Drug Development and Therapeutic Trials for Africa Core Facility" ;
NIFRID:synonym "Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa)" ;
NIFRID:abbrev "CDT-Africa" ;
definition: "World Bank-supported regional center of excellence focused on building capacity for clinical trials, and developing novel vaccines, diagnostics, and therapeutics. Provides training in clinical trials and translational medicine, to foster homegrown health solutions.Training researchers, scientists, and clinical trial staff across Africa in trial management, data management, and scientific writing." .
SCR:028126 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Rwanda African Center of Excellence in Internet of Things Core Facility" ;
NIFRID:synonym "African Center of Excellence in Internet of Things",
"African Center of Excellence in Internet of Things (ACEIoT)" ;
NIFRID:abbrev "ACEIoT" ;
definition: "Specialized hub funded by the World Bank to train high-level African professionals and researchers in IoT, while fostering innovation in fields like health, agriculture, and energy. It provides advanced laboratory equipment for master's/PhD programs, research, and technical incubation to create sustainable, low-cost technological solutions for the region. Enables practical experiments, product design, and collaboration with local/international partners." .
SCR:028127 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Uganda Martyrs University African Centre of Excellence in Agro-ecology and Livelihood Systems Core Facility" ;
NIFRID:synonym "African Center of Excellence in Agro-ecology and Livelihood Systems (ACALISE)",
"African Centre of Excellence in Agro-ecology and Livelihood Systems (ACALISE)" ;
NIFRID:abbrev "ACALISE" ;
definition: "Provides infrastructure for training, research, and innovation to enhance agricultural productivity in East/Southern Africa. Key facilities include soil lab, feed mill, agricultural mechanization units, radio station for knowledge dissemination, and specialized training/hosting spaces for students and farmers." .
SCR:028128 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Rwanda African Centre of Excellence for Innovative Teaching and Learning Mathematics Science Core Facility" ;
NIFRID:synonym "African Center of Excellence for Innovative Teaching and Learning Mathematics Science (ACEITLMS)",
"African Centre of Excellence for Innovative Teaching and Learning Mathematics Science (ACEITLMS)" ;
NIFRID:abbrev "ACEITLMS" ;
definition: "Center runs three activities namely bringing innovation into teaching and learning, research and training, and community engagement." .
SCR:028129 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Mbarara University of Science and Technology Africa Centre of Excellence Pharm-Bio Technology and Traditional Medicine Core Facility" ;
NIFRID:synonym "Mbarara University of Science and Technology Africa Centre of Excellence Pharm-Bio Technology and Traditional Medicine Centre (PHARMBIOTRAC)",
"Mbarara University of Science and Technology African Center of Excellence Pharm-Bio Technology and Traditional Medicine Center (PHARMBIOTRAC)",
"Pharm-Bio Technology and Traditional Medicine Center (PHARMBIOTRAC)",
"Pharm-Bio Technology and Traditional Medicine Centre (PHARMBIOTRAC)" ;
NIFRID:abbrev "PHARMBIOTRAC" ;
definition: "Core to advance, validate, and standardize traditional medicine and biopharmaceuticals in Africa. It serves as a regional platform for training, research, and innovation to improve health outcomes and reduce reliance on imported medicines." .
SCR:028130 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "University of Zambia Africa Centre of Excellence for Infectious Diseases of Humans and Animals Core Facility" ;
NIFRID:synonym "Africa Centre of Excellence for Infectious Diseases of Humans and Animals (ACEIDHA)",
"African Center of Excellence for Infectious Diseases of Humans and Animals (ACEIDHA)" ;
NIFRID:abbrev "ACEIDHA" ;
definition: "World Bank-funded Training and Research Centre for generating knowledge and skills for infectious disease prevention and control." .
SCR:028131 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Copperbelt University African Centre of Excellence for Sustainable Mining Core Facility" ;
NIFRID:synonym "African Center of Excellence for Sustainable Mining (CBU ACESM)",
"African Centre of Excellence for Sustainable Mining (CBU ACESM)" ;
NIFRID:abbrev "ACESM" ;
definition: "World Bank-funded hub focused on advancing sustainable mining practices in Zambia and Africa through research, education, and training in five core areas: occupational health, environmental restoration, energy/mining design, biodiversity, and community livelihoods. Provides training for postgraduate students and professionals in mining, metallurgy, environmental engineering, and biotechnology." .
SCR:028132 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Addis Ababa University Africa Center of Excellence for Water Management Core Facility" ;
NIFRID:synonym "Africa Center of Excellence for Water Management",
"Africa Center of Excellence for Water Management (ACEWM)" ;
NIFRID:abbrev "ACEWM" ;
definition: "Provides technical, on-the-job training to build expertise in water management. Provides research, and training in water science, policy, and management to foster sustainable, community-driven water solutions across Eastern and Southern Africa." .
SCR:028133 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Egerton University Africa Centre of Excellence in Sustainable Agriculture and Agribusiness Management Core Facility" ;
NIFRID:synonym "Africa Centre of Excellence in Sustainable Agriculture and Agribusiness Management (CESAAM)",
"African Center of Excellence in Sustainable Agriculture and Agribusiness Management (CESAAM)" ;
NIFRID:abbrev "CESAAM" ;
definition: "World Bank-funded hub aimed at improving food security in Africa through high-quality training, research, and technology transfer in sustainable agriculture and agribusiness. It enhances research capacity for postgraduate students and staff, offering specialized laboratories and supporting agribusiness innovations. Provides equipped specialized research laboratories and improved post-graduate study rooms." .
SCR:028134 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Makerere University African Regional Centre of Excellence for Crop Improvement Core Facility" ;
NIFRID:synonym "African Regional Center of Excellence for Crop Improvement (MaRCCI)",
"African Regional Centre of Excellence for Crop Improvement (MaRCCI)",
"Makerere University African Regional Center of Excellence for Crop Improvement",
"Makerere University African Regional Centre of Excellence for Crop Improvement" ;
NIFRID:abbrev "MaRCCI" ;
definition: "Specialized training and research hub designed to strengthen plant breeding and seed systems in Africa.Core facility includes laboratories for seed quality and plant diagnostics, molecular biology/microbial labs, and Bioinformatics Training Facility at the Makerere University Agricultural Research Institute Kabanyolo." .
SCR:028135 a owl:NamedIndividual ;
rdfs:label "University of Malawi Center for Resilient Agri-Food Systems Core Facility" ;
NIFRID:synonym "Center for Resilient Agri-Food Systems (CRAFS)" ;
NIFRID:abbrev "CRAFS" ;
definition: "World Bank-funded center to strengthen agri-food systems through research, postgraduate training, and professional short courses. It fosters innovation in climate-resilient agriculture, food technology, and policy in Malawi and the SADC region.Offers scholarships for regional students, internships for graduates, and specialized training." .
SCR:028136 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Lilongwe University of Agriculture and Natural Resources Centre of Excellence in Transformative Agriculture Commercialisation Core Facility" ;
NIFRID:synonym "Center of Excellence in Transformative Agriculture Commercialisation (TACE)",
"Centre of Excellence in Transformative Agriculture Commercialisation (TACE)" ;
NIFRID:abbrev "TACE" ;
definition: "World Bank-supported aimed at transforming farming into a commercial business through research, postgraduate training, agribusiness incubation, and technical agricultural technologies. Offers mentorship and incubation to help students and youth turn ideas into profitable enterprises.Provides sponsorship for MSc/PhD programs in Irrigation, Food Process Engineering, and Agribusiness Management. Promotes modern techniques, including drone-assisted fertilizer/herbicide spraying, climate-smart farming, and ,ropping to increase productivity." .
SCR:028137 a owl:NamedIndividual ;
rdfs:label "Eduardo Mondlane University Regional Center of Excellence in Agri-food Systems and Nutrition Core Facility" ;
NIFRID:synonym "African Centers of Excellence Regional Center of Excellence in Agri-food Systems and Nutrition",
"Regional Center of Excellence in Agri-food Systems and Nutrition (CE-AFSN)" ;
NIFRID:abbrev "CE-AFSN" ;
definition: "Center transforms African agrifood systems through high-quality research, training, and education. It focuses on improving food security, nutrition, agricultural policy, and climate change resilience, acting as a core hub for Master�s/doctoral scholarships, short courses, and academic exchange visits.Offering training for students and professionals to enhance skills in agricultural policy analysis, risk management, and climate change." .
SCR:028138 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_QuantStudio_6_Pro" ;
rdfs:label "Thermo Fisher: Applied Biosystems | QuantStudio 6 Pro Real Time PCR system" ;
NIFRID:synonym "QuantStudio 6 Pro Real Time PCR system" ;
definition: "qPCR machine designed for rapid, reliable, and automated quantitative PCR (qPCR) in research laboratories. It enables gene expression analysis, SNP genotyping, and pathogen detection using a 96-well or 384-well format. The system features a smart workflow with facial authentication, voice commands, and cloud-based data management." .
SCR:028139 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100017581",
"GRID grid.10818.30",
"ISNI 0000 0004 0620 2260",
"Wikidata Q19888178" ;
rdfs:label "University of Rwanda; Butare; Rwanda" ;
NIFRID:synonym "National University of Rwanda" ;
definition: "National University of Rwanda located in the city of Butare and was established in 1963 by the government in cooperation with the Congregation of the Dominicans from the Province of Quebec, Canada." .
SCR:028140 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.11887.37 ISNI 0000 0000 9428 8105 Crossref Funder ID 501100023918 Wikidata Q4005900" ;
rdfs:label "Sokoine University of Agriculture; Morogoro; Tanzania" ;
definition: "Premier public university in Morogoro, Tanzania, founded in 1984, specializing in agriculture, forestry, veterinary sciences, and natural resources. Located at the foot of the Uluguru Mountains, it ranks among the top universities in Sub-Saharan Africa (27th in 2026), focusing on research-driven development." .
SCR:028141 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.442592.c ISNI 0000 0001 0746 093X Wikidata Q477625" ;
rdfs:label "Mzuzu University; Mzuzu; Malawi" ;
definition: "University established in 1997 in Luwinga, Mzuzu City, is Malawi.Public university and the primary higher education institution in the Northern Region. It offers diverse bachelor, masters, and PhD programs, focusing on education, health sciences, environmental studies, and, notably, science, technology and innovation." .
SCR:028142 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 501100004845",
"GRID grid.192267.9",
"ISNI 0000 0001 0108 7468",
"Wikidata Q5654075" ;
rdfs:label "Haramaya University; Dire Dawa; Ethiopia" ;
definition: "Public research university established in 1954, specializing originally in agriculture. It is one of Ethiopia oldest higher education institutions, offering diverse undergraduate and postgraduate programs across various fields, with a major focus on agricultural research, science, and technology." .
SCR:028143 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.451346.1 ISNI 0000 0004 0468 1595 Crossref Funder ID 501100010483 Wikidata Q15261581" ;
rdfs:label "Nelson Mandela African Institution of Science and Technology; Arusha; Tanzania" ;
definition: "Research-intensive postgraduate institution focused on Science, Engineering, Technology, and Innovation (SETI). It trains next-generation scientists and engineers to foster sustainable development and economic growth in Sub-Saharan Africa." .
SCR:028144 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RavenPro" ;
NIFRID:synonym "Cornell RavenPro" ;
definition: "Software for the acquisition, visualization, measurement, and analysis of sounds. Developed by the Cornell Lab of Ornithology, it is widely used for bioacoustics, allowing researchers to study animal vocalizations and other acoustic signals using spectrograms and waveforms." .
SCR:028145 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.459750.a ISNI 0000 0001 2176 4980 Wikidata Q55616872" ;
rdfs:label "Lilongwe University of Agriculture and Natural Resources; Lilongwe; Malawi" ;
definition: "Public university in Malawi, established in 2011 (operational 2012) through a merger of Bunda College of Agriculture and the Natural Resources College. Based in Lilongwe, it focuses on agricultural sciences, natural resource management, and rural development, offering undergraduate, postgraduate, and online e-campus programs." .
SCR:028146 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.8295.6 ISNI 0000 0001 0943 5818 Wikidata Q890884" ;
rdfs:label "Eduardo Mondlane University; Maputo; Mozambique" ;
definition: "Public university, founded in 1962. It is a comprehensive institution focused on higher education, scientific research, and community extension services to promote innovation and sustainable development. The university offers various faculties, including agriculture, engineering, arts, sciences, and medicine." .
SCR:028147 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.7123.7 ISNI 0000 0001 1250 5688 Crossref Funder ID 501100007941 Wikidata Q1238770" ;
rdfs:label "Addis Ababa University; Addis Ababa; Ethiopia" ;
definition: "Ethiopia's oldest and largest public research university, founded in 1950 and located in the capital, Addis Ababa. It is the premier higher education institution in the country, featuring multiple campuses, extensive postgraduate programs, and ranking high among East African universities. " .
SCR:028148 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Uganda Martyrs University; Kampala; Uganda " ;
definition: "Private Catholic chartered university in Uganda, established in 1993, with its main campus in Nkozi, near the Equator. It offers various degrees across faculties like business, health sciences, and engineering, focusing on ethical values, community engagement, and sustainable development." .
SCR:028149 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.33440.30 ISNI 0000 0001 0232 6272 Crossref Funder ID 501100009915 Wikidata Q514030" ;
rdfs:label "Mbarara University of Science and Technology; Mbarara; Uganda" ;
definition: "Public university in Uganda, established in 1989 in Mbarara to specialize in training health professionals. It is renowned for its focus on science, technology, and community-based education, offering programs in medicine, nursing, laboratory sciences, pharmacy, and computing." .
SCR:028150 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.12984.36 ISNI 0000 0000 8914 5257 Wikidata Q2096836" ;
rdfs:label "University of Zambia; Lusaka; Zambia" ;
definition: "Oldest and largest public university established in 1965 in Lusaka. Operating under the motto "Service and Excellence," it offers over 150 undergraduate and postgraduate programs across 13 schools, with major campuses at Great East Road and Ridgeway. " .
SCR:028151 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Copperbelt University; Kitwe; Zambia" ;
definition: "Public university in Kitwe, Zambia, established in 1987. It is a research-intensive institution focusing on technology, engineering, mining, and business. CBU operates several campuses, including the main Jambo Drive Campus in Riverside, and is known as a top Sub-Saharan African university." .
SCR:028152 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.8301.a ISNI 0000 0001 0431 4443 Crossref Funder ID 501100020278 Wikidata Q3915401" ;
rdfs:label "Egerton University; Nakuru; Kenya" ;
definition: "Public institution of higher learning in Kenya, located in Njoro, 24 km from Nakuru city. Founded in 1939 as a farm school by Lord Maurice Egerton, it specializes in agriculture but offers diverse programs across 10 faculties, including Arts, Law, Commerce, Health Sciences, and Engineering." .
SCR:028153 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.10595.38 ISNI 0000 0001 2113 2211 Wikidata Q671642" ;
rdfs:label "University of Malawi; Zomba; Malawi" ;
definition: "University located in the historic city of Zomba, is the nation's oldest and largest public university, established in 1965. It serves as a major research hub offering diverse bachelor's, master's, and PhD programs, and is recognized for its commitment to high-quality education in southern Malawi." .
SCR:028154 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5825" ;
rdfs:label "Michigan State University Transgenic and Genome Editing Core Facility" ;
NIFRID:synonym "Michigan State University Transgenic and Genome Editing Facility" ;
definition: "Provides comprehensive CRISPR genome editing and transgenic services for animal models and stem cells, with both end-to-end and modular support for model generation. The core also offers full cryopreservation and cryorecovery services, plus rederivation, import/export assistance, genotyping support, and consultation in genome engineering and reproductive biology." .
SCR:028155 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5822" ;
rdfs:label "Indiana University School of Medicine Stark Neurosciences Research Institute Flow Cytometry and Microscopy Core Facility (SNRI-FCMCF)" ;
NIFRID:synonym "Stark Neurosciences Research Institute Flow Cytometry and Microscopy Core Facility (SNRI-FCMCF)" ;
definition: "Core provides access to cost effective instrumentation, software, and scientific consultation. First-come first-serve, fee-for-service core facility with fulltime staff to help users generate rigorous scientific data. Offers two point-scanning confocal microscopes, Nikon A1R and Zeiss LSM900, LSRFortessa X-20 and MACSQuant 10 analytic flow cytometers and 4 laser Sony MA900 cell sorter." .
SCR:028157 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Cancer Research UK Cambridge Institute" ;
NIFRID:synonym "Cambridge Institute",
"Cancer Research UK",
"CRUK Cambridge Institute",
"CRUK CI" ;
definition: "Cancer research institute located on the Cambridge Biomedical Campus, focused on understanding cancer biology to develop new diagnostics and treatments. It brings together multidisciplinary research groups to translate findings into improved patient outcomes. Part of the University of Cambridge, funded by Cancer Research UK." .
SCR:028158 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "RNASeqPower" ;
definition: "Software R package, which is used for calculating sample size and power estimates for RNA-Seq studies." .
SCR:028159 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Biopac | Student Lab system" ;
definition: "Biopac Student Lab system is a flexible, integrated life science teaching solution that includes hardware, software, and curriculum materials. System to conduct basic physiology lab experiments including ECG, EEG, EMG, and EOG. BSL System uses dynamic lessons with students as subjects to increase interest and retention. Students can record data from their own bodies, guided by a detailed lab manual and full color onscreen guide, and analyze the results. Students can then compare data from different experimental conditions with others in their group and with all students in the lab." .
SCR:028160 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "cramino" ;
definition: "Software tool for quick quality assessment of cram and bam files, intended for long read sequencing. Used for for BAM/CRAM quality evaluation, intended for long reads." .
SCR:028161 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EcoTyper" ;
definition: "Software machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data." .
SCR:028162 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "LongPhase" ;
definition: "Ultra-fast chromosome-scale phasing algorithm for small and large variants. Ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms." .
SCR:028163 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Modkit" ;
definition: "Software tool for working with modified bases from Oxford Nanopore. Used for working with modified bases. Used for quickly converting modBAM to bedMethyl files using best practices, but also manipulating modBAM files and generating summary statistics." .
SCR:028164 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "methylartist" ;
definition: "Software tools for parsing and plotting methylation patterns. Used for plotting methylation data in various ways." .
SCR:028165 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "nnU-Net" ;
definition: "Software semantic segmentation method that automatically adapts to given dataset. Self-configuring method for deep learning-based biomedical image segmentation. Used to analyze provided training cases and automatically configure matching U-Net-based segmentation pipeline." .
SCR:028166 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pod5" ;
NIFRID:synonym "POD5",
"pod5-file-format" ;
definition: "File format for storing nanopore DNA data in an easily accessible way. High performance file format for nanopore reads." .
SCR:028167 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "somalier" ;
NIFRID:synonym "Somalier" ;
definition: "Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches." .
SCR:028168 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "dreamlet" ;
definition: "Software R package enables differential expression analysis on multi-sample single cell datasets using linear (mixed) models with precision weights." .
SCR:028169 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "single_cell_toolkit" ;
definition: "Software tools for correcting single cell barcodes for various scATAC-seq techniques and creating fragment files and spltting BAM files per cluster." .
SCR:028170 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pertpy" ;
NIFRID:synonym "Pertpy" ;
definition: "Software end-to-end framework for perturbation analysisis. Ecosystem framework for analyzing large-scale single-cell perturbation experiments." .
SCR:028171 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "tensorQTL" ;
definition: "Software tool designed for mapping Quantitative Trait Loci (QTLs), particularly expression QTLs (eQTLs), by identifying statistical associations between genetic variants (genotypes) and molecular phenotypes (e.g., gene expression levels). Used in large-scale functional genomics projects, such as GTEx, to connect specific genetic variants to phenotypic variation. GPU-enabled QTL mapper, achieving ~200-300 fold faster cis- and trans-QTL mapping compared to CPU-based implementations." .
SCR:028172 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5826" ;
rdfs:label "University of Pittsburgh CRConnect Service Center Core Facility" ;
NIFRID:synonym "University of Pittsburgh CRConnect Service Center" ;
NIFRID:abbrev "CRConnect" ;
definition: "Provides flexible, cost-efficient clinical research coordinator support across disease areas and disciplines at the University of Pittsburgh. Offers full-service or targeted, as needed support. Services include study start up, regulatory assistance, budgeting and contracting, participant recruitment and enrollment, study visit conduct, data and query management, safety oversight, blood draws, and study closeout, as well as coordinating or participating center roles for multi-site trials. CRConnect can deploy highly experienced coordinators for only the services or amount of time required, reducing costs and providing coverage for investigators without full time staffing needs. The team supports a wide range of clinical research across Pitt and UPMC systems, including IND trials (Phase I–IV), multi center studies, IDE trials, interventional and observational studies, and collaborates closely with other Pitt and UPMC shared resources to ensure investigators are directed to the appropriate support." .
SCR:028173 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.270301.7 ISNI 0000 0001 2292 6283 Crossref Funder ID 100019686 Wikidata Q825987" ;
rdfs:label "Whitehead Institute; Cambridge; Massachusetts; United States" ;
NIFRID:synonym "Whitehead Institute for Biomedical Research" ;
definition: "Independent, non-profit research institution closely affiliated with MIT, with many of its members holding faculty positions in the MIT Biology Department. Dedicated to improving human health through basic biomedical research." .
SCR:028174 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5827" ;
rdfs:label "Whitehead Institute WM Keck Light Microscopy Innovation Center Core Facility" ;
NIFRID:synonym "W.M. Keck Microscopy Innovation Center" ;
definition: "Offers guidance and support from the very beginning of project development to data analysis. Offers hands-on, personalized support throughout experimental process including experimental design, instruments training to develop microscopy skills." .
SCR:028175 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "VitroVivo Biotech" ;
NIFRID:synonym "VitroVivo Biotech - Histological Products and Services" ;
definition: "Specialized biotechnology company that provides histology services, molecular pathology services, and specialized research reagents to accelerate biomedical research. They assist scientists in academia and industry with tissue preparation, immunostaining, 3D cell culture processing, and laser capture microdissection (LCM) for cancer, neuroscience, and drug development studies." .
SCR:028176 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.11194.3c ISNI 0000 0004 0620 0548 Crossref Funder ID 501100009914 Wikidata Q261506" ;
rdfs:label "Makerere University; Kampala; Uganda" ;
definition: "Uganda largest and oldest institution of higher learning, first established as a technical school in 1922, and the oldest currently active university in East Africa. It became an independent national university in 1970." .
SCR:028177 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ensembl Linkage Disequilibrium Calculator" ;
NIFRID:synonym "Ensembl Linkage Disequilibrium Calculator (GRCh37)",
"Linkage Disequilibrium (LD) Calculator",
"Linkage Disequilibrium Calculator" ;
definition: "Web tool for calculating Linkage Disequilibrium between variants using genotypes from selected population. We only support LD calculation for variants for which we have genotypes from at least 40 samples in the selected population. At the moment we only have sufficient amounts of genotype data from the 1000 Genomes project for human." .
SCR:028178 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "TOPMed Imputation Server" ;
NIFRID:synonym "NHLBI TOPMed Imputation Server",
"Trans-Omics for Precision Medicine Imputation Server" ;
definition: "Free, secure cloud-based service used to impute missing genetic variants in human DNA data, primarily for genome-wide association studies (GWAS). It uses a massive, diverse reference panel of deeply sequenced human genomes to predict missing genotypes, significantly increasing genetic coverage and improving accuracy, particularly for rare variants. It leverages the Trans-Omics for Precision Medicine (TOPMed) panel, which includes over 400 million variants, allowing researchers to boost their genomic data from millions of SNPs to tens of millions." .
SCR:028179 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OBS Studio" ;
NIFRID:synonym "Open Broadcaster Software" ;
definition: "Software used for live streaming and high-quality screen recording on Windows, Mac, and Linux. Allows to capture, mix, and arrange multiple audio/video sources—such as webcams, desktop screens, and games—in real-time to create, broadcast, or record customized video content. Cross-platform screencasting and live streaming software application." .
SCR:028180 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HiTIMED" ;
NIFRID:synonym "Hierarchical Tumor Immune Microenvironment Epigenetic Deconvolution" ;
definition: "Software DNA methylation-based algorithm, to estimate cell proportions in tumor microenvironment. Profiles tumor, immune, and angiogenic components, allowing researchers to study tumor composition and its clinical implications using archival biospecimens." .
SCR:028181 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HiTAIC" ;
NIFRID:synonym "Hierarchical Tumor Artificial Intelligence Classifier" ;
definition: "Web-based application to trace tumor tissue of origin in primary and metastasized cancers." .
SCR:028182 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5829" ;
rdfs:label "University of Edinburgh UK Zebrafish Imaging and Screening Core Facility" ;
NIFRID:synonym "UK Zebrafish Imaging and Screening Facility" ;
definition: "National facility providing advanced automated chemical and genetic in vivo screening for researchers, utilizing zebrafish embryos for studying disease mechanisms. Dedicated zebrafish-focused research imaging and screening facility adapting and developing cutting edge edge microscopy for automated multiscale imaging." .
SCR:028183 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5830" ;
rdfs:label "Cancer Research UK Cambridge Institute Histopathology and In Situ Hybridisation Core Facility" ;
definition: "Core facilitates all aspects of histopathology including processing, embedding, sectioning, histochemical staining, tissue microarray building, immunohistochemistry, in situ hybridisation, whole slide scanning, and image analysis." .
SCR:028184 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5831" ;
rdfs:label "University of Pittsburgh Health Sciences High Throughput Genomics Core Facility" ;
definition: "Core is CAP/CLIA-certified facility offering comprehensive next generation sequencing (NGS) and bioinformatics services. Supports flexible workflows from nucleic acid extraction and library preparation to sequencing and custom data analysis. Services include DNA/RNA extraction, quality checks, various types of RNA/DNA library prep, NGS, methylation, proteomics (Illumina IPP), metabolomics, lipidomics, pharmacogenomics, and microarray analysis, with options for end-to-end or modular support. Advanced instrumentation includes Illumina NovaSeq X Plus and 6000 platforms, MiSeqDX, Hamilton , Eppendorf, and Tecan liquid handlers, automated extraction systems, and more. HTGC also provides clinical-grade sequencing." .
SCR:028185 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5832" ;
rdfs:label "Rush University Research Bioinformatics Core Facility" ;
NIFRID:synonym "Rush Research Bioinformatics Core",
"Rush Research Bioinformatics Core (RRBC)" ;
definition: "Core empowers researchers from genomic, clinical, and basic sciences disciplines at Rush and beyond with cutting-edge bioinformatics resources. Provides guided data analysis and hypothesis-driven research, large-scale data analysis, analytical plan development and results interpretation, algorithm and script development for custom data processing. Provides innovative infrastructure tools, including the Research Private Cloud and scalable cloud-based solutions. Services include customized analytical solutions, data storage and management workflows, training and support for bioinformatics tools." .
SCR:028186 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SciNetX" ;
definition: "Local desktop and cloud-based bibliometric and network analysis platform offered through a licensed access model.Supports literature-centered bibliometric and scientometric workflows, and it can also be applied to custom datasets with or without associated literature papers, including broader general network analysis use cases." .
SCR:028187 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "VIEWpoly" ;
definition: "Software R package to visualize genetic maps and QTL analysis. Provides graphical user interface to integrate, visualize and explore results from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid species. The app is meant for interactive use and allows users to optionally upload different sources of information, including gene annotation and alignment files, enabling the exploitation and search for candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly', 'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages." .
SCR:028188 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CPSM:Cancer Patient Survival Model" ;
NIFRID:synonym "Cancer Patient Survival Model" ;
definition: "Software R package that provides comprehensive computational pipeline for predicting survival probabilities and risk groups in cancer patients. Includes dedicated modules to perform key steps such as data preprocessing, training/test splitting, and normalization." .
SCR:028190 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bsaseq" ;
definition: "Software Python package for bulk segregant analysis (BSA) and QTL mapping from pooled whole-genome sequencing data. Takes variant call format (VCF) input and produces ranked candidate genomic regions and genes through sliding window analysis with tricube kernel smoothing, Z-score and G-statistic significance testing, and optional snpEff functional annotation. Supports recessive and dominant inheritance modes, multi-sample bulk pooling, and integration with Nextflow and Snakemake workflow managers. Distributed via PyPI, Bioconda, and Docker." .
SCR:028191 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Xenium Ranger" ;
definition: "Software suite for analyzing and visualizing in situ gene expression data produced by Xenium Analyzer. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data." .
SCR:028192 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Texas State University 3-Zone Tube Furnace" ;
NIFRID:synonym "3-Zone Tube Furnace" ;
definition: "Custom system intended for flexible annealing or chemical vapor deposition processing at temperatures < 1000oC. Process and/or purge gases (Ar, 4%H2 in Ar, N2) are introduced via a manifold into the quartz tube at either atmospheric or sub-atmospheric pressures. The maximum sample size is 60mm (~2\")." .
SCR:028193 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CBAE Compliance Algorithm" ;
definition: "Software deterministic reproducibility evaluation toolkit for biological machine learning pipelines. Implements 18-assertion compliance evaluation across 5 dimensions: explicitness, data provenance, reproducibility, stability, and bounded deployment envelope. Includes synthetic example dataset for reviewer verification without patient data." .
SCR:028194 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Texas State University AJA Magnetron Sputter System" ;
NIFRID:synonym "AJA International",
"Inc. ATC Orion Sputter Coater",
"Texas State University Magnetron Sputtering System" ;
definition: "Our AJA International, Inc. ATC Orion is a thin film deposition system based on physical ablation of target material by five (2RF/3DC) independently powered magnetron sputter sources. Substrates with maximum diameter of 100mm are load lock transferred to main chamber on Molybdenum substrate holder with variety of features including heating, rotation, Z motion, and RF biasing. Main chamber vacuum system consists of turbo-molecular pump, gate valve, mechanical pump, and 3 vacuum gauges. Quartz crystal monitor may be employed internally for rate calibration. Internal interlocks protect system/user from aberrant power, water, and vacuum states. Labview-based computer control allows for process development and automated sequencing. Physical vapor deposition system that deposits uniform thin films using magnetron sputtering in controlled vacuum environment." .
SCR:028195 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "HP-Phasing" ;
definition: "Software bioinformatics tool for Helicobacter pylori genotyping." .
SCR:028196 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MicroFinder" ;
definition: "Software pipeline to aid the curation of bird genome assemblies by identifying putative microchromosome scaffolds and moving them to start of the genome assembly FASTA file. Hi-C contact map can then be made using the MicroFinder-ordered assembly file for downstream manual curation. Conserved gene-set mapping and assembly ordering for manual curation of bird microchromosomes. Order FASTA file by microchromosome specific genes." .
SCR:028197 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Living Systems Instrumentation" ;
definition: "Company designs and manufactures specialized laboratory equipment for in vitro research on blood vessels and soft tissues. Based in Vermont, they provide tools for studying vessel pressure, flow, and diameter, primarily used by researchers to understand vascular physiology and disease. Instruments for in-vitro research studies of pressurized, perfused, cannulated blood vessels." .
SCR:028198 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5833" ;
rdfs:label "Paris Brain Institute PHENO Zfish Core Facility" ;
NIFRID:synonym "Institut du Cerveau PHENO Zfish",
"Paris Brain Institute PHENO Zebrafish Core Facility",
"Paris Brain Institute PHENO Zfish" ;
definition: "Facility provides infrastructure and technical expertise for maintenance, breeding, and experimental use of Danio rerio. The facility ensures standardized husbandry, health monitoring, and traceability of zebrafish lines in compliance with regulatory and ethical guidelines. Services include colony management, maintenance and distribution of wild-type, mutant, and transgenic lines, and support for experimental workflows. The platform offers technical services such as embryo microinjection (e.g., genome editing using CRISPR/Cas9), phenotypic screening, fin clipping for genotyping, and in vitro fertilization. Training and technical support are available for zebrafish handling, experimental design, and data reproducibility." .
SCR:028199 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5835" ;
rdfs:label "Texas State University Nanofabrication Research Service Center Core Facility" ;
NIFRID:synonym "Texas State University Nanofabrication Research Service Center (NRSC)" ;
definition: "Multi-user clean room facility where students and researchers can fabricate films, structures, and devices at micrometer and nanometer scale. Users must enter through the gowning area that contains garments required to protect the cleanroom from particles. The class 10,000 instruction area houses high temperature furnaces, physical vapor deposition systems, wet chemical benches, chemical storage, and electrical test equipment utilized by undergraduate courses. The class 1000 research area houses deposition, etching, thermal treatment, and metrology equipment to support sponsored research and graduate coursework. The class 100 research space hosts the most sensitive lithography process equipment. The utility chase houses support equipment such as water cooling, vacuum pumps, exhaust abatement, and compressed gas delivery systems." .
SCR:028200 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Texas State University E-Beam Evaporator system" ;
NIFRID:synonym "E-Beam Deposition System",
"E-Beam Evaporator (PVD75 E-Beam)",
"Electron Beam Evaporator" ;
definition: "Facility Angstrom Engineering EvoVac is a thin film deposition system based on evaporation of source material that can deposit a wide range of materials including metals and inorganic compounds. Resistive evaporation results when electrical current heats a boat filled with source material whereas electron beam evaporation utilizes filament emission and magnetic focusing of a high energy electron beam which is swept within a crucible of deposition material. The deposition processes occur in a vacuum to permit long mean free paths from indexed multi-pocket sources at rates and terminal thicknesses controlled using a quartz rate sensor. The substrate can be heated, rotated, and plasma cleaned to control film morphology, uniformity, and adhesion. Vacuum-based deposition system that uses an electron beam to evaporate materials for high-purity thin film coatings with precise thickness control." .
SCR:028201 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Texas State University PEALD System" ;
NIFRID:synonym "PEALD System (FlexAL-PEALD)" ;
definition: "Facility plasma-enhanced atomic layer deposition (PEALD) system from Arradiance utilizes high-speed pulse valves to sequentially deliver reactants that combine to deposit thin films on the surface of a sample at temperatures up to 300C. Eight precursor positions (4 metalorganic + 4 oxidizer) and three plasma gases (N2, O2, H2) enable a wide range of films and process optimization. Plasma-enhanced atomic layer deposition system used for conformal, atomic-scale thin film growth with excellent uniformity and thickness control." .
SCR:028202 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Texas State University PECVD System" ;
NIFRID:synonym "PECVD System (Versaline PECVD)",
"Plasma-Enhanced Chemical Vapor Deposition system" ;
definition: "Facility plasma-enhanced chemical vapor deposition (PECVD) system from AGS utilizes plasma decomposition of silane (SiH4) in in presence of an oxygen or nitrogen source to deposit SiO2 and Si3N4 dielectric thin films. The capacitive coupled plasma reduces the required temperature for deposition to a minimum of ~150degC. A plasma-enhanced chemical vapor deposition system is used to deposit high-quality thin films at reduced temperatures for semiconductor and materials applications." .
SCR:028203 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Texas State University Oxford ICP/RIE system" ;
NIFRID:synonym "Oxford ICP/RIE (PlasmaPro 100)" ;
definition: "Facility Oxford ICP-RIE Plaslab 180 utilizes a 3kW RF power supply to generate a remote plasma of Cl2, BCl3, H2, Ar, NF3, O2, SF6, and/or C4F8 gas species that can be further accelerated (300W table bias) toward a substrate resulting in a combination of physical and chemical dry etching for material removal. The turbomolecular pumped system achieves a base pressure < 1E-7 Torr and is equipped with chuck temperature control from -110 to 350 degrees C. Advanced dry etching system combining inductively coupled plasma (ICP) and reactive ion etching (RIE) for highly anisotropic, high-precision material removal in semiconductor and nanofabrication processes." .
SCR:028204 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Texas State University Rapid Thermal Annealer" ;
NIFRID:synonym "Rapid Thermal Annealer (AS-One 150)" ;
definition: "Fcility AGA Heatpulse 610 is a benchtop rapid thermal annealer (RTA/RTP) that utilizes high power lamps to heat treat thin films and substrates for processes such as contact formation, silicide formation, and dopant diffusion/activation. Temperature control via PID loop has a maximum heating rate of ~50 C/s and maximum temperature of 1000 C. The chamber can also be atmospheric purged with N2, Ar, 4% H2balAr, or O2. A rapid thermal processing system that enables fast heating and cooling cycles for semiconductor wafers, used for dopant activation, oxidation, and material modification." .
SCR:028207 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Texas State University Wafer Bonder system" ;
NIFRID:synonym "Wafer Bonder (EVG520)" ;
definition: "Facility EVG 501 wafer bonder system applies pressure up to 10kN and temperature up to 450C to samples with prepared surfaces (specific chemical surface termination). When the system mechanically brings these surfaces into contact the temperature and pressure sequence activates chemical bonds at the interfaces that fuse the sample surfaces together. A precision wafer bonding system used to join semiconductor wafers using thermal, adhesive, or anodic bonding techniques for device integration." .
SCR:028211 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Bruker_DektakXT" ;
rdfs:label "Bruker | DektakXT Stylus Profiler" ;
NIFRID:synonym "DektakXT Stylus Profiler" ;
definition: "Advanced, stylus-based surface profiler used for high-precision, 2D and 3D surface topography measurements, including step height, surface roughness, and waviness. System measures roughness in the nanometer range. It provides a step-height repeatability of 5Å. It uses a diamond-tip stylus to physically trace samples, offering sub-nanometer vertical resolution and high repeatability." .
SCR:028212 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Filmetrics_F20" ;
rdfs:label "Filmetrics F20 Thin Film Measurement System" ;
NIFRID:synonym "Filmetrics F20 Thin-Film Analyzer" ;
definition: "Filmetrics F20 is a versatile, benchtop thin-film measurement system designed to measure the thickness, refractive index, and extinction coefficient of thin films. Using spectral reflectance in less than a second, it measures single or multi-layer stacks." .
SCR:028213 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5836" ;
rdfs:label "Sunnybrook Research Institute Centre for Flow Cytometry and Scanning Microscopy Core Facility" ;
NIFRID:synonym "Sunnybrook Research Institute Centre for Flow Cytometry and Scanning Microscopy" ;
NIFRID:abbrev "SRI_CCSM" ;
definition: "Core offers services including cell sorting,cell analysis, user training for the flow cytometer benchtop analyzers, user training for the widefield and confocal microscopes." .
SCR:028214 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ISNI 0000 0004 0469 1398 Crossref Funder ID 100011021 Wikidata Q7640792" ;
rdfs:label "Sunnybrook Research Institute; Toronto; Canada" ;
definition: "Premier Canadian academic medical research center located in Toronto, affiliated with the University of Toronto and Sunnybrook Health Sciences Centre focusing on translating scientific discoveries into clinical practice, with specialties in medical imaging, biology, and clinical trials." .
SCR:028215 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5837" ;
rdfs:label "University of Pittsburgh Hillman Cancer Center Population-based Cancer Data and Analytics Core Facility" ;
NIFRID:synonym "Population-based Cancer Data and Analytics (PANDA)",
"University of Pittsburgh Hillman Cancer Center Population-based Cancer Data and Analytics (PANDA)",
"UPMC Hillman Cancer Center Population-based Cancer Data and Analytics (PANDA)" ;
definition: "Core provides infrastructure and analytic support for population-based cancer research at UPMC Hillman Cancer Center. PANDA helps investigators access, manage, link, and analyze population-based cancer datasets to study cancer surveillance, treatment access, and survival in western Pennsylvania and across the United States using datasets such as SEER-Medicare, the Pennsylvania Cancer Registry (PACR), Pennsylvania Health Care Cost Containment Council (PHC4) hospital discharge data, the National Cancer Database (NCDB), and the UPMC Network Cancer Registry, along with area-level and geospatial data relevant to the Hillman catchment area.PANDA provides consultation on study design and data selection, assistance with data management and linkage, analytic dataset creation, population-level and geospatial analyses, and support for manuscripts and grant applications." .
SCR:028216 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5834" ;
rdfs:label "Mayo Clinic Genetic Screening and Engineering Core Facility" ;
NIFRID:synonym "Genetic Screening and Engineering Core - Mayo Clinic" ;
definition: "Core offers tools to precisely modify the genome of cells and organisms using CRISPR-Cas9-based editing, CRISPR interference (CRISPRi), and CRISPR activation (CRISPRa) systems. Our platforms enable high-throughput genetic screening, gene knockouts, transcriptional modulation, and sequence editing with high efficiency and scalability." .
SCR:028217 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bionoculars" ;
NIFRID:synonym "BiOnOculars" ;
definition: "Web tool to search life science articles with AI you can verify and control. Life science search engine designed to hit the sweet spot between classical search and AI-assisted research." .
SCR:028218 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIMP Analytics" ;
NIFRID:synonym "Neuroanatomy-Anchored Information Management Platform (NIMP)" ;
NIFRID:abbrev "NIMP" ;
definition: "Neuroanatomy-anchored Information Management Platform for collaborative BICAN data generation developed by UTHealth Houston. Serves as metadata tracking engine to support generation, management, and sharing of brain research data. Integrates data production pipelines across brain banks, laboratories, sequencing centers, and data archives. Platform enables integrative and collaborative, consortium-scale FAIR data generation within the BICAN project. Platform is designed to manage complex dataset, including tissue samples and sequencing data, through Specimen Portal and Sequence Library Portal. Portals provide multiple types of data interfaces through dashboards, APIs, faceted queries, and batch data ingestion and exporting." .
SCR:028219 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Vilber_Fusion_FX7" ;
rdfs:label "Vilber Lourmat Fusion FX7 imaging system" ;
NIFRID:synonym "Fusion FX7" ;
definition: "Image acquisition system to capture of chemiluminescence and fluorescence images. Using cooled CCD technology in combination with motorised optical lens, Fusion FX7 offers very high sensitivity and extended dynamic range. Data produced are directly compatible with image analysis software developed by VILBER and 1D image can be transformed into 3D results with Bio-1D and the Bio-Gene software." .
SCR:028220 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Tokyo Chemical Industry" ;
NIFRID:synonym "Ltd. (TCI)",
"Tokyo Chemical Industry Co Ltd",
"Tokyo Chemical Industry Co." ;
definition: "Tokyo Chemical Industry Co., Ltd. (TCI) is a leading global manufacturer of specialty organic chemicals, founded in 1946. They produce over 30,000 research chemicals, including laboratory chemicals, reagents, and functional materials. TCI also acts as a supplier, offering custom synthesis and bulk production from milligrams to tons." .
SCR:028221 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 501100008017",
"GRID grid.14925.3b",
"ISNI 0000 0001 2284 9388",
"Wikidata Q266227" ;
rdfs:label "Gustave Roussy Institute" ;
definition: "Gustave Roussy is Europe’s leading comprehensive cancer center, located in Villejuif near Paris, France. It is a premier institution dedicated entirely to cancer treatment, research, and teaching, often ranked among the top oncology hospitals worldwide. Founded in 1925, it specializes in personalized medicine, rare cancers, and complex tumors." .
SCR:028222 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5839" ;
rdfs:label "Gustave Roussy Microscopy and Cytometry Core Facility" ;
NIFRID:synonym "Gustave Roussy Microscopy and Cytometry Core Facility (PFIC)" ;
NIFRID:abbrev "PFIC" ;
definition: "Core supports fundamental, translational, and clinical research by providing advanced services and expertise in cytometry, photonic microscopy, mass imaging, in vivo imaging, and bioinformatics. The cytometry and mass imaging unit offers flow, spectral and mass cytometry, cell sorting, multiplex panel development, and high‑dimensional data analysis. Photonic microscopy unit provides comprehensive support from sample preparation to image processing, with access to widefield, confocal, multiphoton and super‑resolution systems, and benefits from national recognition through IBISA and France BioImaging labels. The platform also hosts clinical transfer imaging activities (SP2I), developing optical tools for surgery and pathology in close collaboration with clinicians, with numerous funded projects and industrial partnerships." .
SCR:028223 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "iRegulon" ;
definition: "Software tool to reverse-engineer transcriptional regulatory networks from co-expressed gene sets by identifying master transcription factors (TFs) and their direct target genes. It operates by scanning for enriched TF binding motifs in promoter regions, utilizing over 10,000 position weight matrices (PWMs) for human, mouse, and Drosophila. Used to enable gene regulatory network mapping directly based on motif enrichment in co-expressed gene set." .
SCR:028224 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "EpiProfile" ;
NIFRID:synonym "EpiProfile 2.0" ;
definition: "Software tool for processing Epi-Proteomics mass spectrometry data. Discriminates isobaric histone peptides using distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples. EpiProfile 2.0 is extended version of v1.0 for enhanced quantification of histone peptides based on LC-MS/MS analysis." .
SCR:028225 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "H-Optimus-0" ;
definition: "Open-source foundation model for histology. Vision transformer model trained on haematoxylin and eosin stained tissue whole slide histology images. AI foundation model for pathology, developed by French startup Bioptimus. Launched as one of the largest open-source models for digital pathology, it is trained on histopathology slides for tasks like tissue classification, mutation prediction, and cancer subtyping." .
SCR:028226 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NIH NCI Cancer Data Access System Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial Portal" ;
NIFRID:synonym "Colorectal and Ovarian (PLCO) Cancer Screening Trial",
"Lung",
"Prostate" ;
definition: "National Cancer Institute (NCI)-sponsored randomized, controlled study (1993–2001) of ~155,000 adults aged 55-74 to evaluated whether organized, regular screenings could reduce cancer deaths compared to usual care. Portal provides randomized, controlled trial data used to determine whether certain screening exams reduce mortality from prostate, lung, colorectal and ovarian cancer." .
SCR:028227 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NuHTC" ;
NIFRID:synonym "Nuclei Hybrid Task Cascade",
"NuHTC nuclear segmentation pipeline" ;
definition: "Software nuclei instance segmentation and classification framework based on hybrid task cascade." .
SCR:028228 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5840" ;
rdfs:label "University of Iowa Roy J Carver Center for Imaging Core Facility" ;
NIFRID:synonym "Roy J. Carver Center for Imaging (CCI) at the University of Iowa" ;
definition: "Core offers light microscopy and imaging services. Provides access to and training on various confocal microscopes." .
SCR:028229 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5841" ;
rdfs:label "University of Iowa Roy J Carver Center for Genomics Core Facility" ;
NIFRID:synonym "Roy J. Carver Center for Genomics (CCG)" ;
definition: "The Roy J. Carver Center for Genomics (CCG) is a research and service center within the Department of Biology on the campus of the University of Iowa (UI). The CCG maintains a centralized laboratory with equipment and instruments available for investigators to use in their molecular research." .
SCR:028230 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5842" ;
rdfs:label "Baylor College of Medicine Human Tissue Acquisition and Pathology Core Facility" ;
definition: "Tissue bank and full service histology core. Provides support for tissue banks staining imaging and spatial applications." .
SCR:028231 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5838" ;
rdfs:label "Cincinnati Children's Hospital Medical Center Qualitative Methods and Analysis Collaborative Core Facility" ;
NIFRID:synonym "Cincinnati Children's Hospital Medical Center Qualitative Methods and Analysis Collaborative (QMAC)",
"Qualitative Methods and Analysis Collaborative (QMAC)" ;
definition: "Core promotes conduct of high-quality qualitative research with focus on integrating key stakeholder perspectives into research designs. It helps investigators with study design, funding proposals, data collection, and analysis to understand contextual, sociocultural, and experiential factors in health." .
SCR:028232 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CellTool" ;
definition: "Stand-alone open-source software with graphical user interface for analysis of time-lapse microscopy images. Combines bio-image analysis and mathematical modeling for study of DNA repair dynamics." .
SCR:028233 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "InteractiVenn" ;
definition: "Web-based tool for analysis of sets through Venn diagrams. Allows set unions in Venn diagrams to be explored thoroughly, by consequence extending the ability to analyze combinations of sets with additional observations, yielded by novel interactions between joined sets." .
SCR:028241 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CIMA_BMI_paper" ;
definition: "Source analysis and data processing code for article titled \"Single-Cell Multi-Omics Insights into BMI-Mediated Immune-Related Disease Risk\"." .
SCR:028242 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Gene Expression Profiling Interactive Analysis 3" ;
NIFRID:abbrev "GEPIA3" ;
definition: "Web based tool as advanced version of GEPIA that provides comprehensive analysis of gene/protein interactions across various cancer types. This version facilitates the investigation of treatment sensitivity utilizing both real-world patient data and cell line screens for over 1000 therapeutic agents, as well as the integration of RNA alterations derived from the pan-cancer analysis of whole genomes project. GEPIA3 represents a significant enhancement of the original platform, enabling in-depth exploration of gene regulation and cancer phenotypes, thereby supporting the identification of novel biomarkers and therapeutic targets." .
SCR:028243 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5844" ;
rdfs:label "University of Glasgow Cancer Sciences Flow Cytometry Core Facility" ;
NIFRID:synonym "Cancer Sciences Flow Cytometry Facility" ;
definition: "Cancer Sciences Flow Cytometry Facility is a joint facility between the School of Cancer Sciences at the University of Glasgow and the CRUK Scotland Institute. Provides access to flow cytometry instrumentation and support from technical experts in analysis and cell sorting." .
SCR:028244 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5846" ;
rdfs:label "Queen's University Translational Institute of Medicine TIME Core Facility" ;
NIFRID:synonym "TIME's Core Facility" ;
definition: "Core to maximize sharing of research platforms and expertise between research groups in the Department of Medicine and their collaborators. Provides research equipment and expertise to accelerate translation of laboratory discoveries into clinical applications to improve patient care. It supports translational research through advanced tools, expertise in biotechnology, biomolecular sciences, and the development of new treatments and biomarkers, aiming to advance first-in-person clinical trials." .
SCR:028245 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5847" ;
rdfs:label "University of Maine CORE Electron Microscopy Laboratory Core Facility" ;
NIFRID:synonym "University of Maine Electron Microscopy Laboratory",
"University of Maine Electron Microscopy Laboratory Core Facility" ;
definition: "Core offers tools and technical expertise for research and training in microscopy with both light and electron microscopes. Maintains and operates electron microscopes (SEM with EDS), confocal laser scanning microscope, and tancillary equipment needed for preparation of specimens for EM and other microscopy. Light microscopes encompass optics for bright-field, phase-contrast, Nomarski differential-interference, polarizing, and fluorescence imaging." .
SCR:028246 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5848" ;
rdfs:label "University of Maine CORE Small Animal Research Core Facility" ;
NIFRID:synonym "UMaine Small Animal Research Facility (SARF)",
"University of Maine Small Animal Research Core Facility",
"University of Maine Small Animal Research Facility" ;
definition: "Core provides animal care and assists investigators in fulfilling their obligation to plan and conduct animal research in accordance with scientific, humane and ethical principles. SARF has a multizone temperature and airflow control to allow for various environments necessary to research projects. SARF also features quarantine suite with separate entrance and personal protective equipment (PPE), and is outfitted with RAIR HD Super Mouse 750 ventilated rack holding 126 cages. Daily care and feeding is provided by trained staff, and surgery prep, surgical area, and recovery area are available for use." .
SCR:028247 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5849" ;
rdfs:label "University of Maine CORE Zebrafish Core Facility" ;
NIFRID:synonym "University of Maine Zebrafish Core Facility",
"University of Maine Zebrafish Facility" ;
definition: "Facility is outfitted with the Aquatic Habitats for Accelerated Bioresearch (AHAB) fish rearing system (Aquatic Habitats, Apopka, FL). This system is composed of five-foot wide, five-level, stainless steel racks using any combination of tank sizes (3 and 10 liter). Water input lines deliver UV-sterilized water to each tank through an independent valve. The fish tanks have self-cleaning bottoms and the effluent system features an optically clear design. The filter system requires minimal maintenance, and maintains high water quality, dramatically reduced disease and mortality." .
SCR:028248 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5850" ;
rdfs:label "University of Maine CORE Environmental DNA Laboratory Core Facility" ;
NIFRID:synonym "UMaine Coordinated Operating Research Entities eDNA Service Center Lab",
"UMaine CORE eDNA Service Center Lab" ;
definition: "Core offers processing and testing of environmental DNA samples, assay development, field surveys and training services. The equipment housed in the center allows users to receive fluorescence-based qPCR analyses, for quantifying DNA concentration and abundances, and plate preparation." .
SCR:028249 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5851" ;
rdfs:label "University of Maine CORE Microfabrication Cleanroom Core Facility" ;
NIFRID:synonym "CORE Microfabrication Cleanroom" ;
definition: "Facility supports micro- and nanoscale fabrication, microsensor development, and atomic-scale materials synthesis. Provides comprehensive technical capabilities, including microlithography (mask aligners, photoresist processing, laser lithography), thin film deposition (e-beam evaporation, sputtering, PECVD, atomic layer deposition), and advanced characterization tools (profilometry, spectroscopic ellipsometry). Fabrication processes are supported by both dry etching (DRIE, RIE) and wet chemical processing (RCA clean, KOH etch, solvent benches), as well as thermal processing systems such as diffusion furnaces and rapid thermal annealing." .
SCR:028250 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5843" ;
rdfs:label "University of Maine DNA Sequencing Facility" ;
NIFRID:synonym "DNA Sequencing Facility" ;
definition: "DNA Sequencing facility provides Sanger sequencing and other services to labs on campus and beyond. Users can choose the degree of in-house processing to accommodate individual needs, providing flexibility for clients of all levels." .
SCR:028251 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "regioneR" ;
definition: "Software R package to work with genomic regions. In addition to predefined randomization and evaluation strategies, regioneR is fully customizable. Implements function to evaluate local specificity of detected association. Used for association analysis of genomic regions based on permutation tests." .
SCR:028252 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "regioneReloaded" ;
definition: "Software package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and creation of graphs. Incorporates strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. Builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs." .
SCR:028253 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Loom" ;
NIFRID:synonym ".loom",
"Loom File Format" ;
definition: "Loom is an efficient HDF5-based file format for storing large, high-dimensional single-cell genomics datasets, including data, metadata, and clustering results. Loom file format is designed to efficiently hold large omics datasets. Typically, such data takes the form of a large matrix of numbers, along with metadata for the rows and columns. Loom files (.loom) are created in the HDF5 file format, which supports an internal collection of numerical multidimensional datasets. HDF5 is supported by many computer languages, including Python, R, MATLAB, Mathematica, C, C++, Java, and Ruby." .
SCR:028254 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Cell-Annotation-and-Taxonomy Standard" ;
definition: "Structured schema used in single-cell biology to standardize how cell types are annotated, classified, and stored. It is frequently associated with the Allen Institute and Brain Initiative Cell Census Network (BICAN) to map cell taxonomy, linking cell sets to ontologies and providing evidence for annotations" .
SCR:028255 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Human Striatum Slide-tags Viewer" ;
definition: "On-line viewer for human striatum slide-tags spatial transcriptomics (10X Chromium 5' GEX) data set generated by the Macosko Lab comprising ~1.1 million cells from 19 human striatum donors." .
SCR:028256 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "PanDepth" ;
definition: "Software tool for calculating sequence depth." .
SCR:028257 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "wgbstools" ;
definition: "Software tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies." .
SCR:028258 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Azure_AC3000" ;
rdfs:label "Azure Ao Absorbance Microplate Reader AC3000" ;
definition: "Filter-based 96-well plate absorbance microplate reader for ELISA, Bradford, Lowry assays and more." .
SCR:028259 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Azure_200" ;
rdfs:label "Azure 200 imaging system" ;
NIFRID:synonym "Azure 200" ;
definition: "Touchscreen-based gel documentation imaging system. It is designed for UV, color imaging, blue-excited DNA dyes, and Coomassie gel imaging." .
SCR:028260 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Azure 280 imaging system" ;
NIFRID:synonym "Azure 280" ;
definition: "Imaging system with the same sensitivity as chemiluminescent detection on film, but without need for darkroom and the expense of film developer." .
SCR:028261 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Azure_400" ;
rdfs:label "Azure 400 imaging system" ;
NIFRID:synonym "Azure 400" ;
definition: "Imaging system capable of three-channel visible fluorescence detection. Enables sensitive multiplex detection of Western blots, fluorescent biomolecules and Cy2/Cy3/Cy5 or similar fluorochromes. Allows you to simultaneously image and quantify up to three different targets." .
SCR:028262 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Azure_500" ;
rdfs:label "Azure 500 imaging system" ;
NIFRID:synonym "Azure 500" ;
definition: "Multichannel, multimodal fluorescent imager, with IR, visible light, and UV excitation channels. Able to image and quantify two different targets in the same position more efficiently using near-infrared (NIR). Normalize to fluorescent total protein stain or a housekeeping protein in the green channel without needing to strip and re-probe your Western blots." .
SCR:028263 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Azure_Cielo_3" ;
rdfs:label "Azure Cielo 3 RT PCR system" ;
NIFRID:synonym "Azure Cielo 3" ;
definition: "Azure Cielo 3 is 96 well Real Time-PCR Machine available with 3 sample channels. Used for RT-PCR amplification and SYBR Green fluorescence detection. Engineered for variety of qPCR applications, with high sensitivity and wide dynamic range. Fast qPCR detection system for high-quality data with smart protocols, and robust durability." .
SCR:028264 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Azure_Cielo_6" ;
rdfs:label "Azure Cielo 6 RT PCR system" ;
NIFRID:synonym "Azure Cielo 6" ;
definition: "Azure Cielo 6 is 96 well Real Time-PCR Machine available with 6 sample channels. Used for RT-PCR amplification and SYBR Green fluorescence detection. Engineered for variety of qPCR applications, with high sensitivity and wide dynamic range. Fast qPCR detection system for high-quality data with smart protocols, and robust durability." .
SCR:028265 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Azure_IS4100" ;
rdfs:label "Azure Sapphire FL+ Biomolecular Imager IS4100" ;
NIFRID:synonym "Sapphire FL+ Biomolecular Imager IS4100" ;
definition: "Large format scanner for precise quantitation of molecular assays. Imaging System 4100 is high-performance laser-based scanner variant designed for fluorescence, phosphor, and chemiluminescence imaging." .
SCR:028266 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Azure_IS1015" ;
rdfs:label "Azure Sapphire Eraser IS1015" ;
NIFRID:synonym "Azure Sapphire Eraser" ;
definition: "Laboratory instrument used to erase residual signals from storage phosphor screens (imaging plates). It utilizes LED light source within drawer-based design to clear screens up to prepare them for reuse in radioactive sample imaging. Used for ensuring that high-sensitivity phosphor imaging assays are free from background noise from previous experiments." .
SCR:028267 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Azure_CS1000" ;
rdfs:label "Azure chemiSOLO imager CS1000" ;
NIFRID:synonym "Azure chemiSOLO imager",
"chemiSOLO",
"chemiSOLO imager" ;
definition: "Compact chemiluminescent imager for quantitative chemiluminescent and visible protein gels." .
SCR:028268 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Taxonomy for Transition Programming" ;
definition: "Research-based framework designed to guide planning, organization, and evaluation of transition services for students with disabilities. It serves as comprehensive tool to improve post-school outcomes in employment, education, and independent living. It encompasses several key dimensions, including student-focused planning, student development, interagency collaboration, family involvement, and program structure and attributes." .
SCR:028269 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5854" ;
rdfs:label "University of Wyoming Stable Isotope Core Facility" ;
NIFRID:synonym "University of Wyoming Stable Isotope Facility" ;
definition: "Facility performs stable isotope analysis and some sample preparation. Analyses include CNS(solid), OH(solid and liquid), DIC(liquids) and CO(solid carbonate, bone, enamel, etc...). Sample prep includes water extractions, soil acidification, grinding, encapsulation, and others." .
SCR:028270 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5853" ;
rdfs:label "University of Colorado Boulder Biochemistry Nuclear Magnetic Resonance Core Facility" ;
NIFRID:synonym "CU Boulder Biochemistry Nuclear Magnetic Resonance (NMR) facility",
"CUB-BioNMR",
"University of Colorado Boulder CUB-BioNMR" ;
definition: "Facility maintains 400MHz Bruker NMR capable of running NMR experiments, including solution NMR spectroscopy for small molecules, macromolecules, polymers, and proteins. The on-site analytical tools (Topspin, MestRenova) are here to facilitate your research success." .
SCR:028271 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Korea Sequence Read Archive" ;
NIFRID:synonym "KoNA: Korean Nucleotide Archive",
"Korea Sequence Read Archive (KRA)" ;
definition: "Publicly available repository of high throughput sequencing data. KRA stores qualified raw sequencing data and alignment information and facilitates reproducibility through cloud-based data analysis service. Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data has been migrated to KRA." .
SCR:028272 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bootstrap Your Own Latent (BYOL)" ;
definition: "Software is the implementation of re-training and linear evaluation pipeline of BYOL. Bootstrap your own latent new approach to self-supervised learning." .
SCR:028273 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5857" ;
rdfs:label "University of Tennessee KnoxvilleAdvanced Microscopy and Imaging Center AMIC Core Facility" ;
NIFRID:synonym "Advanced Microscopy and Imaging Center (AMIC)" ;
definition: "Multi-user, multi-disciplinary facility that provides microscopy and imaging services. It houses instrumentation for optical microscopy including laser scanning confocal microscopy and total internal reflection microscopy (TIRF), scanning as well as transmission electron microscopy, MALDI mass spectrometry imaging, and an X-ray MicroCT. Offers complete technical support, individual training and courses that cover both the practical applications and physical principles of microscopy. Provides consultations for development of microscopy projects for inclusion in grant proposals." .
SCR:028274 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5855" ;
rdfs:label "NYU Langone Health Environmental Exposure and Analytical Chemistry Laboratory Core Facility" ;
NIFRID:synonym "Environmental Exposure and Analytical Chemistry Laboratory",
"NYU Langone Health Environmental Exposure and Analytical Chemistry Laboratory" ;
definition: "Facility for trace-level analysis of anthropogenic organic chemicals in environmental and biological specimens.Specializes in mass spectrometry based analysis, including targeted and nontargeted methods. Capable of quantifying nearly all the organic analytes monitored by the Centers for Disease Control and Prevention (CDC) in the National Health and Nutrition Examination Survey (NHANES) program. Commonly assayed targets include phthalates, bisphenols, per- and polyfluoroalkyl substances (PFAS), glyphosate, organophosphate flame retardants, organophosphate pesticides, and other compound classes at biologically and environmentally relevant concentrations. Our nontargeted analysis workflows are capable of detecting hundreds to thousands of chemical features in a single sample, enabling the identification of unknown organic compounds without a priori target selection.Laboratory operates as a shared resource within NYU Langone's Division of Advanced Research Technologies (DART), which is part of the Office of Science and Research (OSR). We provide precise chemical analysis to support studies on environmental exposures and their health impacts." .
SCR:028275 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5858" ;
rdfs:label "Paris Brain Institute Histomics Core Facility" ;
definition: "Core offers workspaces and equipment for your histology techniques, as well as advice, training, and services." .
SCR:028276 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5861" ;
rdfs:label "Cancer Research UK Cambridge Institute Proteomic Facility" ;
definition: "Core offers services for identification, quantification, and structural characterisation of proteins using next–generation mass spectrometry platforms. Uses mass spectrometry platforms that include Orbitrap Lumos, Ascend and Astral Zoom systems. Services include designing of experimental strategies, implementing and validating previously developed proteomic workflows to profile proteins from diverse biological samples, as well as developing methods and assays when required. Core focuses and specializes in using stable isotopic labelling strategies (Tandem Mass Tags) as well as label-free methods using different acquisition methods (DDA and DIA) for relative quantification of protein expression levels and enrichment within protein complexes. Develops and runs PRM (parallel reaction monitoring) assays for targeted quantification of defined panels of proteins." .
SCR:028277 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5862" ;
rdfs:label "Medical College of Wisconsin Children’s Research Institute CRI Imaging Core Facility" ;
definition: "Imaging core houses microscopic imaging systems including several confocal microscopes, laser microdissection system and whole slide scanners. Core users will be trained and consulted on instrumentation, software, and analysis." .
SCR:028278 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5863" ;
rdfs:label "Medical College of Wisconsin Neuroscience Research Center NRC Microscopy Core Facility" ;
definition: "Core offers confocal imaging systems for specialized imaging of neuronal tissue, including AxL Cleared Tissue Light Sheet Microscope along with appropriate software including Bitplane Imaris 10.0 F1 package and SVI Huygens Professional deconvolution software. The availability of a cleared tissue instrument enables unparalleled visualization of developmental processes, injury recovery, and disease-related pathology." .
SCR:028279 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5864" ;
rdfs:label "Northwestern University Center for Regenerative Nanomedicine Peptide Synthesis Core Facility" ;
NIFRID:synonym "Peptide Synthesis Core Facility at the Center for Regenerative Nanomedicine (CRN)" ;
definition: "Core offers custom peptide services. Facility provides expertise and instrumentation dedicated to chemical synthesis, purification, and characterization of peptides and peptide materials. Provides standard and catalog peptides, and synthesis of specialty custom peptides modified to fit specific research needs." .
SCR:028280 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BD_FACSDiscover_A8" ;
rdfs:label "BD FACSDiscover A8 Cell Analyzer" ;
NIFRID:synonym "BD FACSDiscover A8" ;
definition: "Flow cytometer that combines real-time imaging with spectral flow cytometry. Enables researchers to analyze cell morphology, protein location, and molecular characteristics simultaneously at high speeds, offering deeper single-cell insights than traditional flow cytometry." .
SCR:028281 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_BD_FACSymphony_S6" ;
rdfs:label "BD FACSymphony S6 Cell Sorter" ;
NIFRID:synonym "BD FACSymphony S6" ;
definition: "High-performance, multicolor flow cytometer used to analyze and isolate (sort) specific cell populations with high precision, measuring up to 50–60 parameters. Offers 6-way sorting, indexing for single-cell sorting (e.g., RNA-seq), and BSL-2 biosafety containment." .
SCR:028282 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Sony_ID7000" ;
rdfs:label "Sony ID7000 Spectral Cell Analyzer" ;
NIFRID:synonym "Sony ID7000" ;
definition: "Flow cytometer designed for comprehensive, high-parameter analysis of heterogeneous cell populations. It utilizes spectral technology supporting up to 7 lasers and 186 detectors to detect dim/rare populations and distinguish over 44 colors, making it ideal for advanced immunology and oncology research." .
SCR:028283 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5865" ;
rdfs:label "Medical College of Wisconsin Comprehensive Rodent Metabolic Phenotyping Core Facility" ;
NIFRID:synonym "Comprehensive Rodent Metabolic Phenotyping Core (CRMPC) at the Medical College of Wisconsin" ;
definition: "Core provides guided access to technologies for dissection of metabolic function in rodents and other small animals. Provides development, testing, and standardization of metabolic technologies and workflows to leverage both mouse and rat models of interest to the MCW research community. Offers 16-cage multiplexed metabolic phenotyping system (Promethion, Sable Systems International) that provides detailed mechanistic dissection of resting metabolic rate (RMR), physical activity, and ingestive behaviors of rodents in home style cage designs across the light cycle. Core combines RMR assessments with direct/combined calorimetry (total heat dissipation) to enable assessment of anaerobic forms of energy expenditure. Additional services include body composition analysis, metabolic caging, indirect calorimetry, bioimpedance spectroscopy, thermal imaging. Core experts provide guidance for experimental design, execution of studies, statistical analysis of resulting data, and regulatory assistance and compliance." .
SCR:028284 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SWC-Studio" ;
definition: "Software toolkit for inspection, validation, repair, and reproducible processing of neuronal morphology reconstructions stored in SWC format. It provides a desktop GUI, a command-line interface, and a Python API for issue-driven curation, automated neurite labeling, radii cleaning, simplification, geometry editing, batch processing, and structured reporting." .
SCR:028285 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5867" ;
rdfs:label "BOKU University Bioactive Molecules Screening and Analysis BMOSA Core Facility" ;
NIFRID:synonym "BOKU Core Facility Bioactive Molecules Screening and Analysis (BMOSA)" ;
definition: "Core provides high throughput microbiology screening services and high-end mass spectrometry for diverse range of molecules." .
SCR:028286 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5868" ;
rdfs:label "University of Toronto Research and Innovation Core Facility" ;
NIFRID:synonym "RICore:One Integrated Core",
"University of Toronto Mississauga Research and Innovation Core" ;
definition: "Core brings together UTM’s Growth Facilities, Imaging Facility, Life Sciences Facilities, and NMR Centre into a unified ecosystem that supports academic researchers with shared tools, expert support, and hands‑on training. Provided services include design of multi-scale experimental workflows,cross-platform training,coordinated sample preparation across scales,seamless facility operations,facilitation of data integration, and troubleshooting." .
SCR:028287 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_69" ;
rdfs:label "Roswell Park Comprehensive Cancer Center Gene Targeting and Transgenic Core Facility" ;
NIFRID:synonym "Gene Targeting and Transgenic Facility",
"Roswell Park Comprehensive Cancer Center Gene Targeting and Transgenic Facility" ;
definition: "Core provides investigators in the Western New York area with genetically modified animals for their research through gene targeting and transgenic methodologies." .
SCR:028288 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5860" ;
rdfs:label "Medical College of Wisconsin Children's Research Institute Histology Core Facility" ;
NIFRID:synonym "Children's Research Institute Histology Core",
"Medical College of Wisconsin Children's Research Institute Histology Core" ;
definition: "Core offers histological and immunohistochemical services.Our staff includes ASCP certified Histologists and American Board of Pathology certified Pathologists who provide service, assistance, and quality control. Provided services include grossing specimens, frozen and fixed tissue sectioning, routine H&E and specialized histochemical staining, cytospin preparations, IHC/IF and antibody optimizations using investigator provided antibodies. Provides training for immunohistochemical and histochemical techniques." .
SCR:028289 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5869" ;
rdfs:label "Ohio State University Molecular Biology and Genomics Core Facility" ;
NIFRID:synonym "Ohio State University Molecular Biology and Genomics Core (MBGC)" ;
definition: "Core provides integrated, end-to-end support for molecular biology and genomics research. Services include DNA/RNA extraction, sample quality control, genotyping, qPCR/ddPCR, and next-generation sequencing using Illumina and Oxford Nanopore platforms. In addition to laboratory services, MBGC offers consultation, experimental design guidance, troubleshooting, and training to support high-quality and reproducible research outcomes." .
SCR:028290 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Biacore_S200" ;
rdfs:label "Biacore S200 High Throughput Drug Screening Surface Plasmon Resonance System" ;
NIFRID:synonym "Biacore S200 High Throughput Drug Screening SPR System",
"Biacore S200 system",
"Surface Plasmon Resonance (SPR) biosensor system" ;
definition: "Biosensor system designed for rapid, automated analysis of biomolecular interactions. It excels in characterizing and screening small molecule drug candidates and antibody interactions with high sensitivity, offering rapid fragment screening and affinity determination. Detects low molecular weight (LMW) compounds and weak binding interactions. Optimized for rapid screening of libraries with automated data evaluation for up to 384-well plates. Measures binding interactions in real-time without labeling." .
SCR:028291 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "fqtrim" ;
definition: "Software tool for filtering and trimming next generation sequencing reads." .
SCR:028292 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Servalcat" ;
definition: "Software package for atomic model refinement and map calculation. Software for structure refinement and validation for crystallography and single particle analysis." .
SCR:028293 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5870" ;
rdfs:label "University of Wyoming Center for Advanced Scientific Instrumentation CASI Core Facility" ;
definition: "Core provides instrumentation and service for the University of Wyoming scientific research community. Services include X-ray, Electron Microscopy, and Light microscopy analysis." .
SCR:028294 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Beckman_DU-640" ;
rdfs:label "Beckman DU-640 Spectrophotometer" ;
definition: "Microprocessor controlled UV-Vis spectrophotometer designed for quantitative and qualitative analysis of liquid samples. Used to scan, measure absorbance, and analyze samples within 190 to 1100 nm range, specializing in nucleic acid (DNA/RNA) quantification, protein assays (Bradford/Lowry), and enzyme kinetics. It is part of DU-600 series. DU-640 features micro-focused beam technology for samples as small as 5ul, full-screen scanning, and rapid data storage/analysis without external computer." .
SCR:028295 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "AMT Imaging" ;
NIFRID:synonym "Advanced Microscopy Techniques (AMT)" ;
definition: "Manufacturer and distributor of high-resolution digital imaging systems specifically designed for Transmission Electron Microscopes (TEM). Based in Woburn, Massachusetts, and founded in 1990, the company specializes in developing CCD and sCMOS camera systems for life sciences and materials science applications." .
SCR:028296 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_PowerLab_C" ;
rdfs:label "ADInstruments PowerLab C data acquisition device" ;
NIFRID:synonym "PowerLab C" ;
definition: "Digital data acquisition device used in life science research and education. It converts analog signals from sensors/transducers (e.g., blood pressure, ECG, EEG) into digital data, allowing real-time recording, visualization, and analysis of physiological signals on computer using LabChart software." .
SCR:028297 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ONI Nanoimager" ;
definition: "Compact, benchtop super-resolution fluorescence microscope designed for single-molecule localization microscopy (SMLM) and real-time tracking, allowing imaging of fixed and live cells with a resolution under 20 nm. It enables dSTORM, PALM, PAINT, smFRET, and TIRF imaging on standard lab bench. Used for quantitative studies of biological processes, including protein interactions in fixed/live cells, extracellular vesicle (EV) characterization, and lipid nanoparticle (LNP) analysis for drug delivery research." .
SCR:028298 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Quantum Design DynaCool Physical Properties Measurement System" ;
NIFRID:synonym "Quantum Design DynaCool PPMS" ;
definition: "Automated, cryogen-free laboratory instrument used to measure electrical, magnetic, and thermal properties of materials. It controls temperatures from 1.8K to 400K and magnetic fields from 9T to 14T without liquid helium, using a pulse tube cooler." .
SCR:028299 a owl:NamedIndividual ;
rdfs:label "African Centers of Excellence" ;
NIFRID:abbrev "ACES" ;
definition: "An organization of core facilities in east Africa, spanning multiple countries whose goal is to support research, health, industry and education within Africa. " .
SCR:028300 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MTS Criterion Electromechanical Test System" ;
definition: "High-precision, tabletop or floor-standing machine used for performing static (monotonic) materials testing, including tension, compression, flex/bend, and shear tests. Designed to measure mechanical properties of materials, such as plastics, metals, composites, and adhesives, ensuring they meet quality and durability standards. Offers a force capacity range typically between 1N to 600kN." .
SCR:028301 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5871" ;
rdfs:label "Emory University Translational Neuroscience Core Facility" ;
NIFRID:synonym "Emory University Translational Neuroscience Core",
"Translational Neuroscience Core" ;
definition: "Core provides services primarily on animal models to enable preclinical testing and translational research, accelerating the development of human neurological therapies. It specializes in neurosurgical procedures in rodents and large animals, specializing in gene/stem cell therapy and device testing." .
SCR:028302 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5875" ;
rdfs:label "University of Pittsburgh Pediatric Clinical Research Services PCRS Core Facility" ;
NIFRID:synonym "University of Pittsburgh Pediatric Clinical Research Services (PCRS)" ;
definition: "Core is responsible for overall clinical research management for studies engaging a pediatric population, both grant funded and industry sponsored clinical and translational research studies. For both Children Hospital of Pittsburgh and Magee-Women Hospital, the PCRS group provides comprehensive study engagement and helps investigators enroll research subjects. Services are available in two areas, allowing the group to best meet the needs of Pitt physicians and the patients they serve." .
SCR:028303 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5874" ;
rdfs:label "Medical College of Wisconsin MCW Engineering Core Facility" ;
NIFRID:synonym "MCW - Engineering Core",
"Medical College of Wisconsin MCW - Engineering Core" ;
definition: "Core is a specialized team of biomedical engineers dedicated to supporting MCW medical research effort by expertly designing, fabricating, repairing, and calibrating research instrumentation tailored to lab-specific needs. By providing these services in-house at a fraction of the cost of commercial vendors, the Core enables cutting-edge research while maximizing budget efficiency." .
SCR:028304 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5872" ;
rdfs:label "University of Florida Nanoscale Research Facility NRF Core Facility" ;
NIFRID:synonym "Nanoscale Research Facility (NRF)",
"University of Florida Nanoscale Research Facility (NRF)" ;
definition: "Core supports and enhance research and education by providing access to characterization and process instrumentation. Expert staff provides the assistance and guidance necessary so that students, faculty, and industry get the most effective and appropriate use of facility resources. NRF facilities encompass 100+ instruments, tools and techniques as well as a 7,000 sq. ft. Class 100-1000 Cleanroom facility. Facilities also include instrumentation that allows characterization of radioactive samples." .
SCR:028306 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5879" ;
rdfs:label "Fred Hutch Cancer Center Translational Pathology Core Facility" ;
NIFRID:synonym "Fred Hutch Cancer Center Translational Pathology" ;
definition: "Core provides high-plex immunohistochemistry (PhenoCycler/CODEX) on human and mouse FFPE tissues, image analysis (IHC, mIHC, high-plex), and support for collaborative and fee-for-service projects." .
SCR:028307 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5877" ;
rdfs:label "Northwestern University Magnet Low Temperature and Optics Facility MLTOF Core Facility" ;
NIFRID:synonym "Low Temperature and Optics Facility (MLTOF)",
"Magnet" ;
definition: "Core offers instrumentation for electrical/magnetic/optical characterization of thin film and semi-conductor materials and devices. Temperature range depending on technique is -1.8K to 400K." .
SCR:028308 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Skin Drug Delivery" ;
definition: "Software tools to measure the penetration depth of a fluorescently stained molecule into the skin." .
SCR:028309 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5884" ;
rdfs:label "Yale Center for Molecular Discovery YCMD Core Facility" ;
NIFRID:synonym "Yale Center for Molecular Discovery (YCMD)" ;
definition: "Full-service core facility specializing in high throughput assay development and screening of chemical and genomic probes." .
SCR:028310 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_NEPA21_Type_II" ;
rdfs:label "Nepa Gene Super Electroporator NEPA21 Type II" ;
NIFRID:synonym "Super Electroporator NEPA21 Type II" ;
definition: "Specialized gene transfection system designed to introduce molecules (DNA, RNA, siRNA, CRISPR/Cas9) into difficult-to-transfect cells, tissues, and embryos. It uses a unique 4-step, multi-pulse technology to maximize transfection efficiency while maintaining high cell viability." .
SCR:028311 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ClinoStar_2" ;
rdfs:label "CelVivo ClinoStar 2 bioreactor" ;
NIFRID:synonym "ClinoStar 2 bioreactor" ;
definition: "Automated 3D cell culture bioreactor designed to grow large, functional organoids and spheroids by simulating microgravity via a clinostat. It provides a low-shear environment, enhancing nutrient/oxygen diffusion and cellular communication to produce more physiologically relevant tissue models compared to traditional methods." .
SCR:028312 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_WOLF_G2" ;
rdfs:label "NanoCellect WOLF G2 cell sorter" ;
NIFRID:synonym "WOLF G2 cell sorter" ;
definition: "Benchtop microfluidic cell sorter designed to gently analyze, sort, and plate live cells (stem cells, antibody-producing cells, immune cells) using low pressure and sterile, disposable fluidics. It enables high-viability sorting while preventing cross-contamination." .
SCR:028313 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Breedverse" ;
definition: "Software R packages with Shiny Interface. Modular R Shiny application that serves as a unified hub that lets users install and launch specialized breeding analysis tools - all from a single interface, with no command-line setup required." .
SCR:028314 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GenoBrew" ;
definition: "Software user-friendly Shiny interface for measuring marker panel efficiency according to previous datasets and visualizing CNV profiles." .
SCR:028315 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5828" ;
rdfs:label "Medical College of Wisconsin Cancer Center Stem Cell and Organoid Core Facility" ;
NIFRID:synonym "MCW-Stem Cell & Organoid Core (MCW-SCOC)",
"Medical College of Wisconsin Cancer Center MCW-Stem Cell & Organoid Core (MCW-SCOC)" ;
definition: "Facility provides access to human stem cells, 3D organoids, and other human-relevant disease models to support more predictive drug discovery, improved safety and toxicity assessment, and deeper mechanistic insight. Leveraging organoid and microphysiological platforms, the core enables next-generation therapeutics and clinical trial-in-a-dish approaches that advance biomedical innovation and precision medicine." .
SCR:028316 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5881" ;
rdfs:label "University of California Davis DNA Technologies and Expression Analysis Core Facility" ;
NIFRID:synonym "DNA Technologies and Expression Analysis Core" ;
definition: "Core offers high-throughput sequencing, genotyping, single-cell multi-omics, and spatial biology services as well as training and consultation. Next Generation Sequencing (NGS) technologies including Illumina and Element Biosciences short-read sequencing, PacBio and Nanopore long-read sequencing services provide sequencing and library preparation for these platforms. Genotyping is performed on the Fluidigm EP1 System for low to medium assay numbers, genotyping-by-sequencing assays, and with a range of genotyping-by-sequencing technologies (e.g. multiplexed amplicon, single-primer extension, reduced representation, and skim-seq protocols). Gene expression analysis is carried out by RNA-seq on short-read sequencers as well as full-length transcript sequencing on long-read systems. Single-cell transcriptome (high-throughput single-cell gene expression profiling) and multi-ome studies are enabled by our 10X Genomics Chromium X system and Parse Biosciences assays. Spatial transcriptome profiling is supported on the Xenium and Visium HD platforms with the help of our CytAssist instrument for fresh-frozen, fixed-frozen, and FFPE tissue sections. We offer annual Illumina and PacBio sequencing library preparation workshops, free consultations on project considerations and experimental design, and custom sequencing library prep solutions." .
SCR:028317 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5885" ;
rdfs:label "University of North Carolina at Chapel Hill Lineberger Office of Genomics Research Core Facility" ;
definition: "Cancer genomics project management and data sharing support facility." .
SCR:028318 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5887" ;
rdfs:label "University of Cincinnati Genomics, Epigenomics and Sequencing Core Facility" ;
NIFRID:synonym "Epigenomics and Sequencing Core",
"Epigenomics and Sequencing Core Facility",
"Genomics",
"University of Cincinnati College of Medicine Genomics" ;
NIFRID:abbrev "GES Core" ;
definition: "Facility focused on next-generation sequencing services. Offers advanced capabilities in next-generation sequencing, single-cell sequencing, and genomics and epigenomics services." .
SCR:028319 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5888" ;
rdfs:label "Nationwide Children's Hospital Flow Cytometry and Immune Monitoring Core Facility" ;
NIFRID:synonym "Nationwide Children's Hospital Flow Cytometry and Immune Monitoring Core" ;
definition: "Core provides instrumentation, training, and high-level scientific and technical expertise relating to conventional and spectral cytometry, cell sorting, small particle analysis, ELISA/ELISpot, PBMC processing and cryopreservation, and multiplex assays." .
SCR:028320 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_ZEISS_Xradia_620_Versa" ;
rdfs:label "Zeiss Xradia 620 Versa X-ray microscope" ;
NIFRID:synonym "ZEISS Xradia 620 Versa" ;
definition: "High-resolution 3D X-ray microscope (micro-CT) designed for non-destructive, submicron imaging of internal structures in materials science, electronics, and life sciences. It allows researchers to visualize 3D details at 500 nm resolution without cutting samples, using \"Resolution at a Distance\" (RaaD™) technology to image large or complex items." .
SCR:028321 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Zeiss_LSM5_PASCAL" ;
rdfs:label "Zeiss LSM5 PASCAL confocal laser scanning microscope system" ;
NIFRID:synonym "University of Melbourne Zeiss LSM5 PASCAL confocal laser scanning microscope system" ;
definition: "Specialized, compact confocal laser scanning microscope designed for high-resolution 3D fluorescence imaging. Key features include 2048 x 2048 pixel resolution, a point-scan mechanism, and compatibility with Zeiss Zen software for 3D reconstruction and image processing." .
SCR:028322 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5890" ;
rdfs:label "University College London Single Cell and Spatial Omics Platform Core Facility" ;
NIFRID:synonym "Single Cell and Spatial Omics Platform" ;
definition: "Core offers services in the field of bulk, single cell, spatial omics, FACs sorting and sequencing." .
SCR:028323 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "numbat" ;
NIFRID:synonym "Numbat" ;
definition: "Software tool for haplotype aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome. Haplotype aware analysis of somatic copy number variations from single-cell transcriptomes. It integrates signals from gene expression, allelic ratio, and population-derived haplotype information to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship." .
SCR:028324 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "BoneMarrowMap" ;
definition: "Software R package to enable rapid reference mapping and annotation of new scRNA-seq data across the spectrum of normal and malignant hematopoietic contexts. Single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic stem and progenitor cells and differentiated populations." .
SCR:028325 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker CellScape spatial proteomics system" ;
NIFRID:synonym "Bruker CellScape",
"Canopy Biosciences CellScape",
"CellScape Precise Spatial Multiplexing platform",
"CellScape XR" ;
definition: "Automated microscopy system for high-plex, subcellular spatial proteomics. System integrates automated microscope, fluidics unit for automated staining, and analysis software. It utilizes cyclic immunofluorescence with EpicIF technology to image, remove signals, and restain tissues to map proteins at single-cell resolution. System is developed by Canopy Biosciences, a Bruker Company, and is often used alongside AI-powered data analysis tools to classify cell phenotypes and visualize tissue architecture." .
SCR:028326 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5891" ;
rdfs:label "ÉTS Montréal LaCIME Scientific Platform Core Facility" ;
NIFRID:synonym "LaCIME scientific platform",
"School of Higher Technology LaCIME scientific platform" ;
definition: "Core provides equipment for the fabrication and advanced characterization of cyber-physical microdevices, particularly printed cyber-physical microdevices. Provide students and researchers with environment where engineers receive training with advanced skills in the analog, digital and mixed domains." .
SCR:028327 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5892" ;
rdfs:label "Mayo Clinic Genome Analysis Core Facility" ;
definition: "Core provides genomics services including next-generation sequencing, gene expression, and genotyping. It enables studies on human disease mechanisms, cancer, and rare diseases." .
SCR:028328 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100012992",
"GRID grid.459234.d",
"ISNI 0000 0001 2222 4302",
"Wikidata Q3577916" ;
rdfs:label "École de Technologie Supérieure; Montreal; Canada" ;
NIFRID:synonym "ETS Montreal",
"École de Technologie Supérieure" ;
definition: "Public engineering school in Montreal, Canada, affiliated with the Université du Québec system. Founded in 1974, it specializes in applied engineering education and research, with a strong focus on cooperative education (mandatory internships), industry collaboration, and practical, hands-on training for bachelor, master, and doctorate students." .
SCR:028330 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Longitudinal survival analysis and two-group comparison for predicting the progression of mild cognitive impairment to Alzheimer" ;
definition: "Project to compare two approaches for the construction of longitudinal predictive models, which were used here to estimate the conversion of mild cognitive impairment (MCI) to AD." .
SCR:028337 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Titi Monkey MRI Brain Atlas" ;
definition: "MRI-based atlas package for the titi monkey brain that includes a single subject atlas (UC Davis Titi monkey Neuroimaging Atlas (UCD-TiNA)), alongside a population atlas (UCD-TiNA_group) and a manually segmented atlas compilation (UCD-TiNA_mac)." .
SCR:028338 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Ion Torrent Genexus Purification System" ;
definition: "Automated instrument designed to extract, purify, and quantify nucleic acids (DNA/RNA) from diverse biological samples, preparing them for Next-Generation Sequencing (NGS). It accelerates laboratory workflows, allowing 20 minutes of hands-on time to yield NGS ready samples in ~2 hours." .
SCR:028339 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Plotter" ;
definition: "Web application made for plotting genomic data. Used for genomic composite visualization for bioinformaticians and bench scientists to visualize and analyze signal occupancy across genomic regions." .
SCR:028340 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "OncoDB" ;
NIFRID:synonym "OncoDB2.0" ;
definition: "Database offers integrated multi-omic data for patients across 33 cancer types. It encompasses gene expression, DNA methylation, somatic mutations, proteomic profiles, and chromatin accessibility, drawing from TCGA, GTEx, and CPTAC projects. Users can compare gene expression, DNA methylation, and protein levels between tumor and normal tissues, identifying differentially expressed genes and proteins, and examining gene-to-gene correlations. Provides oncogene mutation profiles and allows for survival analysis based on gene expression and methylation, linked to clinical parameters. Facilitates exploration of multi-omic correlations, such as gene expression with DNA methylation, and their variations with mutation status. Extends its analytical capabilities to include six major oncoviruses, offering insights into their impact on gene expression, methylation, and patient survival." .
SCR:028341 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Multi-Dimensional Viewer" ;
NIFRID:synonym "Multi-Dimensional Viewer (MDV)" ;
definition: "Web tool for analyzing, annotating and sharing multi-dimensional data. Visualisation platform used for spatial analysis." .
SCR:028342 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ChatMDV" ;
definition: "Software tool as natural language interface integrated with MDV that allows users to generate high-quality interactive visualisations through natural language commands. ChatMDV employs a retrieval-augmented generation (RAG) pipeline combined with large language models (LLMs) to translate user queries into reproducible Python code and interactive output. Module to add chatbot functionality to query Multi-Dimensional Viewer projects." .
SCR:028343 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Personal Cancer Genome Reporter" ;
NIFRID:synonym "Personal Cancer Genome Reporter (PCGR)" ;
definition: "Stand-alone software package for translation of individual tumor genomes for precision cancer medicine. PCGR interprets primarily somatic SNVs/InDels and copy number aberrations. The software extends basic gene and variant annotations from the Ensembl's Variant Effect Predictor (VEP) with oncology-relevant, up-to-date annotations, and produces interactive HTML reports intended for clinical interpretation." .
SCR:028344 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Xevo_G3_TOF" ;
rdfs:label "Waters Xevo G3 TOF MS Mass Spectrometry System" ;
NIFRID:synonym "Waters Xevo G3 QTof MS",
"Xevo G3 QToF Mass Spectrometer",
"Xevo G3 Quadrupole Time-of-Flight System",
"Xevo G3 TOF MS" ;
definition: "High-resolution, benchtop Quadrupole Time-of-Flight mass spectrometer designed for characterizing small molecules and biotherapeutics. Used for analyzing complex samples, offering quantitative/qualitative data, and seamless integration with ACQUITY Premier LC systems." .
SCR:028345 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "pairwiseCI" ;
definition: "Software R package provides wrapper functions to compute parametric, nonparametric, and bootstrap confidence intervals (CIs) for comparing two samples, specifically designed for all-pairs or many-to-one comparisons. It enables, but does not enforce, adjustments for multiple testing." .
SCR:028346 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.422632.3",
"ISNI 0000 0004 7591 144X",
"Wikidata Q30283823" ;
rdfs:label "New York Structural Biology Center" ;
NIFRID:synonym "New York Structural Biology Center (NYSBC)" ;
definition: "Non-profit research consortium located in Harlem, NY, providing advanced structural biology technologies to academic and commercial researchers. Founded by nine institutions, it specializes in cryo-electron microscopy (Cryo-EM), NMR spectroscopy, and X-ray crystallography to analyze molecular structures for drug discovery." .
SCR:028347 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MICE" ;
definition: "Source code for work submitted to journal. Multimodal foundation model for pan-cancer prognosis prediction developed on 14,468 patients across 30 cancer types using a collaborative multi-expert architecture that retains unique signals from each modality while modeling their interactions." .
SCR:028348 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ccRCC" ;
NIFRID:synonym "Clear cell renal cell carcinoma (ccRCC)" ;
definition: "Software code used in the multi-omics study of clear cell Renal Cell Carcinoma (ccRCC)." .
SCR:028349 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Combining a patch-based approach with a non-rigid registration-based label fusion method for the hippocampal segmentation" ;
NIFRID:synonym "LF_Patches: Hippocampal Segmentation via Patch-based Label Fusion and Non-rigid Registration" ;
definition: "Software MATLAB toolbox for the automatic segmentation of the hippocampus in brain MRI images. It implements a novel patch-based label fusion method that cooperates with a non-rigid registration-based label fusion approach. Used to automatically and accurately segment the hippocampus in MRI scans by combining two techniques." .
SCR:028350 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5894" ;
rdfs:label "University College London Molecular Biology Core Facility" ;
NIFRID:synonym "University College London Molecular Biology Facility" ;
definition: "Facility contains equipment for all basic molecular biology needs. Training and help are provided. Provides molecular biology services ranging from DNA preparations to cloning and mutagenesis projects." .
SCR:028351 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "METABRIC" ;
NIFRID:synonym "Molecular Taxonomy of the Breast Cancer International Consortium (METABRIC)" ;
definition: "Molecular Taxonomy of the Breast Cancer International Consortium (METABRIC) is a landmark study and dataset comprising primary breast tumour samples with detailed genomic, transcriptomic, and clinical data. It identified ten distinct \"integrative clusters\" (IntClust) based on copy number aberrations and gene expression, revealing new, clinically relevant subtypes with varying prognoses." .
SCR:028352 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Orbitrap_Astral_Zoom" ;
rdfs:label "Thermo Scientific Orbitrap Astral Zoom Mass Spectrometer" ;
NIFRID:synonym "Orbitrap Astral Zoom mass spectrometer" ;
definition: "Spectrometer includes: Fast Ion Filter, Bent Trap for Pre-Accumulation, High-speed Quadrupole, Faster Stepped Collision Energy, Enhanced Dynamic Range mode, TMT HR mode, low input mode, Enhanced Spectral Processing, support for Hybrid DIA experiments, and expanded BioPharma option including Thermo Scientific™ Astral™ analyzer support for top-down and middle-down measurements. Used to accelerate deep proteomics and single-cell analysis. Combines fast scan rates with high-resolution, accurate-mass (HRAM) measurements to detect more proteins, analyze thousands of cells daily, and improve precision oncology or clinical biomarker discovery." .
SCR:028353 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JSM-7800F" ;
rdfs:label "JEOL JSM-7800F Field Emission Scanning Electron Microscope" ;
NIFRID:synonym "JSM-7800F Field Emission Scanning Electron Microscope" ;
definition: "Ultra-high-resolution, Schottky field-emission scanning electron microscope (FE-SEM) designed for advanced nano-characterization, combining in-lens technology with a super hybrid lens to achieve 0.8 nm resolution. It is utilized for high-resolution imaging, elemental analysis (EDS/WDS), and crystallographic analysis (EBSD) of materials, magnetic samples, and non-conductive specimens, even at very low voltages (down to 10 V)." .
SCR:028354 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_CAMECA_SX100" ;
rdfs:label "CAMECA SX100 Electron Probe Microanalyzer" ;
NIFRID:synonym "SX100 Electron Probe Microanalyzer" ;
definition: "Fully automated instrument used for nondestructive, in-situ, micro-scale elemental characterization. It is generally equipped with five vertical crystal spectrometers (WDS) and an energy dispersive analyzer (EDS), operating via proprietary Windows-based Peak Sight software or updated with third-party software like Probe for EPMA." .
SCR:028355 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Krios_G3i" ;
rdfs:label "Thermo Scientific Krios G3i Cryo-Transmission Electron Microscope" ;
NIFRID:synonym "Krios G3i Cryo-TEM",
"Krios G3i Cryo-Transmission Electron Microscope",
"Thermo Scientific™ Krios™ G3i Cryo-Transmission Electron Microscope (Cryo-TEM)" ;
definition: "High-end 300kV instrument designed for automated, high-resolution 3D imaging of biological samples, such as proteins and viruses, at molecular or atomic levels. It enables researchers to study samples in their native, hydrated state, primarily for drug discovery and structural biology." .
SCR:028356 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Attune_CytPix" ;
rdfs:label "Invitrogen Attune CytPix Flow Cytometer" ;
NIFRID:synonym "Attune CytPix Flow Cytometer" ;
definition: "Attune CytPix Flow Cytometer combines acoustic focusing flow cytometry with a high-speed camera to simultaneously collect fluorescent data and high-resolution brightfield images for each cell. It is used for automated, AI-driven morphological analysis alongside traditional immunophenotyping, allowing users to validate cell populations, identify cell-to-cell interactions, and verify cell health (e.g., apoptosis, contamination) in real-time. Attune CytPix is a benchtop analysis cytometer with 4 lasers (488, 405, 561, and 633nm) and a brightfield camera." .
SCR:028357 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5899" ;
rdfs:label "University of Manchester Biomolecular NMR Core Facility" ;
NIFRID:synonym "Manchester Biomolecular NMR Facility" ;
definition: "Core provides advanced NMR spectroscopy for researching the atomic-level structure, dynamics, and interactions of biological macromolecules. It supports structural biology, biocatalysis, and drug discovery by analyzing proteins, DNA, RNA, and carbohydrates. Includes 800MHz NMR spectrometer with H/F-C-N Cryoprobe." .
SCR:028358 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5900" ;
rdfs:label "New York Structural Biology Center SEMC Core Facility" ;
NIFRID:synonym "New York Structural Biology Center Simons Electron Microscopy Center",
"Simons Electron Microscopy Center (SEMC)" ;
definition: "Provides advanced resources in structural biology. Offers access to instruments, including multiple transmission electron microscopes (TEMs) and cryo-FIB/SEM systems. Trains scientists, from beginners to experienced users, on sample preparation (plunge/high-pressure freezers) and advanced EM techniques. Helps researchers solve the 3D structures of proteins and cellular components at atomic resolution." .
SCR:028359 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Bruker_Invenio_S" ;
rdfs:label "Bruker Invenio S FT-IR Spectrometer" ;
NIFRID:synonym "Bruker Invenio S" ;
definition: "Bruker Invenio S is an entry-level FT-IR spectrometer designed for routine productivity and basic research and development. Analytical instrument that identifies chemical compounds and molecular structures by measuring how samples absorb infrared light. Offers upgradable Invenio platform featuring the Transit channel and MultiTect technology." .
SCR:028360 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Jasco_P-2000" ;
rdfs:label "Jasco P-2000 Digital Polarimeter" ;
definition: "Customizable polarimeter used to measure the optical rotation of chiral compounds. It identifies, analyzes, and determines the purity and concentration of liquids (specifically optically active samples) in pharmaceutical, chemical, and food manufacturing industries, featuring customizable light sources for UV-Vis to NIR regions." .
SCR:028361 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Jasco_V-750" ;
rdfs:label "Jasco V-750 UV-Vis Spectrophotometer" ;
definition: "High resolution UV-Visible spectrophotometer with double-beam, single monochromator, variable spectral bandwidth and a photomultiplier tube (PMT) detector. Used for measuring absorbance, transmittance, and reflectance of liquid or solid samples across the UV-visible range 190-900nm. Used for quantitative analysis (concentration measurement) and spectral characterization." .
SCR:028362 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bruker Sierra SPR-32 Pro Analyzer" ;
NIFRID:synonym "Bruker Sierra SPR-32 Analyzer" ;
definition: "High-throughput, 32-spot Surface Plasmon Resonance (SPR) system. The \"Pro\" designation commonly used by Bruker highlights its capabilities, including 8 flow cells with 4 spots each, designed for rapid, label-free molecular interaction analysis. Used for the Real-Time, Label-Free characterization of molecular interactions." .
SCR:028363 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5907" ;
rdfs:label "University of California at Berkeley Cal-Cryo QB3-Berkeley Core Facility" ;
NIFRID:synonym "Cal-Cryo QB3-Berkeley" ;
definition: "Core provides researchers with access to Cryo Electron Microscopes and related tools for high resolution structural biology imaging experiments." .
SCR:028364 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_3D_Cell_Explorer_96focus" ;
rdfs:label "Nanolive 3D Cell Explorer 96focus Imaging System" ;
NIFRID:synonym "3D Cell Explorer 96focus" ;
definition: "Label-free live-cell imaging system designed for high-content screening. Label free live cell imaging microscope allows to instantly observe and analyze the inside of living cells in 3D without using toxic stains, leveraging AI-powered digital assays and holographic tomography to automate workflows and provide fast, high-resolution data." .
SCR:028365 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "SCANDAN-DICOM-labelling" ;
definition: "Software tool for rules for DICOM tag based labelling. Regular expression used during the SCANDAN project to label MRI scans based on DICOM tag." .
SCR:028366 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ggstatsplot" ;
definition: "Software R package extension of ggplot2 designed to create information rich plots that include details from statistical tests directly within the visual output. Used to enhance {ggplot2} plots with statistical analysis." .
SCR:028367 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5859" ;
rdfs:label "Roswell Park Comprehensive Cancer Center Bioanalytics, Metabolomics and Pharmacokinetics Shared Resource BMPK Core Facility" ;
NIFRID:synonym "Bioanalytics",
"Metabolomics & Pharmacokinetics Shared Resource (BMPK)" ;
definition: "Core provides highly sensitive measurements for an extensive array of chemotherapeutic agents and metabolites to support basic research and preclinical/clinical drug development." .
SCR:028368 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5896" ;
rdfs:label "Roswell Park Comprehensive Cancer Center Genomics Shared Resource GSR Core Facility" ;
NIFRID:synonym "Genomics Shared Resource (GSR)" ;
definition: "Core offers services including expert technical staff performing all aspects of sample preparation, QC, assay design and analysis. Provides integrated set of tools and services for genomic analysis. Expertise and services include clone generation, high throughput mapping, array technology development. Offers genomics platforms including data analysis, training and education on instruments and methodologies, complete discovery/screening to validation services, and full Laboratory Information Management System (LIMS) request, workflow and sample management." .
SCR:028369 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5895" ;
rdfs:label "Medical University of South Carolina Hollings Cancer Center Cell and Molecular Imaging Core Facility" ;
NIFRID:synonym "Cell & Molecular Imaging" ;
definition: "Core provides MUSC Hollings Cancer Center members with sophisticated equipment, technologies, training, and expertise required for successful, cell and tissue-based microscopic imaging and image analysis.Optical Microscopy Services include equipment and expertise to facilitate imaging of tissues and cells by Hollings members. Innovative Techniques service include development and application of new imaging techniques to meet the emerging scientific needs of Hollings members.Education and Training services include education, trainning, and consultation on imaging technologies that enable scientific discovery, including a biennial Charleston Workshop on Light Microscopy for the Biomedical Sciences, as well as a lecture series on cell and molecular imaging, especially as it relates to tumor biology." .
SCR:028370 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5901" ;
rdfs:label "Roswell Park Comprehensive Cancer Center Bioinformatics Shared Resource BIOINF Core Facility" ;
NIFRID:synonym "Bioinformatics Shared Resource (BIOINF)" ;
definition: "Core provides bioinformatics assistance for design, analysis and interpretation of genomics, proteomics and other studies for better understanding of cancer biology, thereby facilitating translation of cancer omics discoveries to cancer treatment. Provides services in design of experiments, raw omics data processing, data analysis and interpretation, data mining and integration, informatics infrastructure for data sharing and management, review and prepare grants and manuscripts, software evaluation, new method and database development,bioinformatics education and training for investigators." .
SCR:028371 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5904" ;
rdfs:label "Roswell Park Comprehensive Cancer Center Biostatistics and Statistical Genomics Shared Resource BSGSR Core Facility" ;
NIFRID:synonym "Biostatistics & Statistical Genomics Shared Resource (BSGSR)" ;
definition: "Core offers services in design, oversight, implementation, analysis, publication, and reporting of scientific studies including articulating study objectives and hypotheses, grant writing, conceiving appropriate cost-effective designs and models for achievement of study objectives, monitoring interim and final analyses, and co-authoring abstracts and manuscripts." .
SCR:028372 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5902" ;
rdfs:label "Roswell Park Comprehensive Cancer Center Biomedical Research Informatics Shared Resource BRISR Core Facility" ;
NIFRID:synonym "Biomedical Research Informatics Shared Resource (BRISR)" ;
definition: "Core provides consultations and services for investigators and study teams in the areas of clinical research, informatics, and data science. BRISR helps researchers harness internal and external data resources and provide informatics-driven solutions for clinical and translational research. Offers the infrastructure and processes to establish and monitor data standards, quality integration and distribution, educational and training opportunities. Provide services in three main areas: (1) Clinical data management and delivery for research, (2) Custom software development for research, and (3) Artificial intelligence analysis for clinical and bioinformatics research." .
SCR:028373 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5903" ;
rdfs:label "Roswell Park Comprehensive Cancer Center GMP Engineering and Cell Manufacturing Core Facility" ;
NIFRID:synonym "GMP Engineering & Cell Manufacturing Facility (GEM)" ;
definition: "Core provides clean rooms, cell therapy equipment, manufacturing know-how, capabilities and comprehensive suite of quality assurance and control procedures." .
SCR:028374 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_685" ;
rdfs:label "University of Tennessee at Knoxville Genomics Core Facility" ;
NIFRID:synonym "UT Genomics Core" ;
definition: "Genomics core is a self-supporting core facility specializing in Sanger sequencing, SNP/fragment analysis, and Next Generation DNA Sequencing using Illumina's MiSeq platform. Provides sequencing services." .
SCR:028375 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5898" ;
rdfs:label "University of Massachusetts Chan Medical School BioImage Data Management and Sharing Core Facility" ;
NIFRID:synonym "BioImage Data Management and Sharing Core" ;
definition: "Core helps research scientists and imaging core facilities produce, handle, safeguard, and share high-quality bioimage data. Ensures compliance with standards for image data management and sharing. Helps to plan experiments, track experimental conditions, and produce data.BioImage DMS eases the burden of data publication and sharing when the project is published." .
SCR:028376 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5906" ;
rdfs:label "Roswell Park Comprehensive Cancer Center Biorepository and Laboratory Services Shared Resource BLS Core Facility" ;
NIFRID:synonym "Biorepository & Laboratory Services Shared Resource (BLS)" ;
definition: "Core is comprehensive data and biospecimen bank (malignant and normal tissue and their derivatives, blood and bone marrow) for research along with a range of services that accompany biospecimens. Facilitates access to human tissue, blood and bone marrow for investigators with Institutional Review Board (IRB) approved protocols emphasizing translational research. Helps investigators to establish Biospecimen and Data Research (BDR) protocols and supports the submission of grants by providing feasibility analysis, cost estimates and letters of support." .
SCR:028377 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5897" ;
rdfs:label "Rensselaer Polytechnic Institute RPI-Proteomics Core Facility" ;
NIFRID:synonym "RPI-Proteomics" ;
definition: "Facility provides mass spectrometry-based analytical support.Houses multiple mass spectrometry platforms with complementary ionization capabilities, including EI, APCI, ESI, and MALDI, enabling qualitative and quantitative analysis of diverse sample types across a range of volatility, polarity, and molecular weight. Several systems are coupled with chromatographic separation platforms, allowing complex mixtures to be separated prior to mass spectrometric analysis. Supports research in areas including proteomics, small-molecule analysis, carbohydrate and glycosaminoglycan-related analysis, metabolomics-oriented method development, and drug-discovery-related projects.Particular strength of the Core is the analysis of complex biomolecules, including proteins, peptides, carbohydrates, and heparin/glycosaminoglycan-related samples. The Core works closely with investigators to evaluate feasibility, develop appropriate workflows, and interpret mass spectrometry data in the context of each project." .
SCR:028378 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5905" ;
rdfs:label "Roswell Park Comprehensive Cancer Center Advanced Tissue Imaging Shared Resource ATISR Core Facility" ;
NIFRID:synonym "Advanced Tissue Imaging Shared Resource (ATISR)" ;
definition: "Core offers streamlined, multiplexed tissue analysis services including tissue sectioning, staining, imaging, spatial RNA sequencing, analysis and interpretation of results." .
SCR:028379 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_26" ;
rdfs:label "University of Vermont Office of Animal Care Management Core Facility" ;
NIFRID:synonym "Office of Animal Care Management" ;
definition: "Core oversees the operation of research animal facilities at the University of Vermont. Animal facilities houses mainly mice and rats. Animal models facilitate discovery in the areas of infectious disease, endocrinology and metabolic disease, cancer and chemotherapy, immunology and respiratory disease, among others. The University of Vermont's Animal Care program is fully accredited by the Association for the Assessment and Accreditation of Laboratory Animal Care (AAALAC, International)." .
SCR:028380 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Waters_SQ_Detector_2" ;
rdfs:label "Waters SQ Detector 2 Mass Spectrometer" ;
NIFRID:synonym "Waters SQ Detector 2" ;
definition: "Compact benchtop single quadrupole mass spectrometer designed for routine, high-performance liquid chromatography (LC-MS) applications. Used for molecular weight confirmation, impurity identification, and quantitative analysis. Compatible with a broad range of chromatography platforms and ionization sources, including APCI and UniSpray, the SQ Detector 2 is the ultimate single quadrupole mass detector for chromatography." .
SCR:028381 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Waters_BGM" ;
rdfs:label "Waters Binary Gradient Modules Mixing Pumps" ;
NIFRID:synonym "Waters Binary Gradient Modules (BGM)" ;
definition: "High pressure, precision solvent mixing pumps designed for HPLC and preparative scale purification. They mix two different solvents to create precise gradient compositions, allowing for, or improving, the separation and isolation of target compounds in chemical or biological samples." .
SCR:028382 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5910" ;
rdfs:label "Medical College of Wisconsin Cancer Center Biostatistics Shared Resource Core Facility" ;
definition: "Core services include experimental design, sample size calculation, randomization, analysis plans, data analysis, grant and manuscript preparation, full clinical trial support, and innovative targeted methods development." .
SCR:028383 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_JEOL_JEM_120i" ;
rdfs:label "JEOL JEM-120i Transmission Electron Microscope" ;
NIFRID:synonym "JEOL JEM 120i TEM" ;
definition: "Modern 120 kV Transmission Electron Microscope (TEM) designed for high-throughput screening and ease of use in biological, materials science, and nanotechnology research. Resolution: Achieves 0.14 nm (High Resolution) to 0.2 nm (High Contrast) lattice resolution. Magnification: Range from x50 to x1,500,000 (HR) or x1,200,000 (HC). Imaging System: Includes a 4-megapixel, high-speed, high-sensitivity JEOL CMOS camera (NeoView) as standard, with options for a 19-megapixel (SightSKY) camera. Versatile Applications: It can be used for cryo-TEM screening, material sciences, and high-throughput asbestos analysis." .
SCR:028384 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5912" ;
rdfs:label "Johns Hopkins University School of Medicine Center for Proteomics Discovery CPD Core Facility" ;
definition: "Core facility that helps biomedical researchers design and execute proteomics (and metabolomics/lipidomics) studies from sample preparation and LC-MS/MS data acquisition to protein/PTM identification and quantification and advanced bioinformatics/statistical analysis. CPD supports workflows, including label-free (DIA/DDA) and TMT multiplexed quantitative proteomics, phosphoproteomics/other PTMs, targeted PRM, single-cell proteomics, spatial proteomics, cell-type-specific proteomics, thermal proteome profiling, and more." .
SCR:028385 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Amersham_ImageQuant_800" ;
rdfs:label "Amersham ImageQuant 800 Imaging System" ;
NIFRID:synonym "Amersham ImageQuant 800",
"Amersham ImageQuant 800 Western Blot Imaging System" ;
definition: "Compact imaging system designed for chemiluminescence, fluorescence (including IR) and colorimetric detection. Built with advanced charge-coupled device (CCD) technology, it delivers high-resolution, publication-quality images across a wide range of applications—including gels, membrane blots, multiwell plates and petri dishes." .
SCR:028386 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Thermo_Scientific_BB15_CO2" ;
rdfs:label "ThermoFisher Scientific BB15 CO2 incubator" ;
NIFRID:synonym "Thermo Scientific BB 15 CO₂" ;
definition: "Laboratory instrument designed for cell and tissue culture, providing precise temperature (up to 55°C) and CO2 control for optimal, stable growth conditions. It features air-jacketed heating, a fast-recovering humidification system, and options for stainless steel or copper interiors to reduce contamination risk." .
SCR:028387 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Cytek_Amnis_ImageStreamX_Mk_II" ;
rdfs:label "Cytek Amnis ImageStreamX Mk II Imaging Flow Cytometer" ;
NIFRID:synonym "Cytek Amnis ImageStreamX Mk II system" ;
definition: "Benchtop, multispectral imaging flow cytometer that merges the high-throughput, quantitative capabilities of flow cytometry with the visual detail of microscopy. It captures up to 12 channels of images including brightfield, darkfield, and fluorescence for every cell in flow, allowing researchers to study protein localization, cell-cell interactions, and morphology at a rate of thousands of cells per second." .
SCR:028388 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5909" ;
rdfs:label "Roswell Park Comprehensive Cancer Center Translational Imaging Shared Resource TISR Core Facility" ;
NIFRID:synonym "Translational Imaging Shared Resource (TISR)" ;
definition: "Core provides specialized preclinical imaging services including image acquisition, quantitative image analysis, multidimensional renderings and data sets for research purposes." .
SCR:028389 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5908" ;
rdfs:label "Roswell Park Comprehensive Cancer Center Comparative Oncology Shared Resource COSR Core Facility" ;
NIFRID:synonym "Comparative Oncology Shared Resource (COSR)" ;
definition: "Core offers services for preclinical models including barrier facilities with fully automated environmental controls for the housing of research models. Specialized husbandry with trained staff who perform all manipulations inside Biosafety cabinets for maintenance of a pathogen-free environment for models held in micro isolation (MI) housing systems. In addition to housing pre-clinical models in state-of-the-art facilities, COSR provides Specialized Surgical Services and procedural training, consultation in experimental design, irradiation services, in-house hematological testing, genotyping services, design and conduct of pre-clinical toxicological studies." .
SCR:028390 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5911" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Human Pluripotent Stem Cell Core Facility" ;
NIFRID:synonym "CHOP Human Pluripotent Stem Cell Core" ;
definition: "Core generates induced pluripotent stem cell (iPSC) lines from somatic cells including peripheral blood mononuclear cells and fibroblasts. The Core has established standard operating procedures for Pluripotent stem cell growth and maintenance, Genome editing technologies including CRISPR-CAS9 and Differentiation to germ layer and derivative tissues of interest. Provides enrichment training courses for investigators interested in learning how to work with pluripotent stem cells and/or establish the pluripotent stem cell technology in their own labs." .
SCR:028391 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Predicting Alzheimer’s conversion in mild cognitive impairment patients using longitudinal neuroimaging and clinical markers" ;
definition: "Project to quantify the impact of longitudinal predictive models with single- or multisource data for predicting MCI-to-AD conversion and identifying a very small subset of features that are highly predictive of conversion." .
SCR:028392 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bokeh" ;
definition: "Software Python package for interactive and static data visualization.Interactive visualization library for modern web browsers. Provides concise construction of graphics and affords high-performance interactivity across large or streaming datasets." .
SCR:028393 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Environmental influences on Child Health Outcomes" ;
NIFRID:synonym "Environmental influences on Child Health Outcomes (ECHO)",
"NIH Environmental influences on Child Health Outcomes" ;
definition: "ECHO project to better understand the effects of physical, chemical, and biological exposures, social and behavioral factors, and the natural and built environments on child health and development, with focus in the following areas: Pre-, peri-, and post-natal outcomes; Upper and lower airway; Obesity; Neurodevelopment; and Positive health To achieve this goal, the ECHO program supports multiple, synergistic, longitudinal studies of existing and ongoing study cohorts." .
SCR:028394 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5917" ;
rdfs:label "Field Museum of Natural History Scanning Electron Microscopy Laboratory Core Facility" ;
definition: "Interdepartmental core facility for scanning electron microscope imaging and elemental analysis of objects. Provides Hitachi SU7000 field emission scanning electron microscope, an Oxford Ultim Max 170 infinity EDS detector with BEX (backscatter electron and X-ray imaging detector), a Leica EM Ace600 sputter coater and a Hitachi IM4000II ion milling system." .
SCR:028395 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Crossref Funder ID 100009304",
"GRID grid.299784.9",
"ISNI 0000 0001 0476 8496",
"Wikidata Q1122595" ;
rdfs:label "Field Museum of Natural History" ;
definition: "Scientific and educational institution dedicated to exploring the diversity of life on Earth and human culture. It is renowned for its collection of over 40 million artifacts and specimens, including world-class dinosaur fossils, ancient cultural exhibits, and active scientific research labs." .
SCR:028396 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5941" ;
rdfs:label "Field Museum of Natural History Elemental Analysis Core Facility" ;
NIFRID:synonym "Elemental Analysis Facility (EAF)",
"Field Museum of Natural History Elemental Analysis Facility" ;
definition: "Core consists of an Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) laboratory, an X-ray Fluorescence laboratory, a Raman laboratory, and an optical mineralogy laboratory. Museum curators and researchers are using this instrumentation extensively to further research programs on early state expansion in the Andes, evolving social networks on the north coast of Papua New Guinea, the social dynamics of early village societies and the emergence of early states, African pre-industrial civilizations and, trade and exchange around the Indian Ocean (Laure Dussubieux). In addition to research conducted by Field Museum staff, the EAF collaborates with scientists from other institutions, bringing researchers and students from all over the country to The Field Museum to learn about compositional analysis of ancient materials to enhance their research on a very wide range of anthropological topics." .
SCR:028397 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5918" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Transgenic Core Facility" ;
NIFRID:synonym "CHOP Transgenic Core" ;
definition: "Transgenic Core at Childrens Hospital Research Institute, working in partnership with the University of Pennsylvania CRISPR Core Facility, build complex mouse and rat models,genetically manipulating the mouse and rat genome to meet specific research needs utilizing genetic engineering approaches. Core provides services for the generation and preservation of genetically altered mice or rats." .
SCR:028398 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5922" ;
rdfs:label "Children's Hospital of Philadelphia CHOP High Throughput Sequencing Core Facility" ;
NIFRID:synonym "High Throughput Sequencing Core",
"High Throughput Sequencing Core (HTS Core)" ;
definition: "Core is service facility providing instrumentation, library preparation, and sequencing services to CHOP, UPenn, and external investigators in genomic, epigenomic and transcriptomic studies." .
SCR:028399 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5925" ;
rdfs:label "Children's Hospital of Philadelphia CHOP CAG Biorepository Core Facility" ;
NIFRID:synonym "CAG Biorepository Core" ;
definition: "Pediatric biobank, hosting more than 600,000 biological samples that have been genotyped or sequenced in CAGs CLIA and CAP-accredited high-throughput centers. This core offers services in DNA and RNA extraction and QC." .
SCR:028400 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5926" ;
rdfs:label "Children's Hospital of Philadelphia CHOP CAG Genotyping Core Facility" ;
NIFRID:synonym "CAG Genotyping Core" ;
definition: "Core is equipped with liquid handling technology and experienced staff members. Offers both standard and custom Illumina array project design. With the capacity to process >2300 samples/week and generate >480 million genotypes per day, the genotyping core fully integrates with our Biorepository and Bioinformatics group, offering the collaborator the opportunity for a seamless experience from DNA extraction to data release." .
SCR:028401 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5929" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Single Cell Technology Core Facility" ;
NIFRID:synonym "Single Cell Technology Core" ;
definition: "Core offers services and access to single-cell, spatial and in situ technologies. Provides instruments, experienced research assistants and bioinformaticians to experimental and computational support. Services include 10x Genomics single cell assays, 10x Genomics Visium CytAssist and Visium HD spatial transcriptomics, 10x Genomics Xenium in situ spatial transcriptomics, Vizgen MERSCOPE in situ spatial transcriptomics, NanoString GeoMx Digital Spatial Profiler RNA and protein assays." .
SCR:028402 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5937" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Clinical Vector Characterization Core Facility" ;
NIFRID:synonym "Clinical Vector Characterization" ;
definition: "Core provides manufacturing of clinical and pre-clinical Adeno-Associated Virus (AAV) vectors of serotypes 1, 2, 5, 6, 8, 9, and Lentivirus (LV) vectors. Novel or modified serotypes will require development prior to scale-up. Products for clinical use are manufactured in compliance with Current Good Manufacturing Practices (cGMP) for Phase 1 and 2 clinical trials. To support pre-clinical work, including pharmacology and toxicology studies, core offers products manufactured using a GMP-comparable process. Research-grade products for proof-of- principle and bridging studies are also offered.Core Facility uses a patented vector production technology and a highly efficient purification process that uses combined column and gradient centrifugation-based process steps. This system has manufactured clinical-grade AAV vectors. Prior to the final release of the clinical vectors, the vector product is subjected to numerous tests to ensure quality. Core also provides federal regulatory documentation and necessary certifications." .
SCR:028403 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5923" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Clinical In Vivo Gene Therapy Core Facility" ;
NIFRID:synonym "Clinical In Vivo Gene Therapy Core" ;
definition: "Core experts offers complex gene therapy trials. Ensures licensed gene therapies are available in our clinics." .
SCR:028404 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5920" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Large Animal Imaging Facility LAIF Core Facility" ;
NIFRID:synonym "Children's Hospital of Philadelphia CHOP Large Animal Imaging Core (LAIF)",
"LAIF Core",
"Large Animal Imaging Facility (LAIF)" ;
definition: "Core facilitates advanced MR image-guided interventional and noninvasive procedures to support research across a broad range of disease areas, including neurodegenerative, cardiothoracic, and reproductive disorders. Imaging capabilities span structural MRI, diffusion imaging, DCE and ASL perfusion, spectroscopy, angiography, cardiac imaging, tissue elastography, functional imaging, flow quantification, and quantitative T1, T2, and T2* mapping.In collaboration with the Division of Veterinary Resources (DVR), we encourage investigators to consult with our teams on all scientific, medical, technical, and compliance aspects of studies involving large animal models. Investigators are expected to obtain Institutional Animal Care and Use Committee (IACUC) approval before initiating study activities. Core provides comprehensive data processing, post-processing, and quantitative image analysis support to help investigators extract meaningful outcomes from complex imaging datasets. These services include image reconstruction workflows, multimodal image registration, segmentation, volumetric and regional quantification, diffusion and tract-based analysis, spectroscopy processing, and development of customized pipelines tailored to specific study needs.Provides support in generating high-quality preliminary data for grant applications, instrument proposals, and translational research initiatives by helping design imaging strategies, optimize acquisition protocols, and deliver rigorous quantitative analyses that strengthen scientific aims.For larger research programs, the LAIF Core can assist with processing and managing large-scale imaging datasets to support longitudinal studies, multisubject analyses, and publication-ready results." .
SCR:028405 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5921" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Small Animal Imaging Facility SAIF Core Facility" ;
NIFRID:synonym "Small Animal Imaging Facility (SAIF)" ;
definition: """Core serves CHOP researchers with translational imaging capabilities. Provided imaging platform integrates multiple modalities including MRI, PET, CT, Optical, and US for monitoring disease progression and therapeutic response in vivo in small animal models.
Services include Selecting the optimal imaging modality, Design and optimization of acquisition protocols, Expert execution of in vivo imaging experiments, Training for new users on image acquisition, Advanced data analysis and project management.Provides technical expertise and translational capability.""" .
SCR:028406 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5934" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Pathology Core Facility" ;
NIFRID:synonym "Pathology Core Laboratory Children's Hospital of Philadelphia Research Institute" ;
definition: "Core provides histopathology, Immunohistochemistry, tissue microarray, and imaging services. Staff offer experience in all aspects of tissue processing, histological techniques, antibody work-up, and morphologic analysis. Offers tools to facilitate high throughput analysis of tissue sections and imaging. The Pathology Core is located in the A Level of Colket Translational Research Building (CTRB) Room A410. Staff is available for consultation, troubleshooting, and assistance in planning and interpreting experiments histopathology and related techniques." .
SCR:028407 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5939" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Comparative Medicine Services Core Facility" ;
NIFRID:synonym "Comparative Medicine Service Core" ;
definition: "Core provides support for nonclinical research programs. Offers expertise to design, conduct, and oversee a wide range of animal studies. Services include Grant and funding application support, Budget development and financial planning, Experimental design and study planning, Study protocol drafting, implementation, and management, IACUC protocol guidance and consultation, Standard Operating Procedure (SOP) development, management, and archiving, Training delivery and documentation, Study execution and data generation, Secure archiving of study materials and data. Core offers expertise in Pharmacokinetic studies, Biodistribution studies, Toxicology and reproductive toxicology studies, Medical device testing, Surgical model development." .
SCR:028408 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5935" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Microbiome Center Core Facility" ;
NIFRID:synonym "CHOP Microbiome Center" ;
definition: "Core is sequencing and analytical resource of the PennCHOP Microbiome Program, providing end-to-end solutions for microbiome research. Sequencing lab offers expertise in next-generation DNA sequencing for microbiome studies, working with customers to provide optimized workflows and protocols customized for each study. Provides expertise in bioinformatics and statistical analysis of microbiome data. Develops an analytical plan specific to your project and can integrate microbiome data with other data sources, such as metabolomics or dietary intake information." .
SCR:028409 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5938" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Research Vector Core Facility" ;
NIFRID:synonym "Research Vector Core (RVC)" ;
definition: "Core provides premium recombinant adeno-associated viral (AAV) and lentiviral vectors to support basic research and preclinical studies. Provides expertise in producing custom vector constructs at multiple scales, rigorous quality control standards, and technical support. Services enable gene transfer and accelerate translational research and therapeutic development." .
SCR:028410 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5940" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Biostatistics and Data Management Core Facility" ;
NIFRID:synonym "Biostatistics and Data Management Core" ;
definition: "Core offers biostatistics and data management services, expertise in the design of experiments, planning of clinical protocols, analysis and interpretation of data, and presentation and dissemination of results. Services include designing case report forms, developing databases, creating data management plans, developing metrics to report on study progress, and delivering high quality datasets for analysis. Core offers free limited consulting for data management and statistical questions. Offers experience with the submission of a Biologics License Application (BLA). Core is available to investigators seeking guidance with clinical trial start-up, oversight, and regulatory submission." .
SCR:028411 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5930" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Small Molecule and Metabolite Core Facility" ;
NIFRID:synonym "Small Molecule and Metabolite Core" ;
definition: "Core focuses on quantitative bioanalytical assay development, validation and implementation for drugs, metabolites and biomarkers in blood, serum, plasma, urine, ultrafiltrate and microdialysate utilizing mass spectrometry techniques." .
SCR:028412 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5932" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Qualitative Research Core Facility" ;
NIFRID:synonym "Qualitative Research Core" ;
definition: "Core supports all Children's Hospital of Philadelphia Research Institute personnel and faculty who are interested in utilizing qualitative methods. Provides research support across a broad range of settings, including in-hospital clinical research, primary care, public health, and community-based settings. Services include free introductory videos, yearly seminars, customized project workshops, and hands-on project support and grantmaking." .
SCR:028414 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5919" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Aquatic Zebrafish Core Facility" ;
NIFRID:synonym "Aquatic Zebrafish Core" ;
definition: "Core offers zebrafish research services and provides fish husbandry. Services include experiments designing and performing, teaching zebrafish techniques.Provides special expertise in disease modeling by creation of mutant and transgenic lines, analysis of disease phenotypes, and drug testing." .
SCR:028415 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5936" ;
rdfs:label "Children's Hospital of Philadelphia CHOP Engineered Cell Therapy Core Facility" ;
NIFRID:synonym "CHOP Engineered Cell Therapy Cores" ;
definition: "Core provides services and expertise to advance chimeric antigen receptor (CAR) T or other cell therapy research.Services include guidance in the design, construction, and selection of CARs and other cell therapies against a multitude of targets and diseases. Core offers small-scale lentivirus production and small-scale T cell transduction and expansion for experimental purposes." .
SCR:028416 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5927" ;
rdfs:label "Children's Hospital of Philadelphia CHOP CAG Sequencing Core Facility" ;
NIFRID:synonym "CAG Sequencing Core",
"CAG Sequencing Laboratory" ;
definition: "Cores Sequencing operations are integrated with Biorepository and Bioinformatics teams to keep all stages of a collaborators studies connected. Core offers genomics services in NovaSeq, Single Cell 10xGenomics, various library preparations including bulk RNAseq, Whole Genome/Whole Exome, and Sanger Sequencing including fragment analysis." .
SCR:028417 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scRNAseq" ;
definition: "Software R package for collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata." .
SCR:028418 a NLX:63400,
owl:NamedIndividual .
SCR:028419 a NLX:63400,
owl:NamedIndividual .
SCR:028420 a NLX:63400,
owl:NamedIndividual .
SCR:028421 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "leidenalg" ;
definition: "Software Python package for network analysis and Leiden community detection/clustering algorithm commonly used in single cell analysis for biology." .
SCR:028422 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5946" ;
rdfs:label "Charité Berlin University of Medicine Scientific Workshop Core Facility" ;
definition: "Core Facility for the development and manufacturing of experimental medical devices. Offers advise on experimental design, draft technical proposals, and support in the realization of prototypes and patent ideas." .
SCR:028423 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Waters_Discovery_TGA_5500" ;
rdfs:label "Waters Discovery TGA 5500 Thermal Analyzer" ;
NIFRID:synonym "Waters Discovery TGA 5500" ;
definition: "Thermogravimetric analyzer used to measure a material’s weight change (decomposition, oxidation, or dehydration) as it is heated, cooled, or held at a constant temperature. It is used in research and quality control to analyze polymers, pharmaceuticals, and composites for stability and composition." .
SCR:028424 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Peptoma" ;
NIFRID:synonym "Peptide Open Science Platform",
"PEPTOMA AI Engine" ;
definition: "Web open decentralized science platform for peptide sequence analysis and community annotation. Researchers submit amino acid sequences for AI-powered bioactivity scoring, structure prediction, and toxicity assessment. Results are publicly annotated by the community and secured on the Solana blockchain for verifiable, censorship-resistant research records." .
SCR:028425 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CycSim" ;
definition: "Software tool as context-based long-read simulator that models sequence-context-dependent errors from empirical sequencing data, coupled with a Bayesian optimization framework for systematic parameter tuning." .
SCR:028426 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CCIVR" ;
NIFRID:synonym "Comprehensive Cis-NATs Identifier Via RNA-seq data" ;
definition: "Software Python package tool that facilitates the identification of total cis-NATs (cis-natural antisense transcripts) from gene datasets." .
SCR:028427 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "CoolBox" ;
definition: "Software Jupyter notebook based genomic data visualization toolkit." .
SCR:028428 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Bride of Frankensystem" ;
NIFRID:abbrev "BOFS" ;
definition: "Software open-source Python/Flask framework for building online behavioral experiments and surveys. You describe your study in plain-text files: a TOML config for settings and page flow, JSON files for questionnaires, and HTML files for custom pages. BOFS handles participant routing, condition assignment, consent forms, data storage, and provides an admin panel for monitoring and export." .
SCR:028429 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5950" ;
rdfs:label "Ohio State University Immune Monitoring and Discovery Platform IMDP Core Facility" ;
NIFRID:synonym "Immune Monitoring and Discovery Platform (IMDP)" ;
definition: "Core provides technologies and expertise to accelerate discoveries in cancer immunology and immunotherapy. Offers advanced tools for immune profiling, spatial biology, and translational studies, enabling innovation that drives new therapies for patients." .
SCR:028430 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5952" ;
rdfs:label "University College London Cancer Institute Pathology Translational Technology Platform TTP Core Facility" ;
NIFRID:synonym "facility",
"Pathology Translational Technology Platform (TTP)",
"UCL Cancer Institute Pathology TTP" ;
definition: "Facility provides a range of histology and tissue-based molecular services to research scientists within the UCL Cancer Institute and across UCL.The facility also maintains a range of equipment available for use by UCL researchers to support a range of projects involving human and animal samples. We work in close collaboration with the UCL / UCLH Biobank for Studying Health and Disease and the UCL/UCLH Cancer Biomarker Centre (CBC) which provides a framework for the governance of research involving human samples and supports researchers in meeting regulatory standards." .
SCR:028431 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5953" ;
rdfs:label "Cancer Research UK Scotland Institute Research Integrity Service Core Facility" ;
NIFRID:synonym "CRUK Scotland Institute Research Integrity Service" ;
definition: "Core enables and promotes responsible research practices to generate trustworthy data, and to safeguard research data. The service is comprised of 4 pillars; governance, good research practice support, stewardship and knowledge exchange." .
SCR:028432 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5954" ;
rdfs:label "University of Maryland Baltimore Confocal Microscopy Core Facility" ;
NIFRID:synonym "University of Maryland School of Medicine Confocal Microscopy Facility" ;
definition: "Core provides researchers with confocal imaging equipment to enable acquisition of high resolution images (both in vivo and in vitro). Offers training and assistance in the use of confocal microscopes. Optimization of data acquisition and image processing are both part of the training, thus enabling researchers to efficiently design studies, acquire image data and extract relevant data features." .
SCR:028433 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_GE_PETtrace_800" ;
rdfs:label "GE Healthcare PETtrace 800 cyclotron system" ;
NIFRID:synonym "GE PETtrace 800 cyclotron" ;
definition: "Compact, automated, dual-particle cyclotron system designed for fast, easy and efficient production of PET tracers. It offers the efficiency required to facilitate your clinical schedules, flexibility for research protocols and the performance necessary to meet regional distribution demands. The PETtrace 800 is built around a compact negative ion cyclotron with a vertical mid-plane of proven design, featuring both protons and deuterons allowing maximum flexibility and low-cost isotope production." .
SCR:028434 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "ARTMS QUANTM Irradiation System" ;
NIFRID:synonym "QUANTM Irradiation System (QIS)" ;
definition: "Specialized, automated, cyclotron-based system designed for the decentralized, high-volume production of medical radioisotopes, such as Gallium-68,Technetium-99m, and Zirconium-89. It allows hospitals and radiopharmacies to produce PET and SPECT imaging agents locally, bypassing supply chain disruptions and reducing dependence on traditional nuclreactors." .
SCR:028435 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5945" ;
rdfs:label "University of Washington Histology and Imaging Core Facility" ;
NIFRID:synonym "HIC - Histology and Imaging Core" ;
definition: "Core provides histology, immunohistochemistry, imaging, quantitative image analysis, and pathology consultation services. Offers experience, expertise and instrumentation across all platforms. Through the partnership with the Comparative Pathology Program (CPP), we have board certifies veterinary pathologists on staff who are available for research consultation and collaboration." .
SCR:028436 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Immunosenescence" ;
definition: "Software code and pipelines for the study of pan-cancer myeloid immunosenescence. Analytical framework integrates bulk RNA-seq (GTEx/TCGA) and multi-cohort single-cell RNA sequencing (scRNA-seq) data to construct high-resolution myeloid atlases, cellular communication networks, and clinical prognostic signatures." .
SCR:028439 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "bedGraphToBigWig" ;
definition: "Command-line utility provided by the UCSC Genome Browser to convert text-based bedGraph files into indexed binary bigWig files. It is specifically used in bioinformatics to transform dense, continuous genome coverage data into a format that enables fast visualization and remote viewing in genome browsers like IGV or the UCSC Genome Browser." .
SCR:028440 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GATK HaplotypeCaller" ;
definition: "Software tool for identifying single nucleotide polymorphisms (SNPs) and insertion/deletion (indels) variants, offering high accuracy via local de-novo assembly of reads. It works by identifying \"active regions\" with potential variation, reassembling those reads, and calculating genotype likelihoods, making it superior for complex variant detection." .
SCR:028441 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GATK VariantFiltration" ;
definition: "Software command-line tool designed for hard-filtering variant callsets (VCF files) by applying user-defined criteria to annotate, rather than remove, low-quality variants. It marks fails in the FILTER field (e.g., using JEXL expressions to filter by DP, QD, or FS), making it essential for filtering small datasets, non-model organisms, or whenever Variant Quality Score Recalibration (VQSR) is not feasible" .
SCR:028442 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DADIMODO" ;
definition: "Software program designed for refining atomic models of multidomain proteins or complexes using Small-Angle X-ray Scattering (SAXS) data. It is specifically used in structural biology to help determine the 3D structure of complex molecules in solution." .
SCR:028443 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "GlycoShape" ;
definition: "Database of glycans 3D structural data and information that can be downloaded or used with Re-Glyco to rebuild glycoproteins from the RCSB PDB or EMBL-EBI AlphaFold repositories. Glycan structure database and toolbox designed to restore glycoproteins to their native and functional form." .
SCR:028444 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "DAMMIF" ;
NIFRID:synonym "Dummy Atom Model Fast" ;
definition: """Software tool for rapidly determining the low-resolution three-dimensional shape of biological macromolecules in solution using Small-Angle X-ray Scattering (SAXS) data.
Used for rapid ab-initio shape determination in small-angle scattering.""" .
SCR:028445 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "MANC-RISK-SCREEN" ;
definition: "Software application as discrete event simulation model built in the R programming language which simulates individual women through different risk-stratified breast screening programmes. Used to evaluate the costs, outcomes, and cost-effectiveness of different breast cancer screening strategies, particularly risk-stratified approaches in the UK. It helps policymakers determine the best screening intervals for women based on risk rather than just age." .
SCR:028446 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Charité Primary Tissue Pipeline" ;
definition: "Specialized service at Charité – Universitätsmedizin Berlin that provides researchers with fresh, high-quality primary human biospecimens. By bypassing standard supply chains, it connects operating and clinical wards directly to research laboratories, supporting human-based methods to reduce reliance on animal experimentation. Operates as a central contact point, taking care of the logistics from project initiation to sample transfer. It coordinates with surgical clinics, pathology departments, and tissue repositories. Alongside the living biospecimens, the pipeline helps safely transfer relevant, pseudonymized patient data to research groups." .
SCR:028447 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Olympus_BX60" ;
rdfs:label "Olympus | BX60 Fluorescent Microscope" ;
definition: "Research-grade upright compound microscope used to visualize fluorescently labeled cells, tissues, and biological markers. Equipped with interchangeable filter cubes (e.g., DAPI, FITC, TRITC), it excites specific fluorophores to study gene expression, protein localization, and cellular dynamics. Beyond fluorescence, it supports brightfield, phase contrast, and Differential Interference Contrast (DIC) for examining unlabeled or transparent specimens. Often fitted with trinocular head and high-resolution digital camera to capture publication quality micrographs and record time-lapse imagery." .
SCR:028448 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MabtecH_IRIS_2" ;
rdfs:label "Mabtech|IRIS 2 Reader" ;
definition: "Laboratory instrument designed to analyze and quantify ELISpot, FluoroSpot, and FociSpot assays in 96-well plates. Used by immunologists and vaccine researchers to study individual immune cells and detect secretions like antibodies and cytokines. Capable of analyzing up to four analytes simultaneously." .
SCR:028449 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "HemoGenix" ;
definition: "Specialty contract research laboratory and biotechnology company that provides stem cell testing and in vitro toxicity screening, particularly for the blood-forming (hematopoietic) system. Provides high-throughput hematotoxicity screening and testing with its proprietary HALO®-Tox HT Platform. Provides the expertise to help in predicting toxicity, risk and safety of a drug or other agent." .
SCR:028450 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Ensigna Biosystems" ;
definition: "Contract research organization based in San Leandro, California, that specializes in molecular pathology, genomics, and tissue analysis. Services for drug discovery, biomarker development, and personalized medicine. Provides histopathology and genomic services to the pharmaceutical and biotechnology industries." .
SCR:028451 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "readr" ;
NIFRID:synonym "readr:Read Rectangular Text Data" ;
definition: "Software R package read flat files (csv, tsv, fwf) into R. Used to read rectangular data like 'csv', 'tsv', and 'fwf'. Designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes." .
SCR:028452 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5956" ;
rdfs:label "University of Oklahoma Health Sciences Center Tissue Pathology and Biospecimen Core Facility" ;
NIFRID:synonym "Tissue Pathology and Biospecimen core" ;
definition: "Core provides tissue processing, histology and staining services. Services include embedding, sectioning, histochemical staining of mounted slides, immunohistochemical (IHC) staining for paraffin embedded and frozen tissues, immunocytochemical (ICC) staining for cultured cells (as tissue sections or cytospin slides), evaluation of new antibodies for IHC staining, enzyme histochemistry and special staining.Provides defined analyses including RNA / DNA preparation, reverse transcription and cDNA synthesis from total RNA, construction, staining and analysis of tissue microarrays, and construction and analysis of reverse proteomics array from user-defined biospecimens.Core is flexible to accommodate the development of new techniques and expanding its services based on the research requirements of SCC members and other investigators." .
SCR:028453 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5958" ;
rdfs:label "University of Wisconsin Madison Newcomb Imaging Center NIC Core Facility" ;
NIFRID:synonym "Newcomb Imaging Center",
"NIC",
"UW-Madison" ;
definition: "Core provides services in confocal microscopy (CLSM, including FRET, ion imaging, and colocalization), scanning electron microscopy (SEM, including ESEM for wet samples), SEM prep instrumentation (critical point dryer and sputter coater), epifluorescence microscopy and polarizing microscopy." .
SCR:028454 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5955" ;
rdfs:label "Memorial Sloan Kettering Cancer Center MSKCC Clinical Grade Production Core Facility" ;
NIFRID:synonym "MSKCC-Clinical Grade Production Core Facility" ;
definition: "cGMP facility responsible for the bulk product manufacture, purification, and characterization of clinical-grade materials. Offers vialing of sterile investigational products such as peptides, proteins, carbohydrates, and adjuvants. Service also conducts lot release tests which are required for products release for preclinical and investigational use either in-house or with validated contract vendors." .
SCR:028455 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5962" ;
rdfs:label "Loma Linda University School of Medicine Advanced Imaging and Microscopy Core Facility" ;
definition: "Core offers microscopy services. Provides three offline analysis systems with Intel Xeon-based processors. Two of these are custom-built Origin computers and the third is a Dell Precision computer. All analysis workstations have the most recent versions of the Fiji build of Image J and RStudio." .
SCR:028456 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Matrix:Sparse and Dense Matrix Classes and Methods" ;
NIFRID:abbrev "Matrix" ;
definition: "Software R package for rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries." .
SCR:028457 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "uwot" ;
NIFRID:synonym "uwot: The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction" ;
definition: "Software R package implementing the UMAP dimensionality reduction method. It also provides means to transform new data and to carry out supervised dimensionality reduction." .
SCR:028458 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5959" ;
rdfs:label "Georgetown University NanoScience and Microtechnology Laboratory GNuLab Core Facility" ;
NIFRID:synonym "GNuLab - Georgetown NanoScience and Microtechnology Laboratory" ;
definition: "This 3,300 square foot clean room is located in the Department of Physics in Regents Hall and includes instrumentation for fabrication and characterization of materials and electronic devices. Users have access to a Scanning Electron Microscope with ebeam lithography and EDS; optical lithography; magnetron sputtering; thermal evaporation; reactive ion etching; atomic layer deposition; chemical vapor deposition; wirebonding; a profilometer and various optical microscopes." .
SCR:028464 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "Taiji" ;
definition: "Software integrative analysis pipeline for analyzing bulk/single-cell ATAC-seq and RNA-seq data. Integrative multi-omics data analysis framework. It can be used as a standalone pipeline to analyze ATAC-seq, RNA-seq, single cell ATAC-seq or Drop-seq data. Used to integrate diverse datasets and use these information to construct regulatory network and identify candidate driver genes." .
SCR:028465 a NLX:152328,
owl:NamedIndividual ;
rdfs:label "Anton Paar" ;
definition: "Austrian company that develops and manufactures high-end laboratory, analytical, and process measurement instruments. Their equipment is widely used in scientific research, quality control, and manufacturing." .
SCR:028466 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "NanoporeDB" ;
definition: "Open-access structural database dedicated to the exploration, analysis, and design of protein nanopores, which serve as essential molecular gateways in biological membranes and form the basis of many advanced biosensing and sequencing technologies. This platform integrates large-scale structure-guided mining and deep learning-based modeling using AlphaFold-Multimer and AlphaFold3 to provide high-confidence multimeric nanopore structures. Each entry includes detailed information on membrane embedding, pore geometry annotation, and constriction profiling to support functional and biophysical interpretation." .
SCR:028467 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5967" ;
rdfs:label "Michigan State University Proteomics Core Facility" ;
definition: "Core provides mass spectrometry resources and expertise to assist researchers in the identification and characterization of proteins and peptides. Experiments from simple protein discovery to complex differential proteome profiling, post-translational modification mapping and protein/peptide quantification can be performed using our instrumentation and software." .
SCR:028468 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_MultiFocus" ;
rdfs:label "Faxitron Bioptics | MultiFocus X-ray system" ;
NIFRID:synonym "Faxitron MultiFocus",
"MultiFocus X-ray system" ;
definition: "Faxitron MultiFocus (now part of the Hologic portfolio) is a benchtop digital X-ray system designed for high-resolution specimen imaging, life sciences, and industrial applications. It features advanced Automatic Exposure Control and high geometric magnification for precise analysis" .
SCR:028469 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_FluoView_FV4000" ;
rdfs:label "Olympus | FluoView FV4000 Confocal Laser Scanning Microscope" ;
NIFRID:synonym "FLUOVIEW FV4000",
"FLUOVIEW FV4000 Confocal Laser Scanning Microscope",
"FluoView FV4000 Confocal Laser Scanning Microscope" ;
definition: "Confocal laser scanning microscope used to capture high-resolution, multi-color 3D images of biological samples. It is primarily used in neuroscience, cell biology, and developmental biology to image both fixed tissues and live cells. Detects from 400 nm to 900 nm. Supports up to 10 laser lines for advanced, simultaneous multiplexing." .
SCR:028470 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Nano-400A" ;
rdfs:label "Allsheng | Nano-400A spectrophotometer" ;
NIFRID:synonym "Nano-400A spectrophotometer",
"Nano-400A ultra-micro spectrophotometer" ;
definition: "Ultra-micro UV spectrophotometer used in life science and biology labs to measure the concentration and purity of DNA, RNA, and protein samples. Measures DNA and RNA concentrations at a fixed wavelength of 260 nm.Measures purified protein concentration at 280 nm. Requires only 1 to 2 ul of sample, eliminating the need for cuvettes or capillaries." .
SCR:028471 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "Model_Number_Stratagene_2400" ;
rdfs:label "Stratagene | 2400 Stratalinker UV Crosslinker" ;
NIFRID:synonym "2400 Stratalinker UV Crosslinker" ;
definition: "Stratagene UV crosslinker is designed to crosslink DNA or RNA to nylon, nitrocellulose, or nylon-reinforced nitrocellulose membranes. The crosslinking process takes only 25–50 seconds, in contrast to the traditional method of baking filters at 80°C for 2 hours. Additionally, crosslinking has been shown to significantly increase hybridization signals when compared to oven-baking. For optimal crosslinking performance, each Stratalinker UV crosslinker is equipped with an internal photodetector designed to compensate for the natural shift in power output of aging ultraviolet bulbs." .
SCR:028472 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "scatterpie" ;
NIFRID:synonym "scatterpie: Scatter Pie Plot" ;
definition: "Software R package to create scatterpie plots, especially useful for plotting pies on a map. Used to display proportional or compositional data across spatial coordinates (such as maps) or scatter plot axes." .
SCR:028473 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "xgt" ;
definition: "Software tool for querying and parsing of Genome Taxonomy Database's data.Command-line tool for querying the Genome Taxonomy Database (GTDB) directly from your terminal or scripts. It covers the core GTDB REST API, genome cards, metadata, taxonomic history, taxon lineages, and search, and adds features designed for real research workflows: batch input from files or stdin, automatic pagination, retry logic, flexible output formats (JSON, CSV, TSV), and per-item file splitting for large datasets." .
SCR:028474 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5969" ;
rdfs:label "University of Technology of Compiègne CARMOD meta-platform Core Facility" ;
NIFRID:synonym "University of Technology of Compiègne CARMOD meta-platform",
"Université de Technologie de Compiègne (UTC) CARMOD meta-platform" ;
definition: "CARMOD (characterization and modelling) meta-platform is a core research and technology unit within the Biomechanics and Bioengineering (BMBI) laboratory at the University of Technology of Compiègne.Interdisciplinary core facility dedicated to the mechanical characterization of biological systems, tissues, and biomechanical signals. Provides technological platforms dedicated to the characterization and modeling of biomechanical systems and electrophysiological signals. Offers expertise spanning various scales from the nanoscale to the entire organ in vivo as well as various characterization modalities and physical and numerical modeling." .
SCR:028475 a NLX:63400,
owl:NamedIndividual ;
rdfs:label "starCAT" ;
NIFRID:synonym "starCellAnnoTator",
"starCellAnnoTator (starCAT)" ;
definition: "Software pipeline that improves T cell characterization by simultaneously quantifying predefined gene expression programs (scRNA-Seq) capturing activation states and cellular subsets. Used to score cells based on a fixed, multidataset catalog of Gene Expression Programs from any tissues or cell-type." .
SCR:028476 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5963" ;
rdfs:label "Medical University of South Carolina MUSC Mouse Behavior Phenotyping Core Facility" ;
NIFRID:synonym "Medical University of South Carolina MUSC Mouse Behavior Phenotyping Core",
"MUSC Mouse Behavior Phenotyping Core" ;
definition: "Core provides equipment, expertise, service and training for testing a range of common mouse behaviors to study neurological disorders, such as Autism Spectrum Disorder, intellectual disability, anxiety/depression, and Alzheimer Disease. Performs behavioral testing, data analysis, and data interpretation.Offers personnel training for investigator to have access to the behavior equipment if they prefer to test the mice themselves" .
SCR:028477 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5966" ;
rdfs:label "Sam Houston State University SHSU-Microscopy Core Facility" ;
NIFRID:synonym "SHSU-Microscopy Core Facility" ;
definition: "Core provides specialized imaging services for primarily biological research, with additional applications for materials chemistry, forensic science, and engineering technology. Available instrumentation includes various light microscopes, a laser-scanning confocal, scanning and transmission electron microscopes, and X-ray imaging." .
SCR:028478 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5965" ;
rdfs:label "University of Colorado Anschutz Medical Campus DMBC Microscopy Core Facility" ;
NIFRID:synonym "CU-AMC Developmental Biology Microscopy Consortium",
"University of Colorado Anschutz Medical Campus CU-AMC Developmental Biology Microscopy Consortium" ;
definition: "Core offers services from bench to publication to all consortium members. Provides access to the facilities's microscopes and analysis workstations. Provides training, education, support, and mentorship in all aspects of preparing, acquiring, processing, analyzing, and publishing microscopy data." .
SCR:028479 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5968" ;
rdfs:label "University of Louisville Micro/Nano Technology Center Bioimaging Core Facility" ;
NIFRID:synonym "Micro/Nano Technology Center Bioimaging Core",
"University of Louisville Micro/Nano Technology Center Bioimaging Core" ;
definition: "Core provides biological electron microscopy services including sample preparation, SEM and TEM imaging, array tomography, and cryo-EM plunge freezing." .
SCR:028480 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5964" ;
rdfs:label "Medical College of Wisconsin Children's Research Institute Flow Cytometry Core Facility" ;
NIFRID:synonym "Children's Research Institute Flow Cytometry Core" ;
definition: "Core provides access to analytical cytometers and cell sorters for trained users and operator-assisted cell sorting by appointment during business hours. Assists with protocol and assay development, including sample preparation, selection of antibodies and fluorochromes, proper staining and compensation controls, and selection of appropriate buffers. Offers assistance with data analysis using FlowJo, FCS Express, DIVA and SpectroFlo software is also available by appointment." .
SCR:028481 a NLX:63400,
owl:NamedIndividual ;
oboInOwl:hasDbXref "ABRF_5798" ;
rdfs:label "University of Louisville Micro/Nano Technology Center Imaging and Characterization Core Facility" ;
NIFRID:synonym "Micro/Nano Technology Center Imaging and Characterization Core",
"University of Louisville Micro/Nano Technology Center Imaging and Characterization Core" ;
definition: "Core provides advanced imaging and characterization capabilities including SEM, AFM, and infrared thermal microscopy supporting research in engineering, materials science, biology, and more. Offers imaging and characterization for semiconductors and/or other Micro/Nano scale devices." .
SCR:028482 a NLX:152328,
owl:NamedIndividual ;
oboInOwl:hasDbXref "GRID grid.263046.5",
"ISNI 0000 0001 2291 1903",
"Wikidata Q1422594" ;
rdfs:label "Sam Houston State University; Texas; USA" ;
definition: "Public research university in Huntsville, Texas. Founded in 1879, it is the third-oldest public college or university in Texas. It is one of the first normal schools west of the Mississippi River and the first in Texas." .
### Annotations
SCR:000641 replacedBy: SCR:012988 .
SCR:000830 replacedBy: SCR:013347 .
SCR:000846 replacedBy: SCR:009075 .
SCR:000847 replacedBy: SCR:009216 .
SCR:000848 replacedBy: SCR:013442 .
SCR:000851 replacedBy: SCR:007625 .
SCR:000951 replacedBy: SCR:007394 .
SCR:001055 replacedBy: SCR:016601 .
SCR:001373 replacedBy: SCR:000824 .
SCR:001812 replacedBy: SCR:001754 .
SCR:001888 replacedBy: SCR:001621 .
SCR:001948 replacedBy: SCR:000445 .
SCR:002025 replacedBy: SCR:001832 .
SCR:002078 replacedBy: SCR:014199 .
SCR:002104 replacedBy: SCR:001835 .
SCR:002151 replacedBy: SCR:017637 .
SCR:002911 replacedBy: SCR:005663 .
SCR:002914 replacedBy: SCR:018271 .
SCR:003033 replacedBy: SCR:001881 .
SCR:003491 replacedBy: SCR:000476 .
SCR:003614 replacedBy: SCR:010243 .
SCR:004150 replacedBy: SCR:002022 .
SCR:004576 replacedBy: SCR:019284 .
SCR:004769 replacedBy: SCR:005818 .
SCR:005058 replacedBy: SCR:002004 .
SCR:005074 replacedBy: SCR:011249 .
SCR:005244 replacedBy: SCR:007030 .
SCR:005512 replacedBy: SCR:005615 .
SCR:005539 replacedBy: SCR:014583 .
SCR:005976 replacedBy: SCR:014363 .
SCR:006392 replacedBy: SCR:006389 .
SCR:007057 replacedBy: SCR:007058 .
SCR:007215 replacedBy: SCR:001520 .
SCR:007239 replacedBy: SCR:000825 .
SCR:007247 replacedBy: SCR:000123 .
SCR:007295 replacedBy: SCR:002861 .
SCR:007303 replacedBy: SCR:005012 .
SCR:007368 replacedBy: SCR:002823 .
SCR:007388 replacedBy: SCR:005663 .
SCR:007609 replacedBy: SCR:002320 .
SCR:007842 replacedBy: SCR:013807 .
SCR:007970 replacedBy: SCR:002853 .
SCR:008276 replacedBy: SCR:004699 .
SCR:008430 replacedBy: SCR:005559 .
SCR:008479 replacedBy: SCR:002621 .
SCR:008627 replacedBy: SCR:002050 .
SCR:008779 replacedBy: SCR:000210 .
SCR:009091 replacedBy: SCR:007140 .
SCR:009099 replacedBy: SCR:013132 .
SCR:009101 replacedBy: SCR:009170 .
SCR:009102 replacedBy: SCR:009154 .
SCR:009103 replacedBy: SCR:007420 .
SCR:009106 replacedBy: SCR:009123 .
SCR:009108 replacedBy: SCR:013134 .
SCR:009109 replacedBy: SCR:009155 .
SCR:009219 replacedBy: SCR:009365 .
SCR:009312 replacedBy: SCR:009371 .
SCR:009347 replacedBy: SCR:006312 .
SCR:009366 replacedBy: SCR:013127 .
SCR:009367 replacedBy: SCR:007550 .
SCR:009368 replacedBy: SCR:006282 .
SCR:009372 replacedBy: SCR:013124 .
SCR:009373 replacedBy: SCR:007514 .
SCR:009374 replacedBy: SCR:007315 .
SCR:009405 replacedBy: SCR:009376 .
SCR:009408 replacedBy: SCR:007414 .
SCR:009582 replacedBy: SCR:007350 .
SCR:009594 replacedBy: SCR:001592 .
SCR:010229 replacedBy: SCR:000465 .
SCR:010517 replacedBy: SCR:003988 .
SCR:010649 replacedBy: SCR:007358 .
SCR:010795 replacedBy: SCR:008302 .
SCR:010892 replacedBy: SCR:004513 .
SCR:010949 replacedBy: SCR:007834 .
SCR:010999 replacedBy: SCR:019170 .
SCR:011002 replacedBy: SCR:009994 .
SCR:011034 replacedBy: SCR:010151 .
SCR:011043 replacedBy: SCR:017761 .
SCR:011134 replacedBy: SCR:005054 .
SCR:011782 replacedBy: SCR:001852 .
SCR:011850 replacedBy: SCR:000585 .
SCR:011924 replacedBy: SCR:002676 .
SCR:011948 replacedBy: SCR:008249 .
SCR:012092 replacedBy: SCR:001235 .
SCR:012383 replacedBy: SCR:025218 .
SCR:012479 replacedBy: SCR:005780 .
SCR:012514 replacedBy: SCR:017929 .
SCR:012572 replacedBy: SCR:009793 .
SCR:012659 replacedBy: SCR:012480 .
SCR:012849 replacedBy: SCR:006678 .
SCR:012935 replacedBy: SCR:012909 .
SCR:013106 replacedBy: SCR:006717 .
SCR:013197 replacedBy: SCR:008617 .
SCR:013200 replacedBy: SCR:013189 .
SCR:013230 replacedBy: SCR:006907 .
SCR:013238 replacedBy: SCR:013189 .
SCR:013270 replacedBy: SCR:008452 .
SCR:013307 replacedBy: SCR:014597 .
SCR:013506 replacedBy: SCR:013504 .
SCR:013551 replacedBy: SCR:003792 .
SCR:013553 replacedBy: SCR:008426 .
SCR:013567 replacedBy: SCR:008406 .
SCR:013647 replacedBy: SCR:007712 .
SCR:013734 replacedBy: SCR:005522 .
SCR:014141 replacedBy: SCR:005656 .
SCR:014198 replacedBy: SCR:010279 .
SCR:014203 replacedBy: SCR:013733 .
SCR:014211 replacedBy: SCR:013715 .
SCR:014216 replacedBy: SCR:000325 .
SCR:014234 replacedBy: SCR:014199 .
SCR:014248 replacedBy: SCR:013672 .
SCR:014267 replacedBy: SCR:013057 .
SCR:014298 replacedBy: SCR:014199 .
SCR:014305 replacedBy: SCR:007353 .
SCR:014327 replacedBy: SCR:012312 .
SCR:014441 replacedBy: SCR:002184 .
SCR:014533 replacedBy: SCR:003743 .
SCR:014603 replacedBy: SCR:008472 .
SCR:014747 replacedBy: SCR:010494 .
SCR:014925 replacedBy: SCR:014928 .
SCR:014940 replacedBy: SCR:000614 .
SCR:014984 replacedBy: SCR:014650 .
SCR:014986 replacedBy: SCR:010752 .
SCR:015105 replacedBy: SCR:018206 .
SCR:015358 replacedBy: SCR:008997 .
SCR:015366 replacedBy: SCR:018672 .
SCR:015623 replacedBy: SCR:004162 .
SCR:015636 replacedBy: SCR:014212 .
SCR:015716 replacedBy: SCR:006962 .
SCR:015719 replacedBy: SCR:014806 .
SCR:015767 replacedBy: SCR:008915 .
SCR:015771 replacedBy: SCR:005361 .
SCR:015803 replacedBy: SCR:007369 .
SCR:015807 replacedBy: SCR:002798 .
SCR:015853 replacedBy: SCR:010910 .
SCR:015893 replacedBy: SCR:004869 .
SCR:015894 replacedBy: SCR:012880 .
SCR:015899 replacedBy: SCR:004463 .
SCR:015907 replacedBy: SCR:015324 .
SCR:015922 replacedBy: SCR:015320 .
SCR:015923 replacedBy: SCR:015905 .
SCR:015924 replacedBy: SCR:015914 .
SCR:015925 replacedBy: SCR:015908 .
SCR:015926 replacedBy: SCR:015912 .
SCR:015927 replacedBy: SCR:015910 .
SCR:015928 replacedBy: SCR:015913 .
SCR:015958 replacedBy: SCR:013672 .
SCR:015981 replacedBy: SCR:008417 .
SCR:015988 replacedBy: SCR:010228 .
SCR:015992 replacedBy: SCR:002724 .
SCR:016005 replacedBy: SCR:016001 .
SCR:016009 replacedBy: SCR:016008 .
SCR:016010 replacedBy: SCR:016008 .
SCR:016013 replacedBy: SCR:016012 .
SCR:016014 replacedBy: SCR:016012 .
SCR:016062 replacedBy: SCR:001591 .
SCR:016076 replacedBy: SCR:011735 .
SCR:016099 replacedBy: SCR:002815 .
SCR:016238 replacedBy: SCR:014551 .
SCR:016245 replacedBy: SCR:011853 .
SCR:016247 replacedBy: SCR:016248 .
SCR:016327 replacedBy: SCR:017847 .
SCR:016332 replacedBy: SCR:016331 .
SCR:016462 replacedBy: SCR:006675 .
SCR:016468 replacedBy: SCR:014942 .
SCR:016487 replacedBy: SCR:016486 .
SCR:016537 replacedBy: SCR:016441 .
SCR:016553 replacedBy: SCR:016493 .
SCR:016578 replacedBy: SCR:004630 .
SCR:016579 replacedBy: SCR:003496 .
SCR:016621 replacedBy: SCR:016435 .
SCR:016622 replacedBy: SCR:014280 .
SCR:016626 replacedBy: SCR:011625 .
SCR:016675 replacedBy: SCR:000977 .
SCR:016676 replacedBy: SCR:011273 .
SCR:016709 replacedBy: SCR:007255 .
SCR:016717 replacedBy: SCR:015539 .
SCR:016758 replacedBy: SCR:016497 .
SCR:016856 replacedBy: SCR:016855 .
SCR:016879 replacedBy: SCR:007369 .
SCR:016882 replacedBy: SCR:003199 .
SCR:016894 replacedBy: SCR:016893 .
SCR:016901 replacedBy: SCR:006800 .
SCR:016946 replacedBy: SCR:011847 .
SCR:017155 replacedBy: SCR:017894 .
SCR:017243 replacedBy: SCR:017045 .
SCR:017266 replacedBy: SCR:015820 .
SCR:017379 replacedBy: SCR:012820 .
SCR:017419 replacedBy: SCR:003238 .
SCR:017473 replacedBy: SCR:002865 .
SCR:017475 replacedBy: SCR:006532 .
SCR:017493 replacedBy: SCR:006793 .
SCR:017495 replacedBy: SCR:017354 .
SCR:017497 replacedBy: SCR:003152 .
SCR:017502 replacedBy: SCR:005780 .
SCR:017503 replacedBy: SCR:013157 .
SCR:017504 replacedBy: SCR:002560 .
SCR:017520 replacedBy: SCR:006585 .
SCR:017526 replacedBy: SCR:003015 .
SCR:017527 replacedBy: SCR:005571 .
SCR:017529 replacedBy: SCR:006539 .
SCR:017530 replacedBy: SCR:017001 .
SCR:017615 replacedBy: SCR:004177 .
SCR:017627 replacedBy: SCR:011620 .
SCR:017630 replacedBy: SCR:014074 .
SCR:017649 replacedBy: SCR:014659 .
SCR:017663 replacedBy: SCR:000242 .
SCR:017665 replacedBy: SCR:013331 .
SCR:017675 replacedBy: SCR:017640 .
SCR:017678 replacedBy: SCR:017437 .
SCR:017704 replacedBy: SCR:017688 .
SCR:017705 replacedBy: SCR:017700 .
SCR:017706 replacedBy: SCR:017687 .
SCR:017707 replacedBy: SCR:017686 .
SCR:017708 replacedBy: SCR:017690 .
SCR:017709 replacedBy: SCR:017691 .
SCR:017710 replacedBy: SCR:017694 .
SCR:017711 replacedBy: SCR:017689 .
SCR:017712 replacedBy: SCR:017696 .
SCR:017713 replacedBy: SCR:017692 .
SCR:017714 replacedBy: SCR:017693 .
SCR:017715 replacedBy: SCR:017695 .
SCR:017716 replacedBy: SCR:017701 .
SCR:017717 replacedBy: SCR:017698 .
SCR:017718 replacedBy: SCR:017703 .
SCR:017719 replacedBy: SCR:017697 .
SCR:017720 replacedBy: SCR:017699 .
SCR:017721 replacedBy: SCR:017702 .
SCR:017771 replacedBy: SCR:017879 .
SCR:017832 replacedBy: SCR:014877 .
SCR:017875 replacedBy: SCR:017767 .
SCR:017876 replacedBy: SCR:017773 .
SCR:017880 replacedBy: SCR:017945 .
SCR:017884 replacedBy: SCR:017770 .
SCR:017925 replacedBy: SCR:017692 .
SCR:018035 replacedBy: SCR:016517 .
SCR:018091 replacedBy: SCR:018934 .
SCR:018096 replacedBy: SCR:000025 .
SCR:018130 replacedBy: SCR:018128 .
SCR:018150 replacedBy: SCR:016269 .
SCR:018192 replacedBy: SCR:018183 .
SCR:018202 replacedBy: SCR:016548 .
SCR:018204 replacedBy: SCR:001030 .
SCR:018205 replacedBy: SCR:012429 .
SCR:018244 replacedBy: SCR:018164 .
SCR:018264 replacedBy: SCR:009754 .
SCR:018268 replacedBy: SCR:012487 .
SCR:018269 replacedBy: SCR:017767 .
SCR:018279 replacedBy: SCR:018251 .
SCR:018300 replacedBy: SCR:001030 .
SCR:018318 replacedBy: SCR:018251 .
SCR:018327 replacedBy: SCR:015629 .
SCR:018351 replacedBy: SCR:018338 .
SCR:018356 replacedBy: SCR:016999 .
SCR:018376 replacedBy: SCR:002677 .
SCR:018388 replacedBy: SCR:015645 .
SCR:018407 replacedBy: SCR:003070 .
SCR:018408 replacedBy: SCR:015018 .
SCR:018441 replacedBy: SCR:018430 .
SCR:018442 replacedBy: SCR:018433 .
SCR:018443 replacedBy: SCR:018431 .
SCR:018444 replacedBy: SCR:018435 .
SCR:018445 replacedBy: SCR:018432 .
SCR:018446 replacedBy: SCR:018440 .
SCR:018447 replacedBy: SCR:018438 .
SCR:018448 replacedBy: SCR:018436 .
SCR:018449 replacedBy: SCR:018439 .
SCR:018450 replacedBy: SCR:018437 .
SCR:018451 replacedBy: SCR:018434 .
SCR:018509 replacedBy: SCR:016625 .
SCR:018546 replacedBy: SCR:010246 .
SCR:018577 replacedBy: SCR:018044 .
SCR:018601 replacedBy: SCR:018029 .
SCR:018619 replacedBy: SCR:019705 .
SCR:018682 replacedBy: SCR:002105 .
SCR:018691 replacedBy: SCR:015435 .
SCR:018727 replacedBy: SCR:018726 .
SCR:018741 replacedBy: SCR:018740 .
SCR:018744 replacedBy: SCR:018736 .
SCR:018748 replacedBy: SCR:018747 .
SCR:018750 replacedBy: SCR:002380 .
SCR:018760 replacedBy: SCR:016308 .
SCR:018767 replacedBy: SCR:015643 .
SCR:018791 replacedBy: SCR:018790 .
SCR:018800 replacedBy: SCR:018796 .
SCR:018803 replacedBy: SCR:014627 .
SCR:018816 replacedBy: SCR:018337 .
SCR:018817 replacedBy: SCR:018274 .
SCR:018818 replacedBy: SCR:015041 .
SCR:018856 replacedBy: SCR:018876 .
SCR:018858 replacedBy: SCR:018606 .
SCR:018868 replacedBy: SCR:009984 .
SCR:018869 replacedBy: SCR:014551 .
SCR:018892 replacedBy: SCR:018840 .
SCR:018948 replacedBy: SCR:002526 .
SCR:018991 replacedBy: SCR:001432 .
SCR:019000 replacedBy: SCR:017401 .
SCR:019004 replacedBy: SCR:018996 .
SCR:019005 replacedBy: SCR:017322 .
SCR:019027 replacedBy: SCR:018989 .
SCR:019051 replacedBy: SCR:016477 .
SCR:019096 replacedBy: SCR:016479 .
SCR:019113 replacedBy: SCR:019112 .
SCR:019160 replacedBy: SCR:019156 .
SCR:019161 replacedBy: SCR:019155 .
SCR:019224 replacedBy: SCR:019222 .
SCR:019248 replacedBy: SCR:004997 .
SCR:019325 replacedBy: SCR:017757 .
SCR:019328 replacedBy: SCR:018371 .
SCR:019336 replacedBy: SCR:019332 .
SCR:019384 replacedBy: SCR:017206 .
SCR:019388 replacedBy: SCR:018433 .
SCR:019389 replacedBy: SCR:018043 .
SCR:019394 replacedBy: SCR:019393 .
SCR:019395 replacedBy: SCR:018435 .
SCR:019398 replacedBy: SCR:018435 .
SCR:019403 replacedBy: SCR:019401 .
SCR:019408 replacedBy: SCR:019406 .
SCR:019419 replacedBy: SCR:019415 .
SCR:019429 replacedBy: SCR:019428 .
SCR:019434 replacedBy: SCR:019431 .
SCR:019475 replacedBy: SCR:019473 .
SCR:019498 replacedBy: SCR:018058 .
SCR:019516 replacedBy: SCR:019515 .
SCR:019521 replacedBy: SCR:019515 .
SCR:019564 replacedBy: SCR:018625 .
SCR:019569 replacedBy: SCR:018437 .
SCR:019570 replacedBy: SCR:018434 .
SCR:019574 replacedBy: SCR:018438 .
SCR:019575 replacedBy: SCR:018440 .
SCR:019577 replacedBy: SCR:018436 .
SCR:019580 replacedBy: SCR:018641 .
SCR:019583 replacedBy: SCR:018439 .
SCR:019587 replacedBy: SCR:018642 .
SCR:019598 replacedBy: SCR:019592 .
SCR:019600 replacedBy: SCR:018655 .
SCR:019602 replacedBy: SCR:018655 .
SCR:019605 replacedBy: SCR:018655 .
SCR:019643 replacedBy: SCR:018370 .
SCR:019668 replacedBy: SCR:018370 .
SCR:019672 replacedBy: SCR:019664 .
SCR:019673 replacedBy: SCR:019652 .
SCR:019676 replacedBy: SCR:018044 .
SCR:019682 replacedBy: SCR:019681 .
SCR:019713 replacedBy: SCR:019712 .
SCR:019717 replacedBy: SCR:019712 .
SCR:019720 replacedBy: SCR:019625 .
SCR:019729 replacedBy: SCR:019728 .
SCR:019739 replacedBy: SCR:019689 .
SCR:019747 replacedBy: SCR:019735 .
SCR:019752 replacedBy: SCR:018637 .
SCR:019755 replacedBy: SCR:019754 .
SCR:019758 replacedBy: SCR:019757 .
SCR:019779 replacedBy: SCR:018696 .
SCR:019784 replacedBy: SCR:019781 .
SCR:019800 replacedBy: SCR:017142 .
SCR:019838 replacedBy: SCR:018634 .
SCR:019843 replacedBy: SCR:019831 .
SCR:019871 replacedBy: SCR:019862 .
SCR:019875 replacedBy: SCR:019599 .
SCR:019922 replacedBy: SCR:018576 .
SCR:019925 replacedBy: SCR:018581 .
SCR:019930 replacedBy: SCR:018578 .
SCR:019955 replacedBy: SCR:018049 .
SCR:019963 replacedBy: SCR:018579 .
SCR:019964 replacedBy: SCR:018614 .
SCR:019972 replacedBy: SCR:018613 .
SCR:019974 replacedBy: SCR:019971 .
SCR:020003 replacedBy: SCR:018582 .
SCR:020008 replacedBy: SCR:018399 .
SCR:020011 replacedBy: SCR:020006 .
SCR:020123 replacedBy: SCR:016383 .
SCR:020125 replacedBy: SCR:016377 .
SCR:020127 replacedBy: SCR:016386 .
SCR:020128 replacedBy: SCR:016388 .
SCR:020129 replacedBy: SCR:018580 .
SCR:020131 replacedBy: SCR:016385 .
SCR:020132 replacedBy: SCR:020130 .
SCR:020133 replacedBy: SCR:016382 .
SCR:020134 replacedBy: SCR:016379 .
SCR:020135 replacedBy: SCR:018593 .
SCR:020136 replacedBy: SCR:016378 .
SCR:020137 replacedBy: SCR:016380 .
SCR:020138 replacedBy: SCR:016384 .
SCR:020139 replacedBy: SCR:018583 .
SCR:020141 replacedBy: SCR:016381 .
SCR:020142 replacedBy: SCR:018589 .
SCR:020143 replacedBy: SCR:018575 .
SCR:020150 replacedBy: SCR:016387 .
SCR:020153 replacedBy: SCR:020146 .
SCR:020200 replacedBy: SCR:018586 .
SCR:020203 replacedBy: SCR:018587 .
SCR:020204 replacedBy: SCR:018588 .
SCR:020213 replacedBy: SCR:018640 .
SCR:020216 replacedBy: SCR:018713 .
SCR:020219 replacedBy: SCR:018896 .
SCR:020220 replacedBy: SCR:018713 .
SCR:020228 replacedBy: SCR:018713 .
SCR:020230 replacedBy: SCR:020222 .
SCR:020244 replacedBy: SCR:018589 .
SCR:020255 replacedBy: SCR:018592 .
SCR:020257 replacedBy: SCR:018595 .
SCR:020260 replacedBy: SCR:018590 .
SCR:020261 replacedBy: SCR:018596 .
SCR:020262 replacedBy: SCR:018597 .
SCR:020280 replacedBy: SCR:020267 .
SCR:020292 replacedBy: SCR:018602 .
SCR:020301 replacedBy: SCR:018599 .
SCR:020314 replacedBy: SCR:018605 .
SCR:020315 replacedBy: SCR:018600 .
SCR:020322 replacedBy: SCR:018606 .
SCR:020325 replacedBy: SCR:018603 .
SCR:020327 replacedBy: SCR:018605 .
SCR:020330 replacedBy: SCR:018606 .
SCR:020342 replacedBy: SCR:018607 .
SCR:020345 replacedBy: SCR:020339 .
SCR:020347 replacedBy: SCR:018612 .
SCR:020348 replacedBy: SCR:018604 .
SCR:020349 replacedBy: SCR:019753 .
SCR:020365 replacedBy: SCR:019581 .
SCR:020389 replacedBy: SCR:018610 .
SCR:020391 replacedBy: SCR:018609 .
SCR:020392 replacedBy: SCR:018608 .
SCR:020397 replacedBy: SCR:018621 .
SCR:020409 replacedBy: SCR:019573 .
SCR:020413 replacedBy: SCR:018617 .
SCR:020414 replacedBy: SCR:018618 .
SCR:020417 replacedBy: SCR:018622 .
SCR:020418 replacedBy: SCR:018624 .
SCR:020420 replacedBy: SCR:018623 .
SCR:020421 replacedBy: SCR:018620 .
SCR:020426 replacedBy: SCR:020241 .
SCR:020445 replacedBy: SCR:020265 .
SCR:020502 replacedBy: SCR:018626 .
SCR:020504 replacedBy: SCR:018629 .
SCR:020507 replacedBy: SCR:018628 .
SCR:020508 replacedBy: SCR:018630 .
SCR:020512 replacedBy: SCR:018632 .
SCR:020521 replacedBy: SCR:018635 .
SCR:020527 replacedBy: SCR:020297 .
SCR:020528 replacedBy: SCR:020522 .
SCR:020532 replacedBy: SCR:018631 .
SCR:020537 replacedBy: SCR:018640 .
SCR:020540 replacedBy: SCR:018636 .
SCR:020541 replacedBy: SCR:018646 .
SCR:020557 replacedBy: SCR:018638 .
SCR:020560 replacedBy: SCR:016517 .
SCR:020563 replacedBy: SCR:019840 .
SCR:020568 replacedBy: SCR:018650 .
SCR:020735 replacedBy: SCR:020729 .
SCR:020749 replacedBy: SCR:020744 .
SCR:020870 replacedBy: SCR:018639 .
SCR:020871 replacedBy: SCR:019946 .
SCR:020877 replacedBy: SCR:018649 .
SCR:020879 replacedBy: SCR:018644 .
SCR:020886 replacedBy: SCR:018648 .
SCR:020912 replacedBy: SCR:018645 .
SCR:020941 replacedBy: SCR:013049 .
SCR:020944 replacedBy: SCR:015247 .
SCR:020961 replacedBy: SCR:018565 .
SCR:020965 replacedBy: SCR:018181 .
SCR:020988 replacedBy: SCR:020985 .
SCR:021007 replacedBy: SCR:021004 .
SCR:021132 replacedBy: SCR:006659 .
SCR:021246 replacedBy: SCR:011936 .
SCR:021251 replacedBy: SCR:021235 .
SCR:021271 replacedBy: SCR:001757 .
SCR:021306 replacedBy: SCR:021298 .
SCR:021347 replacedBy: SCR:011668 .
SCR:021549 replacedBy: SCR:017904 .
SCR:021598 replacedBy: SCR:017904 .
SCR:021619 replacedBy: SCR:021585 .
SCR:021634 replacedBy: SCR:017637 .
SCR:021668 replacedBy: SCR:021667 .
SCR:021690 replacedBy: SCR:021313 .
SCR:021784 replacedBy: SCR:009783 .
SCR:021851 replacedBy: SCR:021843 .
SCR:021895 replacedBy: SCR:021894 .
SCR:021896 replacedBy: SCR:021894 .
SCR:021907 replacedBy: SCR:021906 .
SCR:021932 replacedBy: SCR:021929 .
SCR:021949 replacedBy: SCR:014229 .
SCR:021965 replacedBy: SCR:016479 .
SCR:021974 replacedBy: SCR:001905 .
SCR:022220 replacedBy: SCR:022118 .
SCR:022445 replacedBy: SCR:004275 .
SCR:022553 replacedBy: SCR:022552 .
SCR:022652 replacedBy: SCR:009969 .
SCR:022777 replacedBy: SCR:016592 .
SCR:022781 replacedBy: SCR:022776 .
SCR:022792 replacedBy: SCR:019264 .
SCR:022881 replacedBy: SCR:022867 .
SCR:023017 replacedBy: SCR:000667 .
SCR:023167 replacedBy: SCR:023164 .
SCR:023235 replacedBy: SCR:017794 .
SCR:023395 replacedBy: SCR:023389 .
SCR:023813 replacedBy: SCR:023499 .
SCR:024174 replacedBy: SCR:017228 .
SCR:024416 replacedBy: SCR:001953 .
SCR:024705 replacedBy: SCR:002526 .
SCR:025136 replacedBy: SCR:012264 .
SCR:025417 replacedBy: SCR:025413 .
SCR:025534 replacedBy: SCR:017165 .
SCR:025680 replacedBy: SCR:025709 .
SCR:025708 replacedBy: SCR:023413 .
SCR:025922 replacedBy: SCR:020267 .
SCR:026208 replacedBy: SCR:006579 .
SCR:026993 replacedBy: SCR:026992 .
SCR:027365 replacedBy: SCR:027357 .
SCR:027541 replacedBy: SCR:027118 .
### Serialized using the ttlser deterministic serializer v1.2.3